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    Cpsf6 cleavage and polyadenylation specific factor 6 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 299811, updated on 2-May-2024

    Summary

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    Official Symbol
    Cpsf6provided by RGD
    Official Full Name
    cleavage and polyadenylation specific factor 6provided by RGD
    Primary source
    RGD:1304640
    See related
    Ensembl:ENSRNOG00000005927 AllianceGenome:RGD:1304640
    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 exon-exon junction complex binding activity; mRNA binding activity; and ribosomal large subunit binding activity. Predicted to contribute to RNA binding activity. Predicted to be involved in several processes, including mRNA alternative polyadenylation; pre-mRNA cleavage required for polyadenylation; and protein-containing complex assembly. Predicted to be located in cytoplasm and nuclear lumen. Predicted to be part of mRNA cleavage and polyadenylation specificity factor complex and ribonucleoprotein complex. Orthologous to human CPSF6 (cleavage and polyadenylation specific factor 6). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Biased expression in Thymus (RPKM 309.7), Spleen (RPKM 209.2) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    Location:
    7q22
    Exon count:
    15
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 7 NC_086025.1 (54798452..54887711, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 7 NC_051342.1 (52956589..53001783, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 7 NC_005106.4 (60385688..60417661, complement)

    Chromosome 7 - NC_086025.1Genomic Context describing neighboring genes Neighboring gene lysozyme C type 2 Neighboring gene small nucleolar RNA SNORA48 Neighboring gene lysozyme 2 Neighboring gene uncharacterized LOC120093601 Neighboring gene uncharacterized LOC134479595

    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. Subnuclear localization and dynamics of the Pre-mRNA 3' end processing factor mammalian cleavage factor I 68-kDa subunit. Cardinale S, et al. Mol Biol Cell, 2007 Apr. PMID 17267687, Free PMC Article
    2. A mechanism for the regulation of pre-mRNA 3' processing by human cleavage factor Im. Brown KM, et al. Mol Cell, 2003 Dec. PMID 14690600
    3. Human pre-mRNA cleavage factor Im is related to spliceosomal SR proteins and can be reconstituted in vitro from recombinant subunits. Rüegsegger U, et al. Mol Cell, 1998 Jan. PMID 9659921
    4. Differential role for phosphorylation in alternative polyadenylation function versus nuclear import of SR-like protein CPSF6. Jang S, et al. Nucleic Acids Res, 2019 May 21. PMID 30916345, Free PMC Article
    5. Crystal structure of a human cleavage factor CFI(m)25/CFI(m)68/RNA complex provides an insight into poly(A) site recognition and RNA looping. Yang Q, et al. Structure, 2011 Mar 9. PMID 21295486, Free PMC Article

    See all (18) citations in PubMed

    GeneRIFs: Gene References Into Functions

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    contributes_to RNA binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables exon-exon junction complex binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables mRNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables mRNA binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables ribosomal large subunit 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 alternative polyadenylation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in mRNA alternative polyadenylation ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in mRNA processing ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of RNA export from nucleus ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in protein heterotetramerization ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in protein tetramerization ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    located_in cytoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in interchromatin granule 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
    		  
    part_of mRNA cleavage factor complex ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nuclear speck ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleus ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in paraspeckles ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in perichromatin fibrils ISO
    Inferred from Sequence Orthology
    more info
    		  
    part_of ribonucleoprotein complex ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    cleavage and polyadenylation specificity factor subunit 6
    Names
    cleavage and polyadenylation specific factor 6, 68kDa

    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_001106785.1 → NP_001100255.1  cleavage and polyadenylation specificity factor subunit 6

      See identical proteins and their annotated locations for NP_001100255.1

      Status: PROVISIONAL

      Source sequence(s)
      CH473960
      UniProtKB/TrEMBL
      A6IGS7, D3ZPL1
      Related
      ENSRNOP00000008193.6, ENSRNOT00000008193.7
      Conserved Domains (1) summary
      cd12643
      Location:82 → 158
      RRM_CFIm68; RNA recognition motif (RRM) found in pre-mRNA cleavage factor Im 68 kDa subunit (CFIm68 or CPSF6) and similar proteins

