(72 nodes) Telomere maintenance network (Oryzias latipes)

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:
	rad51d	RAD51 paralog D. (332 aa)
	pot1	Protection of telomeres 1 homolog. (812 aa)
	parp3	Poly [ADP-ribose] polymerase. (526 aa)
	xrcc6	X-ray repair complementing defective repair in Chinese hamster cells 6. (611 aa)
	ercc4	Excision repair cross-complementation group 4. (889 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. (655 aa)
	fbxo4	F-box protein 4. (405 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. (598 aa)
	prkdc	Protein kinase, DNA-activated, catalytic subunit; Belongs to the PI3/PI4-kinase family. (3962 aa)
	dclre1b	DNA cross-link repair 1B. (582 aa)
	smc5	Structural maintenance of chromosomes 5. (1072 aa)
	mre11	Double-strand break repair protein; Involved in DNA double-strand break repair (DSBR). Possesses single-strand endonuclease activity and double-strand-specific 3'-5' exonuclease activity. Also involved in meiotic DSB processing. (694 aa)
	telo2	TEL2, telomere maintenance 2, homolog (S. cerevisiae). (829 aa)
	pif1	ATP-dependent DNA helicase PIF1; DNA-dependent ATPase and 5'-3' DNA helicase required for the maintenance of both mitochondrial and nuclear genome stability. (631 aa)
	tfpt	TCF3 (E2A) fusion partner. (196 aa)
	terf2	HTH myb-type domain-containing protein. (627 aa)
	atr	ATR serine/threonine kinase; Belongs to the PI3/PI4-kinase family. (2160 aa)
	LOC101163867	Si:dkey-119f1.1. (1129 aa)
	H2MFR5_ORYLA	ATP-dependent DNA helicase; Belongs to the helicase family. (432 aa)
	tert	Telomerase reverse transcriptase; Telomerase is a ribonucleoprotein enzyme essential for the replication of chromosome termini in most eukaryotes. It elongates telomeres. It is a reverse transcriptase that adds simple sequence repeats to chromosome ends by copying a template sequence within the RNA component of the enzyme. (1090 aa)
	mcrs1	Microspherule protein 1. (460 aa)
	ccne2	Cyclin E2; Belongs to the cyclin family. (393 aa)
	ercc1	Excision repair cross-complementation group 1. (341 aa)
	xrcc5	X-ray repair cross-complementing protein 5; Single-stranded DNA-dependent ATP-dependent helicase. Belongs to the ku80 family. (725 aa)
	dclre1c	DNA cross-link repair 1C, PSO2 homolog (S. cerevisiae). (622 aa)
	LOC110015669	Uncharacterized protein. (183 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 [...] (396 aa)
	ino80	INO80 complex ATPase subunit. (1547 aa)
	H2MVD7_ORYLA	DNA repair protein; Involved in the homologous recombination repair (HRR) pathway of double-stranded DNA, thought to repair chromosomal fragmentation, translocations and deletions; Belongs to the RecA family. RAD51 subfamily. (308 aa)
	LOC111946820	Structural maintenance of chromosomes 6. (1041 aa)
	dkc1	Dyskeratosis congenita 1, dyskerin. (507 aa)
	LOC101161711	Zinc finger and BTB domain containing 48. (625 aa)
	Rad51c	RAD51 paralog C. (307 aa)
	gar1	H/ACA ribonucleoprotein complex subunit; Required for ribosome biogenesis. Part of a complex which catalyzes pseudouridylation of rRNA. This involves the isomerization of uridine such that the ribose is subsequently attached to C5, instead of the normal N1. Pseudouridine ("psi") residues may serve to stabilize the conformation of rRNAs. (283 aa)
