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Cpsf3 cleavage and polyadenylation specific factor 3 [ Rattus norvegicus (Norway rat) ]

Gene ID: 298916, updated on 27-Nov-2024

Summary

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Official Symbol
Cpsf3provided by RGD
Official Full Name
cleavage and polyadenylation specific factor 3provided by RGD
Primary source
RGD:1305767
See related
EnsemblRapid:ENSRNOG00000052418 AllianceGenome:RGD:1305767
Gene type
protein coding
RefSeq status
PROVISIONAL
Organism
Rattus norvegicus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Summary
Predicted to enable RNA binding activity; RNA nuclease activity; and metal ion binding activity. Predicted to be involved in co-transcriptional mRNA 3'-end processing, cleavage and polyadenylation pathway; mRNA 3'-end processing by stem-loop binding activity and cleavage; and positive regulation of G1/S transition of mitotic cell cycle. Predicted to be part of mRNA cleavage and polyadenylation specificity factor complex. Orthologous to human CPSF3 (cleavage and polyadenylation specific factor 3). [provided by Alliance of Genome Resources, Nov 2024]
Expression
Biased expression in Kidney (RPKM 195.4), Thymus (RPKM 194.1) and 9 other tissues See more
Orthologs
human mouse all
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Genomic context

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See Cpsf3 in Genome Data Viewer
Location:
6q16
Exon count:
20
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCr8 (GCF_036323735.1) 6 NC_086024.1 (46564855..46592776)
RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 6 NC_051341.1 (40836121..40864129)
106 previous assembly Rnor_6.0 (GCF_000001895.5) 6 NC_005105.4 (43363792..43391712)

Chromosome 6 - NC_086024.1Genomic Context describing neighboring genes Neighboring gene ArfGAP with SH3 domain, ankyrin repeat and PH domain 2 Neighboring gene U6 spliceosomal RNA Neighboring gene integrin subunit beta 1 binding protein 1 Neighboring gene small nucleolar RNA SNORA21 Neighboring gene isoamyl acetate hydrolyzing esterase 1 Neighboring gene ADAM metallopeptidase domain 17 Neighboring gene U6 spliceosomal RNA

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. Studies of the 5' exonuclease and endonuclease activities of CPSF-73 in histone pre-mRNA processing. Yang XC, et al. Mol Cell Biol, 2009 Jan. PMID 18955505, Free PMC Article
  2. Conserved motifs in both CPSF73 and CPSF100 are required to assemble the active endonuclease for histone mRNA 3'-end maturation. Kolev NG, et al. EMBO Rep, 2008 Oct. PMID 18688255, Free PMC Article
  3. CKIalpha is associated with and phosphorylates star-PAP and is also required for expression of select star-PAP target messenger RNAs. Gonzales ML, et al. J Biol Chem, 2008 May 2. PMID 18305108, Free PMC Article
  4. 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
  5. Smicl is a novel Smad interacting protein and cleavage and polyadenylation specificity factor associated protein. Collart C, et al. Genes Cells, 2005 Sep. PMID 16115198

See all (9) 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

  • MGC124885

Gene Ontology Provided by RGD

Function Evidence Code Pubs
enables 5'-3' RNA exonuclease activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables 5'-3' RNA exonuclease activity ISO
Inferred from Sequence Orthology
more info
  
enables RNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables RNA binding ISO
Inferred from Sequence Orthology
more info
  
enables RNA endonuclease activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables RNA endonuclease activity ISO
Inferred from Sequence Orthology
more info
  
enables metal ion binding ISO
Inferred from Sequence Orthology
more info
  
Process Evidence Code Pubs
involved_in biological_process ND
No biological Data available
more info
  
involved_in co-transcriptional mRNA 3'-end processing, cleavage and polyadenylation pathway ISO
Inferred from Sequence Orthology
more info
  
involved_in mRNA 3'-end processing ISO
Inferred from Sequence Orthology
more info
  
involved_in mRNA 3'-end processing by stem-loop binding and cleavage IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in mRNA 3'-end processing by stem-loop binding and cleavage ISO
Inferred from Sequence Orthology
more info
  
involved_in positive regulation of G1/S transition of mitotic cell cycle ISO
Inferred from Sequence Orthology
more info
  
Component Evidence Code Pubs
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
  

General protein information

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Preferred Names
cleavage and polyadenylation specificity factor subunit 3
Names
cleavage and polyadenylation specific factor 3, 73kDa
cleavage and polyadenylation specificity factor 3

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_001030030.1 → NP_001025201.1  cleavage and polyadenylation specificity factor subunit 3

    See identical proteins and their annotated locations for NP_001025201.1

    Status: PROVISIONAL

    Source sequence(s)
    BC099817
    UniProtKB/TrEMBL
    A6HAV9, G3V6W7, Q499P4
    Related
    ENSRNOP00000082326.2, ENSRNOT00000106025.2
    Conserved Domains (5) summary
    smart01027
    Location:246 → 367
    Beta-Casp; Beta-Casp domain
    smart01098
    Location:477 → 682
    CPSF73-100_C; This is the C-terminal conserved region of the pre-mRNA 3'-end-processing of the polyadenylation factor CPSF-73/CPSF-100 proteins
    COG1236
    Location:14 → 454
    YSH1; RNA processing exonuclease, beta-lactamase fold, Cft2 family [Translation, ribosomal structure and biogenesis]
    pfam07521
    Location:380 → 420
    RMMBL; RNA-metabolizing metallo-beta-lactamase
    cd16292
    Location:12 → 205
    CPSF3-like_MBL-fold; cleavage and polyadenylation specificity factor (CPSF) subunit 3 and related proteins; MBL-fold metallo-hydrolase domain

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_086024.1 Reference GRCr8

    Range
    46564855..46592776
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_039111955.2 → XP_038967883.1  cleavage and polyadenylation specificity factor subunit 3 isoform X1

    UniProtKB/TrEMBL
    A6HAW0
    Related
    ENSRNOP00000108743.1, ENSRNOT00000128022.1
    Conserved Domains (3) summary
    COG1236
    Location:14 → 454
    YSH1; RNA processing exonuclease, beta-lactamase fold, Cft2 family [Translation, ribosomal structure and biogenesis]
    cd16292
    Location:12 → 205
    CPSF3-like_MBL-fold; cleavage and polyadenylation specificity factor (CPSF) subunit 3 and related proteins; MBL-fold metallo-hydrolase domain
    pfam11718
    Location:479 → 595
    CPSF73-100_C; Pre-mRNA 3'-end-processing endonuclease polyadenylation factor C-term

  2. XM_039111954.2 → XP_038967882.1  cleavage and polyadenylation specificity factor subunit 3 isoform X2

    UniProtKB/TrEMBL
    A0A8I6AQC0
    Related
    ENSRNOP00000096053.1, ENSRNOT00000094148.2
    Conserved Domains (2) summary
    COG1236
    Location:1 → 417
    YSH1; RNA processing exonuclease, beta-lactamase fold, Cft2 family [Translation, ribosomal structure and biogenesis]
    pfam11718
    Location:442 → 645
    CPSF73-100_C; Pre-mRNA 3'-end-processing endonuclease polyadenylation factor C-term
Nucleotide Protein Strain
Heading Accession and Version

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