6J51

RNA polymerase II elongation complex bound with Spt4/5 and foreign DNA, stalled at SHL(-1) of the nucleosome, weak Elf1 (+1 position)

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
J	SCOP2B Superfamily	RNA polymerase subunit RPB10	8063366	3001213	SCOP2B (2022-06-29)
K	SCOP2B Superfamily	RBP11-like subunits of RNA polymerase	8080724	3001655	SCOP2B (2022-06-29)
L	SCOP2B Superfamily	RNA polymerase subunits	8080893	3001823	SCOP2B (2022-06-29)
P [auth M]	SCOP2 Family	ELF1 zinc binding domain-like	8097423	4003934	SCOP2 (2022-06-29)
P [auth M]	SCOP2 Superfamily	Zinc beta-ribbon	8097424	3001238	SCOP2 (2022-06-29)
S [auth a]	SCOP2B Superfamily	Core histone-like	8070527	3001387	SCOP2B (2022-06-29)
W [auth e]	SCOP2B Superfamily	Core histone-like	8070527	3001387	SCOP2B (2022-06-29)
T [auth b]	SCOP2B Superfamily	Core histone-like	8070545	3001387	SCOP2B (2022-06-29)
X [auth f]	SCOP2B Superfamily	Core histone-like	8070545	3001387	SCOP2B (2022-06-29)
U [auth c]	SCOP2B Superfamily	Core histone-like	8039342	3001387	SCOP2B (2022-06-29)
Y [auth g]	SCOP2B Superfamily	Core histone-like	8039342	3001387	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	HRDC-like	8078369	3000132	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	RPB6/omega subunit-like	8078373	3000189	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	RBP8/CHS5 N-terminal domain-like	8093395	3002702	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	RBP8/CHS5 N-terminal domain-like	8078385	3002702	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	RNA_pol_Rpb1_2	e6j51A3	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: double psi	F: RNA_pol_Rpb1_2	ECOD (1.6)
A	RNA_pol_Rpb1_2_1	e6j51A7	A: a+b two layers	X: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase (From Topology)	H: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase (From Topology)	T: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase	F: RNA_pol_Rpb1_2_1	ECOD (1.6)
A	RNA_pol_Rpb1_7	e6j51A6	A: a+b two layers	X: permuted ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit (From Topology)	H: permuted ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit (From Topology)	T: permuted ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit	F: RNA_pol_Rpb1_7	ECOD (1.6)
A	RNA_pol_Rpb1_7_1	e6j51A1	A: a+b two layers	X: ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit (From Topology)	H: ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit (From Topology)	T: ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit	F: RNA_pol_Rpb1_7_1	ECOD (1.6)
A	RNA_pol_Rpb1_1	e6j51A2	A: a+b complex topology	X: N-terminal domain in RNA-polymerase beta-prime subunit (From Topology)	H: N-terminal domain in RNA-polymerase beta-prime subunit (From Topology)	T: N-terminal domain in RNA-polymerase beta-prime subunit	F: RNA_pol_Rpb1_1	ECOD (1.6)
A	RNA_pol_Rpb1_5_3rd	e6j51A9	A: a+b complex topology	X: central helical domain in RNA-polymerase beta-prime subunit (From Topology)	H: central helical domain in RNA-polymerase beta-prime subunit (From Topology)	T: central helical domain in RNA-polymerase beta-prime subunit	F: RNA_pol_Rpb1_5_3rd	ECOD (1.6)
A	RNA_pol_Rpb1_6	e6j51A5	A: a+b complex topology	X: helical domain in yeast RNA-polymerases	H: third helical domain in yeast RNA-polymerase II beta-prime subunit (From Topology)	T: third helical domain in yeast RNA-polymerase II beta-prime subunit	F: RNA_pol_Rpb1_6	ECOD (1.6)
A	RNA_pol_Rpb1_4	e6j51A4	A: a+b complex topology	X: second helical domain in RNA-polymerase beta-prime subunit (From Topology)	H: second helical domain in RNA-polymerase beta-prime subunit (From Topology)	T: second helical domain in RNA-polymerase beta-prime subunit	F: RNA_pol_Rpb1_4	ECOD (1.6)
A	RNA_pol_Rpb1_3	e6j51A8	A: a+b complex topology	X: first helical domain in RNA-polymerase beta-prime subunit (From Topology)	H: first helical domain in RNA-polymerase beta-prime subunit (From Topology)	T: first helical domain in RNA-polymerase beta-prime subunit	F: RNA_pol_Rpb1_3	ECOD (1.6)
J	RNA_pol_N	e6j51J1	A: alpha arrays	X: HTH	H: RPB10 (From Topology)	T: RPB10	F: RNA_pol_N	ECOD (1.6)
K	RNA_pol_L_2	e6j51K1	A: a+b two layers	X: DCoH-like	H: RBP11-like subunits of RNA polymerase (From Topology)	T: RBP11-like subunits of RNA polymerase	F: RNA_pol_L_2	ECOD (1.6)
L	DNA_RNApol_7kD	e6j51L1	A: few secondary structure elements	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: DNA_RNApol_7kD	ECOD (1.6)
P [auth M]	Elf1	e6j51M1	A: few secondary structure elements	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: Elf1	ECOD (1.6)
Q [auth V]	Spt4	e6j51V1	A: few secondary structure elements	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: Spt4	ECOD (1.6)
R [auth W]	Ribosomal_L26_1	e6j51W1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: Ribosomal_L26_1	ECOD (1.6)
R [auth W]	KOW_RPL26	e6j51W3	A: beta barrels	X: SH3	H: SH3	T: SH3	F: KOW_RPL26	ECOD (1.6)
R [auth W]	Spt5-NGN	e6j51W2	A: a+b two layers	X: Alpha-beta plaits	H: N-utilization substance G protein NusG, N-terminal domain (From Topology)	T: N-utilization substance G protein NusG, N-terminal domain	F: Spt5-NGN	ECOD (1.6)
S [auth a]	Histone	e6j51a1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: Histone	ECOD (1.6)
W [auth e]	Histone	e6j51e1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: Histone	ECOD (1.6)
B	RNA_pol_Rpb2_6_3rd_2	e6j51B3	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: double psi	F: RNA_pol_Rpb2_6_3rd_2	ECOD (1.6)
B	RNA_pol_Rpb2_6_2nd_1	e6j51B5	A: a+b complex topology	X: alpha/beta-Hammerhead/Barrel-sandwich hybrid	H: alpha/beta-Hammerhead/Barrel-sandwich hybrid	T: Single hybrid motif	F: RNA_pol_Rpb2_6_2nd_1	ECOD (1.6)
B	RNA_pol_Rpb2_3	e6j51B7	A: a+b complex topology	X: N-terminal domain in beta subunit of DNA dependent RNA-polymerase (From Topology)	H: N-terminal domain in beta subunit of DNA dependent RNA-polymerase (From Topology)	T: N-terminal domain in beta subunit of DNA dependent RNA-polymerase	F: RNA_pol_Rpb2_3	ECOD (1.6)
B	RNA_pol_Rpb2_1	e6j51B4	A: a+b complex topology	X: insertion domain in beta subunit of DNA dependent RNA-polymerase (From Topology)	H: insertion domain in beta subunit of DNA dependent RNA-polymerase (From Topology)	T: insertion domain in beta subunit of DNA dependent RNA-polymerase	F: RNA_pol_Rpb2_1	ECOD (1.6)
B	RNA_pol_Rpb2_45_1	e6j51B2	A: a+b complex topology	X: barrel domain in beta subunit of DNA dependent RNA-polymerase (From Topology)	H: barrel domain in beta subunit of DNA dependent RNA-polymerase (From Topology)	T: barrel domain in beta subunit of DNA dependent RNA-polymerase	F: RNA_pol_Rpb2_45_1	ECOD (1.6)
B	RNA_pol_Rpb2_7	e6j51B6	A: a+b complex topology	X: C-terminal domain in beta subunit of DNA dependent RNA-polymerase (From Topology)	H: C-terminal domain in beta subunit of DNA dependent RNA-polymerase (From Topology)	T: C-terminal domain in beta subunit of DNA dependent RNA-polymerase	F: RNA_pol_Rpb2_7	ECOD (1.6)
B	RNA_pol_Rpb2_4	e6j51B1	A: a+b complex topology	X: inserted a+b domain in yeast RNA polymerase beta subunit (From Topology)	H: inserted a+b domain in yeast RNA polymerase beta subunit (From Topology)	T: inserted a+b domain in yeast RNA polymerase beta subunit	F: RNA_pol_Rpb2_4	ECOD (1.6)
T [auth b]	Histone_1	e6j51b1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: Histone_1	ECOD (1.6)
X [auth f]	Histone_1	e6j51f1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: Histone_1	ECOD (1.6)
U [auth c]	Histone_1	e6j51c1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: Histone_1	ECOD (1.6)
Y [auth g]	Histone_1	e6j51g1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: Histone_1	ECOD (1.6)
V [auth d]	Histone	e6j51d1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: Histone	ECOD (1.6)
Z [auth h]	Histone	e6j51h1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: Histone	ECOD (1.6)
C	RNA_pol_L_1	e6j51C2	A: a+b two layers	X: DCoH-like	H: RBP11-like subunits of RNA polymerase (From Topology)	T: RBP11-like subunits of RNA polymerase	F: RNA_pol_L_1	ECOD (1.6)
C	RNA_pol_A_bac_1	e6j51C1	A: a+b complex topology	X: Ribosomal protein TL5/L25 C-terminal domain-like	H: Insert subdomain of RNA polymerase alpha subunit (From Topology)	T: Insert subdomain of RNA polymerase alpha subunit	F: RNA_pol_A_bac_1	ECOD (1.6)
D	RNA_pol_Rpb4	e6j51D1	A: alpha arrays	X: HhH/H2TH	H: SAM/DNA-glycosylase	T: SAM domain-like	F: RNA_pol_Rpb4	ECOD (1.6)
E	RNA_pol_Rpb5_C	e6j51E1	A: a+b two layers	X: RPB5-like RNA polymerase subunit (From Topology)	H: RPB5-like RNA polymerase subunit (From Topology)	T: RPB5-like RNA polymerase subunit	F: RNA_pol_Rpb5_C	ECOD (1.6)
E	RNA_pol_Rpb5_N	e6j51E2	A: a/b three-layered sandwiches	X: Restriction endonuclease-like	H: Eukaryotic RPB5 N-terminal domain (From Topology)	T: Eukaryotic RPB5 N-terminal domain	F: RNA_pol_Rpb5_N	ECOD (1.6)
F	RNA_pol_Rpb6_1	e6j51F1	A: alpha arrays	X: RPB6/omega subunit-like (From Homology)	H: RPB6/omega subunit-like	T: RPB6	F: RNA_pol_Rpb6_1	ECOD (1.6)
G	S1_1	e6j51G1	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: S1_1	ECOD (1.6)
G	SHS2_Rpb7-N	e6j51G2	A: a+b two layers	X: Dodecin subunit-like	H: Flavin-binding protein dodecin-like (From Topology)	T: Flavin-binding protein dodecin-like	F: SHS2_Rpb7-N	ECOD (1.6)
H	RNA_pol_Rpb8	e6j51H1	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: RNA_pol_Rpb8	ECOD (1.6)
I	RNA_POL_M_15KD	e6j51I1	A: few secondary structure elements	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: RNA_POL_M_15KD	ECOD (1.6)
I	TFIIS_C	e6j51I2	A: few secondary structure elements	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: TFIIS_C	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF00623	RNA polymerase Rpb1, domain 2 (RNA_pol_Rpb1_2)	RNA polymerase Rpb1, domain 2	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 2, contains the active site ...	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 2, contains the active site. The invariant motif -NADFDGD- binds the active site magnesium ion [1,2].	Domain
A	PF04990	RNA polymerase Rpb1, domain 7 (RNA_pol_Rpb1_7)	RNA polymerase Rpb1, domain 7	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 7, represents a mobile modu ...	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 7, represents a mobile module of the RNA polymerase. Domain 7 forms a substantial interaction with the lobe domain of Rpb2 (Pfam:PF04561) [1,2].	Domain
A	PF05000	RNA polymerase Rpb1, domain 4 (RNA_pol_Rpb1_4)	RNA polymerase Rpb1, domain 4	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 4, represents the funnel do ...	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 4, represents the funnel domain. The funnel contain the binding site for some elongation factors [1,2].	Domain
A	PF04983	RNA polymerase Rpb1, domain 3 (RNA_pol_Rpb1_3)	RNA polymerase Rpb1, domain 3	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 3, represents the pore doma ...	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 3, represents the pore domain. The 3' end of RNA is positioned close to this domain. The pore delimited by this domain is thought to act as a channel through which nucleotides enter the active site and/or where the 3' end of the RNA may be extruded during back-tracking [1,2].	Domain
