(50 nodes) RNA polymerase II, holoenzyme network (Verticillium alfalfae)

Nodes:

Network nodes represent proteins

splice isoforms or post-translational modifications are collapsed, i.e. each node represents all the proteins produced by a single, protein-coding gene locus.

Node Color

colored nodes:
query proteins and first shell of interactors

white nodes:
second shell of interactors

Node Content

empty nodes:
proteins of unknown 3D structure

filled nodes:
a 3D structure is known or predicted

Edges:

Edges represent protein-protein associations

associations are meant to be specific and meaningful, i.e. proteins jointly contribute to a shared function; this does not necessarily mean they are physically binding to each other.

Known Interactions

from curated databases

experimentally determined

Predicted Interactions

gene neighborhood

gene fusions

gene co-occurrence

Others

textmining

co-expression

protein homology

Your Input:
	VDBG_09348	DUF618 domain-containing protein. (409 aa)
	VDBG_00773	Transcription initiation factor IIA subunit 2; TFIIA is a component of the transcription machinery of RNA polymerase II and plays an important role in transcriptional activation; Belongs to the TFIIA subunit 2 family. (115 aa)
	VDBG_01446	Metallothionein-I gene transcription activator. (81 aa)
	VDBG_00138	DNA-directed RNA polymerase II. (75 aa)
	VDBG_01069	Cell division control protein. (345 aa)
	VDBG_01082	DNA-directed RNA polymerases I. (231 aa)
	VDBG_01726	Plus3 domain-containing protein. (588 aa)
	VDBG_02832	DNA repair helicase RAD25. (518 aa)
	VDBG_03011	General transcription and DNA repair factor IIH; Component of the general transcription and DNA repair factor IIH (TFIIH) core complex, which is involved in general and transcription-coupled nucleotide excision repair (NER) of damaged DNA and, when complexed to TFIIK, in RNA transcription by RNA polymerase II; Belongs to the GTF2H2 family. (468 aa)
	VDBG_02525	DNA-directed RNA polymerase subunit; DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Belongs to the archaeal rpoM/eukaryotic RPA12/RPB9/RPC11 RNA polymerase family. (132 aa)
	VDBG_03410	RNA polymerase II transcription factor B subunit 1. (630 aa)
	VDBG_03422	DNA repair helicase RAD3. (756 aa)
	VDBG_03996	Uncharacterized protein. (356 aa)
	VDBG_04181	Serine/threonine-protein kinase crk1; Belongs to the protein kinase superfamily. (413 aa)
	VDBG_03609	Transcription initiation factor TFIID subunit 12. (763 aa)
	VDBG_04315	DNA-directed RNA polymerase subunit beta; DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. (1260 aa)
	VDBG_03708	Transcription initiation factor TFIID subunit 1. (1106 aa)
	VDBG_03761	DNA-directed RNA polymerases I/II/III subunit 10. (76 aa)
	VDBG_03832	Transcription initiation factor TFIId 127kD subunit. (1552 aa)
	VDBG_04535	Uncharacterized protein. (106 aa)
	VDBG_04843	Transcription initiation factor TFIID subunit 7. (506 aa)
	VDBG_04852	DNA-directed RNA polymerase II subunit RPB7. (177 aa)
	VDBG_04869	Bromodomain associated domain-containing protein. (262 aa)
	VDBG_05130	RPOL4c domain-containing protein. (160 aa)
	VDBG_05354	Uncharacterized protein. (167 aa)
	VDBG_05416	RNA polymerase II subunit 3. (84 aa)
	VDBG_05446	Transcription initiation factor TFIID subunit 10; Functions as a component of the DNA-binding general transcription factor complex TFIID and the transcription regulatory histone acetylation (HAT) complexes SAGA and SLIK. Binding of TFIID to a promoter (with or without TATA element) is the initial step in preinitiation complex (PIC) formation. TFIID plays a key role in the regulation of gene expression by RNA polymerase II through different activities such as transcription activator interaction, core promoter recognition and selectivity, TFIIA and TFIIB interaction, chromatin modificati [...] (224 aa)
	VDBG_05543	Meiotic recombination protein rec14. (310 aa)
	VDBG_05562	RNA polymerase II transcription factor B subunit 4. (384 aa)
	VDBG_05852	Transcription initiation factor iif. (368 aa)
	VDBG_06481	TAFII28 domain-containing protein. (291 aa)
	VDBG_06895	Tetratricopeptide repeat protein. (991 aa)
	VDBG_06898	Predicted protein. (259 aa)
	VDBG_07047	Bromodomain associated domain-containing protein. (316 aa)
	VDBG_07204	RNA polymerase II transcription factor B subunit 3. (353 aa)
	VDBG_07235	Uncharacterized protein. (181 aa)
	VDBG_07372	Uncharacterized protein. (416 aa)
	VDBG_07406	DNA-directed RNA polymerase subunit; DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. (1756 aa)
	VDBG_07593	Transcription initiation factor TFIID complex 60 kDa subunit. (398 aa)
	VDBG_08075	Transcription initiation factor IIE subunit beta; Recruits TFIIH to the initiation complex and stimulates the RNA polymerase II C-terminal domain kinase and DNA-dependent ATPase activities of TFIIH. Both TFIIH and TFIIE are required for promoter clearance by RNA polymerase. (277 aa)
	VDBG_09412	Transcription initiation factor TFIID subunit 5. (759 aa)
	VDBG_08319	Transcription initiation factor IIF subunit alpha; TFIIF is a general transcription initiation factor that binds to RNA polymerase II and helps to recruit it to the initiation complex in collaboration with TFIIB. It promotes transcription elongation. Belongs to the TFIIF alpha subunit family. (721 aa)
	VDBG_08370	Uncharacterized protein. (275 aa)
	VDBG_08235	DNA-directed RNA polymerases I, II, and III subunit RPABC3; DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Common component of RNA polymerases I, II and III which synthesize ribosomal RNA precursors, mRNA precursors and many functional non- coding RNAs, and small RNAs, such as 5S rRNA and tRNAs, respectively. (152 aa)
	VDBG_08793	DNA-directed RNA polymerases I. (149 aa)
	VDBG_08945	Uncharacterized protein. (491 aa)
	VDBG_09023	Cyclin CCL1. (365 aa)
	VDBG_09222	RNA polymerase II transcription factor B subunit 2; Component of the general transcription and DNA repair factor IIH (TFIIH) core complex which is involved in general and transcription-coupled nucleotide excision repair (NER) of damaged DNA. Belongs to the TFB2 family. (476 aa)
	VDBG_09316	Uncharacterized protein. (414 aa)
	VDBG_09336	Transcription initiation factor IIE subunit alpha. (411 aa)

