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

Gene ID: 305120, updated on 27-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
  • 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 MAP kinase serine/threonine phosphatase activity IEA
Inferred from Electronic Annotation
more info
  
enables RNA polymerase II CTD heptapeptide repeat S2 phosphatase activity IEA
Inferred from Electronic Annotation
more info
  
enables RNA polymerase II CTD heptapeptide repeat S5 phosphatase activity IEA
Inferred from Electronic Annotation
more info
  
enables RNA polymerase II CTD heptapeptide repeat S7 phosphatase activity IEA
Inferred from Electronic Annotation
more info
  
enables RNA polymerase II CTD heptapeptide repeat T4 phosphatase activity IEA
Inferred from Electronic Annotation
more info
  
enables RNA polymerase II CTD heptapeptide repeat Y1 phosphatase activity IEA
Inferred from Electronic Annotation
more info
  
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 calmodulin-dependent protein phosphatase activity IEA
Inferred from Electronic Annotation
more info
  
enables histone H2AXS140 phosphatase activity 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 chromatin remodeling IEA
Inferred from Electronic Annotation
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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