(56 nodes) Precatalytic spliceosome, and snRNA binding network (Opisthorchis viverrini)

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:
	T265_16193	Uncharacterized protein. (74 aa)
	T265_11847	WD_REPEATS_REGION domain-containing protein. (364 aa)
	T265_11627	Uncharacterized protein. (294 aa)
	T265_11303	Reverse transcriptase domain-containing protein. (919 aa)
	T265_12062	RRM domain-containing protein. (544 aa)
	T265_11882	SF3b1 domain-containing protein. (1307 aa)
	T265_11823	CPSF A subunit region. (1226 aa)
	T265_10389	Matrin-type domain-containing protein. (486 aa)
	LSM1	U6 snRNA-associated Sm-like protein LSm1; Probably involved with other LSm subunits in the general process of degradation of mRNAs. (220 aa)
	T265_10294	WD_REPEATS_REGION domain-containing protein. (450 aa)
	T265_10890	WD_REPEATS_REGION domain-containing protein. (923 aa)
	T265_09690	EFG_C domain-containing protein. (95 aa)
	T265_10482	Uncharacterized protein. (514 aa)
	T265_08856	Uncharacterized protein. (59 aa)
	T265_08740	Uncharacterized protein. (422 aa)
	T265_09870	Uncharacterized protein. (491 aa)
	T265_09689	Uncharacterized protein. (1279 aa)
	T265_07598	Nop domain-containing protein. (895 aa)
	T265_08572	Uncharacterized protein. (326 aa)
	T265_10171	Uncharacterized protein. (488 aa)
	T265_06824	KH domain-containing protein. (597 aa)
	T265_14961	Uncharacterized protein. (1068 aa)
	LSM4	U6 snRNA-associated Sm-like protein LSm4; Binds specifically to the 3'-terminal U-tract of U6 snRNA. (161 aa)
	T265_14392	MPN domain-containing protein. (2287 aa)
	T265_05930	Uncharacterized protein. (190 aa)
	T265_14671	Sm domain-containing protein. (92 aa)
	T265_08739	Uncharacterized protein. (266 aa)
	T265_06282	Small nuclear ribonucleoprotein Sm D1; Essential for pre-mRNA splicing. Implicated in the formation of stable, biologically active snRNP structures. Belongs to the snRNP core protein family. (124 aa)
	T265_06228	Uncharacterized protein. (575 aa)
	T265_06108	Small nuclear ribonucleoprotein G. (199 aa)
	T265_07581	RRM domain-containing protein. (123 aa)
	T265_07341	Small nuclear ribonucleoprotein E; Associated with the spliceosome snRNP U1, U2, U4/U6 and U5. Belongs to the snRNP Sm proteins family. (86 aa)
	T265_04172	Uncharacterized protein. (945 aa)
	T265_07357	Sm domain-containing protein. (178 aa)
	T265_04068	Sm domain-containing protein. (788 aa)
	T265_03368	Uncharacterized protein. (1670 aa)
	T265_13987	Uncharacterized protein. (399 aa)
	T265_06230	Uncharacterized protein. (717 aa)
	T265_05809	Sm domain-containing protein. (277 aa)
	T265_05583	PPIase cyclophilin-type domain-containing protein. (1368 aa)
	T265_03378	Sm domain-containing protein. (291 aa)
	T265_11628	Uncharacterized protein. (1974 aa)
	T265_01556	U1 small nuclear ribonucleoprotein C; Component of the U1 snRNP, which is essential for recognition of the pre-mRNA 5' splice-site and the subsequent assembly of the spliceosome. U1-C is directly involved in initial 5' splice-site recognition for both constitutive and regulated alternative splicing. The interaction with the 5' splice-site seems to precede base-pairing between the pre-mRNA and the U1 snRNA; Belongs to the U1 small nuclear ribonucleoprotein C family. (142 aa)
	T265_04319	Splicing factor 3B subunit 5; Belongs to the SF3B5 family. (85 aa)
	T265_03828	Uncharacterized protein. (363 aa)
	T265_01022	PSP domain-containing protein. (891 aa)
	T265_13216	Uncharacterized protein. (447 aa)
	T265_09428	RRM domain-containing protein. (616 aa)
	T265_09278	Small nuclear ribonucleoprotein Sm D2. (124 aa)
	LSM3	U6 snRNA-associated Sm-like protein LSm3; Binds specifically to the 3'-terminal U-tract of U6 snRNA. (104 aa)
	T265_02055	Thioredoxin-like protein; Plays role in pre-mRNA splicing. Belongs to the DIM1 family. (169 aa)
	T265_07600	Uncharacterized protein. (78 aa)
	T265_05682	Matrin-type domain-containing protein. (572 aa)
	T265_05545	Uncharacterized protein. (937 aa)
	T265_12691	Uncharacterized protein. (434 aa)
	T265_00099	Sm domain-containing protein. (439 aa)

Your Current Organism:

