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

    Gene ID: 432508, updated on 11-Apr-2024

    Summary

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    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 AllianceGenome:MGI:1913948
    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; HPBRII-4; HPBRII-7; 4733401N12Rik
    Summary
    Predicted to enable exon-exon junction complex binding activity; mRNA binding activity; and ribosomal large subunit binding activity. Predicted to contribute to RNA binding activity. Predicted to be involved in several processes, including mRNA alternative polyadenylation; pre-mRNA cleavage required for polyadenylation; and protein-containing complex assembly. Located in nucleus. Is expressed in several structures, including brain and retina nuclear layer. Orthologous to human CPSF6 (cleavage and polyadenylation specific factor 6). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Ubiquitous expression in whole brain E14.5 (RPKM 23.5), CNS E14 (RPKM 23.0) and 28 other tissues See more
    Orthologs
    human all
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    Genomic context

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    Location:
    10 D2; 10 65.41 cM
    Exon count:
    12
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 10 NC_000076.7 (117180572..117212903, complement)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 10 NC_000076.6 (117344667..117376998, complement)

    Chromosome 10 - NC_000076.7Genomic Context describing neighboring genes Neighboring gene lysozyme 2 Neighboring gene lysozyme 1 Neighboring gene STARR-positive B cell enhancer mm9_chr10:116767566-116767867 Neighboring gene STARR-seq mESC enhancer starr_27980 Neighboring gene STARR-positive B cell enhancer ABC_E11460 Neighboring gene STARR-positive B cell enhancer ABC_E11461 Neighboring gene predicted gene, 40770 Neighboring gene STARR-positive B cell enhancer ABC_E6926 Neighboring gene ribosomal protein L18a pseudogene

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • 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

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    Related articles in PubMed

    1. Pre-messenger RNA cleavage factor I (CFIm): potential role in alternative polyadenylation during spermatogenesis. Sartini BL, et al. Biol Reprod, 2008 Mar. PMID 18032416
    2. CFIm-mediated alternative polyadenylation safeguards the development of mammalian pre-implantation embryos. Li N, et al. Stem Cell Reports, 2023 Jan 10. PMID 36563685, Free PMC Article
    3. Reverse engineering a mouse embryonic stem cell-specific transcriptional network reveals a new modulator of neuronal differentiation. De Cegli R, et al. Nucleic Acids Res, 2013 Jan. PMID 23180766, Free PMC Article
    4. Nuclear m6A reader YTHDC1 regulates alternative polyadenylation and splicing during mouse oocyte development. Kasowitz SD, et al. PLoS Genet, 2018 May. PMID 29799838, Free PMC Article
    5. Integrative genomics positions MKRN1 as a novel ribonucleoprotein within the embryonic stem cell gene regulatory network. Cassar PA, et al. EMBO Rep, 2015 Oct. PMID 26265008, Free PMC Article

    See all (42) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Downregulation of CPSF6 leads to global mRNA 3' UTR shortening and enhanced antiviral immune responses.
      Title: Downregulation of CPSF6 leads to global mRNA 3' UTR shortening and enhanced antiviral immune responses.
    2. Pre-messenger RNA cleavage factor I (CFIm): potential role in alternative polyadenylation during spermatogenesis.
      Title: Pre-messenger RNA cleavage factor I (CFIm): potential role in alternative polyadenylation during spermatogenesis.
    3. Here we report that the CFIm subunits NUDT21/CPSF5 and CPSF6 are highly enriched in mouse male germ cells relative to somatic cells.
      Title: Pre-messenger RNA cleavage factor I (CFIm): potential role in alternative polyadenylation during spermatogenesis.
    Submit: New GeneRIF Correction

    Variation

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    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    • Endonuclease-mediated (1) 

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    contributes_to RNA binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables exon-exon junction complex binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables mRNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables mRNA binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables nucleic acid binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables ribosomal large subunit binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    Process Evidence Code Pubs
    involved_in localization ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in mRNA 3'-end processing ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in mRNA alternative polyadenylation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in mRNA alternative polyadenylation ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in mRNA processing ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of RNA export from nucleus ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in protein heterotetramerization ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in protein tetramerization ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    located_in cytoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in interchromatin granule ISO
    Inferred from Sequence Orthology
    more info
    		  
    part_of mRNA cleavage and polyadenylation specificity factor complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of mRNA cleavage and polyadenylation specificity factor complex ISO
    Inferred from Sequence Orthology
    more info
    		  
    part_of mRNA cleavage factor complex ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nuclear speck ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleus ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in paraspeckles ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in perichromatin fibrils ISO
    Inferred from Sequence Orthology
    more info
    		  
    part_of ribonucleoprotein complex ISO
    Inferred from Sequence Orthology
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    cleavage and polyadenylation specificity factor subunit 6

