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Cpsf4l cleavage and polyadenylation specific factor 4-like [ Mus musculus (house mouse) ]

Gene ID: 52670, updated on 5-Mar-2024

Summary

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Official Symbol
Cpsf4lprovided by MGI
Official Full Name
cleavage and polyadenylation specific factor 4-likeprovided by MGI
Primary source
MGI:MGI:1277182
See related
Ensembl:ENSMUSG00000018727 AllianceGenome:MGI:1277182
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
D11Ertd636e; 0610010C04Rik; 1500000C01Rik
Summary
Predicted to be involved in pre-mRNA cleavage required for polyadenylation. Predicted to be part of mRNA cleavage and polyadenylation specificity factor complex. Is expressed in central nervous system and retina. Orthologous to human CPSF4L (cleavage and polyadenylation specific factor 4 like). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Biased expression in testis adult (RPKM 18.1), ovary adult (RPKM 3.8) and 5 other tissues See more
Orthologs
human all
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Genomic context

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Location:
11 E2; 11 79.17 cM
Exon count:
10
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 11 NC_000077.7 (113588997..113601125, complement)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 11 NC_000077.6 (113698171..113710167, complement)

Chromosome 11 - NC_000077.7Genomic Context describing neighboring genes Neighboring gene solute carrier family 39 (metal ion transporter), member 11 Neighboring gene STARR-positive B cell enhancer ABC_E4012 Neighboring gene somatostatin receptor 2 Neighboring gene CapStarr-seq enhancer MGSCv37_chr11:113545452-113545561 Neighboring gene STARR-positive B cell enhancer ABC_E4013 Neighboring gene STARR-seq mESC enhancer starr_31100 Neighboring gene component of oligomeric golgi complex 1 Neighboring gene STARR-seq mESC enhancer starr_31103 Neighboring gene VCP nuclear cofactor family member 1 Neighboring gene mitochondrial nucleoid associated protein 1 Neighboring gene STARR-positive B cell enhancer ABC_E8469 Neighboring gene CDC42 effector protein 4 Neighboring gene predicted gene 11736

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. Cracking the egg: molecular dynamics and evolutionary aspects of the transition from the fully grown oocyte to embryo. Evsikov AV, et al. Genes Dev, 2006 Oct 1. PMID 17015433, Free PMC Article
  2. EUCOMM--the European conditional mouse mutagenesis program. Friedel RH, et al. Brief Funct Genomic Proteomic, 2007 Sep. PMID 17967808
  3. Large-scale cDNA analysis reveals phased gene expression patterns during preimplantation mouse development. Ko MS, et al. Development, 2000 Apr. PMID 10725249
  4. BGEM: an in situ hybridization database of gene expression in the embryonic and adult mouse nervous system. Magdaleno S, et al. PLoS Biol, 2006 Apr. PMID 16602821, Free PMC Article
  5. Genome-wide expression profiling of mid-gestation placenta and embryo using a 15,000 mouse developmental cDNA microarray. Tanaka TS, et al. Proc Natl Acad Sci U S A, 2000 Aug 1. PMID 10922068, Free PMC Article

See all (16) citations in PubMed

GeneRIFs: Gene References Into Functions

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)
  • Endonuclease-mediated (2) 

General gene information

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Markers

Homology

Gene Ontology Provided by MGI

Component Evidence Code Pubs
part_of mRNA cleavage and polyadenylation specificity factor complex IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
putative cleavage and polyadenylation specificity factor subunit 4-like protein

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_001164532.1 → NP_001158004.1  putative cleavage and polyadenylation specificity factor subunit 4-like protein isoform 3

    See identical proteins and their annotated locations for NP_001158004.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) uses an alternate in-frame splice site in the 5' coding region, compared to variant 1, resulting in an isoform (3) that is longer than isoform 1.
    Source sequence(s)
    AK161074, DV648079, DV657463, DV659633
    Consensus CDS
    CCDS48977.1
    UniProtKB/TrEMBL
    E9Q2N0
    Related
    ENSMUSP00000097819.5, ENSMUST00000100248.6
    Conserved Domains (1) summary
    COG5084
    Location:82 → 230
    YTH1; Cleavage and polyadenylation specificity factor (CPSF) Clipper subunit and related makorin family Zn-finger proteins [General function prediction only]

  2. NM_001362806.1 → NP_001349735.1  putative cleavage and polyadenylation specificity factor subunit 4-like protein isoform 4

    Status: VALIDATED

    Source sequence(s)
    AL603706, DV655803, DV657463
    Conserved Domains (1) summary
    COG5084
    Location:36 → 177
    YTH1; Cleavage and polyadenylation specificity factor (CPSF) Clipper subunit and related makorin family Zn-finger proteins [General function prediction only]

