(36 nodes) LSM domain superfamily network (Theobroma cacao)

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:
	TCM_019522	Decapping 5, putative isoform 2. (601 aa)
	TCM_000986	MSCS-like 2. (744 aa)
	TCM_000988	MSCS-like 2. (566 aa)
	LSM5	U6 snRNA-associated Sm-like protein LSm5; Plays a role in U6 snRNP assembly and function. Binds to the 3' end of U6 snRNA. (87 aa)
	LSM4	U6 snRNA-associated Sm-like protein LSm4; Binds specifically to the 3'-terminal U-tract of U6 snRNA. (149 aa)
	TCM_002491	Sm domain-containing protein. (359 aa)
	TCM_005909	Small nuclear ribonucleoprotein family protein. (99 aa)
	TCM_046691	Small nuclear ribonucleoprotein Sm D1; Involved in splicing regulation. Facilitates post- transcriptional gene silencing (PTGS) by limiting the degradation of transgene aberrant RNAs by the RNA quality control (RQC) machinery, thus favoring their entry into cytoplasmic siRNA bodies where they can trigger PTGS. Does not participate in the production of small RNAs. Belongs to the snRNP core protein family. (174 aa)
	TCM_004456	BTB-POZ and MATH domain 2. (493 aa)
	TCM_006558	Mechanosensitive ion channel domain-containing protein isoform 1. (549 aa)
	TCM_006563	Mechanosensitive ion channel domain-containing protein. (419 aa)
	TCM_005285	Mechanosensitive ion channel protein isoform 1. (546 aa)
	TCM_006546	Mechanosensitive ion channel family protein. (213 aa)
	TCM_011884	Decapping 5. (673 aa)
	TCM_011273	Small nuclear ribonucleoprotein Sm D2. (107 aa)
	TCM_019826	Small nuclear ribonucleoprotein family protein isoform 1. (91 aa)
	TCM_022624	Small nuclear ribonucleoprotein G. (80 aa)
	LSM8	U6 snRNA-associated Sm-like protein LSm8; Plays role in pre-mRNA splicing as component of the U4/U6-U5 tri-snRNP complex that is involved in spliceosome assembly, and as component of the precatalytic spliceosome (spliceosome B complex). The heptameric LSM2-8 complex binds specifically to the 3'-terminal U-tract of U6 snRNA. (98 aa)
	TCM_025703	Mechanosensitive ion channel protein. (708 aa)
	TCM_034315	Mechanosensitive ion channel protein. (799 aa)
	TCM_034385	Small nuclear ribonucleoprotein Sm D3; Core component of the spliceosomal U1, U2, U4 and U5 small nuclear ribonucleoproteins (snRNPs), the building blocks of the spliceosome. (132 aa)
	TCM_034509	MSCS-like 3 isoform 1. (707 aa)
	TCM_032110	Mechanosensitive ion channel protein. (898 aa)
	LSM3	U6 snRNA-associated Sm-like protein LSm3; Binds specifically to the 3'-terminal U-tract of U6 snRNA. (97 aa)
	TCM_012240	Binding-like protein isoform 1. (723 aa)
	TCM_016705	Decapping 5-like, putative isoform 1. (574 aa)
	TCM_026981	Small nuclear ribonucleoprotein associated protein B. (291 aa)
	TCM_016671	Mechanosensitive ion channel protein. (708 aa)
	TCM_027096	Small nuclear ribonucleoprotein E; Associated with the spliceosome snRNP U1, U2, U4/U6 and U5. Belongs to the snRNP Sm proteins family. (114 aa)
	LSM1	U6 snRNA-associated Sm-like protein LSm1; Component of the cytoplasmic LSM1-LSM7 complex which is involved in mRNA degradation. (128 aa)
	TCM_029454	Small nuclear ribonucleoprotein family protein isoform 2. (140 aa)
	TCM_037568	Mechanosensitive channel of small conductance-like 10, putative isoform 1. (949 aa)
	TCM_037366	Mechanosensitive ion channel protein. (779 aa)
	LSM1-2	U6 snRNA-associated Sm-like protein LSm1; Component of the cytoplasmic LSM1-LSM7 complex which is involved in mRNA degradation. (128 aa)
	TCM_038810	Small nuclear ribonucleoprotein E; Associated with the spliceosome snRNP U1, U2, U4/U6 and U5. Belongs to the snRNP Sm proteins family. (88 aa)
	TCM_039217	Small nuclear ribonucleoprotein F. (88 aa)

