(27 nodes) Homologous DNA Pairing and Strand Exchange, and Double-strand break repair via synthesis-dependent strand annealing network (Callorhinchus milii)

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:
	recql4	Uncharacterized protein. (1406 aa)
	fancm	Uncharacterized protein. (1846 aa)
	tdrd3	Uncharacterized protein. (758 aa)
	top3b	DNA topoisomerase; Introduces a single-strand break via transesterification at a target site in duplex DNA. Releases the supercoiling and torsional tension of DNA introduced during the DNA replication and transcription by transiently cleaving and rejoining one strand of the DNA duplex. The scissile phosphodiester is attacked by the catalytic tyrosine of the enzyme, resulting in the formation of a DNA-(5'-phosphotyrosyl)-enzyme intermediate and the expulsion of a 3'-OH DNA strand. Belongs to the type IA topoisomerase family. (861 aa)
	rpa3	Uncharacterized protein. (121 aa)
	top3a	DNA topoisomerase; Introduces a single-strand break via transesterification at a target site in duplex DNA. Releases the supercoiling and torsional tension of DNA introduced during the DNA replication and transcription by transiently cleaving and rejoining one strand of the DNA duplex. The scissile phosphodiester is attacked by the catalytic tyrosine of the enzyme, resulting in the formation of a DNA-(5'-phosphotyrosyl)-enzyme intermediate and the expulsion of a 3'-OH DNA strand. Belongs to the type IA topoisomerase family. (931 aa)
	rmi2	RecQ-mediated genome instability protein 2. (148 aa)
	dna2	Uncharacterized protein. (1488 aa)
	dmc1	Uncharacterized protein; Belongs to the RecA family. (326 aa)
	ENSCMIP00000026210	Uncharacterized protein. (1093 aa)
	xrcc2	RECA_2 domain-containing protein. (302 aa)
	rad51d	RECA_2 domain-containing protein. (298 aa)
	xrcc3	RECA_2 domain-containing protein. (356 aa)
	rmi1	DUF1767 domain-containing protein. (638 aa)
	rad51	DNA repair protein RAD51 homolog; Plays an important role in homologous strand exchange, a key step in DNA repair through homologous recombination. Binds to single and double-stranded DNA and exhibits DNA-dependent ATPase activity. Catalyzes the recognition of homology and strand exchange between homologous DNA partners to form a joint molecule between a processed DNA break and the repair template. Binds to single-stranded DNA in an ATP-dependent manner to form nucleoprotein filaments which are essential for the homology search and strand exchange. Belongs to the RecA family. RAD51 sub [...] (337 aa)
	rad51b	RECA_2 domain-containing protein. (457 aa)
	rpa2	Replication protein A2, 32kDa. (275 aa)
	meiob	Uncharacterized protein. (472 aa)
	recql5	Uncharacterized protein. (1072 aa)
	ENSCMIP00000043864	Uncharacterized protein. (319 aa)
	blm	ATP-dependent DNA helicase; Belongs to the helicase family. RecQ subfamily. (972 aa)
	ENSCMIP00000044115	BLM_N domain-containing protein. (350 aa)
	rad51c	RECA_2 domain-containing protein. (346 aa)
	brca2	Tower domain-containing protein. (3025 aa)
	rpa1	Replication protein A subunit; As part of the heterotrimeric replication protein A complex (RPA/RP-A), binds and stabilizes single-stranded DNA intermediates, that form during DNA replication or upon DNA stress. It prevents their reannealing and in parallel, recruits and activates different proteins and complexes involved in DNA metabolism. Thereby, it plays an essential role both in DNA replication and the cellular response to DNA damage. (601 aa)
	exo1	Uncharacterized protein. (846 aa)
	rad52	Uncharacterized protein. (415 aa)

Your Current Organism:

Callorhinchus milii

NCBI taxonomy Id: 7868
Other names: Australian ghost shark, C. milii, elephant fish, elephant shark, ghost shark, makorepe, plownose chimaera, reperepe

