sf3b1 splicing factor 3b, subunit 1 [Danio rerio (zebrafish)] - Gene

Summary

Official Symbol: sf3b1provided by ZNC
Official Full Name: splicing factor 3b, subunit 1provided by ZNC
Primary source: ZFIN:ZDB-GENE-040827-3
See related: Ensembl:ENSDARG00000056138 AllianceGenome:ZFIN:ZDB-GENE-040827-3
Gene type: protein coding
RefSeq status: MODEL
Organism: Danio rerio
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
Also known as: wu:fb99f09
Summary: Predicted to enable mRNA binding activity. Acts upstream of or within several processes, including hemopoiesis; melanocyte differentiation; and neural crest cell development. Predicted to be located in nucleus. Predicted to be part of U2 snRNP and spliceosomal complex. Is expressed in brain; neural tube; and trunk. 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]
Orthologs: human mouse all
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Genomic context

Location:: chromosome: 9

Exon count:: 26

Annotation release	Status	Assembly	Chr	Location
106	current	GRCz11 (GCF_000002035.6)	9	NC_007120.7 (32161623..32177156, complement)
105	previous assembly	GRCz10 (GCF_000002035.5)	9	NC_007120.6 (32350877..32366395, complement)

Chromosome 9 - NC_007120.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

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Expression

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See details

Project title: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
Description: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
BioProject: PRJEB1986
Analysis date: Fri Dec 8 19:48:10 2017

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Data indicate that splicing factor 3b, subunit 1 (sf3b1) mutation causes aberrant splicing of sf3b1 resulting in functional and predicted non-functional transcripts and a 90% reduction in full-length Sf3b1 protein.
Title: The zebrafish sf3b1b460 mutant reveals differential requirements for the sf3b1 pre-mRNA processing gene during neural crest development.

Submit: New GeneRIF Correction

Pathways from PubChem

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General gene information

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Markers

fb99f09.x1 (e-PCR)
- UniSTS:203640

fb13g01.y1 (e-PCR)
- UniSTS:190110

Homology

NCBI Orthologs

Orthologs from OrthoDB

Gene Ontology Provided by ZFIN

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
acts_upstream_of_or_within RNA splicing	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within definitive hemopoiesis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within hematopoietic stem cell differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within mRNA processing	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within melanocyte differentiation	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within melanocyte differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within myeloid cell development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within neural crest cell development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within regulation of apoptotic process	IGI Inferred from Genetic Interaction more info	PubMed
involved_in spliceosomal complex assembly	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within spliceosomal complex assembly	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
part_of U12-type spliceosomal complex	IBA Inferred from Biological aspect of Ancestor more info
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

Names: tst

NCBI Reference Sequences (RefSeq)

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RefSeqs of Annotated Genomes: Danio rerio Annotation Release 106 details...

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

Reference GRCz11 Primary Assembly

Genomic

NC_007120.7 Reference GRCz11 Primary Assembly

Range

32161623..32177156 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_679219.5 → XP_684311.1 splicing factor 3B subunit 1 isoform X1

UniProtKB/TrEMBL

A0A8N7TAM0, F1QQZ1

Related

ENSDARP00000073029.5, ENSDART00000078568.5

Conserved Domains (6) summary

smart01104
Location:231 → 393

CTD; Spt5 C-terminal nonapeptide repeat binding Spt4

COG5181
Location:457 → 1312

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

cd00020
Location:991 → 1092

ARM; Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, ...

pfam08920
Location:343 → 454

SF3b1; Splicing factor 3B subunit 1

pfam12815
Location:269 → 341

CTD; Spt5 C-terminal nonapeptide repeat binding Spt4

sd00044
Location:861 → 885

HEAT; HEAT repeat [structural motif]
XM_005167787.3 → XP_005167844.1 splicing factor 3B subunit 1 isoform X2

UniProtKB/TrEMBL

A0A8M2BF81

Conserved Domains (5) summary

smart01104
Location:231 → 350

CTD; Spt5 C-terminal nonapeptide repeat binding Spt4

COG5181
Location:414 → 1269

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

cd00020
Location:948 → 1049

ARM; Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, ...

pfam08920
Location:300 → 411

SF3b1; Splicing factor 3B subunit 1

sd00044
Location:818 → 842

HEAT; HEAT repeat [structural motif]
XM_005167788.4 → XP_005167845.1 splicing factor 3B subunit 1 isoform X3

UniProtKB/TrEMBL

A0A8M2BF86

Conserved Domains (6) summary

smart01104
Location:77 → 239

CTD; Spt5 C-terminal nonapeptide repeat binding Spt4

COG5181
Location:303 → 1158

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

cd00020
Location:837 → 938

ARM; Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, ...

pfam08920
Location:189 → 300

SF3b1; Splicing factor 3B subunit 1

pfam12815
Location:115 → 187

CTD; Spt5 C-terminal nonapeptide repeat binding Spt4

sd00044
Location:707 → 731

HEAT; HEAT repeat [structural motif]
XM_009304794.3 → XP_009303069.1 splicing factor 3B subunit 1 isoform X5

See identical proteins and their annotated locations for XP_009303069.1

UniProtKB/TrEMBL

A0A8M3AW70
XM_009304793.3 → XP_009303068.1 splicing factor 3B subunit 1 isoform X4

UniProtKB/TrEMBL

A0A8M3B2S8