A	PF04992	RNA polymerase Rpb1, domain 6 (RNA_pol_Rpb1_6)	RNA polymerase Rpb1, domain 6	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 6, represents a mobile modu ...	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 6, represents a mobile module of the RNA polymerase. Domain 6 forms part of the shelf module [1,2]. This family appears to be specific to the largest subunit of RNA polymerase II.	Domain
A	PF04998	RNA polymerase Rpb1, domain 5 (RNA_pol_Rpb1_5)	RNA polymerase Rpb1, domain 5	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 5, represents the discontin ...	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 5, represents the discontinuous cleft domain that is required to from the central cleft or channel where the DNA is bound [1,2].	Domain
A	PF04997	RNA polymerase Rpb1, domain 1 (RNA_pol_Rpb1_1)	RNA polymerase Rpb1, domain 1	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 1, represents the clamp do ...	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 1, represents the clamp domain, which a mobile domain involved in positioning the DNA, maintenance of the transcription bubble and positioning of the nascent RNA strand [1,2].	Domain
J	PF01194	RNA polymerases N / 8 kDa subunit (RNA_pol_N)	RNA polymerases N / 8 kDa subunit	-	Domain
K	PF01193	RNA polymerase Rpb3/Rpb11 dimerisation domain (RNA_pol_L)	RNA polymerase Rpb3/Rpb11 dimerisation domain	The two eukaryotic subunits Rpb3 and Rpb11 dimerise to from a platform onto which the other subunits of the RNA polymerase assemble (D/L in archaea). The prokaryotic equivalent of the Rpb3/Rpb11 platform is the alpha-alpha dimer. The dimerisation do ...	The two eukaryotic subunits Rpb3 and Rpb11 dimerise to from a platform onto which the other subunits of the RNA polymerase assemble (D/L in archaea). The prokaryotic equivalent of the Rpb3/Rpb11 platform is the alpha-alpha dimer. The dimerisation domain of the alpha subunit/Rpb3 is interrupted by an insert domain (Pfam:PF01000). Some of the alpha subunits also contain iron-sulphur binding domains (Pfam:PF00037). Rpb11 is found as a continuous domain. Members of this family include: alpha subunit from eubacteria, alpha subunits from chloroplasts, Rpb3 subunits from eukaryotes, Rpb11 subunits from eukaryotes, RpoD subunits from archaeal spp, and RpoL subunits from archaeal spp.	Domain
K	PF13656	RNA polymerase Rpb3/Rpb11 dimerisation domain (RNA_pol_L_2)	RNA polymerase Rpb3/Rpb11 dimerisation domain	The two eukaryotic subunits Rpb3 and Rpb11 dimerise to from a platform onto which the other subunits of the RNA polymerase assemble (D/L in archaea). The prokaryotic equivalent of the Rpb3/Rpb11 platform is the alpha-alpha dimer. The dimerisation do ...	The two eukaryotic subunits Rpb3 and Rpb11 dimerise to from a platform onto which the other subunits of the RNA polymerase assemble (D/L in archaea). The prokaryotic equivalent of the Rpb3/Rpb11 platform is the alpha-alpha dimer. The dimerisation domain of the alpha subunit/Rpb3 is interrupted by an insert domain (Pfam:PF01000). Some of the alpha subunits also contain iron-sulphur binding domains (Pfam:PF00037). Rpb11 is found as a continuous domain. Members of this family include: alpha subunit from eubacteria, alpha subunits from chloroplasts, Rpb3 subunits from eukaryotes, Rpb11 subunits from eukaryotes, RpoD subunits from archaeal spp, and RpoL subunits from archaeal spp. Many of the members of this family carry only the N-terminal region of Rpb11.	Domain
L	PF03604	DNA directed RNA polymerase, 7 kDa subunit (DNA_RNApol_7kD)	DNA directed RNA polymerase, 7 kDa subunit	-	Domain
P [auth M]	PF05129	Transcription elongation factor Elf1 like (Elf1)	Transcription elongation factor Elf1 like	This family of short proteins contains a putative zinc binding domain with four conserved cysteines. Swiss:P36053 has been identified as a transcription elongation factor in Saccharomyces cerevisiae [1].	Domain
Q [auth V]	PF06093	Spt4/RpoE2 zinc finger (Spt4)	Spt4/RpoE2 zinc finger	This family consists of several eukaryotic transcription elongation Spt4 proteins as well as archaebacterial RpoE2 [2]. Three transcription-elongation factors Spt4, Spt5, and Spt6 are conserved among eukaryotes and are essential for transcription via ...	This family consists of several eukaryotic transcription elongation Spt4 proteins as well as archaebacterial RpoE2 [2]. Three transcription-elongation factors Spt4, Spt5, and Spt6 are conserved among eukaryotes and are essential for transcription via the modulation of chromatin structure. Spt4 and Spt5 are tightly associated in a complex, while the physical association of the Spt4-Spt5 complex with Spt6 is considerably weaker. It has been demonstrated that Spt4, Spt5, and Spt6 play roles in transcription elongation in both yeast and humans including a role in activation by Tat. It is known that Spt4, Spt5, and Spt6 are general transcription-elongation factors, controlling transcription both positively and negatively in important regulatory and developmental roles [1]. RpoE2 is one of 13 subunits in the archaeal RNA polymerase. These proteins contain a C4-type zinc finger, and the structure has been solved in [3]. The structure reveals that Spt4-Spt5 binding is governed by an acid-dipole interaction between Spt5 and Spt4, and the complex binds to and travels along the elongating RNA polymerase. The Spt4-Spt5 complex is likely to be an ancient, core component of the transcription elongation machinery.	Domain
R [auth W]	PF03439	Early transcription elongation factor of RNA pol II, NGN section (Spt5-NGN)	Early transcription elongation factor of RNA pol II, NGN section	-	Family
R [auth W]	PF11942	Spt5 transcription elongation factor, acidic N-terminal (Spt5_N)	Spt5 transcription elongation factor, acidic N-terminal	This is the very acidic N-terminal region of the early transcription elongation factor Spt5 [1]. The Spt5-Spt4 complex regulates early transcription elongation by RNA polymerase II and has an imputed role in pre-mRNA processing via its physical assoc ...	This is the very acidic N-terminal region of the early transcription elongation factor Spt5 [1]. The Spt5-Spt4 complex regulates early transcription elongation by RNA polymerase II and has an imputed role in pre-mRNA processing via its physical association with mRNA capping enzymes. The actual function of this N-terminal domain is not known although it is dispensable for binding to Spt4 [2].	Domain
R [auth W]	PF00467	KOW motif (KOW)	KOW motif	-	Family
S [auth a], W [auth e]	PF00125	Core histone H2A/H2B/H3/H4 (Histone)	Core histone H2A/H2B/H3/H4	-	Domain
B	PF04561	RNA polymerase Rpb2, domain 2 (RNA_pol_Rpb2_2)	RNA polymerase Rpb2, domain 2	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Rpb2 is the second largest subunit of the RNA po ...	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Rpb2 is the second largest subunit of the RNA polymerase. This domain forms one of the two distinctive lobes of the Rpb2 structure. This domain is also known as the lobe domain [1]. DNA has been demonstrated to bind to the concave surface of the lobe domain, and plays a role in maintaining the transcription bubble [1]. Many of the bacterial members contain large insertions within this domain, as region known as dispensable region 1 (DRI).	Domain
B	PF04560	RNA polymerase Rpb2, domain 7 (RNA_pol_Rpb2_7)	RNA polymerase Rpb2, domain 7	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Rpb2 is the second largest subunit of the RNA p ...	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Rpb2 is the second largest subunit of the RNA polymerase. This domain comprised of the structural domains anchor and clamp [1]. The clamp region (C-terminal) contains a zinc-binding motif [1]. The clamp region is named due to its interaction with the clamp domain found in Rpb1. The domain also contains a region termed "switch 4". The switches within the polymerase are thought to signal different stages of transcription [1].	Domain
B	PF04565	RNA polymerase Rpb2, domain 3 (RNA_pol_Rpb2_3)	RNA polymerase Rpb2, domain 3	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Domain 3, s also known as the fork domain and is ...	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Domain 3, s also known as the fork domain and is proximal to catalytic site [1].	Domain
B	PF04566	RNA polymerase Rpb2, domain 4 (RNA_pol_Rpb2_4)	RNA polymerase Rpb2, domain 4	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Domain 4, is also known as the external 2 domain ...	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Domain 4, is also known as the external 2 domain [1].	Domain
B	PF04563	RNA polymerase beta subunit (RNA_pol_Rpb2_1)	RNA polymerase beta subunit	-	Family
B	PF00562	RNA polymerase Rpb2, domain 6 (RNA_pol_Rpb2_6)	RNA polymerase Rpb2, domain 6	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain represents the hybrid binding domain ...	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain represents the hybrid binding domain and the wall domain [1]. The hybrid binding domain binds the nascent RNA strand / template DNA strand in the Pol II transcription elongation complex. This domain contains the important structural motifs, switch 3 and the flap loop and binds an active site metal ion[1]. This domain is also involved in binding to Rpb1 and Rpb3 [1]. Many of the bacterial members contain large insertions within this domain, as region known as dispensable region 2 (DRII).	Domain
B	PF04567	RNA polymerase Rpb2, domain 5 (RNA_pol_Rpb2_5)	RNA polymerase Rpb2, domain 5	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Domain 5, is also known as the external 2 domain ...	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Domain 5, is also known as the external 2 domain [1].	Domain
T [auth b], X [auth f]	PF15511	Centromere kinetochore component CENP-T histone fold (CENP-T_C)	Centromere kinetochore component CENP-T histone fold	CENP-T is a family of vertebral kinetochore proteins that associates directly with CENP-W. The N-terminus of CENP-T proteins interacts directly with the Ndc80 complex in the outer kinetochore. Importantly, the CENP-T-W complex does not directly asso ...	CENP-T is a family of vertebral kinetochore proteins that associates directly with CENP-W. The N-terminus of CENP-T proteins interacts directly with the Ndc80 complex in the outer kinetochore. Importantly, the CENP-T-W complex does not directly associate with CENP-A, but with histone H3 in the centromere region. CENP-T and -W form a hetero-tetramer with CENP-S and -X and bind to a ~100 bp region of nucleosome-free DNA forming a nucleosome-like structure. The DNA-CENP-T-W-S-X complex is likely to be associated with histone H3-containing nucleosomes rather than with CENP-nucleosomes. This domain is the C-terminal histone fold domain of CENP-T, which associates with chromatin [2-3].	Domain
U [auth c], Y [auth g]	PF16211	C-terminus of histone H2A (Histone_H2A_C)	C-terminus of histone H2A	-	Family
U [auth c], Y [auth g]	PF00125	Core histone H2A/H2B/H3/H4 (Histone)	Core histone H2A/H2B/H3/H4	-	Domain
V [auth d], Z [auth h]	PF00125	Core histone H2A/H2B/H3/H4 (Histone)	Core histone H2A/H2B/H3/H4	-	Domain
