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    cpsf6 cleavage and polyadenylation specific factor 6 [ Danio rerio (zebrafish) ]

    Gene ID: 327069, updated on 28-Oct-2024

    Summary

    Official Symbol
    cpsf6provided by ZNC
    Official Full Name
    cleavage and polyadenylation specific factor 6provided by ZNC
    Primary source
    ZFIN:ZDB-GENE-030131-5277
    See related
    Ensembl:ENSDARG00000018618 AllianceGenome:ZFIN:ZDB-GENE-030131-5277
    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
    zgc:85819; wu:fa22f12
    Summary
    Predicted to enable mRNA binding activity. Predicted to be involved in mRNA 3'-end processing; positive regulation of RNA export from nucleus; and protein heterotetramerization. Predicted to act upstream of or within mRNA processing. Is active in paraspeckles. Is expressed in several structures, including blastomere; central nervous system; digestive system; eye; and yolk. Orthologous to human CPSF6 (cleavage and polyadenylation specific factor 6). [provided by Alliance of Genome Resources, Oct 2024]
    Orthologs
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    Genomic context

    See cpsf6 in Genome Data Viewer
    Location:
    chromosome: 4
    Exon count:
    11
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCz11 (GCF_000002035.6) 4 NC_007115.7 (2043989..2059268, complement)
    105 previous assembly GRCz10 (GCF_000002035.5) 4 NC_007115.6 (2195798..2209984, complement)

    Chromosome 4 - NC_007115.7Genomic Context describing neighboring genes Neighboring gene si:ch73-177h5.3 Neighboring gene si:dkey-97m3.1 Neighboring gene YEATS domain containing 4 Neighboring gene fibroblast growth factor receptor substrate 2a

    Genomic regions, transcripts, and products

    Expression

    • 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

    Pathways from PubChem

    General gene information

    Markers

    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 mRNA binding ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    enables nucleic acid binding IEA
    Inferred from Electronic Annotation
    more info
     
    Process Evidence Code Pubs
    involved_in co-transcriptional mRNA 3'-end processing, cleavage and polyadenylation pathway ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in mRNA alternative polyadenylation IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in mRNA alternative polyadenylation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    acts_upstream_of_or_within mRNA processing IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of RNA export from nucleus ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in protein heterotetramerization ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    Component Evidence Code Pubs
    located_in cytoplasm IEA
    Inferred from Electronic Annotation
    more info
     
    located_in cytoplasm ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in interchromatin granule ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    part_of mRNA cleavage and polyadenylation specificity factor complex IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    part_of mRNA cleavage factor complex ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in nuclear speck ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in nucleoplasm ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in nucleus IEA
    Inferred from Electronic Annotation
    more info
     
    located_in nucleus ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    is_active_in paraspeckles IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in paraspeckles ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in perichromatin fibrils ISS
    Inferred from Sequence or Structural Similarity
    more info
     

    General protein information

    Preferred Names
    cleavage and polyadenylation specificity factor subunit 6
    Names
    cleavage and polyadenylation specific factor 6, 68kDa

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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_001017993.1NP_001017993.1  cleavage and polyadenylation specificity factor subunit 6

      See identical proteins and their annotated locations for NP_001017993.1

      Status: PROVISIONAL

      Source sequence(s)
      AY398330
      UniProtKB/Swiss-Prot
      Q6NWC6
      Related
      ENSDARP00000076726.4, ENSDART00000082289.6
      Conserved Domains (1) summary
      cd12643
      Location:82158
      RRM_CFIm68; RNA recognition motif of pre-mRNA cleavage factor Im 68 kDa subunit (CFIm68 or CPSF6) and similar proteins

    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_007115.7 Reference GRCz11 Primary Assembly

      Range
      2043989..2059268 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_005164453.5XP_005164510.1  cleavage and polyadenylation specificity factor subunit 6 isoform X3

      See identical proteins and their annotated locations for XP_005164510.1

      UniProtKB/Swiss-Prot
      Q6NWC6, Q6TH26
      Related
      ENSDARP00000110285.2, ENSDART00000129521.4
      Conserved Domains (1) summary
      cd12643
      Location:82158
      RRM_CFIm68; RNA recognition motif of pre-mRNA cleavage factor Im 68 kDa subunit (CFIm68 or CPSF6) and similar proteins
    2. XM_005164452.5XP_005164509.1  cleavage and polyadenylation specificity factor subunit 6 isoform X2

      UniProtKB/TrEMBL
      A0A8M2BBP6
      Conserved Domains (2) summary
      cd12643
      Location:82158
      RRM_CFIm68; RNA recognition motif of pre-mRNA cleavage factor Im 68 kDa subunit (CFIm68 or CPSF6) and similar proteins
      pfam16294
      Location:492526
      RSB_motif; RNSP1-SAP18 binding (RSB) motif
    3. XM_005164451.5XP_005164508.1  cleavage and polyadenylation specificity factor subunit 6 isoform X1

      UniProtKB/TrEMBL
      A0A2R8RIN6, A0A8M2BBU1
      Related
      ENSDARP00000145832.1, ENSDART00000188177.1
      Conserved Domains (2) summary
      cd12643
      Location:82158
      RRM_CFIm68; RNA recognition motif of pre-mRNA cleavage factor Im 68 kDa subunit (CFIm68 or CPSF6) and similar proteins
      pfam16294
      Location:505539
      RSB_motif; RNSP1-SAP18 binding (RSB) motif