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    Cpsf4 cleavage and polyadenylation specific factor 4 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 304277, updated on 3-Dec-2024

    Summary

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    Official Symbol
    Cpsf4provided by RGD
    Official Full Name
    cleavage and polyadenylation specific factor 4provided by RGD
    Primary source
    RGD:620440
    See related
    EnsemblRapid:ENSRNOG00000000985 AllianceGenome:RGD:620440
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Summary
    Predicted to enable sequence-specific double-stranded DNA binding activity. Predicted to be involved in mRNA 3'-end processing. Predicted to be located in nucleoplasm. Predicted to be part of mRNA cleavage and polyadenylation specificity factor complex. Orthologous to human CPSF4 (cleavage and polyadenylation specific factor 4). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Biased expression in Kidney (RPKM 140.0), Thymus (RPKM 115.1) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Cpsf4 in Genome Data Viewer
    Location:
    12p11
    Exon count:
    8
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 12 NC_086030.1 (14543536..14559350, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 12 NC_051347.1 (9429765..9445586, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 12 NC_005111.4 (11199893..11215690, complement)

    Chromosome 12 - NC_086030.1Genomic Context describing neighboring genes Neighboring gene histidine triad nucleotide binding protein 1 like 2 Neighboring gene zinc finger protein 394 Neighboring gene ATP synthase membrane subunit f Neighboring gene pentatricopeptide repeat domain 1 Neighboring gene BUD31 homolog Neighboring gene PDGFA associated protein 1

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • 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

    Bibliography

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    Related articles in PubMed

    1. Influenza virus NS1 protein interacts with the cellular 30 kDa subunit of CPSF and inhibits 3'end formation of cellular pre-mRNAs. Nemeroff ME, et al. Mol Cell, 1998 Jun. PMID 9651582
    2. The poly A polymerase Star-PAP controls 3'-end cleavage by promoting CPSF interaction and specificity toward the pre-mRNA. Laishram RS, et al. EMBO J, 2010 Dec 15. PMID 21102410, Free PMC Article
    3. The mRNA-bound proteome and its global occupancy profile on protein-coding transcripts. Baltz AG, et al. Mol Cell, 2012 Jun 8. PMID 22681889
    4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). Gerhard DS, et al. Genome Res, 2004 Oct. PMID 15489334, Free PMC Article
    5. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, et al. Proc Natl Acad Sci U S A, 2002 Dec 24. PMID 12477932, Free PMC Article

    See all (6) citations in PubMed

    GeneRIFs: Gene References Into Functions

    Pathways from PubChem

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    General gene information

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    Markers

    Homology

    Clone Names

    • MGC108785

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables RNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables sequence-specific double-stranded DNA binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables zinc ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in mRNA 3'-end processing IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in mRNA processing IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in intracellular membrane-bounded organelle 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 IEA
    Inferred from Electronic Annotation
    more info
    		  
    part_of mRNA cleavage and polyadenylation specificity factor complex ISO
    Inferred from Sequence Orthology
    more info
    		  
    part_of mRNA cleavage and polyadenylation specificity factor complex ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in nucleoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    cleavage and polyadenylation specificity factor subunit 4
    Names
    CPSF 30 kDa subunit
    cleavage and polyadenylation specific factor 4, 30kD subunit
    cleavage and polyadenylation specificity factor 30 kDa subunit

    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_001012351.3 → NP_001012351.1  cleavage and polyadenylation specificity factor subunit 4 isoform 1

      See identical proteins and their annotated locations for NP_001012351.1

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000012
      UniProtKB/Swiss-Prot
      Q5FVR7
      UniProtKB/TrEMBL
      A0A8I5Y5Y1
      Related
      ENSRNOP00000068209.1, ENSRNOT00000076369.3
      Conserved Domains (2) summary
      COG5084
      Location:25 → 176
      YTH1; Cleavage and polyadenylation specificity factor (CPSF) Clipper subunit and related makorin family Zn-finger proteins [General function prediction only]
      COG5222
      Location:192 → 232
      COG5222; Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]

    2. NM_001401115.1 → NP_001388044.1  cleavage and polyadenylation specificity factor subunit 4 isoform 2

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000012
      UniProtKB/TrEMBL
      A0A8I5Y5Y1
      Related
      ENSRNOP00000046991.4, ENSRNOT00000042474.8

    3. NM_001401116.1 → NP_001388045.1  cleavage and polyadenylation specificity factor subunit 4 isoform 3

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000012
      UniProtKB/TrEMBL
      A0A8I5Y5Y1
      Related
      ENSRNOP00000085636.2, ENSRNOT00000099433.2

    RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

    Reference GRCr8

    Genomic

    1. NC_086030.1 Reference GRCr8

      Range
      14543536..14559350 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_063271252.1 → XP_063127322.1  cleavage and polyadenylation specificity factor subunit 4 isoform X1

    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q5FVR7.1 GenPept UniProtKB/Swiss-Prot:Q5FVR7

    Gene LinkOut

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

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