C	PF01193	RNA polymerase Rpb3/Rpb11 dimerisation domain (RNA_pol_L)	RNA polymerase Rpb3/Rpb11 dimerisation domain	The two eukaryotic subunits Rpb3 and Rpb11 dimerise to from a platform onto which the other subunits of the RNA polymerase assemble (D/L in archaea). The prokaryotic equivalent of the Rpb3/Rpb11 platform is the alpha-alpha dimer. The dimerisation do ...	The two eukaryotic subunits Rpb3 and Rpb11 dimerise to from a platform onto which the other subunits of the RNA polymerase assemble (D/L in archaea). The prokaryotic equivalent of the Rpb3/Rpb11 platform is the alpha-alpha dimer. The dimerisation domain of the alpha subunit/Rpb3 is interrupted by an insert domain (Pfam:PF01000). Some of the alpha subunits also contain iron-sulphur binding domains (Pfam:PF00037). Rpb11 is found as a continuous domain. Members of this family include: alpha subunit from eubacteria, alpha subunits from chloroplasts, Rpb3 subunits from eukaryotes, Rpb11 subunits from eukaryotes, RpoD subunits from archaeal spp, and RpoL subunits from archaeal spp.	Domain
C	PF01000	RNA polymerase Rpb3/RpoA insert domain (RNA_pol_A_bac)	RNA polymerase Rpb3/RpoA insert domain	Members of this family include: alpha subunit from eubacteria alpha subunits from chloroplasts Rpb3 subunits from eukaryotes RpoD subunits from archaeal	Domain
D	PF03874	RNA polymerase Rpb4 (RNA_pol_Rpb4)	RNA polymerase Rpb4	-	Family
E	PF01191	RNA polymerase Rpb5, C-terminal domain (RNA_pol_Rpb5_C)	RNA polymerase Rpb5, C-terminal domain	The assembly domain of Rpb5 [1]. The archaeal equivalent to this domain is subunit H. Subunit H lacks the N-terminal domain.	Domain
E	PF03871	RNA polymerase Rpb5, N-terminal domain (RNA_pol_Rpb5_N)	RNA polymerase Rpb5, N-terminal domain	Rpb5 has a bipartite structure which includes a eukaryote-specific N-terminal domain and a C-terminal domain resembling the archaeal RNAP subunit H [1,2]. The N-terminal domain is involved in DNA binding and is part of the jaw module in the RNA p ...	Rpb5 has a bipartite structure which includes a eukaryote-specific N-terminal domain and a C-terminal domain resembling the archaeal RNAP subunit H [1,2]. The N-terminal domain is involved in DNA binding and is part of the jaw module in the RNA pol II structure [3]. This module is important for positioning the downstream DNA.	Domain
F	PF01192	RNA polymerase Rpb6 (RNA_pol_Rpb6)	RNA polymerase Rpb6	-	Family
G	PF03876	SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397 (SHS2_Rpb7-N)	SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397	Rpb7 bind to Rpb4 to form a heterodimer. This complex is thought to interact with the nascent RNA strand during RNA polymerase II elongation[1]. This family includes the homologs from RNA polymerase I and III. In RNA polymerase I, Rpa43 is at leas ...	Rpb7 bind to Rpb4 to form a heterodimer. This complex is thought to interact with the nascent RNA strand during RNA polymerase II elongation[1]. This family includes the homologs from RNA polymerase I and III. In RNA polymerase I, Rpa43 is at least one of the subunits contacted by the transcription factor TIF-IA [2]. The N terminus of Rpb7p/Rpc25p/MJ0397 has a SHS2 domain that is involved in protein-protein interaction [3].	Domain
G	PF00575	S1 RNA binding domain (S1)	S1 RNA binding domain	The S1 domain occurs in a wide range of RNA associated proteins. It is structurally similar to cold shock protein which binds nucleic acids. The S1 domain has an OB-fold structure.	Domain
H	PF03870	RNA polymerase Rpb8 (RNA_pol_Rpb8)	RNA polymerase Rpb8	-	Family
I	PF02150	RNA polymerases M/15 Kd subunit (RNA_POL_M_15KD)	RNA polymerases M/15 Kd subunit	-	Domain
I	PF01096	Transcription factor S-II (TFIIS) (TFIIS_C)	Transcription factor S-II (TFIIS)	-	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	DNA-directed RNA polymerase subunit	DNA binding binding organic cyclic compound binding nucleic acid binding DNA-directed 5'-3' RNA polymerase activity 5'-3' RNA polymerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA polymerase activity transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups cation binding DNA binding binding organic cyclic compound binding nucleic acid binding DNA-directed 5'-3' RNA polymerase activity 5'-3' RNA polymerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA polymerase activity transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups cation binding ion binding metal ion binding small molecule binding	cellular biosynthetic process cellular metabolic process RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription organic cyclic compound metabolic process nucleic acid biosynthetic process transcription by RNA polymerase II organic substance metabolic process cellular biosynthetic process cellular metabolic process RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription organic cyclic compound metabolic process nucleic acid biosynthetic process transcription by RNA polymerase II organic substance metabolic process biosynthetic process organic cyclic compound biosynthetic process organic substance biosynthetic process metabolic process cellular process macromolecule metabolic process	membrane-bounded organelle intracellular organelle intracellular anatomical structure organelle nucleus intracellular membrane-bounded organelle cellular anatomical entity transferase complex, transferring phosphorus-containing groups protein-containing complex catalytic complex RNA polymerase complex DNA-directed RNA polymerase complex transferase complex intracellular protein-containing complex
J	RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III	DNA binding binding organic cyclic compound binding nucleic acid binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding DNA-directed 5'-3' RNA polymerase activity 5'-3' RNA polymerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid DNA binding binding organic cyclic compound binding nucleic acid binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding DNA-directed 5'-3' RNA polymerase activity 5'-3' RNA polymerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA polymerase activity transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups	cellular biosynthetic process cellular metabolic process RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription organic cyclic compound metabolic process nucleic acid biosynthetic process organic substance metabolic process biosynthetic process cellular biosynthetic process cellular metabolic process RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription organic cyclic compound metabolic process nucleic acid biosynthetic process organic substance metabolic process biosynthetic process organic cyclic compound biosynthetic process organic substance biosynthetic process metabolic process cellular process macromolecule metabolic process transcription by RNA polymerase III transcription by RNA polymerase II transcription initiation at RNA polymerase II promoter DNA-templated transcription initiation transcription by RNA polymerase I	membrane-bounded organelle protein-containing complex intracellular anatomical structure RNA polymerase I complex nucleus membrane-enclosed lumen nuclear protein-containing complex transferase complex intracellular organelle lumen intracellular organelle non-membrane-bounded organelle catalytic complex intracellular membrane-bounded organelle cellular anatomical entity membrane-bounded organelle protein-containing complex intracellular anatomical structure RNA polymerase I complex nucleus membrane-enclosed lumen nuclear protein-containing complex transferase complex intracellular organelle lumen intracellular organelle non-membrane-bounded organelle catalytic complex intracellular membrane-bounded organelle cellular anatomical entity nucleolus transferase complex, transferring phosphorus-containing groups nuclear DNA-directed RNA polymerase complex organelle lumen organelle intracellular non-membrane-bounded organelle RNA polymerase complex DNA-directed RNA polymerase complex intracellular protein-containing complex nuclear lumen RNA polymerase III complex RNA polymerase II, holoenzyme nucleoplasm RNA polymerase II, core complex
K	RNA polymerase II subunit B12.5	DNA binding binding organic cyclic compound binding nucleic acid binding 5'-3' RNA polymerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA polymerase activity transferase activity RNA-dependent RNA polymerase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups DNA-directed 5'-3' RNA polymerase activity DNA binding binding organic cyclic compound binding nucleic acid binding 5'-3' RNA polymerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA polymerase activity transferase activity RNA-dependent RNA polymerase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups DNA-directed 5'-3' RNA polymerase activity RNA polymerase II activity protein binding protein dimerization activity	cellular biosynthetic process RNA metabolic process DNA-templated transcription termination RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process transcription by RNA polymerase II organic substance metabolic process organic substance biosynthetic process cellular metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression cellular biosynthetic process RNA metabolic process DNA-templated transcription termination RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process transcription by RNA polymerase II organic substance metabolic process organic substance biosynthetic process cellular metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process organic cyclic compound metabolic process biosynthetic process organic cyclic compound biosynthetic process metabolic process cellular process macromolecule metabolic process termination of RNA polymerase II transcription transcription initiation at RNA polymerase II promoter DNA-templated transcription initiation transcription elongation by RNA polymerase II DNA-templated transcription elongation	membrane-bounded organelle RNA polymerase II, holoenzyme protein-containing complex intracellular anatomical structure nucleus membrane-enclosed lumen nuclear protein-containing complex transferase complex intracellular organelle lumen intracellular organelle nucleoplasm RNA polymerase II, core complex catalytic complex intracellular membrane-bounded organelle membrane-bounded organelle RNA polymerase II, holoenzyme protein-containing complex intracellular anatomical structure nucleus membrane-enclosed lumen nuclear protein-containing complex transferase complex intracellular organelle lumen intracellular organelle nucleoplasm RNA polymerase II, core complex catalytic complex intracellular membrane-bounded organelle cellular anatomical entity transferase complex, transferring phosphorus-containing groups nuclear DNA-directed RNA polymerase complex organelle lumen organelle RNA polymerase complex DNA-directed RNA polymerase complex intracellular protein-containing complex nuclear lumen