  3. NM_026682.2 → NP_080958.2  putative cleavage and polyadenylation specificity factor subunit 4-like protein isoform 1

    See identical proteins and their annotated locations for NP_080958.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) encodes isoform 1.
    Source sequence(s)
    AK161074, DV657463, DV659633
    Consensus CDS
    CCDS25603.2
    UniProtKB/TrEMBL
    G3UWW6
    Related
    ENSMUSP00000133451.2, ENSMUST00000173655.8
    Conserved Domains (1) summary
    COG5084
    Location:36 → 178
    YTH1; Cleavage and polyadenylation specificity factor (CPSF) Clipper subunit and related makorin family Zn-finger proteins [General function prediction only]

  4. NM_029794.2 → NP_084070.1  putative cleavage and polyadenylation specificity factor subunit 4-like protein isoform 2

    See identical proteins and their annotated locations for NP_084070.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR, lacks a portion of the 5' coding region, uses a downstream translational start codon, and lacks an alternate exon that causes a frameshift in the 3' coding region, compared to variant 1. The encoded isoform (2) is shorter at the N-terminus and includes a distinct C-terminus, compared to isoform 1.
    Source sequence(s)
    AK005072, DV657463
    Consensus CDS
    CCDS25602.1
    UniProtKB/TrEMBL
    Q9DBA5
    Related
    ENSMUSP00000018871.2, ENSMUST00000018871.8
    Conserved Domains (1) summary
    COG5084
    Location:3 → 110
    YTH1; Cleavage and polyadenylation specificity factor (CPSF) Clipper subunit and related makorin family Zn-finger proteins [General function prediction only]

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_000077.7 Reference GRCm39 C57BL/6J

    Range
    113588997..113601125 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_030246127.2 → XP_030101987.1  putative cleavage and polyadenylation specificity factor subunit 4-like protein isoform X15

    Conserved Domains (1) summary
    COG5084
    Location:3 → 125
    YTH1; Cleavage and polyadenylation specificity factor (CPSF) Clipper subunit and related makorin family Zn-finger proteins [General function prediction only]

  2. XM_036156832.1 → XP_036012725.1  putative cleavage and polyadenylation specificity factor subunit 4-like protein isoform X14

    UniProtKB/TrEMBL
    A2A6P9, Q91YP9
    Related
    ENSMUSP00000102228.2, ENSMUST00000106617.8
    Conserved Domains (1) summary
    COG5084
    Location:3 → 126
    YTH1; Cleavage and polyadenylation specificity factor (CPSF) Clipper subunit and related makorin family Zn-finger proteins [General function prediction only]

  3. XM_006533705.5 → XP_006533768.1  putative cleavage and polyadenylation specificity factor subunit 4-like protein isoform X9

    Conserved Domains (1) summary
    COG5084
    Location:36 → 161
    YTH1; Cleavage and polyadenylation specificity factor (CPSF) Clipper subunit and related makorin family Zn-finger proteins [General function prediction only]

  4. XM_006533707.5 → XP_006533770.1  putative cleavage and polyadenylation specificity factor subunit 4-like protein isoform X11

    See identical proteins and their annotated locations for XP_006533770.1

    Conserved Domains (1) summary
    COG5084
    Location:36 → 177
    YTH1; Cleavage and polyadenylation specificity factor (CPSF) Clipper subunit and related makorin family Zn-finger proteins [General function prediction only]

  5. XM_006533704.5 → XP_006533767.1  putative cleavage and polyadenylation specificity factor subunit 4-like protein isoform X8

    Conserved Domains (1) summary
    COG5084
    Location:36 → 162
    YTH1; Cleavage and polyadenylation specificity factor (CPSF) Clipper subunit and related makorin family Zn-finger proteins [General function prediction only]

  6. XM_006533706.5 → XP_006533769.1  putative cleavage and polyadenylation specificity factor subunit 4-like protein isoform X10

    See identical proteins and their annotated locations for XP_006533769.1

    UniProtKB/TrEMBL
    G3UWW6
    Conserved Domains (1) summary
    COG5084
    Location:36 → 178
    YTH1; Cleavage and polyadenylation specificity factor (CPSF) Clipper subunit and related makorin family Zn-finger proteins [General function prediction only]

  7. XM_030246125.2 → XP_030101985.1  putative cleavage and polyadenylation specificity factor subunit 4-like protein isoform X7

