(47 nodes) mRNA Splicing - Minor Pathway network (Xiphophorus couchianus)

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.

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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:
	Srsf7	Serine and arginine rich splicing factor 7b. (147 aa)
	Snrpf	Small nuclear ribonucleoprotein polypeptide F. (87 aa)
	GTF2F2	General transcription factor IIF, polypeptide 2b. (261 aa)
	ENSXCOP00000019505	Uncharacterized protein. (290 aa)
	POLR2B	RNA polymerase II subunit B. (366 aa)
	Zcrb1	Zinc finger CCHC-type and RNA binding motif 1. (148 aa)
	polr2f	Polymerase (RNA) II (DNA directed) polypeptide F. (127 aa)
	Eftud2	Elongation factor Tu GTP binding domain containing 2. (817 aa)
	ENSXCOP00000023505	Uncharacterized protein. (142 aa)
	Ddx42	DEAD (Asp-Glu-Ala-Asp) box helicase 42; Belongs to the DEAD box helicase family. (782 aa)
	Pdcd7	Uncharacterized protein. (514 aa)
	ENSXCOP00000023969	Uncharacterized protein. (250 aa)
	ENSXCOP00000024216	Splicing factor 3b, subunit 1. (1276 aa)
	sf3b4	Splicing factor 3b, subunit 4. (391 aa)
	ENSXCOP00000026847	Uncharacterized protein. (66 aa)
	snrpd1	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. (119 aa)
	snrnp40	Small nuclear ribonucleoprotein 40 (U5). (347 aa)
	polr2c	Polymerase (RNA) II (DNA directed) polypeptide C. (275 aa)
	ncbp2	Nuclear cap-binding protein subunit 2; Component of the cap-binding complex (CBC), which binds co- transcriptionally to the 5' cap of pre-mRNAs and is involved in various processes such as pre-mRNA splicing, translation regulation, nonsense- mediated mRNA decay, RNA-mediated gene silencing (RNAi) by microRNAs (miRNAs) and mRNA export. The CBC complex is involved in mRNA export from the nucleus, leading to the recruitment of the mRNA export machinery to the 5' end of mRNA and to mRNA export in a 5' to 3' direction through the nuclear pore. The CBC complex is also involved in mediating U [...] (164 aa)
	LOC114161558	Uncharacterized protein. (250 aa)
	ENSXCOP00000012414	Serine and arginine rich splicing factor 7a. (127 aa)
	ENSXCOP00000012253	Small nuclear ribonucleoprotein E; Associated with the spliceosome snRNP U1, U2, U4/U6 and U5. Belongs to the snRNP Sm proteins family. (93 aa)
	POLR2E	RNA polymerase II subunit E. (183 aa)
	ENSXCOP00000011879	Small nuclear ribonucleoprotein 70 (U1). (456 aa)
	ENSXCOP00000011827	Splicing factor 3b, subunit 2. (702 aa)
	Sf3b6	Splicing factor 3b, subunit 6. (129 aa)
	prpf6	PRP6 pre-mRNA processing factor 6 homolog (S. cerevisiae). (969 aa)
	Srsf2	Serine and arginine rich splicing factor 2a. (218 aa)
	ENSXCOP00000006473	RNA-binding region (RNP1, RRM) containing 3. (509 aa)
	snrpd3	Small nuclear ribonucleoprotein Sm D3. (127 aa)
	ENSXCOP00000005749	Small nuclear ribonucleoprotein 48 (U11/U12). (323 aa)
	ybx1	Y box binding protein 1. (324 aa)
	polr2h	DNA-directed RNA polymerases I, II, and III subunit RPABC3; DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Common component of RNA polymerases I, II and III which synthesize ribosomal RNA precursors, mRNA precursors and many functional non- coding RNAs, and small RNAs, such as 5S rRNA and tRNAs, respectively. (150 aa)
	Polr2g	Polymerase (RNA) II (DNA directed) polypeptide G-like. (201 aa)
	txnl4a	Thioredoxin-like protein; Plays role in pre-mRNA splicing. Belongs to the DIM1 family. (142 aa)
	YBX2	Y-box binding protein 2. (171 aa)
	Polr2a	DNA-directed RNA polymerase subunit; DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. (1788 aa)
	ENSXCOP00000002251	General transcription factor IIF subunit 2; TFIIF is a general transcription initiation factor that binds to RNA polymerase II and helps to recruit it to the initiation complex in collaboration with TFIIB. It promotes transcription elongation. This subunit shows ATP-dependent DNA-helicase activity. (252 aa)
	polr2i	DNA-directed RNA polymerase subunit; DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Belongs to the archaeal rpoM/eukaryotic RPA12/RPB9/RPC11 RNA polymerase family. (126 aa)
	Snrpd2	Small nuclear ribonucleoprotein Sm D2. (126 aa)
	ENSXCOP00000000399	Zinc finger (CCCH type), RNA-binding motif and serine/arginine rich 2. (554 aa)
	ENSXCOP00000000111	Small nuclear ribonucleoprotein G. (79 aa)
	snrnp25	Small nuclear ribonucleoprotein 25. (179 aa)
	Ddx23	DEAD (Asp-Glu-Ala-Asp) box polypeptide 23; Belongs to the DEAD box helicase family. (765 aa)
	Polr2d	Polymerase (RNA) II (DNA directed) polypeptide D. (104 aa)
	prpf8	Pre-mRNA processing factor 8. (2341 aa)
	Sf3b3	Splicing factor 3b, subunit 3. (976 aa)