L	RNA polymerase subunit ABC10-alpha	DNA binding binding organic cyclic compound binding nucleic acid binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding DNA-directed 5'-3' RNA polymerase activity 5'-3' RNA polymerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid DNA binding binding organic cyclic compound binding nucleic acid binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding DNA-directed 5'-3' RNA polymerase activity 5'-3' RNA polymerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA polymerase activity transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups	cellular biosynthetic process cellular metabolic process RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription organic cyclic compound metabolic process nucleic acid biosynthetic process organic substance metabolic process biosynthetic process cellular biosynthetic process cellular metabolic process RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription organic cyclic compound metabolic process nucleic acid biosynthetic process organic substance metabolic process biosynthetic process organic cyclic compound biosynthetic process organic substance biosynthetic process metabolic process cellular process macromolecule metabolic process	membrane-bounded organelle intracellular organelle intracellular anatomical structure organelle nucleus intracellular membrane-bounded organelle cellular anatomical entity
M [auth P]	RNA (5'-R(PCPCPUPGPGPUPGPUPCPUPUPGPGPGPUPG)-3')	-	-	-
N [auth T]	DNA (198-MER)	-	-	-
O [auth N]	DNA (198-MER)	-	-	-
P [auth M]	Transcription elongation factor 1 homolog	cation binding ion binding binding metal ion binding small molecule binding	-	membrane-bounded organelle intracellular organelle intracellular anatomical structure organelle nucleus intracellular membrane-bounded organelle cellular anatomical entity
Q [auth V]	Transcription elongation factor SPT4	cation binding transition metal ion binding zinc ion binding ion binding binding metal ion binding small molecule binding	regulation of cellular process cellular biosynthetic process RNA metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process organic substance metabolic process organic substance biosynthetic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of cellular process cellular biosynthetic process RNA metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process organic substance metabolic process organic substance biosynthetic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of biological process cellular metabolic process biological regulation primary metabolic process regulation of cellular metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of cellular biosynthetic process organic cyclic compound metabolic process regulation of gene expression biosynthetic process organic cyclic compound biosynthetic process metabolic process regulation of macromolecule biosynthetic process cellular process regulation of DNA-templated transcription macromolecule metabolic process regulation of metabolic process transcription elongation by RNA polymerase II protein-DNA complex organization cellular component organization transcription by RNA polymerase II chromatin organization chromatin remodeling cellular component organization or biogenesis transcription elongation-coupled chromatin remodeling protein-containing complex organization DNA-templated transcription elongation	membrane-bounded organelle protein-containing complex intracellular anatomical structure transcription elongation factor complex DSIF complex nucleus membrane-enclosed lumen nuclear protein-containing complex intracellular membrane-bounded organelle cellular anatomical entity intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen membrane-bounded organelle protein-containing complex intracellular anatomical structure transcription elongation factor complex DSIF complex nucleus membrane-enclosed lumen nuclear protein-containing complex intracellular membrane-bounded organelle cellular anatomical entity intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen intracellular non-membrane-bounded organelle chromosome, centromeric region chromosome chromosomal region non-membrane-bounded organelle
R [auth W]	Protein that forms a complex with Spt4p	transcription regulator activity transcription elongation factor activity	transcription elongation by RNA polymerase II cellular biosynthetic process RNA metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process organic substance metabolic process transcription by RNA polymerase II organic substance biosynthetic process cellular metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression transcription elongation by RNA polymerase II cellular biosynthetic process RNA metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process organic substance metabolic process transcription by RNA polymerase II organic substance biosynthetic process cellular metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process organic cyclic compound metabolic process DNA-templated transcription elongation biosynthetic process organic cyclic compound biosynthetic process metabolic process cellular process macromolecule metabolic process regulation of cellular process regulation of primary metabolic process regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of transcription by RNA polymerase II regulation of biosynthetic process regulation of biological process biological regulation regulation of cellular metabolic process regulation of macromolecule metabolic process regulation of cellular biosynthetic process regulation of gene expression regulation of macromolecule biosynthetic process regulation of DNA-templated transcription regulation of metabolic process regulation of DNA-templated transcription elongation	membrane-bounded organelle protein-containing complex intracellular anatomical structure transcription elongation factor complex DSIF complex nucleus membrane-enclosed lumen nuclear protein-containing complex intracellular membrane-bounded organelle cellular anatomical entity intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen membrane-bounded organelle protein-containing complex intracellular anatomical structure transcription elongation factor complex DSIF complex nucleus membrane-enclosed lumen nuclear protein-containing complex intracellular membrane-bounded organelle cellular anatomical entity intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen
S [auth a], W [auth e]	Histone H3.3	DNA binding protein-containing complex binding binding chromatin binding organic cyclic compound binding nucleic acid binding nucleosome binding nucleosomal DNA binding chromatin DNA binding sequence-specific DNA binding double-stranded DNA binding RNA polymerase II transcription regulatory region sequence-specific DNA binding cis-regulatory region sequence-specific DNA binding sequence-specific double-stranded DNA binding DNA binding protein-containing complex binding binding chromatin binding organic cyclic compound binding nucleic acid binding nucleosome binding nucleosomal DNA binding chromatin DNA binding sequence-specific DNA binding double-stranded DNA binding RNA polymerase II transcription regulatory region sequence-specific DNA binding cis-regulatory region sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding transcription regulatory region nucleic acid binding RNA polymerase II cis-regulatory region sequence-specific DNA binding protein heterodimerization activity protein binding protein dimerization activity core promoter sequence-specific DNA binding RNA polymerase II core promoter sequence-specific DNA binding structural molecule activity structural constituent of chromatin	protein-containing complex organization protein-DNA complex assembly protein-DNA complex organization cellular component organization cellular component biogenesis cellular component assembly chromatin organization protein-containing complex assembly chromatin remodeling cellular process cellular component organization or biogenesis nucleosome assembly nucleosome organization regulation of biological process protein-containing complex organization protein-DNA complex assembly protein-DNA complex organization cellular component organization cellular component biogenesis cellular component assembly chromatin organization protein-containing complex assembly chromatin remodeling cellular process cellular component organization or biogenesis nucleosome assembly nucleosome organization regulation of biological process regulation of growth regulation of cellular process regulation of cellular component organization positive regulation of biological process biological regulation growth positive regulation of cell growth regulation of cell growth cell growth positive regulation of growth positive regulation of cellular process organelle organization telomere organization chromosome organization	extracellular region cellular anatomical entity extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle organelle extracellular space vesicle extracellular membrane-bounded organelle protein-containing complex intracellular anatomical structure protein-DNA complex nucleosome extracellular region cellular anatomical entity extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle organelle extracellular space vesicle extracellular membrane-bounded organelle protein-containing complex intracellular anatomical structure protein-DNA complex nucleosome chromatin chromosome intracellular organelle intracellular non-membrane-bounded organelle non-membrane-bounded organelle chromosome, telomeric region chromosomal region nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen
B	DNA-directed RNA polymerase subunit beta	DNA binding binding organic cyclic compound binding nucleic acid binding DNA-directed 5'-3' RNA polymerase activity 5'-3' RNA polymerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA polymerase activity transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups ribonucleoside binding DNA binding binding organic cyclic compound binding nucleic acid binding DNA-directed 5'-3' RNA polymerase activity 5'-3' RNA polymerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA polymerase activity transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups ribonucleoside binding nucleoside binding heterocyclic compound binding carbohydrate derivative binding small molecule binding RNA binding cation binding ion binding metal ion binding	cellular biosynthetic process RNA metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process transcription by RNA polymerase II organic substance metabolic process organic substance biosynthetic process transcription initiation at RNA polymerase II promoter cellular metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression cellular biosynthetic process RNA metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process transcription by RNA polymerase II organic substance metabolic process organic substance biosynthetic process transcription initiation at RNA polymerase II promoter cellular metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process DNA-templated transcription initiation organic cyclic compound metabolic process biosynthetic process organic cyclic compound biosynthetic process metabolic process cellular process macromolecule metabolic process regulation of cellular process negative regulation of biological process negative regulation of cellular metabolic process protein-DNA complex organization cellular component organization chromatin organization negative regulation of cellular process chromatin remodeling