(18 nodes) Processing of Intronless Pre-mRNAs, and Termination of RNA polymerase II transcription network (Cavenderia fasciculata)

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:
	DFA_03323	Uncharacterized protein. (589 aa)
	DFA_03330	CCCH-type zinc finger-containing protein. (925 aa)
	DFA_04708	Uncharacterized protein. (78 aa)
	DFA_01942	WD40 repeat-containing protein. (696 aa)
	clp1	Protein CLP1 homolog; Required for endonucleolytic cleavage during polyadenylation- dependent pre-mRNA 3'-end formation; Belongs to the Clp1 family. Clp1 subfamily. (431 aa)
	DFA_00543	WD_REPEATS_REGION domain-containing protein. (251 aa)
	cpsf4	CCCH-type zinc finger-containing protein. (286 aa)
	DFA_00053	Uncharacterized protein. (754 aa)
	papA	Poly(A) polymerase; Polymerase that creates the 3'-poly(A) tail of mRNA's. (803 aa)
	cstf1	WD40 repeat-containing protein. (432 aa)
	fip1l1	Cleavage and polyadenylation specificity factor FIP1. (405 aa)
	cstf3	Cleavage stimulation factor subunit 3. (997 aa)
	cpsf3	Beta-lactamase domain-containing protein. (786 aa)
	sympk	Symplekin. (1201 aa)
	cpsf2	Cleavage and polyadenylation specificity factor subunit 2. (768 aa)
	cstf2	RNA-binding region RNP-1 domain-containing protein. (436 aa)
	cpsf1	CPSF domain-containing protein. (1627 aa)
	pcf11	ENTH domain-containing protein. (705 aa)

Your Current Organism:

Cavenderia fasciculata

NCBI taxonomy Id: 1054147
Other names: C. fasciculata SH3, Cavenderia fasciculata SH3, Dictyostelium fasciculatum SH3, Dictyostelium fasciculatum strain SH3

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
DFA_00053	DFA_00543	F4PXG6	F4PSD6	Uncharacterized protein.	WD_REPEATS_REGION domain-containing protein.	0.786
DFA_00053	DFA_01942	F4PXG6	F4PQU5	Uncharacterized protein.	WD40 repeat-containing protein.	0.910
DFA_00053	DFA_03323	F4PXG6	F4PH93	Uncharacterized protein.	Uncharacterized protein.	0.757
DFA_00053	DFA_03330	F4PXG6	F4PHA0	Uncharacterized protein.	CCCH-type zinc finger-containing protein.	0.874
DFA_00053	DFA_04708	F4PXG6	F4PQB5	Uncharacterized protein.	Uncharacterized protein.	0.852
DFA_00053	clp1	F4PXG6	F4PRU6	Uncharacterized protein.	Protein CLP1 homolog; Required for endonucleolytic cleavage during polyadenylation- dependent pre-mRNA 3'-end formation; Belongs to the Clp1 family. Clp1 subfamily.	0.878
DFA_00053	cpsf1	F4PXG6	F4QEG3	Uncharacterized protein.	CPSF domain-containing protein.	0.932
DFA_00053	cpsf2	F4PXG6	F4Q9E5	Uncharacterized protein.	Cleavage and polyadenylation specificity factor subunit 2.	0.932
DFA_00053	cpsf3	F4PXG6	F4Q8H1	Uncharacterized protein.	Beta-lactamase domain-containing protein.	0.940
DFA_00053	cpsf4	F4PXG6	F4PXF7	Uncharacterized protein.	CCCH-type zinc finger-containing protein.	0.874
DFA_00053	cstf1	F4PXG6	F4Q476	Uncharacterized protein.	WD40 repeat-containing protein.	0.966
DFA_00053	cstf3	F4PXG6	F4Q859	Uncharacterized protein.	Cleavage stimulation factor subunit 3.	0.967
DFA_00053	fip1l1	F4PXG6	F4Q737	Uncharacterized protein.	Cleavage and polyadenylation specificity factor FIP1.	0.963
DFA_00053	papA	F4PXG6	F4PYA7	Uncharacterized protein.	Poly(A) polymerase; Polymerase that creates the 3'-poly(A) tail of mRNA's.	0.916
DFA_00053	pcf11	F4PXG6	F4QFG6	Uncharacterized protein.	ENTH domain-containing protein.	0.914
DFA_00053	sympk	F4PXG6	F4Q935	Uncharacterized protein.	Symplekin.	0.936
DFA_00543	DFA_00053	F4PSD6	F4PXG6	WD_REPEATS_REGION domain-containing protein.	Uncharacterized protein.	0.786
DFA_00543	DFA_01942	F4PSD6	F4PQU5	WD_REPEATS_REGION domain-containing protein.	WD40 repeat-containing protein.	0.998
DFA_00543	DFA_03323	F4PSD6	F4PH93	WD_REPEATS_REGION domain-containing protein.	Uncharacterized protein.	0.976
DFA_00543	DFA_03330	F4PSD6	F4PHA0	WD_REPEATS_REGION domain-containing protein.	CCCH-type zinc finger-containing protein.	0.898