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    Rpap2 RNA polymerase II associated protein 2 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 305120, updated on 2-Nov-2024

    Summary

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    Official Symbol
    Rpap2provided by RGD
    Official Full Name
    RNA polymerase II associated protein 2provided by RGD
    Primary source
    RGD:1309034
    See related
    EnsemblRapid:ENSRNOG00000023484 AllianceGenome:RGD:1309034
    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
    Also known as
    RGD1309034
    Summary
    Predicted to enable RNA polymerase II CTD heptapeptide repeat phosphatase activity. Predicted to be involved in PERK-mediated unfolded protein response and snRNA transcription. Predicted to be located in cytosol and nucleolus. Predicted to be part of transcription preinitiation complex. Predicted to be active in cytoplasm and nucleus. Orthologous to human RPAP2 (RNA polymerase II associated protein 2). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Biased expression in Thymus (RPKM 111.5), Spleen (RPKM 80.8) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Rpap2 in Genome Data Viewer
    Location:
    14p22
    Exon count:
    16
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 14 NC_086032.1 (2253966..2332251, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 14 NC_051349.1 (2109044..2187343, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 14 NC_005113.4 (3125595..3204590, complement)

    Chromosome 14 - NC_086032.1Genomic Context describing neighboring genes Neighboring gene ecotropic viral integration site 5 Neighboring gene ubiquitin-conjugating enzyme E2D 2B Neighboring gene growth factor independent 1 transcriptional repressor Neighboring gene similar to human chromosome 1 open reading frame 146 Neighboring gene glomulin, FKBP associated protein Neighboring gene uncharacterized LOC108352691 Neighboring gene BTB domain containing 8

    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. Ser7 phosphorylation of the CTD recruits the RPAP2 Ser5 phosphatase to snRNA genes. Egloff S, et al. Mol Cell, 2012 Jan 13. PMID 22137580, Free PMC Article
    2. The writers, readers, and functions of the RNA polymerase II C-terminal domain code. Jeronimo C, et al. Chem Rev, 2013 Nov 13. PMID 23837720
    3. Updating the RNA polymerase CTD code: adding gene-specific layers. Egloff S, et al. Trends Genet, 2012 Jul. PMID 22622228
    4. Control of the RNA polymerase II phosphorylation state in promoter regions by CTD interaction domain-containing proteins RPRD1A and RPRD1B. Ni Z, et al. Transcription, 2011 Sep-Oct. PMID 22231121, Free PMC Article
    5. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). Gerhard DS, et al. Genome Res, 2004 Oct. PMID 15489334, Free PMC Article

    See all (7) citations in PubMed

    GeneRIFs: Gene References Into Functions

    Pathways from PubChem

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    General gene information

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    Markers

    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables RNA polymerase II CTD heptapeptide repeat phosphatase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables RNA polymerase II CTD heptapeptide repeat phosphatase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables RNA polymerase II CTD heptapeptide repeat phosphatase activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables RNA polymerase II CTD heptapeptide repeat phosphatase activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables RNA polymerase core enzyme binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables myosin phosphatase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein serine/threonine phosphatase activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables protein serine/threonine phosphatase activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Process Evidence Code Pubs
    involved_in PERK-mediated unfolded protein response IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in PERK-mediated unfolded protein response ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in PERK-mediated unfolded protein response ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in biological_process ND
    No biological Data available
    more info
    		  
    involved_in regulation of transcription by RNA polymerase II IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in snRNA transcription IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in snRNA transcription ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in snRNA transcription ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Component Evidence Code Pubs
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in cytoplasm ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in cytosol IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in cytosol ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleolus IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nucleolus ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nucleus ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleus ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    part_of transcription preinitiation complex IEA
    Inferred from Electronic Annotation
    more info
    		  
    part_of transcription preinitiation complex ISO
    Inferred from Sequence Orthology
    more info
    		  
    part_of transcription preinitiation complex ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  

