(65 nodes) RNA polymerase II, holoenzyme network (Stegastes partitus)

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:
	gtf2a1	General transcription factor IIA, 1. (402 aa)
	cdk20	Cyclin-dependent kinase 20. (238 aa)
	LOC103353985	General transcription factor IIF subunit 2; 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. This subunit shows ATP-dependent DNA-helicase activity. (255 aa)
	leo1	LEO1 homolog, Paf1/RNA polymerase II complex component. (635 aa)
	taf5l	TAF5-like RNA polymerase II, p300/CBP-associated factor (PCAF)-associated factor. (600 aa)
	recql5	RecQ helicase-like 5. (1018 aa)
	gtf2e1	General transcription factor IIE, polypeptide 1, alpha. (446 aa)
	ctr9	CTR9 homolog, Paf1/RNA polymerase II complex component. (1163 aa)
	LOC103371965	TAF3 RNA polymerase II, TATA box binding protein (TBP)-associated facto. (898 aa)
	LOC103356806	SH3-binding domain protein 5-like, a. (435 aa)
	gtf2f1	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. (533 aa)
	mnat1	CDK-activating kinase assembly factor MAT1; Stabilizes the cyclin H-CDK7 complex to form a functional CDK-activating kinase (CAK) enzymatic complex. (311 aa)
	polr2d	Polymerase (RNA) II (DNA directed) polypeptide D. (144 aa)
	tbp	TATA box binding protein. (309 aa)
	gtf2a2	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. (111 aa)
	polr2g	Polymerase (RNA) II (DNA directed) polypeptide G-like. (171 aa)
	ENSSPAP00000020591	TAF4 domain-containing protein. (253 aa)
	polr2m	RNA polymerase II subunit M. (359 aa)
	polr2i	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. (126 aa)
	polr2a	DNA-directed RNA polymerase subunit; DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. (1955 aa)
	taf5	TAF5 RNA polymerase II, TATA box binding protein (TBP)-associated factor. (780 aa)
	POLR2E	RNA polymerase II subunit E. (210 aa)
	gtf2e2	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. (287 aa)
	ENSSPAP00000024879	CID domain-containing protein. (67 aa)
	TAF4	TAFH domain-containing protein. (593 aa)
	rprd2	Regulation of nuclear pre-mRNA domain containing 2b. (910 aa)
	LOC103373818	DNA-directed RNA polymerase II subunit RPB2-like. (501 aa)
	rprd1b	Regulation of nuclear pre-mRNA domain containing 1B. (328 aa)
	polr2k	Uncharacterized protein. (59 aa)
	taf2	TAF2 RNA polymerase II, TATA box binding protein (TBP)-associated factor. (1213 aa)
	gtf2a1l	General transcription factor IIA, 1-like. (361 aa)
	gtf2h1	General transcription factor IIH, polypeptide 1. (550 aa)
	ENSSPAP00000027722	TAF4 domain-containing protein. (288 aa)
	cdk7	Cyclin-dependent kinase 7; Belongs to the protein kinase superfamily. (343 aa)
	paf1	PAF1 homolog, Paf1/RNA polymerase II complex component. (536 aa)
	polr2j	Polymerase (RNA) II (DNA directed) polypeptide J. (117 aa)
	taf13	TATA-box binding protein associated factor 13. (175 aa)
	ENSSPAP00000030471	Uncharacterized protein. (111 aa)
	LOC103371583	General transcription factor IIH subunit. (390 aa)
	supt3h	SPT3 homolog, SAGA and STAGA complex component. (354 aa)
	wdr47	WD repeat domain 47a. (916 aa)
	LOC103365992	Si:dkey-219c3.2. (823 aa)
	gtf2h5	General transcription factor IIH, polypeptide 5. (71 aa)
	LOC103356388	Regulation of nuclear pre-mRNA domain containing 2a. (1097 aa)
	gtf2h3	General transcription factor IIH, polypeptide 3. (300 aa)
	pex2	Peroxisomal biogenesis factor 2. (330 aa)
	cdc73	Cell division cycle 73, Paf1/RNA polymerase II complex component, homolog (S. cerevisiae). (530 aa)
	LOC103368907	TAFH domain-containing protein. (1025 aa)
	cinp	Cyclin-dependent kinase 2 interacting protein. (219 aa)
	taf8	TAF8 RNA polymerase II, TATA box binding protein (TBP)-associated factor. (308 aa)
	LOC103364913	WD repeat domain 47b. (857 aa)
	ccnh	Cyclin H; Belongs to the cyclin family. (319 aa)
	wdr61	WD repeat domain 61. (305 aa)
	rpap2	RNA polymerase II associated protein 2. (667 aa)
	rprd1a	Regulation of nuclear pre-mRNA domain containing 1A. (294 aa)
	ENSSPAP00000007569	General transcription factor IIH, polypeptide 4. (386 aa)
	gtf2h4	General transcription factor IIH subunit 4; 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. (463 aa)
	ENSSPAP00000007455	Uncharacterized protein. (144 aa)
	taf3	PHD-type domain-containing protein. (938 aa)
	taf11	TAF11 RNA polymerase II, TATA box binding protein (TBP)-associated factor. (205 aa)
	POLR2B	DNA-directed RNA polymerase subunit beta; DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. (1174 aa)
	gtf2f2	General transcription factor IIF subunit 2; 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. This subunit shows ATP-dependent DNA-helicase activity. (270 aa)
	taf1	Transcription initiation factor TFIID subunit. (1840 aa)
	ercc3	Excision repair cross-complementation group 3. (783 aa)
	rtf1	RTF1 homolog, Paf1/RNA polymerase II complex component. (677 aa)

