UPF1 protein (Oryzias latipes) - STRING interaction network

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.

Knowledge-based Evidence

from curated databases

textmining

Assay-based Predictions

experimentally determined

co-expression

Genomic Predictions

gene neighborhood

gene co-occurrence

gene fusions

Your Input:

Neighborhood

Gene Fusion

Cooccurrence

Coexpression

Experiments

Databases

Textmining

[Homology]

Score

UPF1

UPF1 RNA helicase and ATPase. (1101 aa)

Predicted Functional Partners:

smg6

0.999

smg5

0.999

UPF2

0.999

smg7

0.999

upf3b

0.998

Smg1

0.996

LOC101167578

0.995

eif4a3

0.995

casc3

0.995

rbm8a

0.994

Your Current Organism:

Oryzias latipes

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

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
LOC101167578	Smg1	ENSORLP00000013686	ENSORLP00000023938	UPF3A regulator of nonsense mediated mRNA decay.	SMG1_N domain-containing protein.	0.781
LOC101167578	UPF1	ENSORLP00000013686	ENSORLP00000010622	UPF3A regulator of nonsense mediated mRNA decay.	UPF1 RNA helicase and ATPase.	0.995
LOC101167578	UPF2	ENSORLP00000013686	ENSORLP00000021507	UPF3A regulator of nonsense mediated mRNA decay.	UPF2 regulator of nonsense mediated mRNA decay.	0.995
LOC101167578	casc3	ENSORLP00000013686	ENSORLP00000043908	UPF3A regulator of nonsense mediated mRNA decay.	Casc3 exon junction complex subunit.	0.933
LOC101167578	eif4a3	ENSORLP00000013686	ENSORLP00000040100	UPF3A regulator of nonsense mediated mRNA decay.	Eukaryotic translation initiation factor 4A3.	0.950
LOC101167578	rbm8a	ENSORLP00000013686	ENSORLP00000020359	UPF3A regulator of nonsense mediated mRNA decay.	RNA-binding protein 8A; Core component of the splicing-dependent multiprotein exon junction complex (EJC) deposited at splice junctions on mRNAs.	0.947
LOC101167578	smg5	ENSORLP00000013686	ENSORLP00000020330	UPF3A regulator of nonsense mediated mRNA decay.	SMG5 nonsense mediated mRNA decay factor.	0.974
LOC101167578	smg6	ENSORLP00000013686	ENSORLP00000004123	UPF3A regulator of nonsense mediated mRNA decay.	SMG6 nonsense mediated mRNA decay factor.	0.938
LOC101167578	smg7	ENSORLP00000013686	ENSORLP00000039487	UPF3A regulator of nonsense mediated mRNA decay.	SMG7 nonsense mediated mRNA decay factor.	0.890
LOC101167578	upf3b	ENSORLP00000013686	ENSORLP00000001267	UPF3A regulator of nonsense mediated mRNA decay.	UPF3B regulator of nonsense mediated mRNA decay.	0.902
Smg1	LOC101167578	ENSORLP00000023938	ENSORLP00000013686	SMG1_N domain-containing protein.	UPF3A regulator of nonsense mediated mRNA decay.	0.781
Smg1	UPF1	ENSORLP00000023938	ENSORLP00000010622	SMG1_N domain-containing protein.	UPF1 RNA helicase and ATPase.	0.996
Smg1	UPF2	ENSORLP00000023938	ENSORLP00000021507	SMG1_N domain-containing protein.	UPF2 regulator of nonsense mediated mRNA decay.	0.968
Smg1	casc3	ENSORLP00000023938	ENSORLP00000043908	SMG1_N domain-containing protein.	Casc3 exon junction complex subunit.	0.464
Smg1	eif4a3	ENSORLP00000023938	ENSORLP00000040100	SMG1_N domain-containing protein.	Eukaryotic translation initiation factor 4A3.	0.947
Smg1	rbm8a	ENSORLP00000023938	ENSORLP00000020359	SMG1_N domain-containing protein.	RNA-binding protein 8A; Core component of the splicing-dependent multiprotein exon junction complex (EJC) deposited at splice junctions on mRNAs.	0.939
Smg1	smg5	ENSORLP00000023938	ENSORLP00000020330	SMG1_N domain-containing protein.	SMG5 nonsense mediated mRNA decay factor.	0.898
Smg1	smg6	ENSORLP00000023938	ENSORLP00000004123	SMG1_N domain-containing protein.	SMG6 nonsense mediated mRNA decay factor.	0.900
Smg1	smg7	ENSORLP00000023938	ENSORLP00000039487	SMG1_N domain-containing protein.	SMG7 nonsense mediated mRNA decay factor.	0.984
Smg1	upf3b	ENSORLP00000023938	ENSORLP00000001267	SMG1_N domain-containing protein.	UPF3B regulator of nonsense mediated mRNA decay.	0.848