    General protein information

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    Preferred Names
    RNA polymerase II subunit B1 CTD phosphatase Rpap2
    Names
    putative RNA polymerase II-associated protein 2
    NP_001014009.1
    XP_006250610.2
    XP_008768150.1
    XP_008768151.1
    XP_063129084.1
    XP_063129085.1
    XP_063129086.1
    XP_063129087.1

    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_001013987.1 → NP_001014009.1  RNA polymerase II subunit B1 CTD phosphatase Rpap2

      See identical proteins and their annotated locations for NP_001014009.1

      Status: PROVISIONAL

      Source sequence(s)
      BC088426
      UniProtKB/Swiss-Prot
      D4A5J9, D4A672, Q5I0E6
      UniProtKB/TrEMBL
      A0A8I5ZL24, A0A8I5ZQT7, A6KPI3
      Related
      ENSRNOP00000080489.1, ENSRNOT00000106624.2
      Conserved Domains (2) summary
      pfam04181
      Location:81 → 152
      RPAP2_Rtr1; Rtr1/RPAP2 family
      pfam15035
      Location:35 → 99
      Rootletin; Ciliary rootlet component, centrosome cohesion

    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_086032.1 Reference GRCr8

      Range
      2253966..2332251 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_063273014.1 → XP_063129084.1  RNA polymerase II subunit B1 CTD phosphatase Rpap2 isoform X3

      UniProtKB/TrEMBL
      A0A8I6AFB1
      Related
      ENSRNOP00000106193.1, ENSRNOT00000135453.1

    2. XM_008769929.4 → XP_008768151.1  RNA polymerase II subunit B1 CTD phosphatase Rpap2 isoform X2

      UniProtKB/TrEMBL
      A0A8I5ZQT7
      Conserved Domains (2) summary
      pfam04181
      Location:89 → 160
      RPAP2_Rtr1; Rtr1/RPAP2 family
      pfam15035
      Location:43 → 107
      Rootletin; Ciliary rootlet component, centrosome cohesion

    3. XM_006250548.5 → XP_006250610.2  RNA polymerase II subunit B1 CTD phosphatase Rpap2 isoform X1

      See identical proteins and their annotated locations for XP_006250610.2

      UniProtKB/TrEMBL
      A0A8I5ZL24, A0A8I5ZQT7, A0A8L2PZW5
      Related
      ENSRNOP00000002815.6, ENSRNOT00000002815.9
      Conserved Domains (2) summary
      pfam04181
      Location:89 → 160
      RPAP2_Rtr1; Rtr1/RPAP2 family
      pfam15035
      Location:43 → 107
      Rootletin; Ciliary rootlet component, centrosome cohesion

    4. XM_063273017.1 → XP_063129087.1  RNA polymerase II subunit B1 CTD phosphatase Rpap2 isoform X6

    5. XM_008769928.4 → XP_008768150.1  RNA polymerase II subunit B1 CTD phosphatase Rpap2 isoform X1

      See identical proteins and their annotated locations for XP_008768150.1

      UniProtKB/TrEMBL
      A0A8I5ZL24, A0A8I5ZQT7, A0A8L2PZW5
      Conserved Domains (2) summary
      pfam04181
      Location:89 → 160
      RPAP2_Rtr1; Rtr1/RPAP2 family
      pfam15035
      Location:43 → 107
      Rootletin; Ciliary rootlet component, centrosome cohesion

    6. XM_063273016.1 → XP_063129086.1  RNA polymerase II subunit B1 CTD phosphatase Rpap2 isoform X5

      Related
      ENSRNOP00000081066.1, ENSRNOT00000119617.2

    7. XM_063273015.1 → XP_063129085.1  RNA polymerase II subunit B1 CTD phosphatase Rpap2 isoform X4

    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q5I0E6.1 GenPept UniProtKB/Swiss-Prot:Q5I0E6

    Gene LinkOut

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