Your Current Organism:

Xiphophorus couchianus

NCBI taxonomy Id: 32473
Other names: Limia couchiana, Monterrey platyfish, X. couchianus

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Browse interactions in tabular form:

node1	node2	node1 accession	node2 accession	node1 annotation	node2 annotation	score
Ddx23	ENSXCOP00000000111	ENSXCOP00000015385	ENSXCOP00000000111	DEAD (Asp-Glu-Ala-Asp) box polypeptide 23; Belongs to the DEAD box helicase family.	Small nuclear ribonucleoprotein G.	0.972
Ddx23	ENSXCOP00000006473	ENSXCOP00000015385	ENSXCOP00000006473	DEAD (Asp-Glu-Ala-Asp) box polypeptide 23; Belongs to the DEAD box helicase family.	RNA-binding region (RNP1, RRM) containing 3.	0.600
Ddx23	ENSXCOP00000011827	ENSXCOP00000015385	ENSXCOP00000011827	DEAD (Asp-Glu-Ala-Asp) box polypeptide 23; Belongs to the DEAD box helicase family.	Splicing factor 3b, subunit 2.	0.889
Ddx23	ENSXCOP00000011879	ENSXCOP00000015385	ENSXCOP00000011879	DEAD (Asp-Glu-Ala-Asp) box polypeptide 23; Belongs to the DEAD box helicase family.	Small nuclear ribonucleoprotein 70 (U1).	0.938
Ddx23	ENSXCOP00000012253	ENSXCOP00000015385	ENSXCOP00000012253	DEAD (Asp-Glu-Ala-Asp) box polypeptide 23; Belongs to the DEAD box helicase family.	Small nuclear ribonucleoprotein E; Associated with the spliceosome snRNP U1, U2, U4/U6 and U5. Belongs to the snRNP Sm proteins family.	0.982
Ddx23	ENSXCOP00000024216	ENSXCOP00000015385	ENSXCOP00000024216	DEAD (Asp-Glu-Ala-Asp) box polypeptide 23; Belongs to the DEAD box helicase family.	Splicing factor 3b, subunit 1.	0.909
Ddx23	Eftud2	ENSXCOP00000015385	ENSXCOP00000023170	DEAD (Asp-Glu-Ala-Asp) box polypeptide 23; Belongs to the DEAD box helicase family.	Elongation factor Tu GTP binding domain containing 2.	0.994
Ddx23	Sf3b3	ENSXCOP00000015385	ENSXCOP00000018080	DEAD (Asp-Glu-Ala-Asp) box polypeptide 23; Belongs to the DEAD box helicase family.	Splicing factor 3b, subunit 3.	0.884
Ddx23	Sf3b6	ENSXCOP00000015385	ENSXCOP00000011203	DEAD (Asp-Glu-Ala-Asp) box polypeptide 23; Belongs to the DEAD box helicase family.	Splicing factor 3b, subunit 6.	0.695
Ddx23	Snrpd2	ENSXCOP00000015385	ENSXCOP00000001338	DEAD (Asp-Glu-Ala-Asp) box polypeptide 23; Belongs to the DEAD box helicase family.	Small nuclear ribonucleoprotein Sm D2.	0.980
