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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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