(23 nodes) RNA Pol II CTD phosphorylation and interaction with CE network (Pseudozyma hubeiensis)

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:
	PHSY_000825	RNA polymerase subunit. (208 aa)
	PHSY_000806	DNA-directed RNA polymerase subunit; DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. (1783 aa)
	PHSY_001307	RPOLD domain-containing protein. (364 aa)
	PHSY_002756	Transcription initiation factor IIF subunit alpha. (795 aa)
	PHSY_003566	Protein kinase domain-containing protein; Belongs to the protein kinase superfamily. (371 aa)
	PHSY_004296	Transcription elongation factor SPT5; The SPT4-SPT5 complex mediates both activation and inhibition of transcription elongation, and plays a role in pre-mRNA processing. This complex seems to be important for the stability of the RNA polymerase II elongation machinery on the chromatin template but not for the inherent ability of this machinery to translocate down the gene. (962 aa)
	PHSY_005225	Transcription factor subunit. (417 aa)
	PHSY_005341	Uncharacterized protein. (614 aa)
	PHSY_005554	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. (507 aa)
	PHSY_005788	DNA repair helicase. (849 aa)
	PHSY_002518	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. (1237 aa)
	PHSY_005902	RNA polymerase II fourth largest subunit. (160 aa)
	PHSY_006312	RNA_pol_L_2 domain-containing protein. (144 aa)
	PHSY_006618	Uncharacterized protein. (422 aa)
	PHSY_003351	CYCLIN domain-containing protein; Belongs to the cyclin family. (467 aa)
	PHSY_003639	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. (161 aa)
	PHSY_007023	RING-type domain-containing protein. (361 aa)
	PHSY_007369	Uncharacterized protein. (948 aa)
	PHSY_006395	DNA-directed RNA polymerase subunit; DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. (264 aa)
	PHSY_007408	Potential subunit common to RNA polymerase I, II and III. (138 aa)
	PHSY_007418	DNA-directed RNA polymerase subunit beta; DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. (1241 aa)
	PHSY_000523	Uncharacterized protein. (200 aa)
	PHSY_000740	RNA cap methyltransferase. (1326 aa)

Your Current Organism:

Pseudozyma hubeiensis

NCBI taxonomy Id: 1305764
Other names: P. hubeiensis SY62, Pseudozyma hubeiensis SY62

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
PHSY_000523	PHSY_000806	R9NWH6	R9NXG0	Uncharacterized protein.	DNA-directed RNA polymerase subunit; DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.	0.954
PHSY_000523	PHSY_000825	R9NWH6	R9NXF2	Uncharacterized protein.	RNA polymerase subunit.	0.998
PHSY_000523	PHSY_001307	R9NWH6	R9NYL7	Uncharacterized protein.	RPOLD domain-containing protein.	0.998
PHSY_000523	PHSY_002518	R9NWH6	R9PA43	Uncharacterized protein.	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.	0.955
PHSY_000523	PHSY_002756	R9NWH6	R9P1Q4	Uncharacterized protein.	Transcription initiation factor IIF subunit alpha.	0.969
PHSY_000523	PHSY_003351	R9NWH6	R9PCI0	Uncharacterized protein.	CYCLIN domain-containing protein; Belongs to the cyclin family.	0.899
PHSY_000523	PHSY_003566	R9NWH6	R9P3G3	Uncharacterized protein.	Protein kinase domain-containing protein; Belongs to the protein kinase superfamily.	0.824
PHSY_000523	PHSY_003639	R9NWH6	R9PD82	Uncharacterized protein.	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.	0.997
PHSY_000523	PHSY_004296	R9NWH6	R9P635	Uncharacterized protein.	Transcription elongation factor SPT5; The SPT4-SPT5 complex mediates both activation and inhibition of transcription elongation, and plays a role in pre-mRNA processing. This complex seems to be important for the stability of the RNA polymerase II elongation machinery on the chromatin template but not for the inherent ability of this machinery to translocate down the gene.	0.971
PHSY_000523	PHSY_005225	R9NWH6	R9P8G4	Uncharacterized protein.	Transcription factor subunit.	0.957
PHSY_000523	PHSY_005341	R9NWH6	R9P8T2	Uncharacterized protein.	Uncharacterized protein.	0.955
PHSY_000523	PHSY_005554	R9NWH6	R9P9C2	Uncharacterized protein.	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.	0.955
PHSY_000523	PHSY_005788	R9NWH6	R9PA18	Uncharacterized protein.	DNA repair helicase.	0.957
PHSY_000523	PHSY_005902	R9NWH6	R9PAD5	Uncharacterized protein.	RNA polymerase II fourth largest subunit.	0.996
PHSY_000523	PHSY_006312	R9NWH6	R9PBD2	Uncharacterized protein.	RNA_pol_L_2 domain-containing protein.	0.997
PHSY_000523	PHSY_006395	R9NWH6	R9PL38	Uncharacterized protein.	DNA-directed RNA polymerase subunit; DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.	0.954
PHSY_000523	PHSY_006618	R9NWH6	R9PCC1	Uncharacterized protein.	Uncharacterized protein.	0.955
PHSY_000523	PHSY_007023	R9NWH6	R9PDW2	Uncharacterized protein.	RING-type domain-containing protein.	0.955
PHSY_000523	PHSY_007369	R9NWH6	R9PEI7	Uncharacterized protein.	Uncharacterized protein.	0.955
PHSY_000523	PHSY_007408	R9NWH6	R9PNX4	Uncharacterized protein.	Potential subunit common to RNA polymerase I, II and III.	0.999