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    cpsf1 cleavage and polyadenylation specific factor 1 [ Danio rerio (zebrafish) ]

    Gene ID: 432372, updated on 2-Nov-2024

    Summary

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    Official Symbol
    cpsf1provided by ZNC
    Official Full Name
    cleavage and polyadenylation specific factor 1provided by ZNC
    Primary source
    ZFIN:ZDB-GENE-040709-2
    See related
    Ensembl:ENSDARG00000034178 AllianceGenome:ZFIN:ZDB-GENE-040709-2
    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
    wu:fb24c01
    Summary
    Predicted to enable NAD+-protein poly-ADP-ribosyltransferase activity and nucleic acid binding activity. Acts upstream of or within cytosolic mRNA polyadenylation; definitive hemopoiesis; and retinal ganglion cell axon guidance. Predicted to be part of mRNA cleavage and polyadenylation specificity factor complex. Predicted to be active in nucleus. Is expressed in brain; gut; head; and pectoral fin. Human ortholog(s) of this gene implicated in myopia. Orthologous to human CPSF1 (cleavage and polyadenylation specific factor 1). [provided by Alliance of Genome Resources, Nov 2024]
    Orthologs
    human mouse all
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    Genomic context

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    See cpsf1 in Genome Data Viewer
    Location:
    chromosome: 19
    Exon count:
    38
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCz11 (GCF_000002035.6) 19 NC_007130.7 (11897631..11950437, complement)
    105 previous assembly GRCz10 (GCF_000002035.5) 19 NC_007130.6 (11979289..12032094, complement)

    Chromosome 19 - NC_007130.7Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC137488481 Neighboring gene aarF domain containing kinase 5 Neighboring gene poly(ADP-ribose) polymerase family member 10 Neighboring gene RNA polymerase II, I and III subunit K

    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. CPSF1 mutations are associated with early-onset high myopia and involved in retinal ganglion cell axon projection. Ouyang J, et al. Hum Mol Genet, 2019 Jun 15. PMID 30689892, Free PMC Article
    2. Characterization and expression pattern of ZB and PS transposons in zebrafish. Wang Y, et al. Gene Expr Patterns, 2021 Dec. PMID 34481069
    3. cpsf1 is required for definitive HSC survival in zebrafish. Bolli N, et al. Blood, 2011 Apr 14. PMID 21330472, Free PMC Article
    4. Single-cell transcriptional analysis of normal, aberrant, and malignant hematopoiesis in zebrafish. Moore FE, et al. J Exp Med, 2016 May 30. PMID 27139488, Free PMC Article
    5. Identification of 315 genes essential for early zebrafish development. Amsterdam A, et al. Proc Natl Acad Sci U S A, 2004 Aug 31. PMID 15256591, Free PMC Article

    See all (8) 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 NAD+-protein poly-ADP-ribosyltransferase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables nucleic acid binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    acts_upstream_of_or_within cytosolic mRNA polyadenylation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within definitive hemopoiesis IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within retinal ganglion cell axon guidance IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    part_of mRNA cleavage and polyadenylation specificity factor complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    cleavage and polyadenylation specificity factor subunit 1
    NP_001108153.2
    XP_005159641.1

    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_001114681.2 → NP_001108153.2  cleavage and polyadenylation specificity factor subunit 1

      Status: PROVISIONAL

      Source sequence(s)
      CU467825
      UniProtKB/Swiss-Prot
      A0A0R4IC37
      UniProtKB/TrEMBL
      A0A8M1NHR0
      Related
      ENSDARP00000130523.2, ENSDART00000163478.2
      Conserved Domains (3) summary
      COG5161
      Location:1 → 1443
      SFT1; Pre-mRNA cleavage and polyadenylation specificity factor [RNA processing and modification]
      pfam03178
      Location:1079 → 1414
      CPSF_A; CPSF A subunit region
      pfam10433
      Location:92 → 674
      MMS1_N; Mono-functional DNA-alkylating methyl methanesulfonate N-term

    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_007130.7 Reference GRCz11 Primary Assembly

      Range
      11897631..11950437 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_005159584.5 → XP_005159641.1  cleavage and polyadenylation specificity factor subunit 1 isoform X1

      UniProtKB/Swiss-Prot
      A0A0R4IC37
      UniProtKB/TrEMBL
      A0A8M2B658, F6NXE7
      Related
      ENSDARP00000023736.9, ENSDART00000024861.11
      Conserved Domains (3) summary
      COG5161
      Location:1 → 1442
      SFT1; Pre-mRNA cleavage and polyadenylation specificity factor [RNA processing and modification]
      pfam03178
      Location:1078 → 1413
      CPSF_A; CPSF A subunit region
      pfam10433
      Location:92 → 673
      MMS1_N; Mono-functional DNA-alkylating methyl methanesulfonate N-term
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    A0A0R4IC37.2 GenPept UniProtKB/Swiss-Prot:A0A0R4IC37

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.