    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_001013391.2 → NP_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, Q8BX86, Q8BXI8
      Related
      ENSMUSP00000068408.7, ENSMUST00000069168.13
      Conserved Domains (1) summary
      cd12643
      Location:82 → 158
      RRM_CFIm68; RNA recognition motif of pre-mRNA cleavage factor Im 68 kDa subunit (CFIm68 or CPSF6) and similar proteins

    2. NM_001310609.1 → NP_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
      ENSMUSP00000134823.2, ENSMUST00000176686.8
      Conserved Domains (1) summary
      cd12643
      Location:82 → 158
      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_000001635.27-RS_2024_02

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

    Reference GRCm39 C57BL/6J

    Genomic

    1. NC_000076.7 Reference GRCm39 C57BL/6J

      Range
      117180572..117212903 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_030245173.1 → XP_030101033.1  cleavage and polyadenylation specificity factor subunit 6 isoform X4

      UniProtKB/Swiss-Prot
      Q6NVF9, Q8BX86, Q8BXI8
      Conserved Domains (1) summary
      cd12643
      Location:82 → 158
      RRM_CFIm68; RNA recognition motif of pre-mRNA cleavage factor Im 68 kDa subunit (CFIm68 or CPSF6) and similar proteins

    2. XM_030245172.1 → XP_030101032.1  cleavage and polyadenylation specificity factor subunit 6 isoform X3

      UniProtKB/TrEMBL
      H3BJ30
      Conserved Domains (1) summary
      cd12643
      Location:82 → 158
      RRM_CFIm68; RNA recognition motif of pre-mRNA cleavage factor Im 68 kDa subunit (CFIm68 or CPSF6) and similar proteins

    3. XM_006513855.3 → XP_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
      ENSMUSP00000135150.2, ENSMUST00000176670.8
      Conserved Domains (2) summary
      COG0724
      Location:9 → 153
      RRM; RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis]
      cd12643
      Location:82 → 158
      RRM_CFIm68; RNA recognition motif of pre-mRNA cleavage factor Im 68 kDa subunit (CFIm68 or CPSF6) and similar proteins

    4. XM_030245171.1 → XP_030101031.1  cleavage and polyadenylation specificity factor subunit 6 isoform X2

      UniProtKB/TrEMBL
      H3BJW3
      Conserved Domains (2) summary
      COG0724
      Location:9 → 153
      RRM; RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis]
      cd12643
      Location:82 → 158
      RRM_CFIm68; RNA recognition motif of pre-mRNA cleavage factor Im 68 kDa subunit (CFIm68 or CPSF6) and similar proteins

    5. XM_006513852.3 → XP_006513915.1  cleavage and polyadenylation specificity factor subunit 6 isoform X1

      See identical proteins and their annotated locations for XP_006513915.1

      Conserved Domains (2) summary
      COG0724
      Location:9 → 153
      RRM; RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis]
      cd12643
      Location:82 → 158
      RRM_CFIm68; RNA recognition motif of pre-mRNA cleavage factor Im 68 kDa subunit (CFIm68 or CPSF6) and similar proteins

    6. XM_006513853.3 → XP_006513916.1  cleavage and polyadenylation specificity factor subunit 6 isoform X1

      See identical proteins and their annotated locations for XP_006513916.1

      Conserved Domains (2) summary
      COG0724
      Location:9 → 153
      RRM; RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis]
      cd12643
      Location:82 → 158
      RRM_CFIm68; RNA recognition motif of pre-mRNA cleavage factor Im 68 kDa subunit (CFIm68 or CPSF6) and similar proteins

    RNA

    1. XR_003948730.1 RNA Sequence

    2. XR_004936222.1 RNA Sequence

    3. XR_004936221.1 RNA Sequence

    4. XR_003948728.1 RNA Sequence

    5. XR_004936220.1 RNA Sequence

    6. XR_004936219.1 RNA Sequence

    7. XR_001779551.2 RNA Sequence

    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q6NVF9.1 GenPept UniProtKB/Swiss-Prot:Q6NVF9

    Gene LinkOut

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

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