U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

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