Opisthorchis viverrini

NCBI taxonomy Id: 6198
Other names: O. viverrini, Southeast Asian liver fluke

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 protiens in your network

Browse interactions in tabular form:

node1	node2	node1 accession	node2 accession	node1 annotation	node2 annotation	score
LSM1	LSM3	A0A074Z2V9	A0A075A7R3	U6 snRNA-associated Sm-like protein LSm1; Probably involved with other LSm subunits in the general process of degradation of mRNAs.	U6 snRNA-associated Sm-like protein LSm3; Binds specifically to the 3'-terminal U-tract of U6 snRNA.	0.999
LSM1	LSM4	A0A074Z2V9	A0A074ZFN5	U6 snRNA-associated Sm-like protein LSm1; Probably involved with other LSm subunits in the general process of degradation of mRNAs.	U6 snRNA-associated Sm-like protein LSm4; Binds specifically to the 3'-terminal U-tract of U6 snRNA.	0.999
LSM1	T265_00099	A0A074Z2V9	A0A075AJZ6	U6 snRNA-associated Sm-like protein LSm1; Probably involved with other LSm subunits in the general process of degradation of mRNAs.	Sm domain-containing protein.	0.729
LSM1	T265_03368	A0A074Z2V9	A0A074ZSK6	U6 snRNA-associated Sm-like protein LSm1; Probably involved with other LSm subunits in the general process of degradation of mRNAs.	Uncharacterized protein.	0.400
LSM1	T265_03378	A0A074Z2V9	A0A074ZW48	U6 snRNA-associated Sm-like protein LSm1; Probably involved with other LSm subunits in the general process of degradation of mRNAs.	Sm domain-containing protein.	0.999
LSM1	T265_04068	A0A074Z2V9	A0A074ZP91	U6 snRNA-associated Sm-like protein LSm1; Probably involved with other LSm subunits in the general process of degradation of mRNAs.	Sm domain-containing protein.	0.980
LSM1	T265_04172	A0A074Z2V9	A0A074ZP66	U6 snRNA-associated Sm-like protein LSm1; Probably involved with other LSm subunits in the general process of degradation of mRNAs.	Uncharacterized protein.	0.517
LSM1	T265_05809	A0A074Z2V9	A0A074ZUH8	U6 snRNA-associated Sm-like protein LSm1; Probably involved with other LSm subunits in the general process of degradation of mRNAs.	Sm domain-containing protein.	0.559
LSM1	T265_06108	A0A074Z2V9	A0A074ZLQ4	U6 snRNA-associated Sm-like protein LSm1; Probably involved with other LSm subunits in the general process of degradation of mRNAs.	Small nuclear ribonucleoprotein G.	0.610
LSM1	T265_06282	A0A074Z2V9	A0A074ZL28	U6 snRNA-associated Sm-like protein LSm1; Probably involved with other LSm subunits in the general process of degradation of mRNAs.	Small nuclear ribonucleoprotein Sm D1; Essential for pre-mRNA splicing. Implicated in the formation of stable, biologically active snRNP structures. Belongs to the snRNP core protein family.	0.703
LSM1	T265_07341	A0A074Z2V9	A0A074ZP55	U6 snRNA-associated Sm-like protein LSm1; Probably involved with other LSm subunits in the general process of degradation of mRNAs.	Small nuclear ribonucleoprotein E; Associated with the spliceosome snRNP U1, U2, U4/U6 and U5. Belongs to the snRNP Sm proteins family.	0.794
LSM1	T265_07357	A0A074Z2V9	A0A074ZP75	U6 snRNA-associated Sm-like protein LSm1; Probably involved with other LSm subunits in the general process of degradation of mRNAs.	Sm domain-containing protein.	0.532
LSM1	T265_09278	A0A074Z2V9	A0A075A5M1	U6 snRNA-associated Sm-like protein LSm1; Probably involved with other LSm subunits in the general process of degradation of mRNAs.	Small nuclear ribonucleoprotein Sm D2.	0.746
LSM1	T265_14671	A0A074Z2V9	A0A074ZIY3	U6 snRNA-associated Sm-like protein LSm1; Probably involved with other LSm subunits in the general process of degradation of mRNAs.	Sm domain-containing protein.	0.999
LSM1	T265_14961	A0A074Z2V9	A0A074ZFK3	U6 snRNA-associated Sm-like protein LSm1; Probably involved with other LSm subunits in the general process of degradation of mRNAs.	Uncharacterized protein.	0.400
LSM3	LSM1	A0A075A7R3	A0A074Z2V9	U6 snRNA-associated Sm-like protein LSm3; Binds specifically to the 3'-terminal U-tract of U6 snRNA.	U6 snRNA-associated Sm-like protein LSm1; Probably involved with other LSm subunits in the general process of degradation of mRNAs.	0.999
LSM3	LSM4	A0A075A7R3	A0A074ZFN5	U6 snRNA-associated Sm-like protein LSm3; Binds specifically to the 3'-terminal U-tract of U6 snRNA.	U6 snRNA-associated Sm-like protein LSm4; Binds specifically to the 3'-terminal U-tract of U6 snRNA.	0.999
LSM3	T265_00099	A0A075A7R3	A0A075AJZ6	U6 snRNA-associated Sm-like protein LSm3; Binds specifically to the 3'-terminal U-tract of U6 snRNA.	Sm domain-containing protein.	0.982
LSM3	T265_01022	A0A075A7R3	A0A075A3R8	U6 snRNA-associated Sm-like protein LSm3; Binds specifically to the 3'-terminal U-tract of U6 snRNA.	PSP domain-containing protein.	0.879
LSM3	T265_01556	A0A075A7R3	A0A074ZY03	U6 snRNA-associated Sm-like protein LSm3; Binds specifically to the 3'-terminal U-tract of U6 snRNA.	U1 small nuclear ribonucleoprotein C; Component of the U1 snRNP, which is essential for recognition of the pre-mRNA 5' splice-site and the subsequent assembly of the spliceosome. U1-C is directly involved in initial 5' splice-site recognition for both constitutive and regulated alternative splicing. The interaction with the 5' splice-site seems to precede base-pairing between the pre-mRNA and the U1 snRNA; Belongs to the U1 small nuclear ribonucleoprotein C family.	0.522