cellular component organization or biogenesis negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of biological process heterochromatin formation protein-containing complex organization epigenetic regulation of gene expression negative regulation of metabolic process biological regulation regulation of cellular metabolic process regulation of macromolecule metabolic process negative regulation of cellular biosynthetic process regulation of cellular biosynthetic process regulatory ncRNA-mediated gene silencing regulation of gene expression negative regulation of gene expression regulatory ncRNA-mediated heterochromatin formation negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of gene expression, epigenetic regulation of macromolecule biosynthetic process regulation of metabolic process	membrane-bounded organelle RNA polymerase II, holoenzyme protein-containing complex intracellular anatomical structure nucleus membrane-enclosed lumen nuclear protein-containing complex transferase complex intracellular organelle lumen intracellular organelle nucleoplasm RNA polymerase II, core complex catalytic complex intracellular membrane-bounded organelle membrane-bounded organelle RNA polymerase II, holoenzyme protein-containing complex intracellular anatomical structure nucleus membrane-enclosed lumen nuclear protein-containing complex transferase complex intracellular organelle lumen intracellular organelle nucleoplasm RNA polymerase II, core complex catalytic complex intracellular membrane-bounded organelle cellular anatomical entity transferase complex, transferring phosphorus-containing groups nuclear DNA-directed RNA polymerase complex organelle lumen organelle RNA polymerase complex DNA-directed RNA polymerase complex intracellular protein-containing complex nuclear lumen pericentric heterochromatin protein-DNA complex chromatin chromosome heterochromatin chromosomal region intracellular non-membrane-bounded organelle chromosome, centromeric region non-membrane-bounded organelle
T [auth b], X [auth f]	Histone H4	DNA binding binding organic cyclic compound binding nucleic acid binding protein heterodimerization activity protein binding protein dimerization activity RNA binding structural molecule activity structural constituent of chromatin	protein-containing complex organization protein-DNA complex assembly protein-DNA complex organization cellular component organization cellular component biogenesis cellular component assembly chromatin organization protein-containing complex assembly chromatin remodeling cellular process cellular component organization or biogenesis nucleosome assembly nucleosome organization organelle organization protein-containing complex organization protein-DNA complex assembly protein-DNA complex organization cellular component organization cellular component biogenesis cellular component assembly chromatin organization protein-containing complex assembly chromatin remodeling cellular process cellular component organization or biogenesis nucleosome assembly nucleosome organization organelle organization telomere organization chromosome organization protein localization protein localization to chromatin cellular localization protein localization to chromosome, centromeric region localization protein localization to chromosome protein localization to organelle cellular macromolecule localization macromolecule localization protein localization to CENP-A containing chromatin multicellular organismal process regulation of cellular process cellular developmental process regulation of developmental process regulation of megakaryocyte differentiation negative regulation of biological process megakaryocyte differentiation cell development regulation of cell differentiation regulation of cell development multicellular organism development negative regulation of megakaryocyte differentiation cell differentiation anatomical structure development negative regulation of cellular process negative regulation of cell differentiation regulation of immune system process regulation of multicellular organismal process developmental process regulation of biological process regulation of multicellular organismal development hemopoiesis negative regulation of developmental process regulation of myeloid cell differentiation biological regulation negative regulation of myeloid cell differentiation myeloid cell differentiation immune system process regulation of hemopoiesis	membrane cellular anatomical entity extracellular region extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle organelle extracellular space vesicle extracellular membrane-bounded organelle protein-containing complex intracellular anatomical structure CENP-A containing chromatin membrane cellular anatomical entity extracellular region extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle organelle extracellular space vesicle extracellular membrane-bounded organelle protein-containing complex intracellular anatomical structure CENP-A containing chromatin protein-DNA complex nucleosome chromosome chromatin chromosomal region intracellular organelle chromosome, centromeric core domain CENP-A containing nucleosome intracellular non-membrane-bounded organelle chromosome, centromeric region non-membrane-bounded organelle chromosome, telomeric region nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen
U [auth c], Y [auth g]	Histone H2A type 1-B/E	DNA binding binding organic cyclic compound binding nucleic acid binding protein heterodimerization activity protein binding protein dimerization activity structural molecule activity structural constituent of chromatin	negative regulation of cell population proliferation regulation of biological process cell population proliferation regulation of cellular process regulation of cell population proliferation negative regulation of cellular process biological regulation negative regulation of biological process cellular process protein localization protein localization to chromatin cellular localization protein localization to chromosome, centromeric region localization negative regulation of cell population proliferation regulation of biological process cell population proliferation regulation of cellular process regulation of cell population proliferation negative regulation of cellular process biological regulation negative regulation of biological process cellular process protein localization protein localization to chromatin cellular localization protein localization to chromosome, centromeric region localization protein localization to chromosome protein localization to organelle cellular macromolecule localization macromolecule localization protein localization to CENP-A containing chromatin protein-DNA complex organization cellular component organization protein-containing complex organization chromatin organization cellular component organization or biogenesis	extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space cellular anatomical entity vesicle extracellular membrane-bounded organelle protein-containing complex intracellular anatomical structure CENP-A containing chromatin protein-DNA complex extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space cellular anatomical entity vesicle extracellular membrane-bounded organelle protein-containing complex intracellular anatomical structure CENP-A containing chromatin protein-DNA complex nucleosome chromosome chromatin chromosomal region intracellular organelle chromosome, centromeric core domain CENP-A containing nucleosome intracellular non-membrane-bounded organelle chromosome, centromeric region non-membrane-bounded organelle nucleus intracellular membrane-bounded organelle
V [auth d], Z [auth h]	Histone H2B type 1-J	DNA binding binding organic cyclic compound binding nucleic acid binding protein heterodimerization activity protein binding protein dimerization activity lipid binding lipopolysaccharide binding carbohydrate derivative binding structural molecule activity structural constituent of chromatin	protein-containing complex organization protein-DNA complex assembly protein-DNA complex organization cellular component organization cellular component biogenesis cellular component assembly chromatin organization protein-containing complex assembly chromatin remodeling cellular process cellular component organization or biogenesis nucleosome assembly nucleosome organization biological process involved in interspecies interaction between organisms protein-containing complex organization protein-DNA complex assembly protein-DNA complex organization cellular component organization cellular component biogenesis cellular component assembly chromatin organization protein-containing complex assembly chromatin remodeling cellular process cellular component organization or biogenesis nucleosome assembly nucleosome organization biological process involved in interspecies interaction between organisms innate immune response in mucosa response to stimulus immune response response to other organism defense response defense response to symbiont response to external stimulus response to biotic stimulus immune system process defense response to other organism response to stress innate immune response response to external biotic stimulus mucosal immune response organ or tissue specific immune response humoral immune response antimicrobial humoral response antimicrobial humoral immune response mediated by antimicrobial peptide disruption of cell in another organism disruption of anatomical structure in another organism killing of cells of another organism cell killing defense response to Gram-negative bacterium defense response to bacterium response to bacterium antibacterial humoral response protein localization protein localization to chromatin cellular localization protein localization to chromosome, centromeric region localization protein localization to chromosome protein localization to organelle cellular macromolecule localization macromolecule localization protein localization to CENP-A containing chromatin cellular response to stimulus response to organic substance regulation of cellular process negative regulation of signaling signaling negative regulation of biological process response to cytokine regulation of signal transduction negative regulation of cell communication cytokine-mediated signaling pathway cell communication cellular response to tumor necrosis factor negative regulation of cellular process tumor necrosis factor-mediated signaling pathway cellular response to cytokine stimulus signal transduction cellular response to organic substance regulation of biological process regulation of signaling cell surface receptor signaling pathway regulation of tumor necrosis factor-mediated signaling pathway negative regulation of response to stimulus regulation of cytokine-mediated signaling pathway biological regulation negative regulation of tumor necrosis factor-mediated signaling pathway negative regulation of signal transduction regulation of response to cytokine stimulus cellular response to chemical stimulus negative regulation of response to cytokine stimulus regulation of response to stimulus negative regulation of cytokine-mediated signaling pathway response to chemical regulation of cell communication response to tumor necrosis factor defense response to Gram-positive bacterium	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol protein-containing complex CENP-A containing chromatin protein-DNA complex nucleosome chromosome chromatin chromosomal region intracellular organelle chromosome, centromeric core domain CENP-A containing nucleosome intracellular anatomical structure cytoplasm cellular anatomical entity cytosol protein-containing complex CENP-A containing chromatin protein-DNA complex nucleosome chromosome chromatin chromosomal region intracellular organelle chromosome, centromeric core domain CENP-A containing nucleosome organelle intracellular non-membrane-bounded organelle chromosome, centromeric region non-membrane-bounded organelle extracellular region extracellular space membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen
AA [auth 0]	DNA (36-MER)	-	-	-
BA [auth 1]	DNA (36-MER)	-	-	-
C	RNA polymerase II third largest subunit B44, part of central core	DNA binding binding organic cyclic compound binding nucleic acid binding protein binding protein dimerization activity DNA-directed 5'-3' RNA polymerase activity 5'-3' RNA polymerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA polymerase activity transferase activity nucleotidyltransferase activity catalytic activity DNA binding binding organic cyclic compound binding nucleic acid binding protein binding protein dimerization activity DNA-directed 5'-3' RNA polymerase activity 5'-3' RNA polymerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA polymerase activity transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups cation binding ion binding metal ion binding small molecule binding	cellular biosynthetic process cellular metabolic process RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription organic cyclic compound metabolic process nucleic acid biosynthetic process organic substance metabolic process biosynthetic process cellular biosynthetic process cellular metabolic process RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription organic cyclic compound metabolic process nucleic acid biosynthetic process organic substance metabolic process biosynthetic process organic cyclic compound biosynthetic process organic substance biosynthetic process metabolic process cellular process macromolecule metabolic process	membrane-bounded organelle protein-containing complex intracellular anatomical structure catalytic complex nucleus nuclear protein-containing complex intracellular membrane-bounded organelle cellular anatomical entity transferase complex transferase complex, transferring phosphorus-containing groups intracellular organelle nuclear DNA-directed RNA polymerase complex organelle RNA polymerase complex membrane-bounded organelle protein-containing complex intracellular anatomical structure catalytic complex nucleus nuclear protein-containing complex intracellular membrane-bounded organelle cellular anatomical entity transferase complex transferase complex, transferring phosphorus-containing groups intracellular organelle nuclear DNA-directed RNA polymerase complex organelle RNA polymerase complex DNA-directed RNA polymerase complex intracellular protein-containing complex
D	RNA polymerase II subunit B32	5'-3' RNA polymerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA polymerase activity transferase activity RNA-dependent RNA polymerase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups protein binding binding translation initiation factor binding nucleoside phosphate binding organic cyclic compound binding 5'-3' RNA polymerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA polymerase activity transferase activity RNA-dependent RNA polymerase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups protein binding binding translation initiation factor binding nucleoside phosphate binding organic cyclic compound binding nucleotide binding heterocyclic compound binding small molecule binding DNA-directed 5'-3' RNA polymerase activity RNA binding nucleic acid binding single-stranded RNA binding DNA binding single-stranded DNA binding	cellular biosynthetic process RNA metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process transcription by RNA polymerase II organic substance metabolic process organic substance biosynthetic process transcription initiation at RNA polymerase II promoter cellular metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression cellular biosynthetic process RNA metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process transcription by RNA polymerase II organic substance metabolic process organic substance biosynthetic process transcription initiation at RNA polymerase II promoter cellular metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process DNA-templated transcription initiation organic cyclic compound metabolic process biosynthetic process organic cyclic compound biosynthetic process metabolic process cellular process macromolecule metabolic process transcription elongation by RNA polymerase II DNA-templated transcription elongation regulation of cellular process positive regulation of protein metabolic process organonitrogen compound biosynthetic process positive regulation of biological process positive regulation of translation positive regulation of cellular metabolic process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process post-transcriptional regulation of gene expression positive regulation of metabolic process positive regulation of biosynthetic process positive regulation of macromolecule metabolic process translational initiation protein metabolic process positive regulation of cellular process regulation of biosynthetic process regulation of biological process organonitrogen compound metabolic process regulation of translational initiation regulation of protein metabolic process biological regulation regulation of cellular metabolic process regulation of macromolecule metabolic process translation regulation of cellular biosynthetic process regulation of gene expression positive regulation of gene expression regulation of translation regulation of macromolecule biosynthetic process positive regulation of translational initiation regulation of metabolic process positive regulation of cellular biosynthetic process negative regulation of biological process negative regulation of cellular metabolic process regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of biological quality RNA catabolic process mRNA catabolic process positive regulation of nucleobase-containing compound metabolic process negative regulation of metabolic process positive regulation of mRNA metabolic process negative regulation of cellular biosynthetic process nucleobase-containing compound catabolic process positive regulation of RNA metabolic process negative regulation of gene expression negative regulation of macromolecule biosynthetic process nucleic acid catabolic process nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay catabolic process mRNA destabilization macromolecule catabolic process regulation of mRNA catabolic process negative regulation of cellular process negative regulation of macromolecule metabolic process RNA destabilization nuclear-transcribed mRNA catabolic process regulation of catabolic process mRNA metabolic process organic cyclic compound catabolic process positive regulation of catabolic process regulation of mRNA stability positive regulation of mRNA catabolic process negative regulation of biosynthetic process regulation of RNA stability regulation of mRNA metabolic process organic substance catabolic process	membrane-bounded organelle RNA polymerase II, holoenzyme protein-containing complex intracellular anatomical structure nucleus membrane-enclosed lumen nuclear protein-containing complex transferase complex intracellular organelle lumen intracellular organelle nucleoplasm RNA polymerase II, core complex catalytic complex intracellular membrane-bounded organelle membrane-bounded organelle RNA polymerase II, holoenzyme protein-containing complex intracellular anatomical structure nucleus membrane-enclosed lumen nuclear protein-containing complex transferase complex intracellular organelle lumen intracellular organelle nucleoplasm RNA polymerase II, core complex catalytic complex intracellular membrane-bounded organelle cellular anatomical entity transferase complex, transferring phosphorus-containing groups nuclear DNA-directed RNA polymerase complex organelle lumen organelle RNA polymerase complex DNA-directed RNA polymerase complex intracellular protein-containing complex nuclear lumen RPB4-RPB7 complex cytoplasmic ribonucleoprotein granule ribonucleoprotein granule intracellular non-membrane-bounded organelle cytoplasm supramolecular complex P-body non-membrane-bounded organelle
E	RNA polymerase subunit ABC27, common to RNA polymerases I, II, and III	DNA binding binding organic cyclic compound binding nucleic acid binding 5'-3' RNA polymerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA polymerase activity transferase activity RNA-dependent RNA polymerase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups DNA-directed 5'-3' RNA polymerase activity DNA binding binding organic cyclic compound binding nucleic acid binding 5'-3' RNA polymerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA polymerase activity transferase activity RNA-dependent RNA polymerase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups DNA-directed 5'-3' RNA polymerase activity RNA polymerase I activity RNA polymerase II activity RNA polymerase III activity	cellular biosynthetic process RNA metabolic process DNA-templated transcription termination RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process organic substance metabolic process transcription by RNA polymerase I organic substance biosynthetic process termination of RNA polymerase I transcription cellular metabolic process primary metabolic process nucleobase-containing compound biosynthetic process cellular biosynthetic process RNA metabolic process DNA-templated transcription termination RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process organic substance metabolic process transcription by RNA polymerase I organic substance biosynthetic process termination of RNA polymerase I transcription cellular metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process organic cyclic compound metabolic process biosynthetic process organic cyclic compound biosynthetic process metabolic process cellular process macromolecule metabolic process termination of RNA polymerase III transcription transcription by RNA polymerase III transcription by RNA polymerase II transcription initiation at RNA polymerase II promoter DNA-templated transcription initiation transcription initiation at RNA polymerase III promoter transcription elongation by RNA polymerase II DNA-templated transcription elongation transcription elongation by RNA polymerase I rRNA transcription rRNA metabolic process nucleolar large rRNA transcription by RNA polymerase I ncRNA metabolic process tRNA metabolic process tRNA transcription tRNA transcription by RNA polymerase III transcription initiation at RNA polymerase I promoter	membrane-bounded organelle protein-containing complex intracellular anatomical structure RNA polymerase I complex nucleus membrane-enclosed lumen nuclear protein-containing complex transferase complex intracellular organelle lumen intracellular organelle non-membrane-bounded organelle catalytic complex intracellular membrane-bounded organelle cellular anatomical entity membrane-bounded organelle protein-containing complex intracellular anatomical structure RNA polymerase I complex nucleus membrane-enclosed lumen nuclear protein-containing complex transferase complex intracellular organelle lumen intracellular organelle non-membrane-bounded organelle catalytic complex intracellular membrane-bounded organelle cellular anatomical entity nucleolus transferase complex, transferring phosphorus-containing groups nuclear DNA-directed RNA polymerase complex organelle lumen organelle intracellular non-membrane-bounded organelle RNA polymerase complex DNA-directed RNA polymerase complex intracellular protein-containing complex nuclear lumen RNA polymerase II, holoenzyme nucleoplasm RNA polymerase II, core complex RNA polymerase III complex