Your Current Organism:

Stegastes partitus

NCBI taxonomy Id: 144197
Other names: S. partitus, bicolor damselfish

Send network to Cytoscape

Export your current network:

... as a bitmap image:

download

file format is 'PNG': portable network graphic

... as a high-resolution bitmap:

download

same PNG format, but at higher resolution

... as a vector graphic:

download

SVG: scalable vector graphic - can be opened and edited in Illustrator, CorelDraw, Dia, etc

... as short tabular text output:

download

TSV: tab separated values - can be opened in Excel and Cytoscape (lists only one-way edges: A-B)

... as tabular text output:

download

TSV: tab separated values - can be opened in Excel (lists reciprocal edges: A-B,B-A)

... as an XML summary:

download

structured XML interaction data, according to the 'PSI-MI' data standard

... protein node degrees:

download

node degree of proteins in your network (given the current score cut-off)

... network coordinates:

download

a flat-file format describing the coordinates and colors of nodes in the network

... protein sequences:

download

MFA: multi-fasta format - containing the aminoacid sequences in the network

... protein annotations:

download

a tab-delimited file describing the names, domains and descriptions of proteins in your network

... functional annotations:

download

a tab-delimited file containing all known functional terms of proteins in your network

Browse interactions in tabular form:

node1	node2	node1 accession	node2 accession	node1 annotation	node2 annotation	score
ENSSPAP00000007455	ENSSPAP00000020591	ENSSPAP00000007455	ENSSPAP00000020591	Uncharacterized protein.	TAF4 domain-containing protein.	0.849
ENSSPAP00000007455	ENSSPAP00000027722	ENSSPAP00000007455	ENSSPAP00000027722	Uncharacterized protein.	TAF4 domain-containing protein.	0.849
ENSSPAP00000007455	LOC103353985	ENSSPAP00000007455	ENSSPAP00000010363	Uncharacterized protein.	General transcription factor IIF subunit 2; 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. This subunit shows ATP-dependent DNA-helicase activity.	0.931
ENSSPAP00000007455	LOC103365992	ENSSPAP00000007455	ENSSPAP00000031248	Uncharacterized protein.	Si:dkey-219c3.2.	0.849
ENSSPAP00000007455	LOC103368907	ENSSPAP00000007455	ENSSPAP00000004006	Uncharacterized protein.	TAFH domain-containing protein.	0.849
ENSSPAP00000007455	LOC103371583	ENSSPAP00000007455	ENSSPAP00000030702	Uncharacterized protein.	General transcription factor IIH subunit.	0.946
ENSSPAP00000007455	LOC103371965	ENSSPAP00000007455	ENSSPAP00000016600	Uncharacterized protein.	TAF3 RNA polymerase II, TATA box binding protein (TBP)-associated facto.	0.890
ENSSPAP00000007455	LOC103373818	ENSSPAP00000007455	ENSSPAP00000025466	Uncharacterized protein.	DNA-directed RNA polymerase II subunit RPB2-like.	0.914
ENSSPAP00000007455	POLR2B	ENSSPAP00000007455	ENSSPAP00000006312	Uncharacterized protein.	DNA-directed RNA polymerase subunit beta; DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.	0.914
ENSSPAP00000007455	POLR2E	ENSSPAP00000007455	ENSSPAP00000023286	Uncharacterized protein.	RNA polymerase II subunit E.	0.965
ENSSPAP00000007455	TAF4	ENSSPAP00000007455	ENSSPAP00000024900	Uncharacterized protein.	TAFH domain-containing protein.	0.849
ENSSPAP00000007455	ccnh	ENSSPAP00000007455	ENSSPAP00000001387	Uncharacterized protein.	Cyclin H; Belongs to the cyclin family.	0.878
ENSSPAP00000007455	cdk20	ENSSPAP00000007455	ENSSPAP00000009446	Uncharacterized protein.	Cyclin-dependent kinase 20.	0.781
ENSSPAP00000007455	cdk7	ENSSPAP00000007455	ENSSPAP00000029052	Uncharacterized protein.	Cyclin-dependent kinase 7; Belongs to the protein kinase superfamily.	0.781
ENSSPAP00000007455	ercc3	ENSSPAP00000007455	ENSSPAP00000006177	Uncharacterized protein.	Excision repair cross-complementation group 3.	0.960
ENSSPAP00000007455	gtf2a1	ENSSPAP00000007455	ENSSPAP00000008217	Uncharacterized protein.	General transcription factor IIA, 1.	0.951
ENSSPAP00000007455	gtf2a1l	ENSSPAP00000007455	ENSSPAP00000026999	Uncharacterized protein.	General transcription factor IIA, 1-like.	0.939
ENSSPAP00000007455	gtf2a2	ENSSPAP00000007455	ENSSPAP00000020222	Uncharacterized protein.	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.	0.968
ENSSPAP00000007455	gtf2e1	ENSSPAP00000007455	ENSSPAP00000015394	Uncharacterized protein.	General transcription factor IIE, polypeptide 1, alpha.	0.973
ENSSPAP00000007455	gtf2e2	ENSSPAP00000007455	ENSSPAP00000024825	Uncharacterized protein.	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.	0.947