    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_086025.1 Reference GRCr8

      Range
      54798452..54887711 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_063263231.1 → XP_063119301.1  cleavage and polyadenylation specificity factor subunit 6 isoform X3

    2. XM_063263234.1 → XP_063119304.1  cleavage and polyadenylation specificity factor subunit 6 isoform X5

    3. XM_063263233.1 → XP_063119303.1  cleavage and polyadenylation specificity factor subunit 6 isoform X5

    4. XM_039078740.2 → XP_038934668.1  cleavage and polyadenylation specificity factor subunit 6 isoform X5

      Conserved Domains (1) summary
      cd12643
      Location:30 → 106
      RRM_CFIm68; RNA recognition motif (RRM) found in pre-mRNA cleavage factor Im 68 kDa subunit (CFIm68 or CPSF6) and similar proteins

    5. XM_063263235.1 → XP_063119305.1  cleavage and polyadenylation specificity factor subunit 6 isoform X5

    6. XM_039078739.2 → XP_038934667.1  cleavage and polyadenylation specificity factor subunit 6 isoform X4

      UniProtKB/TrEMBL
      A6IGS7, D3ZPL1
      Conserved Domains (1) summary
      cd12643
      Location:82 → 158
      RRM_CFIm68; RNA recognition motif (RRM) found in pre-mRNA cleavage factor Im 68 kDa subunit (CFIm68 or CPSF6) and similar proteins

    7. XM_063263232.1 → XP_063119302.1  cleavage and polyadenylation specificity factor subunit 6 isoform X4

      UniProtKB/TrEMBL
      A6IGS7, D3ZPL1

    8. XM_039078738.2 → XP_038934666.1  cleavage and polyadenylation specificity factor subunit 6 isoform X3

      Conserved Domains (1) summary
      cd12643
      Location:82 → 158
      RRM_CFIm68; RNA recognition motif (RRM) found in pre-mRNA cleavage factor Im 68 kDa subunit (CFIm68 or CPSF6) and similar proteins

    9. XM_063263230.1 → XP_063119300.1  cleavage and polyadenylation specificity factor subunit 6 isoform X3

    10. XM_006241374.4 → XP_006241436.1  cleavage and polyadenylation specificity factor subunit 6 isoform X2

      See identical proteins and their annotated locations for XP_006241436.1

      UniProtKB/TrEMBL
      A0A8I6AMJ9, A6IGS9
      Related
      ENSRNOP00000094948.1
      Conserved Domains (1) summary
      cd12643
      Location:82 → 158
      RRM_CFIm68; RNA recognition motif of pre-mRNA cleavage factor Im 68 kDa subunit (CFIm68 or CPSF6) and similar proteins

    11. XM_063263228.1 → XP_063119298.1  cleavage and polyadenylation specificity factor subunit 6 isoform X2

      UniProtKB/TrEMBL
      A0A8I6AMJ9, A6IGS9

    12. XM_006241372.4 → XP_006241434.1  cleavage and polyadenylation specificity factor subunit 6 isoform X1

      See identical proteins and their annotated locations for XP_006241434.1

      Conserved Domains (1) summary
      cd12643
      Location:82 → 158
      RRM_CFIm68; RNA recognition motif of pre-mRNA cleavage factor Im 68 kDa subunit (CFIm68 or CPSF6) and similar proteins

    13. XM_006241373.4 → XP_006241435.1  cleavage and polyadenylation specificity factor subunit 6 isoform X1

      See identical proteins and their annotated locations for XP_006241435.1

      Conserved Domains (1) summary
      cd12643
      Location:82 → 158
      RRM_CFIm68; RNA recognition motif of pre-mRNA cleavage factor Im 68 kDa subunit (CFIm68 or CPSF6) and similar proteins
    Nucleotide Protein Strain
    Heading Accession and Version

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