Ddx23	Snrpf	ENSXCOP00000015385	ENSXCOP00000018407	DEAD (Asp-Glu-Ala-Asp) box polypeptide 23; Belongs to the DEAD box helicase family.	Small nuclear ribonucleoprotein polypeptide F.	0.969
Ddx23	ncbp2	ENSXCOP00000015385	ENSXCOP00000014472	DEAD (Asp-Glu-Ala-Asp) box polypeptide 23; Belongs to the DEAD box helicase family.	Nuclear cap-binding protein subunit 2; Component of the cap-binding complex (CBC), which binds co- transcriptionally to the 5' cap of pre-mRNAs and is involved in various processes such as pre-mRNA splicing, translation regulation, nonsense- mediated mRNA decay, RNA-mediated gene silencing (RNAi) by microRNAs (miRNAs) and mRNA export. The CBC complex is involved in mRNA export from the nucleus, leading to the recruitment of the mRNA export machinery to the 5' end of mRNA and to mRNA export in a 5' to 3' direction through the nuclear pore. The CBC complex is also involved in mediating U [...]	0.587
Ddx23	prpf6	ENSXCOP00000015385	ENSXCOP00000010708	DEAD (Asp-Glu-Ala-Asp) box polypeptide 23; Belongs to the DEAD box helicase family.	PRP6 pre-mRNA processing factor 6 homolog (S. cerevisiae).	0.995
Ddx23	prpf8	ENSXCOP00000015385	ENSXCOP00000016944	DEAD (Asp-Glu-Ala-Asp) box polypeptide 23; Belongs to the DEAD box helicase family.	Pre-mRNA processing factor 8.	0.999
Ddx23	sf3b4	ENSXCOP00000015385	ENSXCOP00000026640	DEAD (Asp-Glu-Ala-Asp) box polypeptide 23; Belongs to the DEAD box helicase family.	Splicing factor 3b, subunit 4.	0.842
Ddx23	snrnp40	ENSXCOP00000015385	ENSXCOP00000026975	DEAD (Asp-Glu-Ala-Asp) box polypeptide 23; Belongs to the DEAD box helicase family.	Small nuclear ribonucleoprotein 40 (U5).	0.991
Ddx23	snrpd1	ENSXCOP00000015385	ENSXCOP00000026925	DEAD (Asp-Glu-Ala-Asp) box polypeptide 23; Belongs to the DEAD box helicase family.	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.	0.976
Ddx23	snrpd3	ENSXCOP00000015385	ENSXCOP00000006205	DEAD (Asp-Glu-Ala-Asp) box polypeptide 23; Belongs to the DEAD box helicase family.	Small nuclear ribonucleoprotein Sm D3.	0.977
Ddx23	txnl4a	ENSXCOP00000015385	ENSXCOP00000002451	DEAD (Asp-Glu-Ala-Asp) box polypeptide 23; Belongs to the DEAD box helicase family.	Thioredoxin-like protein; Plays role in pre-mRNA splicing. Belongs to the DIM1 family.	0.989
Ddx42	ENSXCOP00000000111	ENSXCOP00000023506	ENSXCOP00000000111	DEAD (Asp-Glu-Ala-Asp) box helicase 42; Belongs to the DEAD box helicase family.	Small nuclear ribonucleoprotein G.	0.694