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

    Gene ID: 298916, updated on 2-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 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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