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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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See Cpsf6 in Genome Data Viewer
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

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