F	RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III	DNA binding binding organic cyclic compound binding nucleic acid binding 5'-3' RNA polymerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA polymerase activity transferase activity RNA-dependent RNA polymerase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups DNA-directed 5'-3' RNA polymerase activity DNA binding binding organic cyclic compound binding nucleic acid binding 5'-3' RNA polymerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA polymerase activity transferase activity RNA-dependent RNA polymerase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups DNA-directed 5'-3' RNA polymerase activity RNA polymerase I activity RNA polymerase II activity RNA polymerase III activity	cellular biosynthetic process RNA metabolic process DNA-templated transcription termination RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process organic substance metabolic process transcription by RNA polymerase I organic substance biosynthetic process termination of RNA polymerase I transcription cellular metabolic process primary metabolic process nucleobase-containing compound biosynthetic process cellular biosynthetic process RNA metabolic process DNA-templated transcription termination RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process organic substance metabolic process transcription by RNA polymerase I organic substance biosynthetic process termination of RNA polymerase I transcription cellular metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process organic cyclic compound metabolic process biosynthetic process organic cyclic compound biosynthetic process metabolic process cellular process macromolecule metabolic process termination of RNA polymerase III transcription transcription by RNA polymerase III transcription by RNA polymerase II transcription initiation at RNA polymerase II promoter DNA-templated transcription initiation transcription initiation at RNA polymerase III promoter transcription elongation by RNA polymerase II DNA-templated transcription elongation transcription elongation by RNA polymerase I rRNA transcription rRNA metabolic process nucleolar large rRNA transcription by RNA polymerase I ncRNA metabolic process tRNA metabolic process tRNA transcription tRNA transcription by RNA polymerase III transcription initiation at RNA polymerase I promoter	membrane-bounded organelle protein-containing complex intracellular anatomical structure RNA polymerase I complex nucleus membrane-enclosed lumen nuclear protein-containing complex transferase complex intracellular organelle lumen intracellular organelle non-membrane-bounded organelle catalytic complex intracellular membrane-bounded organelle cellular anatomical entity membrane-bounded organelle protein-containing complex intracellular anatomical structure RNA polymerase I complex nucleus membrane-enclosed lumen nuclear protein-containing complex transferase complex intracellular organelle lumen intracellular organelle non-membrane-bounded organelle catalytic complex intracellular membrane-bounded organelle cellular anatomical entity nucleolus transferase complex, transferring phosphorus-containing groups nuclear DNA-directed RNA polymerase complex organelle lumen organelle intracellular non-membrane-bounded organelle RNA polymerase complex DNA-directed RNA polymerase complex intracellular protein-containing complex nuclear lumen RNA polymerase II, holoenzyme nucleoplasm RNA polymerase II, core complex RNA polymerase III complex
G	RNA polymerase II subunit	binding organic cyclic compound binding nucleic acid binding	cellular biosynthetic process RNA metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process transcription by RNA polymerase II organic substance metabolic process organic substance biosynthetic process transcription initiation at RNA polymerase II promoter cellular metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression cellular biosynthetic process RNA metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process transcription by RNA polymerase II organic substance metabolic process organic substance biosynthetic process transcription initiation at RNA polymerase II promoter cellular metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process DNA-templated transcription initiation organic cyclic compound metabolic process biosynthetic process organic cyclic compound biosynthetic process metabolic process cellular process macromolecule metabolic process regulation of septum digestion after cytokinesis regulation of biological process regulation of cellular process biological regulation septum digestion after cytokinesis cell division	membrane-bounded organelle RNA polymerase II, holoenzyme protein-containing complex intracellular anatomical structure nucleus membrane-enclosed lumen nuclear protein-containing complex transferase complex intracellular organelle lumen intracellular organelle nucleoplasm RNA polymerase II, core complex catalytic complex intracellular membrane-bounded organelle membrane-bounded organelle RNA polymerase II, holoenzyme protein-containing complex intracellular anatomical structure nucleus membrane-enclosed lumen nuclear protein-containing complex transferase complex intracellular organelle lumen intracellular organelle nucleoplasm RNA polymerase II, core complex catalytic complex intracellular membrane-bounded organelle cellular anatomical entity transferase complex, transferring phosphorus-containing groups nuclear DNA-directed RNA polymerase complex organelle lumen organelle RNA polymerase complex DNA-directed RNA polymerase complex intracellular protein-containing complex nuclear lumen
H	DNA-directed RNA polymerases I, II, and III subunit RPABC3	5'-3' RNA polymerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA polymerase activity transferase activity RNA-dependent RNA polymerase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups DNA-directed 5'-3' RNA polymerase activity RNA polymerase I activity RNA polymerase II activity RNA polymerase III activity	cellular biosynthetic process RNA metabolic process DNA-templated transcription termination RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process organic substance metabolic process transcription by RNA polymerase I organic substance biosynthetic process termination of RNA polymerase I transcription cellular metabolic process primary metabolic process nucleobase-containing compound biosynthetic process cellular biosynthetic process RNA metabolic process DNA-templated transcription termination RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process organic substance metabolic process transcription by RNA polymerase I organic substance biosynthetic process termination of RNA polymerase I transcription cellular metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process organic cyclic compound metabolic process biosynthetic process organic cyclic compound biosynthetic process metabolic process cellular process macromolecule metabolic process termination of RNA polymerase III transcription transcription by RNA polymerase III transcription by RNA polymerase II transcription initiation at RNA polymerase II promoter DNA-templated transcription initiation transcription initiation at RNA polymerase III promoter transcription elongation by RNA polymerase II DNA-templated transcription elongation transcription elongation by RNA polymerase I rRNA transcription rRNA metabolic process nucleolar large rRNA transcription by RNA polymerase I ncRNA metabolic process tRNA metabolic process tRNA transcription tRNA transcription by RNA polymerase III transcription initiation at RNA polymerase I promoter	membrane-bounded organelle protein-containing complex intracellular anatomical structure RNA polymerase I complex nucleus membrane-enclosed lumen nuclear protein-containing complex transferase complex intracellular organelle lumen intracellular organelle non-membrane-bounded organelle catalytic complex intracellular membrane-bounded organelle cellular anatomical entity membrane-bounded organelle protein-containing complex intracellular anatomical structure RNA polymerase I complex nucleus membrane-enclosed lumen nuclear protein-containing complex transferase complex intracellular organelle lumen intracellular organelle non-membrane-bounded organelle catalytic complex intracellular membrane-bounded organelle cellular anatomical entity nucleolus transferase complex, transferring phosphorus-containing groups nuclear DNA-directed RNA polymerase complex organelle lumen organelle intracellular non-membrane-bounded organelle RNA polymerase complex DNA-directed RNA polymerase complex intracellular protein-containing complex nuclear lumen RNA polymerase II, holoenzyme nucleoplasm RNA polymerase II, core complex RNA polymerase III complex
I	DNA-directed RNA polymerase subunit	binding organic cyclic compound binding nucleic acid binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding DNA-directed 5'-3' RNA polymerase activity 5'-3' RNA polymerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA polymerase activity binding organic cyclic compound binding nucleic acid binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding DNA-directed 5'-3' RNA polymerase activity 5'-3' RNA polymerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA polymerase activity transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups	cellular biosynthetic process cellular metabolic process RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription organic cyclic compound metabolic process nucleic acid biosynthetic process organic substance metabolic process biosynthetic process cellular biosynthetic process cellular metabolic process RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription organic cyclic compound metabolic process nucleic acid biosynthetic process organic substance metabolic process biosynthetic process organic cyclic compound biosynthetic process organic substance biosynthetic process metabolic process cellular process macromolecule metabolic process	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle cellular anatomical entity nucleolus intracellular organelle lumen intracellular organelle organelle lumen organelle intracellular non-membrane-bounded organelle nuclear lumen non-membrane-bounded organelle membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle cellular anatomical entity nucleolus intracellular organelle lumen intracellular organelle organelle lumen organelle intracellular non-membrane-bounded organelle nuclear lumen non-membrane-bounded organelle RNA polymerase II, holoenzyme protein-containing complex nuclear protein-containing complex transferase complex nucleoplasm RNA polymerase II, core complex catalytic complex transferase complex, transferring phosphorus-containing groups nuclear DNA-directed RNA polymerase complex RNA polymerase complex DNA-directed RNA polymerase complex intracellular protein-containing complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR007066	RNA polymerase Rpb1, domain 3	Domain