	Rif1	Uncharacterized protein. (1520 aa)
	ptges3	Prostaglandin E synthase 3b (cytosolic). (159 aa)
	Atm	Uncharacterized protein. (147 aa)
	LOC101172197	TERF1 (TRF1)-interacting nuclear factor 2. (566 aa)
	dclre1a	C2H2-type domain-containing protein. (548 aa)
	ino80d	INO80 complex subunit Da. (1013 aa)
	terf2ip	Uncharacterized protein. (682 aa)
	blm	Uncharacterized protein. (1393 aa)
	tprkb	Tp53rk binding protein; Belongs to the CGI121/TPRKB family. (174 aa)
	ENSORLP00000027619	TAN domain-containing protein. (321 aa)
	nsmce2	NSE2 (MMS21) homolog, SMC5-SMC6 complex SUMO ligase. (230 aa)
	nhp2	Ribonucloprotein; Common component of the spliceosome and rRNA processing machinery; Belongs to the eukaryotic ribosomal protein eL8 family. (151 aa)
	recql4	RecQ helicase-like 4. (1546 aa)
	znf827	Zinc finger protein 827. (1498 aa)
	LOC101161606	Prostaglandin E synthase 3a (cytosolic). (159 aa)
	Tep1	Uncharacterized protein. (83 aa)
	ENSORLP00000031850	Uncharacterized protein. (396 aa)
	LOC105356481	ATP-dependent DNA helicase; Belongs to the helicase family. (2444 aa)
	ENSORLP00000032485	ATP-dependent DNA helicase; Belongs to the helicase family. (2676 aa)
	ENSORLP00000033799	Uncharacterized protein. (799 aa)
	ENSORLP00000033990	NOP10 ribonucleoprotein homolog (yeast). (64 aa)
	terf1	Telomeric repeat-binding factor; Binds the telomeric double-stranded 5'-TTAGGG-3' repeat. (454 aa)
	stn1	CST complex subunit STN1; Component of the CST complex proposed to act as a specialized replication factor promoting DNA replication under conditions of replication stress or natural replication barriers such as the telomere duplex. The CST complex binds single-stranded DNA with high affinity in a sequence-independent manner, while isolated subunits bind DNA with low affinity by themselves. Initially the CST complex has been proposed to protect telomeres from DNA degradation. However, the CST complex has been shown to be involved in several aspects of telomere replication. (359 aa)
	ENSORLP00000035938	Uncharacterized protein. (521 aa)
	wrap53	WD repeat containing, antisense to TP53. (467 aa)
	LOC101173980	Structure-specific endonuclease subunit SLX1; Catalytic subunit of the SLX1-SLX4 structure-specific endonuclease that resolves DNA secondary structures generated during DNA repair and recombination. Has endonuclease activity towards branched DNA substrates, introducing single-strand cuts in duplex DNA close to junctions with ss-DNA. (269 aa)
	lto1	LTO1 maturation factor of ABCE1. (143 aa)
	rad50	RAD50 homolog, double strand break repair protein. (1311 aa)
	pinx1	PIN2 (TERF1) interacting telomerase inhibitor 1. (352 aa)
	hus1	Checkpoint protein; Belongs to the HUS1 family. (299 aa)
	brca2	BRCA2 DNA repair associated. (3161 aa)
	xrcc1	X-ray repair complementing defective repair in Chinese hamster cells 1. (627 aa)
	ENSORLP00000040907	TROVE domain-containing protein. (289 aa)
	LOC101172442	C2H2-type domain-containing protein. (683 aa)
	uchl5	Ubiquitin carboxyl-terminal hydrolase. (329 aa)
	slx4	SLX4 structure-specific endonuclease subunit homolog (S. cerevisiae). (1590 aa)
	ino80e	INO80 complex subunit E. (257 aa)
	nfrkb	Nuclear factor related to kappaB binding protein. (1274 aa)

