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    Cpsf6 cleavage and polyadenylation specific factor 6 [ Mus musculus (house mouse) ]

    Gene ID: 432508, updated on 31-Jan-2019

    Summary

    Official Symbol
    Cpsf6provided by MGI
    Official Full Name
    cleavage and polyadenylation specific factor 6provided by MGI
    Primary source
    MGI:MGI:1913948
    See related
    Ensembl:ENSMUSG00000055531
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
    Also known as
    CFIM; CFIM68; AI256641; HPBRII-4; HPBRII-7; 4733401N12Rik
    Expression
    Ubiquitous expression in whole brain E14.5 (RPKM 23.5), CNS E14 (RPKM 23.0) and 28 other tissues See more
    Orthologs

    Genomic context

    See Cpsf6 in Genome Data Viewer
    Location:
    10; 10 D2
    Exon count:
    11
    Annotation release Status Assembly Chr Location
    106 current GRCm38.p4 (GCF_000001635.24) 10 NC_000076.6 (117344667..117376990, complement)
    Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 10 NC_000076.5 (116781724..116814029, complement)

    Chromosome 10 - NC_000076.6Genomic Context describing neighboring genes Neighboring gene lysozyme 2 Neighboring gene lysozyme 1 Neighboring gene predicted gene, 40770 Neighboring gene ribosomal protein L18a pseudogene

    Genomic regions, transcripts, and products

    Expression

    • Project title: Mouse ENCODE transcriptome data
    • Description: RNA profiling data sets generated by the Mouse ENCODE project.
    • BioProject: PRJNA66167
    • Publication: PMID 25409824
    • Analysis date: n/a

    Bibliography

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    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 ...

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Homology

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    contributes_to RNA binding ISO
    Inferred from Sequence Orthology
    more info
     
    exon-exon junction complex binding ISO
    Inferred from Sequence Orthology
    more info
     
    mRNA binding ISO
    Inferred from Sequence Orthology
    more info
     
    nucleic acid binding IEA
    Inferred from Electronic Annotation
    more info
     
    ribosomal large subunit binding ISO
    Inferred from Sequence Orthology
    more info
     
    Process Evidence Code Pubs
    mRNA alternative polyadenylation ISO
    Inferred from Sequence Orthology
    more info
     
    mRNA processing ISO
    Inferred from Sequence Orthology
    more info
     
    messenger ribonucleoprotein complex assembly ISO
    Inferred from Sequence Orthology
    more info
     
    positive regulation of RNA export from nucleus ISO
    Inferred from Sequence Orthology
    more info
     
    pre-mRNA cleavage required for polyadenylation ISO
    Inferred from Sequence Orthology
    more info
     
    protein heterotetramerization ISO
    Inferred from Sequence Orthology
    more info
     
    protein tetramerization ISO
    Inferred from Sequence Orthology
    more info
     
    Component Evidence Code Pubs
    cytoplasm ISO
    Inferred from Sequence Orthology
    more info
     
    interchromatin granule ISO
    Inferred from Sequence Orthology
    more info
     
    mRNA cleavage and polyadenylation specificity factor complex ISO
    Inferred from Sequence Orthology
    more info
     
    mRNA cleavage factor complex ISO
    Inferred from Sequence Orthology
    more info
     
    nuclear speck ISO
    Inferred from Sequence Orthology
    more info
     
    nucleoplasm ISO
    Inferred from Sequence Orthology
    more info
     
    nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    nucleus ISO
    Inferred from Sequence Orthology
    more info
     
    paraspeckles ISO
    Inferred from Sequence Orthology
    more info
     
    perichromatin fibrils ISO
    Inferred from Sequence Orthology
    more info
     
    ribonucleoprotein complex ISO
    Inferred from Sequence Orthology
    more info
    PubMed 

    General protein information

    Preferred Names
    cleavage and polyadenylation specificity factor subunit 6

    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_001013391.2NP_001013409.1  cleavage and polyadenylation specificity factor subunit 6 isoform 2

      See identical proteins and their annotated locations for NP_001013409.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) uses an alternate in-frame splice site in the 3' coding region, compared to variant 1. This results in a shorter protein (isoform 2), compared to isoform 1.
      Source sequence(s)
      AK033801, AK077684, AK164584, BC068133, CD547792
      Consensus CDS
      CCDS24193.1
      UniProtKB/Swiss-Prot
      Q6NVF9
      Related
      ENSMUSP00000068408.6, ENSMUST00000069168.12
      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. NM_001310609.1NP_001297538.1  cleavage and polyadenylation specificity factor subunit 6 isoform 1

      See identical proteins and their annotated locations for NP_001297538.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes the longer isoform (1).
      Source sequence(s)
      AC123694, AK049749, AK077684
      Consensus CDS
      CCDS78898.1
      UniProtKB/TrEMBL
      H3BJ30
      Related
      ENSMUSP00000134823.1, ENSMUST00000176686.7
      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: Mus musculus Annotation Release 106

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

    Reference GRCm38.p4 C57BL/6J

    Genomic

    1. NC_000076.6 Reference GRCm38.p4 C57BL/6J

      Range
      117344667..117376990 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006513855.2XP_006513918.1  cleavage and polyadenylation specificity factor subunit 6 isoform X2

      See identical proteins and their annotated locations for XP_006513918.1

      UniProtKB/TrEMBL
      H3BJW3
      Related
      ENSMUSP00000135150.1, ENSMUST00000176670.7
      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_006513854.3XP_006513917.1  cleavage and polyadenylation specificity factor subunit 6 isoform X2

      See identical proteins and their annotated locations for XP_006513917.1

      UniProtKB/TrEMBL
      H3BJW3
      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_006513852.2XP_006513915.1  cleavage and polyadenylation specificity factor subunit 6 isoform X1

      See identical proteins and their annotated locations for XP_006513915.1

      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
    4. XM_006513853.2XP_006513916.1  cleavage and polyadenylation specificity factor subunit 6 isoform X1

      See identical proteins and their annotated locations for XP_006513916.1

      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_006513851.3XP_006513914.1  cleavage and polyadenylation specificity factor subunit 6 isoform X1

      See identical proteins and their annotated locations for XP_006513914.1

      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_006513858.3XP_006513921.1  cleavage and polyadenylation specificity factor subunit 6 isoform X4

      See identical proteins and their annotated locations for XP_006513921.1

      UniProtKB/Swiss-Prot
      Q6NVF9
      Related
      ENSMUSP00000135136.1, ENSMUST00000177145.7
      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_006513856.3XP_006513919.1  cleavage and polyadenylation specificity factor subunit 6 isoform X3

      See identical proteins and their annotated locations for XP_006513919.1

      UniProtKB/TrEMBL
      H3BJ30
      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

    RNA

    1. XR_001779551.1 RNA Sequence

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