Your Current Organism:

Theobroma cacao

NCBI taxonomy Id: 3641
Other names: T. cacao, Theobroma cacao L., cacao, chocolate, cocoa

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
LSM1	LSM1-2	A0A061GBQ5	A0A061GLG0	U6 snRNA-associated Sm-like protein LSm1; Component of the cytoplasmic LSM1-LSM7 complex which is involved in mRNA degradation.	U6 snRNA-associated Sm-like protein LSm1; Component of the cytoplasmic LSM1-LSM7 complex which is involved in mRNA degradation.	0.901
LSM1	LSM3	A0A061GBQ5	A0A061FQC9	U6 snRNA-associated Sm-like protein LSm1; Component of the cytoplasmic LSM1-LSM7 complex which is involved in mRNA degradation.	U6 snRNA-associated Sm-like protein LSm3; Binds specifically to the 3'-terminal U-tract of U6 snRNA.	0.993
LSM1	LSM4	A0A061GBQ5	A0A061DSH4	U6 snRNA-associated Sm-like protein LSm1; Component of the cytoplasmic LSM1-LSM7 complex which is involved in mRNA degradation.	U6 snRNA-associated Sm-like protein LSm4; Binds specifically to the 3'-terminal U-tract of U6 snRNA.	0.984
LSM1	LSM5	A0A061GBQ5	A0A061DMN8	U6 snRNA-associated Sm-like protein LSm1; Component of the cytoplasmic LSM1-LSM7 complex which is involved in mRNA degradation.	U6 snRNA-associated Sm-like protein LSm5; Plays a role in U6 snRNP assembly and function. Binds to the 3' end of U6 snRNA.	0.992
LSM1	LSM8	A0A061GBQ5	A0A061F6F2	U6 snRNA-associated Sm-like protein LSm1; Component of the cytoplasmic LSM1-LSM7 complex which is involved in mRNA degradation.	U6 snRNA-associated Sm-like protein LSm8; Plays role in pre-mRNA splicing as component of the U4/U6-U5 tri-snRNP complex that is involved in spliceosome assembly, and as component of the precatalytic spliceosome (spliceosome B complex). The heptameric LSM2-8 complex binds specifically to the 3'-terminal U-tract of U6 snRNA.	0.953
LSM1	TCM_002491	A0A061GBQ5	A0A061DUE5	U6 snRNA-associated Sm-like protein LSm1; Component of the cytoplasmic LSM1-LSM7 complex which is involved in mRNA degradation.	Sm domain-containing protein.	0.416
LSM1	TCM_005909	A0A061GBQ5	A0A061DVC4	U6 snRNA-associated Sm-like protein LSm1; Component of the cytoplasmic LSM1-LSM7 complex which is involved in mRNA degradation.	Small nuclear ribonucleoprotein family protein.	0.991
LSM1	TCM_011273	A0A061GBQ5	A0A061EGD1	U6 snRNA-associated Sm-like protein LSm1; Component of the cytoplasmic LSM1-LSM7 complex which is involved in mRNA degradation.	Small nuclear ribonucleoprotein Sm D2.	0.631
LSM1	TCM_019826	A0A061GBQ5	A0A061EIY5	U6 snRNA-associated Sm-like protein LSm1; Component of the cytoplasmic LSM1-LSM7 complex which is involved in mRNA degradation.	Small nuclear ribonucleoprotein family protein isoform 1.	0.982
LSM1	TCM_022624	A0A061GBQ5	A0A061EV54	U6 snRNA-associated Sm-like protein LSm1; Component of the cytoplasmic LSM1-LSM7 complex which is involved in mRNA degradation.	Small nuclear ribonucleoprotein G.	0.510
LSM1	TCM_026981	A0A061GBQ5	A0A061G6W4	U6 snRNA-associated Sm-like protein LSm1; Component of the cytoplasmic LSM1-LSM7 complex which is involved in mRNA degradation.	Small nuclear ribonucleoprotein associated protein B.	0.547