Your Current Organism:

Oryzias latipes

NCBI taxonomy Id: 8090
Other names: Japanese medaka, Japanese rice fish, O. latipes, Poecilia latipes, medaka

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
Atm	ENSORLP00000027619	ENSORLP00000026266	ENSORLP00000027619	Uncharacterized protein.	TAN domain-containing protein.	0.929
Atm	ENSORLP00000031850	ENSORLP00000026266	ENSORLP00000031850	Uncharacterized protein.	Uncharacterized protein.	0.691
Atm	H2MVD7_ORYLA	ENSORLP00000026266	ENSORLP00000022767	Uncharacterized protein.	DNA repair protein; Involved in the homologous recombination repair (HRR) pathway of double-stranded DNA, thought to repair chromosomal fragmentation, translocations and deletions; Belongs to the RecA family. RAD51 subfamily.	0.795
Atm	LOC101173980	ENSORLP00000026266	ENSORLP00000037215	Uncharacterized protein.	Structure-specific endonuclease subunit SLX1; Catalytic subunit of the SLX1-SLX4 structure-specific endonuclease that resolves DNA secondary structures generated during DNA repair and recombination. Has endonuclease activity towards branched DNA substrates, introducing single-strand cuts in duplex DNA close to junctions with ss-DNA.	0.634
Atm	RPA1	ENSORLP00000026266	ENSORLP00000004185	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.	0.758
Atm	Rad51c	ENSORLP00000026266	ENSORLP00000024828	Uncharacterized protein.	RAD51 paralog C.	0.785
Atm	Rif1	ENSORLP00000026266	ENSORLP00000025841	Uncharacterized protein.	Uncharacterized protein.	0.723
Atm	atr	ENSORLP00000026266	ENSORLP00000015251	Uncharacterized protein.	ATR serine/threonine kinase; Belongs to the PI3/PI4-kinase family.	0.968
Atm	blm	ENSORLP00000026266	ENSORLP00000027048	Uncharacterized protein.	Uncharacterized protein.	0.890
Atm	brca2	ENSORLP00000026266	ENSORLP00000039367	Uncharacterized protein.	BRCA2 DNA repair associated.	0.832
Atm	dclre1a	ENSORLP00000026266	ENSORLP00000026487	Uncharacterized protein.	C2H2-type domain-containing protein.	0.510
Atm	dclre1b	ENSORLP00000026266	ENSORLP00000007985	Uncharacterized protein.	DNA cross-link repair 1B.	0.519
Atm	dclre1c	ENSORLP00000026266	ENSORLP00000021646	Uncharacterized protein.	DNA cross-link repair 1C, PSO2 homolog (S. cerevisiae).	0.616
Atm	ercc1	ENSORLP00000026266	ENSORLP00000020313	Uncharacterized protein.	Excision repair cross-complementation group 1.	0.574
Atm	ercc4	ENSORLP00000026266	ENSORLP00000003684	Uncharacterized protein.	Excision repair cross-complementation group 4.	0.621
Atm	hus1	ENSORLP00000026266	ENSORLP00000039054	Uncharacterized protein.	Checkpoint protein; Belongs to the HUS1 family.	0.773
Atm	mre11	ENSORLP00000026266	ENSORLP00000009106	Uncharacterized protein.	Double-strand break repair protein; Involved in DNA double-strand break repair (DSBR). Possesses single-strand endonuclease activity and double-strand-specific 3'-5' exonuclease activity. Also involved in meiotic DSB processing.	0.997
Atm	pif1	ENSORLP00000026266	ENSORLP00000010771	Uncharacterized protein.	ATP-dependent DNA helicase PIF1; DNA-dependent ATPase and 5'-3' DNA helicase required for the maintenance of both mitochondrial and nuclear genome stability.	0.446
Atm	prkdc	ENSORLP00000026266	ENSORLP00000006867	Uncharacterized protein.	Protein kinase, DNA-activated, catalytic subunit; Belongs to the PI3/PI4-kinase family.	0.687
Atm	rad50	ENSORLP00000026266	ENSORLP00000037867	Uncharacterized protein.	RAD50 homolog, double strand break repair protein.	0.995