A	IPR007081	RNA polymerase Rpb1, domain 5	Domain
A	IPR007073	RNA polymerase Rpb1, domain 7	Domain
A	IPR045867	DNA-directed RNA polymerase, subunit beta-prime	Family
A	IPR042102	RNA polymerase Rpb1, domain 3 superfamily	Homologous Superfamily
A	IPR007075	RNA polymerase Rpb1, domain 6	Domain
A	IPR000684	RNA polymerase II, heptapeptide repeat, eukaryotic	Repeat
A	IPR007083	RNA polymerase Rpb1, domain 4	Domain
A	IPR038593	RNA polymerase Rpb1, domain 7 superfamily	Homologous Superfamily
A	IPR000722	RNA polymerase, alpha subunit	Domain
A	IPR044893	RNA polymerase Rpb1, clamp domain superfamily	Homologous Superfamily
A	IPR038120	RNA polymerase Rpb1, funnel domain superfamily	Homologous Superfamily
A	IPR006592	RNA polymerase, N-terminal	Domain
A	IPR007080	RNA polymerase Rpb1, domain 1	Domain
J	IPR023580	RNA polymerase subunit RPB10	Homologous Superfamily
J	IPR020789	RNA polymerases, subunit N, zinc binding site	Binding Site
J	IPR000268	DNA-directed RNA polymerase subunit RPABC5/Rpb10	Family
K	IPR009025	DNA-directed RNA polymerase, RBP11-like dimerisation domain	Domain
K	IPR037685	RNA polymerase RBP11	Family
K	IPR022905	DNA-directed RNA polymerase subunit Rpo11-like	Family
K	IPR036603	RNA polymerase, RBP11-like subunit	Homologous Superfamily
K	IPR008193	DNA-directed RNA polymerase Rpb11, 13-16kDa subunit, conserved site	Conserved Site
L	IPR006591	RNA polymerase archaeal subunit P/eukaryotic subunit RPABC4	Family
L	IPR029040	RNA polymerase subunit RPABC4/transcription elongation factor Spt4	Homologous Superfamily
L	IPR039747	DNA-directed RNA polymerases I, II, and III subunit RPABC4	Family
P [auth M]	IPR007808	Transcription elongation factor 1	Family
P [auth M]	IPR038567	Transcription elongation factor 1 superfamily	Homologous Superfamily
Q [auth V]	IPR029040	RNA polymerase subunit RPABC4/transcription elongation factor Spt4	Homologous Superfamily
Q [auth V]	IPR038510	Spt4 superfamily	Homologous Superfamily
Q [auth V]	IPR009287	Transcription initiation Spt4	Family
Q [auth V]	IPR022800	Spt4/RpoE2 zinc finger	Domain
R [auth W]	IPR036735	NusG, N-terminal domain superfamily	Homologous Superfamily
R [auth W]	IPR041976	Spt5, KOW domain repeat 3	Domain
R [auth W]	IPR039385	NGN domain, eukaryotic	Domain
R [auth W]	IPR014722	Large ribosomal subunit protein uL2, domain 2	Homologous Superfamily
R [auth W]	IPR008991	Translation protein SH3-like domain superfamily	Homologous Superfamily
R [auth W]	IPR041973	Spt5, KOW domain repeat 1	Domain
R [auth W]	IPR022581	Spt5 transcription elongation factor, N-terminal	Domain
R [auth W]	IPR005100	NGN domain	Domain
R [auth W]	IPR041977	Spt5, KOW domain repeat 4	Domain
R [auth W]	IPR017071	Transcription elongation factor Spt5, eukaryote	Family
R [auth W]	IPR005824	KOW	Domain
R [auth W]	IPR041975	Spt5, KOW domain repeat 2	Domain
R [auth W]	IPR041978	Spt5, KOW domain repeat 5	Domain
R [auth W]	IPR039659	Transcription elongation factor SPT5	Family
S [auth a], W [auth e]	IPR009072	Histone-fold	Homologous Superfamily
S [auth a], W [auth e]	IPR007125	Histone H2A/H2B/H3	Domain
S [auth a], W [auth e]	IPR000164	Histone H3/CENP-A	Family
B	IPR007642	RNA polymerase Rpb2, domain 2	Domain
B	IPR015712	DNA-directed RNA polymerase, subunit 2	Family
B	IPR037033	DNA-directed RNA polymerase, subunit 2, hybrid-binding domain superfamily	Homologous Superfamily
B	IPR037034	RNA polymerase Rpb2, domain 2 superfamily	Homologous Superfamily
B	IPR007120	DNA-directed RNA polymerase, subunit 2, hybrid-binding domain	Domain
B	IPR007121	RNA polymerase, beta subunit, conserved site	Conserved Site
B	IPR007645	RNA polymerase Rpb2, domain 3	Domain
B	IPR007646	RNA polymerase Rpb2, domain 4	Domain
B	IPR007647	RNA polymerase Rpb2, domain 5	Domain
B	IPR014724	RNA polymerase Rpb2, OB-fold	Homologous Superfamily
B	IPR007644	RNA polymerase, beta subunit, protrusion	Domain
B	IPR007641	RNA polymerase Rpb2, domain 7	Domain
T [auth b], X [auth f]	IPR009072	Histone-fold	Homologous Superfamily
T [auth b], X [auth f]	IPR035425	CENP-T/Histone H4, histone fold	Domain
T [auth b], X [auth f]	IPR001951	Histone H4	Family
T [auth b], X [auth f]	IPR019809	Histone H4, conserved site	Conserved Site
T [auth b], X [auth f]	IPR004823	TATA box binding protein associated factor (TAF), histone-like fold domain	Domain
U [auth c], Y [auth g]	IPR009072	Histone-fold	Homologous Superfamily
U [auth c], Y [auth g]	IPR007125	Histone H2A/H2B/H3	Domain
U [auth c], Y [auth g]	IPR002119	Histone H2A	Family
U [auth c], Y [auth g]	IPR032454	Histone H2A, C-terminal domain	Domain
U [auth c], Y [auth g]	IPR032458	Histone H2A conserved site	Conserved Site
V [auth d], Z [auth h]	IPR009072	Histone-fold	Homologous Superfamily
V [auth d], Z [auth h]	IPR007125	Histone H2A/H2B/H3	Domain
V [auth d], Z [auth h]	IPR000558	Histone H2B	Family
C	IPR011262	DNA-directed RNA polymerase, insert domain	Domain
C	IPR011263	DNA-directed RNA polymerase, RpoA/D/Rpb3-type	Domain
C	IPR036643	DNA-directed RNA polymerase, insert domain superfamily	Homologous Superfamily
C	IPR022842	DNA-directed RNA polymerase subunit Rpo3/Rpb3/RPAC1	Family
C	IPR001514	DNA-directed RNA polymerase, 30-40kDa subunit, conserved site	Conserved Site
C	IPR036603	RNA polymerase, RBP11-like subunit	Homologous Superfamily
D	IPR005574	RNA polymerase subunit Rpb4/RPC9	Family
D	IPR010997	HRDC-like superfamily	Homologous Superfamily
D	IPR006590	RNA polymerase Rpb4/RPC9, core	Domain
D	IPR038324	Rpb4/RPC9 superfamily	Homologous Superfamily
D	IPR045222	DNA-directed RNA polymerase II subunit Rpb4-like	Family
E	IPR014381	DNA-directed RNA polymerase subunit Rpo5/Rpb5	Family
E	IPR036710	RNA polymerase Rpb5, N-terminal domain superfamily	Homologous Superfamily
E	IPR035913	RPB5-like RNA polymerase subunit superfamily	Homologous Superfamily
E	IPR000783	RNA polymerase, subunit H/Rpb5 C-terminal	Domain
E	IPR020608	RNA polymerase, subunit H/Rpb5, conserved site	Conserved Site
E	IPR005571	RNA polymerase, Rpb5, N-terminal	Domain
F	IPR020708	DNA-directed RNA polymerase, 14-18kDa subunit, conserved site	Conserved Site
F	IPR028363	DNA-directed RNA polymerase, subunit RPB6	Family
F	IPR006110	RNA polymerase, subunit omega/Rpo6/RPB6	Family
F	IPR036161	RPB6/omega subunit-like superfamily	Homologous Superfamily
F	IPR006111	Archaeal Rpo6/eukaryotic RPB6 RNA polymerase subunit	Family
G	IPR036898	RNA polymerase Rpb7-like, N-terminal domain superfamily	Homologous Superfamily
G	IPR003029	S1 domain	Domain
G	IPR012340	Nucleic acid-binding, OB-fold	Homologous Superfamily
G	IPR045113	RNA polymerase subunit Rpb7-like	Family
G	IPR005576	RNA polymerase Rpb7-like , N-terminal	Domain
H	IPR005570	DNA-directed RNA polymerases I, II, and III subunit RPABC3	Family
H	IPR012340	Nucleic acid-binding, OB-fold	Homologous Superfamily
I	IPR012164	DNA-directed RNA polymerase subunit/transcription factor S	Family
I	IPR001222	Zinc finger, TFIIS-type	Domain
I	IPR034012	Pol II subunit B9, C-terminal zinc ribbon	Domain
I	IPR019761	DNA-directed RNA polymerase M, 15kDa subunit, conserved site	Conserved Site
I	IPR001529	DNA-directed RNA polymerase, M/15kDa subunit	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
S [auth a], W [auth e]	Pharos: P84243	malignant glioma bone giant cell tumor glioblastoma giant cell glioblastoma mixed glioma glioma lung adenocarcinoma medulloblastoma ovarian cancer psoriasis astrocytoma (excluding glioblastoma) tuberculosis chondroblastoma ependymoma Glioma of Brain, Familial malignant glioma bone giant cell tumor glioblastoma giant cell glioblastoma mixed glioma glioma lung adenocarcinoma medulloblastoma ovarian cancer psoriasis astrocytoma (excluding glioblastoma) tuberculosis chondroblastoma ependymoma Glioma of Brain, Familial intellectual disability lung cancer malignant mesothelioma pituitary cancer subependymal giant cell astrocytoma atopic eczema breast cancer cutaneous lupus erythematosus glioma susceptibility 1 invasive ductal breast carcinoma malignant colon neoplasm malignant pancreatic neoplasm non-small cell lung carcinoma plasma cell myeloma subependymoma atypical teratoid rhabdoid tumor breast carcinoma Down syndrome exocrine pancreatic carcinoma hepatocellular carcinoma
T [auth b], X [auth f]	Pharos: P62805	lung carcinoma Malignant neoplasm of breast non-small cell lung carcinoma Pick disease squamous cell lung carcinoma acute myeloid leukemia atypical teratoid rhabdoid tumor breast carcinoma ductal breast carcinoma in situ exocrine pancreatic carcinoma hepatocellular carcinoma lung adenocarcinoma malignant colon neoplasm malignant pancreatic neoplasm osteoarthritis lung carcinoma Malignant neoplasm of breast non-small cell lung carcinoma Pick disease squamous cell lung carcinoma acute myeloid leukemia atypical teratoid rhabdoid tumor breast carcinoma ductal breast carcinoma in situ exocrine pancreatic carcinoma hepatocellular carcinoma lung adenocarcinoma malignant colon neoplasm malignant pancreatic neoplasm osteoarthritis pilocytic astrocytoma ulcerative colitis allergic rhinitis autism spectrum disorder cystic fibrosis endogenous depression glioblastoma hypertensive disorder lung cancer malignant mesothelioma multiple sclerosis osteosarcoma psoriasis astrocytic tumor breast cancer diabetes mellitus endometriosis gout invasive ductal breast carcinoma
U [auth c], Y [auth g]	Pharos: P04908	juvenile idiopathic arthritis pituitary cancer acute myeloid leukemia autism spectrum disorder hypertensive disorder lung adenocarcinoma medulloblastoma ovarian cancer psoriasis allergic rhinitis breast cancer invasive ductal breast carcinoma Juvenile psoriatic arthritis lung cancer non-small cell lung carcinoma juvenile idiopathic arthritis pituitary cancer acute myeloid leukemia autism spectrum disorder hypertensive disorder lung adenocarcinoma medulloblastoma ovarian cancer psoriasis allergic rhinitis breast cancer invasive ductal breast carcinoma Juvenile psoriatic arthritis lung cancer non-small cell lung carcinoma pancreatic intraductal papillary-mucinous carcinoma squamous cell lung carcinoma atypical teratoid rhabdoid tumor ductal breast carcinoma in situ lung carcinoma osteoarthritis
V [auth d], Z [auth h]	Pharos: P06899	autism spectrum disorder lung adenocarcinoma breast cancer schizophrenia endogenous depression