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

    Gene ID: 446117, updated on 17-Sep-2024

    Summary

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    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

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    See sf3b1 in Genome Data Viewer
    Location:
    chromosome: 9
    Exon count:
    26
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCz11 (GCF_000002035.6) 9 NC_007120.7 (32161847..32177089, complement)
    105 previous assembly GRCz10 (GCF_000002035.5) 9 NC_007120.6 (32350877..32366395, complement)

    Chromosome 9 - NC_007120.7Genomic Context describing neighboring genes Neighboring gene phosphoinositide kinase, FYVE finger containing Neighboring gene ankyrin repeat domain 44 Neighboring gene coenzyme Q10B Neighboring gene rho-associated protein kinase 1-like

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages 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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    Related articles in PubMed

    1. The fate of recent duplicated genes following a fourth-round whole genome duplication in a tetraploid fish, common carp (Cyprinus carpio). Li JT, et al. Sci Rep, 2015 Feb 3. PMID 25645996, Free PMC Article
    2. Spliceosomal component Sf3b1 is essential for hematopoietic differentiation in zebrafish. De La Garza A, et al. Exp Hematol, 2016 Sep. PMID 27260753, Free PMC Article
    3. The zebrafish sf3b1b460 mutant reveals differential requirements for the sf3b1 pre-mRNA processing gene during neural crest development. An M, et al. Int J Dev Biol, 2012. PMID 22562198, Free PMC Article
    4. Phylogenetic and evolutionary relationships and developmental expression patterns of the zebrafish twist gene family. Yeo GH, et al. Dev Genes Evol, 2009 Jun. PMID 19565261
    5. CRISPR gRNA phenotypic screening in zebrafish reveals pro-regenerative genes in spinal cord injury. Keatinge M, et al. PLoS Genet, 2021 Apr. PMID 33914736, Free PMC Article

    See all (9) citations in PubMed

    GeneRIFs: Gene References Into Functions

    Pathways from PubChem

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    General gene information

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    Markers

    Homology

    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: GCF_000002035.6-RS_2024_08

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

    Reference GRCz11 Primary Assembly

    Genomic

    1. NC_007120.7 Reference GRCz11 Primary Assembly

      Range
      32161847..32177089 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_679219.6 → 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]

    2. XM_005167788.5 → XP_005167845.1  splicing factor 3B subunit 1 isoform X2

      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]

    3. XM_068223656.1 → XP_068079757.1  splicing factor 3B subunit 1 isoform X4

    4. XM_009304793.4 → XP_009303068.1  splicing factor 3B subunit 1 isoform X3

      UniProtKB/TrEMBL
      A0A8M3B2S8
    Nucleotide Protein Strain
    Heading Accession and Version

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