U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Links from GEO Profiles

    • Showing Current items.

    Cpsf4 cleavage and polyadenylation specific factor 4 [ Mus musculus (house mouse) ]

    Gene ID: 54188, updated on 5-Mar-2024

    Summary

    Go to the top of the page Help
    Official Symbol
    Cpsf4provided by MGI
    Official Full Name
    cleavage and polyadenylation specific factor 4provided by MGI
    Primary source
    MGI:MGI:1861602
    See related
    Ensembl:ENSMUSG00000029625 AllianceGenome:MGI:1861602
    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
    30kDa
    Summary
    Predicted to enable sequence-specific double-stranded DNA binding activity. Predicted to be involved in pre-mRNA cleavage required for polyadenylation. Predicted to act upstream of or within mRNA processing. Predicted to be located in nucleoplasm. Predicted to be part of mRNA cleavage and polyadenylation specificity factor complex. Is expressed in several structures, including genitourinary system; midbrain ventricular layer; olfactory epithelium; submandibular gland primordium; and telencephalon. Orthologous to human CPSF4 (cleavage and polyadenylation specific factor 4). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Ubiquitous expression in CNS E11.5 (RPKM 23.8), CNS E14 (RPKM 23.1) and 28 other tissues See more
    Orthologs
    human all
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    Go to the top of the page Help
    Location:
    5 G2; 5 85.08 cM
    Exon count:
    8
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 5 NC_000071.7 (145104023..145118851)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 5 NC_000071.6 (145167213..145182041)

    Chromosome 5 - NC_000071.7Genomic Context describing neighboring genes Neighboring gene PDGFA associated protein 1 Neighboring gene STARR-positive B cell enhancer ABC_E8091 Neighboring gene BUD31 homolog Neighboring gene pentatricopeptide repeat domain 1 Neighboring gene STARR-positive B cell enhancer ABC_E6397 Neighboring gene ATP synthase membrane subunit f Neighboring gene zinc finger with KRAB and SCAN domains 14 Neighboring gene STARR-positive B cell enhancer ABC_E1316

    Genomic regions, transcripts, and products

    Go to the top of the page Help

    Go to nucleotide: Graphics FASTA GenBank

    Expression

    Go to the top of the page Help
    • 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

    Go to the top of the pageHelp

    Related articles in PubMed

    1. Drosophila clipper/CPSF 30K is a post-transcriptionally regulated nuclear protein that binds RNA containing GC clusters. Bai C, et al. Nucleic Acids Res, 1998 Apr 1. PMID 9512528, Free PMC Article
    2. Cleavage of RNA hairpins mediated by a developmentally regulated CCCH zinc finger protein. Bai C, et al. Mol Cell Biol, 1996 Dec. PMID 8943320, Free PMC Article
    3. Gene expression analysis of the embryonic subplate. Oeschger FM, et al. Cereb Cortex, 2012 Jun. PMID 21862448, Free PMC Article
    4. Tagging genes with cassette-exchange sites. Cobellis G, et al. Nucleic Acids Res, 2005 Mar 1. PMID 15741177, Free PMC Article
    5. Transcriptome analysis of mouse stem cells and early embryos. Sharov AA, et al. PLoS Biol, 2003 Dec. PMID 14691545, Free PMC Article

    See all (24) citations in PubMed

    GeneRIFs: Gene References Into Functions

    Variation

    Go to the top of the page Help

    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    • Endonuclease-mediated (3) 

    Pathways from PubChem

    Go to the top of the page

    Interactions

    Go to the top of the page Help
    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Go to the top of the page Help

    Markers

    Homology

    Clone Names

    • MGC36996

    Gene Ontology Provided by MGI

    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 nucleic acid 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
    acts_upstream_of_or_within 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 ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleus IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

    Go to the top of the page Help
    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
    clipper homolog
    clipper/CPSF 30K
    musculus clipper/cleavage and polyadenylation specificity factor 30 kDa subunit

    NCBI Reference Sequences (RefSeq)

    Go to the top of the page Help

    NEW Try the new Transcript table

    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_001291248.1 → NP_001278177.1  cleavage and polyadenylation specificity factor subunit 4 isoform a

      See identical proteins and their annotated locations for NP_001278177.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes isoform a.
      Source sequence(s)
      AC127411, AF033201, AI324081, AK046064
      Consensus CDS
      CCDS71710.1
      UniProtKB/TrEMBL
      B2LVG6
      Related
      ENSMUSP00000124966.2, ENSMUST00000162244.8
      Conserved Domains (1) 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]

    2. NM_001291249.1 → NP_001278178.1  cleavage and polyadenylation specificity factor subunit 4 isoform b

      See identical proteins and their annotated locations for NP_001278178.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) uses an alternate in-frame splice site in the 3' coding region, compared to variant 1, resulting in an isoform (b) that is shorter than isoform a.
      Source sequence(s)
      AC127411, AI324081, AK046064, CN723345
      Consensus CDS
      CCDS71711.1
      UniProtKB/TrEMBL
      B2LVG5
      Related
      ENSMUSP00000124899.2, ENSMUST00000160629.8
      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]

    3. NM_001374716.1 → NP_001361645.1  cleavage and polyadenylation specificity factor subunit 4 isoform d

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) represents the longest transcript and encodes the longest isoform (d).
      Source sequence(s)
      AC127411
      Consensus CDS
      CCDS90014.1
      UniProtKB/TrEMBL
      E0CXT7
      Related
      ENSMUSP00000125019.2, ENSMUST00000160422.8
      Conserved Domains (2) summary
      COG5084
      Location:25 → 211
      YTH1; Cleavage and polyadenylation specificity factor (CPSF) Clipper subunit and related makorin family Zn-finger proteins [General function prediction only]
      COG5222
      Location:198 → 258
      COG5222; Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]

    4. NM_178576.3 → NP_848671.1  cleavage and polyadenylation specificity factor subunit 4 isoform c

      See identical proteins and their annotated locations for NP_848671.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) lacks an alternate in-frame exon in the central coding region, and uses an alternate in-frame splice site in the 3' coding region, compared to variant 1. The encoded isoform (c) is shorter than isoform a.
      Source sequence(s)
      AC127411, AI324081, AK046064
      Consensus CDS
      CCDS19859.1
      UniProtKB/Swiss-Prot
      O54930, Q8BQZ5
      Related
      ENSMUSP00000069243.6, ENSMUST00000070487.12
      Conserved Domains (2) summary
      COG5084
      Location:25 → 142
      YTH1; Cleavage and polyadenylation specificity factor (CPSF) Clipper subunit and related makorin family Zn-finger proteins [General function prediction only]
      cl26688
      Location:160 → 200
      DWNN; DWNN domain

    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_000071.7 Reference GRCm39 C57BL/6J

      Range
      145104023..145118851
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8BQZ5.1 GenPept UniProtKB/Swiss-Prot:Q8BQZ5

    Gene LinkOut

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

    Chemical Information
    Molecular Biology Databases
    Research Materials
    Tools
    Miscellaneous