Your Current Organism:

Verticillium alfalfae

NCBI taxonomy Id: 526221
Other names: V. alfalfae VaMs.102, Verticillium alfalfae VaMs.102

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Browse interactions in tabular form:

node1	node2	node1 accession	node2 accession	node1 annotation	node2 annotation	score
VDBG_00138	VDBG_00773	C9S8V4	C9S780	DNA-directed RNA polymerase II.	Transcription initiation factor IIA subunit 2; TFIIA is a component of the transcription machinery of RNA polymerase II and plays an important role in transcriptional activation; Belongs to the TFIIA subunit 2 family.	0.912
VDBG_00138	VDBG_01069	C9S8V4	C9S8Y7	DNA-directed RNA polymerase II.	Cell division control protein.	0.889
VDBG_00138	VDBG_01082	C9S8V4	C9S900	DNA-directed RNA polymerase II.	DNA-directed RNA polymerases I.	0.999
VDBG_00138	VDBG_01446	C9S8V4	C9S887	DNA-directed RNA polymerase II.	Metallothionein-I gene transcription activator.	0.999
VDBG_00138	VDBG_01726	C9S8V4	C9SB67	DNA-directed RNA polymerase II.	Plus3 domain-containing protein.	0.858
VDBG_00138	VDBG_02525	C9S8V4	C9SDJ5	DNA-directed RNA polymerase II.	DNA-directed RNA polymerase subunit; DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Belongs to the archaeal rpoM/eukaryotic RPA12/RPB9/RPC11 RNA polymerase family.	0.999
VDBG_00138	VDBG_02832	C9S8V4	C9SCA8	DNA-directed RNA polymerase II.	DNA repair helicase RAD25.	0.982
VDBG_00138	VDBG_03011	C9S8V4	C9SCT7	DNA-directed RNA polymerase II.	General transcription and DNA repair factor IIH; Component of the general transcription and DNA repair factor IIH (TFIIH) core complex, which is involved in general and transcription-coupled nucleotide excision repair (NER) of damaged DNA and, when complexed to TFIIK, in RNA transcription by RNA polymerase II; Belongs to the GTF2H2 family.	0.984
VDBG_00138	VDBG_03410	C9S8V4	C9SE54	DNA-directed RNA polymerase II.	RNA polymerase II transcription factor B subunit 1.	0.981
VDBG_00138	VDBG_03422	C9S8V4	C9SE89	DNA-directed RNA polymerase II.	DNA repair helicase RAD3.	0.980
VDBG_00138	VDBG_03609	C9S8V4	C9SGG0	DNA-directed RNA polymerase II.	Transcription initiation factor TFIID subunit 12.	0.900
VDBG_00138	VDBG_03708	C9S8V4	C9SH05	DNA-directed RNA polymerase II.	Transcription initiation factor TFIID subunit 1.	0.890
VDBG_00138	VDBG_03761	C9S8V4	C9SH58	DNA-directed RNA polymerase II.	DNA-directed RNA polymerases I/II/III subunit 10.	0.999
VDBG_00138	VDBG_03832	C9S8V4	C9SHC9	DNA-directed RNA polymerase II.	Transcription initiation factor TFIId 127kD subunit.	0.902
VDBG_00138	VDBG_03996	C9S8V4	C9SFA1	DNA-directed RNA polymerase II.	Uncharacterized protein.	0.691
VDBG_00138	VDBG_04181	C9S8V4	C9SG58	DNA-directed RNA polymerase II.	Serine/threonine-protein kinase crk1; Belongs to the protein kinase superfamily.	0.927
VDBG_00138	VDBG_04315	C9S8V4	C9SGY6	DNA-directed RNA polymerase II.	DNA-directed RNA polymerase subunit beta; DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.	0.999
VDBG_00138	VDBG_04535	C9S8V4	C9SHK3	DNA-directed RNA polymerase II.	Uncharacterized protein.	0.865
VDBG_00138	VDBG_04843	C9S8V4	C9SIG1	DNA-directed RNA polymerase II.	Transcription initiation factor TFIID subunit 7.	0.890
VDBG_00138	VDBG_04852	C9S8V4	C9SIH0	DNA-directed RNA polymerase II.	DNA-directed RNA polymerase II subunit RPB7.	0.999