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
ENSCMIP00000026210	ENSCMIP00000043864	ENSCMIP00000026210	ENSCMIP00000043864	Uncharacterized protein.	Uncharacterized protein.	0.973
ENSCMIP00000026210	ENSCMIP00000044115	ENSCMIP00000026210	ENSCMIP00000044115	Uncharacterized protein.	BLM_N domain-containing protein.	0.597
ENSCMIP00000026210	blm	ENSCMIP00000026210	ENSCMIP00000044113	Uncharacterized protein.	ATP-dependent DNA helicase; Belongs to the helicase family. RecQ subfamily.	0.663
ENSCMIP00000026210	brca2	ENSCMIP00000026210	ENSCMIP00000046776	Uncharacterized protein.	Tower domain-containing protein.	0.986
ENSCMIP00000026210	dmc1	ENSCMIP00000026210	ENSCMIP00000023729	Uncharacterized protein.	Uncharacterized protein; Belongs to the RecA family.	0.986
ENSCMIP00000026210	dna2	ENSCMIP00000026210	ENSCMIP00000020988	Uncharacterized protein.	Uncharacterized protein.	0.994
ENSCMIP00000026210	exo1	ENSCMIP00000026210	ENSCMIP00000047918	Uncharacterized protein.	Uncharacterized protein.	0.996
ENSCMIP00000026210	fancm	ENSCMIP00000026210	ENSCMIP00000005855	Uncharacterized protein.	Uncharacterized protein.	0.998
ENSCMIP00000026210	meiob	ENSCMIP00000026210	ENSCMIP00000042229	Uncharacterized protein.	Uncharacterized protein.	0.999
ENSCMIP00000026210	rad51	ENSCMIP00000026210	ENSCMIP00000038027	Uncharacterized protein.	DNA repair protein RAD51 homolog; Plays an important role in homologous strand exchange, a key step in DNA repair through homologous recombination. Binds to single and double-stranded DNA and exhibits DNA-dependent ATPase activity. Catalyzes the recognition of homology and strand exchange between homologous DNA partners to form a joint molecule between a processed DNA break and the repair template. Binds to single-stranded DNA in an ATP-dependent manner to form nucleoprotein filaments which are essential for the homology search and strand exchange. Belongs to the RecA family. RAD51 sub [...]	0.995
ENSCMIP00000026210	rad51b	ENSCMIP00000026210	ENSCMIP00000038776	Uncharacterized protein.	RECA_2 domain-containing protein.	0.994
ENSCMIP00000026210	rad51c	ENSCMIP00000026210	ENSCMIP00000046177	Uncharacterized protein.	RECA_2 domain-containing protein.	0.986
ENSCMIP00000026210	rad51d	ENSCMIP00000026210	ENSCMIP00000028211	Uncharacterized protein.	RECA_2 domain-containing protein.	0.994
ENSCMIP00000026210	rad52	ENSCMIP00000026210	ENSCMIP00000048282	Uncharacterized protein.	Uncharacterized protein.	0.998
ENSCMIP00000026210	recql4	ENSCMIP00000026210	ENSCMIP00000000377	Uncharacterized protein.	Uncharacterized protein.	0.605
ENSCMIP00000026210	recql5	ENSCMIP00000026210	ENSCMIP00000043196	Uncharacterized protein.	Uncharacterized protein.	0.664
ENSCMIP00000026210	rmi1	ENSCMIP00000026210	ENSCMIP00000032831	Uncharacterized protein.	DUF1767 domain-containing protein.	0.990
ENSCMIP00000026210	rmi2	ENSCMIP00000026210	ENSCMIP00000019981	Uncharacterized protein.	RecQ-mediated genome instability protein 2.	0.987
ENSCMIP00000026210	rpa1	ENSCMIP00000026210	ENSCMIP00000046808	Uncharacterized protein.	Replication protein A subunit; As part of the heterotrimeric replication protein A complex (RPA/RP-A), binds and stabilizes single-stranded DNA intermediates, that form during DNA replication or upon DNA stress. It prevents their reannealing and in parallel, recruits and activates different proteins and complexes involved in DNA metabolism. Thereby, it plays an essential role both in DNA replication and the cellular response to DNA damage.	0.999
ENSCMIP00000026210	rpa2	ENSCMIP00000026210	ENSCMIP00000040441	Uncharacterized protein.	Replication protein A2, 32kDa.	0.973