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    sf1 splicing factor 1 [ Danio rerio (zebrafish) ]

    Gene ID: 572785, updated on 9-Dec-2024

    Summary

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    Official Symbol
    sf1provided by ZNC
    Official Full Name
    splicing factor 1provided by ZNC
    Primary source
    ZFIN:ZDB-GENE-030131-2492
    See related
    Ensembl:ENSDARG00000008188 AllianceGenome:ZFIN:ZDB-GENE-030131-2492
    Gene type
    protein coding
    RefSeq status
    PROVISIONAL
    Organism
    Danio rerio
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
    Also known as
    znf162; wu:fc09f06
    Summary
    Predicted to enable mRNA binding activity. Acts upstream of or within retina development in camera-type eye. Predicted to be part of spliceosomal complex. Predicted to be active in nucleus. Orthologous to human SF1 (splicing factor 1). [provided by Alliance of Genome Resources, Dec 2024]
    Orthologs
    human mouse all
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    Genomic context

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    See sf1 in Genome Data Viewer
    Location:
    chromosome: 7
    Exon count:
    12
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCz11 (GCF_000002035.6) 7 NC_007118.7 (22809914..22820816)
    105 previous assembly GRCz10 (GCF_000002035.5) 7 NC_007118.6 (22538737..22549659)

    Chromosome 7 - NC_007118.7Genomic Context describing neighboring genes Neighboring gene RNA binding motif protein 4.2 Neighboring gene RNA binding motif protein 4.1 Neighboring gene phosphorylase, glycogen, muscle b Neighboring gene chloride channel, voltage-sensitive 5b

    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
    • 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. Targeted Disruption of Aromatase Reveals Dual Functions of cyp19a1a During Sex Differentiation in Zebrafish. Yin Y, et al. Endocrinology, 2017 Sep 1. PMID 28575219
    2. The tissue-specific RNA binding protein T-STAR controls regional splicing patterns of neurexin pre-mRNAs in the brain. Ehrmann I, et al. PLoS Genet, 2013 Apr. PMID 23637638, Free PMC Article
    3. Rx3 and Shh direct anisotropic growth and specification in the zebrafish tuberal/anterior hypothalamus. Muthu V, et al. Development, 2016 Jul 15. PMID 27317806, Free PMC Article
    4. Identification of zebrafish insertional mutants with defects in visual system development and function. Gross JM, et al. Genetics, 2005 May. PMID 15716491, Free PMC Article
    5. Online automated in vivo zebrafish phosphoproteomics: from large-scale analysis down to a single embryo. Lemeer S, et al. J Proteome Res, 2008 Apr. PMID 18307296

    See all (15) citations in PubMed

    GeneRIFs: Gene References Into Functions

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by ZFIN

    Function Evidence Code Pubs
    enables RNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables mRNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables nucleic acid binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables pre-mRNA branch point binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables zinc ion 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 mRNA processing IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in mRNA splicing, via spliceosome IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in regulation of mRNA splicing, via spliceosome IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within retina development in camera-type eye IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    is_active_in nucleus 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 1
    Names
    zinc finger protein 162

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_212653.1 → NP_997818.1  splicing factor 1

      See identical proteins and their annotated locations for NP_997818.1

      Status: PROVISIONAL

      Source sequence(s)
      AY391459
      UniProtKB/TrEMBL
      Q6TNQ8
      Related
      ENSDARP00000105365.2, ENSDART00000126037.4
      Conserved Domains (2) summary
      cd02395
      Location:137 → 255
      SF1_like-KH; Splicing factor 1 (SF1) K homology RNA-binding domain (KH). Splicing factor 1 (SF1) specifically recognizes the intron branch point sequence (BPS) UACUAAC in the pre-mRNA transcripts during spliceosome assembly. We show that the KH-QUA2 region of SF1 ...
      pfam16275
      Location:18 → 130
      SF1-HH; Splicing factor 1 helix-hairpin domain

    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_007118.7 Reference GRCz11 Primary Assembly

      Range
      22809914..22820816
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_009303075.3 → XP_009301350.1  splicing factor 1 isoform X1

      UniProtKB/TrEMBL
      A0A0R4IBT0, A0A8M3BAW2
      Related
      ENSDARP00000130303.1, ENSDART00000166900.3
      Conserved Domains (2) summary
      cd02395
      Location:209 → 327
      SF1_like-KH; Splicing factor 1 (SF1) K homology RNA-binding domain (KH). Splicing factor 1 (SF1) specifically recognizes the intron branch point sequence (BPS) UACUAAC in the pre-mRNA transcripts during spliceosome assembly. We show that the KH-QUA2 region of SF1 ...
      pfam16275
      Location:90 → 202
      SF1-HH; Splicing factor 1 helix-hairpin domain

    2. XM_009303076.3 → XP_009301351.1  splicing factor 1 isoform X2

      UniProtKB/TrEMBL
      A0A8M3AU14
      Conserved Domains (2) summary
      cd02395
      Location:209 → 327
      SF1_like-KH; Splicing factor 1 (SF1) K homology RNA-binding domain (KH). Splicing factor 1 (SF1) specifically recognizes the intron branch point sequence (BPS) UACUAAC in the pre-mRNA transcripts during spliceosome assembly. We show that the KH-QUA2 region of SF1 ...
      pfam16275
      Location:90 → 202
      SF1-HH; Splicing factor 1 helix-hairpin domain

    3. XM_009303077.4 → XP_009301352.1  splicing factor 1 isoform X4

      UniProtKB/TrEMBL
      A0A8M3B3Z3
      Conserved Domains (1) summary
      cd02395
      Location:22 → 140
      SF1_like-KH; Splicing factor 1 (SF1) K homology RNA-binding domain (KH). Splicing factor 1 (SF1) specifically recognizes the intron branch point sequence (BPS) UACUAAC in the pre-mRNA transcripts during spliceosome assembly. We show that the KH-QUA2 region of SF1 ...

    4. XM_021477588.2 → XP_021333263.1  splicing factor 1 isoform X3

      UniProtKB/TrEMBL
      A0A8M9Q1R8
      Conserved Domains (2) summary
      smart00343
      Location:279 → 293
      ZnF_C2HC; zinc finger
      cl25681
      Location:36 → 257
      SF1-HH; Splicing factor 1 helix-hairpin domain

    5. XM_021477589.2 → XP_021333264.1  splicing factor 1 isoform X4

      UniProtKB/TrEMBL
      A0A8M3B3Z3
      Conserved Domains (1) summary
      cd02395
      Location:22 → 140
      SF1_like-KH; Splicing factor 1 (SF1) K homology RNA-binding domain (KH). Splicing factor 1 (SF1) specifically recognizes the intron branch point sequence (BPS) UACUAAC in the pre-mRNA transcripts during spliceosome assembly. We show that the KH-QUA2 region of SF1 ...
    Nucleotide Protein Strain
    Heading Accession and Version

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