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RPAP2 RNA polymerase II associated protein 2 [ Homo sapiens (human) ]

Gene ID: 79871, updated on 5-Mar-2024

Summary

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Official Symbol
RPAP2provided by HGNC
Official Full Name
RNA polymerase II associated protein 2provided by HGNC
Primary source
HGNC:HGNC:25791
See related
Ensembl:ENSG00000122484 MIM:611476; AllianceGenome:HGNC:25791
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
Rtr1; C1orf82
Summary
Enables RNA polymerase II CTD heptapeptide repeat phosphatase activity. Involved in dephosphorylation of RNA polymerase II C-terminal domain and snRNA transcription. Located in cytosol and nucleolus. Part of RNA polymerase II, holoenzyme. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in thyroid (RPKM 2.5), endometrium (RPKM 2.0) and 25 other tissues See more
Orthologs
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Genomic context

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See RPAP2 in Genome Data Viewer
Location:
1p22.1
Exon count:
16
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (92299059..92402056)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (92143968..92246943)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (92764616..92867613)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene zinc finger protein 510 pseudogene Neighboring gene chromosome 1 open reading frame 146 Neighboring gene ACTB pseudogene 12 Neighboring gene MPRA-validated peak316 silencer Neighboring gene glomulin, FKBP associated protein Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:92763642-92764538 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1312 Neighboring gene Sharpr-MPRA regulatory region 6980 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1313 Neighboring gene RNA, 7SL, cytoplasmic 824, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1314 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1070 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:92948665-92949264 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:92949865-92950465 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:92951066-92951666 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1074 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1075 Neighboring gene growth factor independent 1 transcriptional repressor

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. The yeast regulator of transcription protein Rtr1 lacks an active site and phosphatase activity. Xiang K, et al. Nat Commun, 2012 Jul 10. PMID 22781759, Free PMC Article
  2. Human RNA polymerase II-associated protein 2 (RPAP2) interacts directly with the RNA polymerase II subunit Rpb6 and participates in pre-mRNA 3'-end formation. Wani S, et al. Drug Discov Ther, 2014 Dec. PMID 25639305
  3. 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
  4. Modulation of the Pol II CTD Phosphorylation Code by Rac1 and Cdc42 Small GTPases in Cultured Human Cancer Cells and Its Implication for Developing a Synthetic-Lethal Cancer Therapy. Zhang B, et al. Cells, 2020 Mar 4. PMID 32143485, Free PMC Article
  5. Phosphorylation-dependent PIH1D1 interactions define substrate specificity of the R2TP cochaperone complex. Hořejší Z, et al. Cell Rep, 2014 Apr 10. PMID 24656813, Free PMC Article

See all (55) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Modulation of the Pol II CTD Phosphorylation Code by Rac1 and Cdc42 Small GTPases in Cultured Human Cancer Cells and Its Implication for Developing a Synthetic-Lethal Cancer Therapy.
    Title: Modulation of the Pol II CTD Phosphorylation Code by Rac1 and Cdc42 Small GTPases in Cultured Human Cancer Cells and Its Implication for Developing a Synthetic-Lethal Cancer Therapy.
  2. Coordination between two branches of the unfolded protein response determines apoptotic cell fate so that PERK attenuates IRE1 via RPAP2 to abort failed endoplasmic reticulum stress adaptation and trigger apoptosis.
    Title: Coordination between Two Branches of the Unfolded Protein Response Determines Apoptotic Cell Fate.
  3. These results suggest that RPAP2 controls Pol II activity through a direct interaction with Rpb6
    Title: Human RNA polymerase II-associated protein 2 (RPAP2) interacts directly with the RNA polymerase II subunit Rpb6 and participates in pre-mRNA 3'-end formation.
  4. During transcription of snRNA genes, Ser7 phosphorylation facilitates recruitment of RPAP2, which in turn both recruits Integrator and dephosphorylates Ser5.
    Title: Ser7 phosphorylation of the CTD recruits the RPAP2 Ser5 phosphatase to snRNA genes.
Submit: New GeneRIF Correction

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ13150

Gene Ontology Provided by GOA

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 IMP
Inferred from Mutant Phenotype
more info
 PubMed 
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 binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein serine/threonine phosphatase activity IDA
Inferred from Direct Assay
more info
 PubMed 
Process Evidence Code Pubs
involved_in PERK-mediated unfolded protein response IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in regulation of transcription by RNA polymerase II IEA
Inferred from Electronic Annotation
more info
  
involved_in snRNA transcription IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
is_active_in cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in cytoplasm IDA
Inferred from Direct Assay
more info
 PubMed 
located_in cytosol IDA
Inferred from Direct Assay
more info
  
located_in nucleolus IDA
Inferred from Direct Assay
more info
  
located_in nucleoplasm TAS
Traceable Author Statement
more info
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in nucleus IDA
Inferred from Direct Assay
more info
 PubMed 
part_of transcription preinitiation complex IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
putative RNA polymerase II subunit B1 CTD phosphatase RPAP2
NP_079089.2
XP_011540469.1
XP_016857852.1
XP_016857853.1
XP_047286776.1
XP_054194773.1
XP_054194774.1
XP_054194775.1
XP_054194776.1

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_024813.3 → NP_079089.2  putative RNA polymerase II subunit B1 CTD phosphatase RPAP2

    See identical proteins and their annotated locations for NP_079089.2

    Status: VALIDATED

    Source sequence(s)
    AC104456, AI612918, AL451010, BC039014
    Consensus CDS
    CCDS740.1
    UniProtKB/Swiss-Prot
    C9JKB5, Q49AS7, Q8IXW5, Q9H8Y2
    Related
    ENSP00000476948.1, ENST00000610020.2
    Conserved Domains (1) summary
    pfam04181
    Location:80 → 152
    RPAP2_Rtr1; Rtr1/RPAP2 family

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    92299059..92402056
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047430820.1 → XP_047286776.1  putative RNA polymerase II subunit B1 CTD phosphatase RPAP2 isoform X1

  2. XM_017002363.3 → XP_016857852.1  putative RNA polymerase II subunit B1 CTD phosphatase RPAP2 isoform X2

  3. XM_011542167.4 → XP_011540469.1  putative RNA polymerase II subunit B1 CTD phosphatase RPAP2 isoform X3

    Conserved Domains (1) summary
    pfam04181
    Location:80 → 152
    RPAP2_Rtr1; Rtr1/RPAP2 family

  4. XM_017002364.3 → XP_016857853.1  putative RNA polymerase II subunit B1 CTD phosphatase RPAP2 isoform X4

    Conserved Domains (1) summary
    pfam04181
    Location:80 → 152
    RPAP2_Rtr1; Rtr1/RPAP2 family

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    92143968..92246943
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054338798.1 → XP_054194773.1  putative RNA polymerase II subunit B1 CTD phosphatase RPAP2 isoform X1

  2. XM_054338799.1 → XP_054194774.1  putative RNA polymerase II subunit B1 CTD phosphatase RPAP2 isoform X2

  3. XM_054338800.1 → XP_054194775.1  putative RNA polymerase II subunit B1 CTD phosphatase RPAP2 isoform X3

  4. XM_054338801.1 → XP_054194776.1  putative RNA polymerase II subunit B1 CTD phosphatase RPAP2 isoform X4

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q8IXW5.1 GenPept UniProtKB/Swiss-Prot:Q8IXW5

Gene LinkOut

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