sftb-1 Splicing factor 3B subunit 1 domain-containing protein [Caenorhabditis elegans] - Gene

Summary

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Gene symbol: sftb-1
Gene description: Splicing factor 3B subunit 1 domain-containing protein
Primary source: WormBase:WBGene00011605
Locus tag: CELE_T08A11.2
See related: AllianceGenome:WB:WBGene00011605
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Caenorhabditis elegans (strain: Bristol N2)
Lineage: Eukaryota; Metazoa; Ecdysozoa; Nematoda; Chromadorea; Rhabditida; Rhabditina; Rhabditomorpha; Rhabditoidea; Rhabditidae; Peloderinae; Caenorhabditis
Summary: Predicted to enable mRNA binding activity. Involved in negative regulation of gene expression. Predicted to be located in nucleus. Predicted to be part of U2 snRNP; U2-type prespliceosome; and catalytic step 2 spliceosome. Human ortholog(s) of this gene implicated in hepatocellular carcinoma and myelodysplastic syndrome. Orthologous to human SF3B1 (splicing factor 3b subunit 1). [provided by Alliance of Genome Resources, Apr 2022]
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Genomic context

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Location:: chromosome: III

Exon count:: 11

Sequence:: Chromosome: III; NC_003281.10 (4263786..4269270, complement)

Chromosome III - NC_003281.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:: NC_003281.10

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Study reproduced three cancer-related SF3B1 missense mutations in the C. elegans ortholog sftb-1 and they do not cause any overt phenotypes, but few alterations in splicing. However, the combination of these mutations has additive effects, hampering SFTB-1 functions and allowing the study of synthetic interactions that may result in a defective spliceosome structure.
Title: CRISPR editing of sftb-1/SF3B1 in Caenorhabditis elegans allows the identification of synthetic interactions with cancer-related mutations and the chemical inhibition of splicing.

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Pathways from PubChem

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Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

T08A11.2 (e-PCR)
- UniSTS:311626

Homology

Orthologs from OrthoDB

Gene Ontology Provided by WormBase

Function	Evidence Code	Pubs
enables mRNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables mRNA binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in negative regulation of gene expression	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in spliceosomal complex assembly	IBA Inferred from Biological aspect of Ancestor more info
involved_in spliceosomal complex assembly	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
part_of U2 snRNP	IBA Inferred from Biological aspect of Ancestor more info
part_of U2-type prespliceosome	IBA Inferred from Biological aspect of Ancestor more info
part_of catalytic step 2 spliceosome	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IEA Inferred from Electronic Annotation more info
part_of spliceosomal complex	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: Splicing factor 3B subunit 1 domain-containing protein

NP_497853.1

Confirmed by transcript evidence

NCBI Reference Sequences (RefSeq)

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Genome Annotation

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference assembly

Genomic

NC_003281.10 Reference assembly

Range

4263786..4269270 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_065452.6 → NP_497853.1 Splicing factor 3B subunit 1 domain-containing protein [Caenorhabditis elegans]

See identical proteins and their annotated locations for NP_497853.1

Status: REVIEWED

UniProtKB/TrEMBL

G5EEQ8

Conserved Domains (4) summary

COG5181
Location:480 → 1319

HSH155; U2 snRNP spliceosome subunit [RNA processing and modification]

sd00044
Location:868 → 892

HEAT; HEAT repeat [structural motif]

pfam08920
Location:316 → 444

SF3b1; Splicing factor 3B subunit 1

pfam17823
Location:185 → 477

DUF5585; Family of unknown function (DUF5585)