    Conserved Domains (1) summary
    COG5084
    Location:86 → 164
    YTH1; Cleavage and polyadenylation specificity factor (CPSF) Clipper subunit and related makorin family Zn-finger proteins [General function prediction only]

  8. XM_030246124.2 → XP_030101984.1  putative cleavage and polyadenylation specificity factor subunit 4-like protein isoform X2

    Conserved Domains (1) summary
    COG5084
    Location:82 → 214
    YTH1; Cleavage and polyadenylation specificity factor (CPSF) Clipper subunit and related makorin family Zn-finger proteins [General function prediction only]

  9. XM_006533701.5 → XP_006533764.1  putative cleavage and polyadenylation specificity factor subunit 4-like protein isoform X4

    See identical proteins and their annotated locations for XP_006533764.1

    UniProtKB/TrEMBL
    E9Q2N0
    Conserved Domains (1) summary
    COG5084
    Location:82 → 230
    YTH1; Cleavage and polyadenylation specificity factor (CPSF) Clipper subunit and related makorin family Zn-finger proteins [General function prediction only]

  10. XM_017314656.3 → XP_017170145.1  putative cleavage and polyadenylation specificity factor subunit 4-like protein isoform X5

    Conserved Domains (1) summary
    COG5084
    Location:84 → 215
    YTH1; Cleavage and polyadenylation specificity factor (CPSF) Clipper subunit and related makorin family Zn-finger proteins [General function prediction only]

  11. XM_030246123.2 → XP_030101983.1  putative cleavage and polyadenylation specificity factor subunit 4-like protein isoform X1

    Conserved Domains (1) summary
    COG5084
    Location:84 → 215
    YTH1; Cleavage and polyadenylation specificity factor (CPSF) Clipper subunit and related makorin family Zn-finger proteins [General function prediction only]

  12. XM_017314657.3 → XP_017170146.1  putative cleavage and polyadenylation specificity factor subunit 4-like protein isoform X6

    Conserved Domains (1) summary
    COG5084
    Location:82 → 231
    YTH1; Cleavage and polyadenylation specificity factor (CPSF) Clipper subunit and related makorin family Zn-finger proteins [General function prediction only]

  13. XM_017314655.3 → XP_017170144.1  putative cleavage and polyadenylation specificity factor subunit 4-like protein isoform X3

    Conserved Domains (1) summary
    COG5084
    Location:82 → 231
    YTH1; Cleavage and polyadenylation specificity factor (CPSF) Clipper subunit and related makorin family Zn-finger proteins [General function prediction only]

  14. XM_036156830.1 → XP_036012723.1  putative cleavage and polyadenylation specificity factor subunit 4-like protein isoform X13

    Conserved Domains (1) summary
    COG5084
    Location:3 → 109
    YTH1; Cleavage and polyadenylation specificity factor (CPSF) Clipper subunit and related makorin family Zn-finger proteins [General function prediction only]

  15. XM_036156829.1 → XP_036012722.1  putative cleavage and polyadenylation specificity factor subunit 4-like protein isoform X12

    UniProtKB/TrEMBL
    Q9DBA5
    Conserved Domains (1) summary
    COG5084
    Location:3 → 110
    YTH1; Cleavage and polyadenylation specificity factor (CPSF) Clipper subunit and related makorin family Zn-finger proteins [General function prediction only]

  16. XM_006533709.5 → XP_006533772.1  putative cleavage and polyadenylation specificity factor subunit 4-like protein isoform X12

    See identical proteins and their annotated locations for XP_006533772.1

    UniProtKB/TrEMBL
    Q9DBA5
    Conserved Domains (1) summary
    COG5084
    Location:3 → 110
    YTH1; Cleavage and polyadenylation specificity factor (CPSF) Clipper subunit and related makorin family Zn-finger proteins [General function prediction only]

  17. XM_006533710.5 → XP_006533773.1  putative cleavage and polyadenylation specificity factor subunit 4-like protein isoform X12

    See identical proteins and their annotated locations for XP_006533773.1

    UniProtKB/TrEMBL
    Q9DBA5
    Conserved Domains (1) summary
    COG5084
    Location:3 → 110
    YTH1; Cleavage and polyadenylation specificity factor (CPSF) Clipper subunit and related makorin family Zn-finger proteins [General function prediction only]

  18. XM_036156831.1 → XP_036012724.1  putative cleavage and polyadenylation specificity factor subunit 4-like protein isoform X13

    Conserved Domains (1) summary
    COG5084
    Location:3 → 109
    YTH1; Cleavage and polyadenylation specificity factor (CPSF) Clipper subunit and related makorin family Zn-finger proteins [General function prediction only]
Nucleotide Protein Strain
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