LSM1	TCM_027096	A0A061GBQ5	A0A061G7A6	U6 snRNA-associated Sm-like protein LSm1; Component of the cytoplasmic LSM1-LSM7 complex which is involved in mRNA degradation.	Small nuclear ribonucleoprotein E; Associated with the spliceosome snRNP U1, U2, U4/U6 and U5. Belongs to the snRNP Sm proteins family.	0.581
LSM1	TCM_034385	A0A061GBQ5	A0A061FED3	U6 snRNA-associated Sm-like protein LSm1; Component of the cytoplasmic LSM1-LSM7 complex which is involved in mRNA degradation.	Small nuclear ribonucleoprotein Sm D3; Core component of the spliceosomal U1, U2, U4 and U5 small nuclear ribonucleoproteins (snRNPs), the building blocks of the spliceosome.	0.560
LSM1	TCM_038810	A0A061GBQ5	A0A061GPH3	U6 snRNA-associated Sm-like protein LSm1; Component of the cytoplasmic LSM1-LSM7 complex which is involved in mRNA degradation.	Small nuclear ribonucleoprotein E; Associated with the spliceosome snRNP U1, U2, U4/U6 and U5. Belongs to the snRNP Sm proteins family.	0.581
LSM1	TCM_039217	A0A061GBQ5	A0A061GXN6	U6 snRNA-associated Sm-like protein LSm1; Component of the cytoplasmic LSM1-LSM7 complex which is involved in mRNA degradation.	Small nuclear ribonucleoprotein F.	0.717
LSM1	TCM_046691	A0A061GBQ5	A0A061DXR8	U6 snRNA-associated Sm-like protein LSm1; Component of the cytoplasmic LSM1-LSM7 complex which is involved in mRNA degradation.	Small nuclear ribonucleoprotein Sm D1; Involved in splicing regulation. Facilitates post- transcriptional gene silencing (PTGS) by limiting the degradation of transgene aberrant RNAs by the RNA quality control (RQC) machinery, thus favoring their entry into cytoplasmic siRNA bodies where they can trigger PTGS. Does not participate in the production of small RNAs. Belongs to the snRNP core protein family.	0.416
LSM1-2	LSM1	A0A061GLG0	A0A061GBQ5	U6 snRNA-associated Sm-like protein LSm1; Component of the cytoplasmic LSM1-LSM7 complex which is involved in mRNA degradation.	U6 snRNA-associated Sm-like protein LSm1; Component of the cytoplasmic LSM1-LSM7 complex which is involved in mRNA degradation.	0.901
LSM1-2	LSM3	A0A061GLG0	A0A061FQC9	U6 snRNA-associated Sm-like protein LSm1; Component of the cytoplasmic LSM1-LSM7 complex which is involved in mRNA degradation.	U6 snRNA-associated Sm-like protein LSm3; Binds specifically to the 3'-terminal U-tract of U6 snRNA.	0.993
LSM1-2	LSM4	A0A061GLG0	A0A061DSH4	U6 snRNA-associated Sm-like protein LSm1; Component of the cytoplasmic LSM1-LSM7 complex which is involved in mRNA degradation.	U6 snRNA-associated Sm-like protein LSm4; Binds specifically to the 3'-terminal U-tract of U6 snRNA.	0.984
LSM1-2	LSM5	A0A061GLG0	A0A061DMN8	U6 snRNA-associated Sm-like protein LSm1; Component of the cytoplasmic LSM1-LSM7 complex which is involved in mRNA degradation.	U6 snRNA-associated Sm-like protein LSm5; Plays a role in U6 snRNP assembly and function. Binds to the 3' end of U6 snRNA.	0.992