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    Cpsf6 cleavage and polyadenylation specific factor 6 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 299811, updated on 19-Apr-2019

    Summary

    Official Symbol
    Cpsf6provided by RGD
    Official Full Name
    cleavage and polyadenylation specific factor 6provided by RGD
    Primary source
    RGD:1304640
    See related
    Ensembl:ENSRNOG00000005927
    Gene type
    protein coding
    RefSeq status
    PROVISIONAL
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Expression
    Biased expression in Thymus (RPKM 309.7), Spleen (RPKM 209.2) and 9 other tissues See more
    Orthologs

    Genomic context

    See Cpsf6 in Genome Data Viewer
    Location:
    7q22
    Exon count:
    12
    Annotation release Status Assembly Chr Location
    106 current Rnor_6.0 (GCF_000001895.5) 7 NC_005106.4 (60385688..60417661, complement)
    104 previous assembly Rnor_5.0 (GCF_000001895.4) 7 NC_005106.3 (60387688..60432254, complement)

    Chromosome 7 - NC_005106.4Genomic Context describing neighboring genes Neighboring gene lysozyme C type 2 Neighboring gene lysozyme 2 Neighboring gene uncharacterized LOC108351459 Neighboring gene uncharacterized LOC108351460

    Genomic regions, transcripts, and products

    Expression

    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Pathways from BioSystems

    • mRNA surveillance pathway, organism-specific biosystem (from KEGG)
      mRNA surveillance pathway, organism-specific biosystemThe mRNA surveillance pathway is a quality control mechanism that detects and degrades abnormal mRNAs. These pathways include nonsense-mediated mRNA decay (NMD), nonstop mRNA decay (NSD), and no-go ...
    • mRNA surveillance pathway, conserved biosystem (from KEGG)
      mRNA surveillance pathway, conserved biosystemThe mRNA surveillance pathway is a quality control mechanism that detects and degrades abnormal mRNAs. These pathways include nonsense-mediated mRNA decay (NMD), nonstop mRNA decay (NSD), and no-go ...

    General gene information

    Markers

    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    contributes_to RNA binding ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    exon-exon junction complex binding IEA
    Inferred from Electronic Annotation
    more info
     
    exon-exon junction complex binding ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    mRNA binding IEA
    Inferred from Electronic Annotation
    more info
     
    mRNA binding ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    molecular_function ND
    No biological Data available
    more info
     
    ribosomal large subunit binding IEA
    Inferred from Electronic Annotation
    more info
     
    ribosomal large subunit binding ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    Process Evidence Code Pubs
    biological_process ND
    No biological Data available
    more info
     
    mRNA alternative polyadenylation IEA
    Inferred from Electronic Annotation
    more info
     
    mRNA alternative polyadenylation ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    mRNA processing ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    messenger ribonucleoprotein complex assembly IEA
    Inferred from Electronic Annotation
    more info
     
    messenger ribonucleoprotein complex assembly ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    positive regulation of RNA export from nucleus IEA
    Inferred from Electronic Annotation
    more info
     
    positive regulation of RNA export from nucleus ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    pre-mRNA cleavage required for polyadenylation IEA
    Inferred from Electronic Annotation
    more info
     
    pre-mRNA cleavage required for polyadenylation ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    protein heterotetramerization IEA
    Inferred from Electronic Annotation
    more info
     
    protein heterotetramerization ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    protein tetramerization ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    Component Evidence Code Pubs
    cellular_component ND
    No biological Data available
    more info
     
    cytoplasm IEA
    Inferred from Electronic Annotation
    more info
     
    cytoplasm ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    interchromatin granule IEA
    Inferred from Electronic Annotation
    more info
     
    interchromatin granule ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    mRNA cleavage and polyadenylation specificity factor complex IEA
    Inferred from Electronic Annotation
    more info
     
    mRNA cleavage and polyadenylation specificity factor complex ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    mRNA cleavage factor complex ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    nuclear speck IEA
    Inferred from Electronic Annotation
    more info
     
    nuclear speck ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    nucleoplasm ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    nucleus ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    paraspeckles IEA
    Inferred from Electronic Annotation
    more info
     
    paraspeckles ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    perichromatin fibrils IEA
    Inferred from Electronic Annotation
    more info
     
    perichromatin fibrils ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    ribonucleoprotein complex IEA
    Inferred from Electronic Annotation
    more info
     
    ribonucleoprotein complex ISO
    Inferred from Sequence Orthology
    more info
    PubMed 

    General protein information

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

    NCBI Reference Sequences (RefSeq)

    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_001106785.1NP_001100255.1  cleavage and polyadenylation specificity factor subunit 6

      See identical proteins and their annotated locations for NP_001100255.1

      Status: PROVISIONAL

      Source sequence(s)
      CH473960
      UniProtKB/TrEMBL
      D3ZPL1
      Related
      ENSRNOP00000008193.6, ENSRNOT00000008193.6
      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: Rattus norvegicus Annotation Release 106 details...Open this link in a new tab

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

    Reference Rnor_6.0 Primary Assembly

    Genomic

    1. NC_005106.4 Reference Rnor_6.0 Primary Assembly

      Range
      60385688..60417661 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_008765390.2XP_008763612.1  cleavage and polyadenylation specificity factor subunit 6 isoform X5

      Conserved Domains (1) summary
      cd12643
      Location:30106
      RRM_CFIm68; RNA recognition motif of pre-mRNA cleavage factor Im 68 kDa subunit (CFIm68 or CPSF6) and similar proteins
    2. XM_008765388.2XP_008763610.1  cleavage and polyadenylation specificity factor subunit 6 isoform X4

      See identical proteins and their annotated locations for XP_008763610.1

      UniProtKB/TrEMBL
      D3ZPL1
      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
    3. XM_008765387.2XP_008763609.1  cleavage and polyadenylation specificity factor subunit 6 isoform X3

      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
    4. XM_006241374.2XP_006241436.1  cleavage and polyadenylation specificity factor subunit 6 isoform X2

      See identical proteins and their annotated locations for XP_006241436.1

      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
    5. XM_008765386.2XP_008763608.1  cleavage and polyadenylation specificity factor subunit 6 isoform X2

      See identical proteins and their annotated locations for XP_008763608.1

      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
    6. XM_006241372.2XP_006241434.1  cleavage and polyadenylation specificity factor subunit 6 isoform X1

      See identical proteins and their annotated locations for XP_006241434.1

      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
    7. XM_006241373.2XP_006241435.1  cleavage and polyadenylation specificity factor subunit 6 isoform X1

      See identical proteins and their annotated locations for XP_006241435.1

      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

    Alternate Rn_Celera

    Genomic

    1. AC_000075.1 Alternate Rn_Celera

      Range
      49730420..49761230 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
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