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

    Gene ID: 79871, updated on 10-Dec-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 PERK-mediated unfolded protein response and snRNA transcription. Located in cytosol and nucleolus. Part of transcription preinitiation complex. [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Ubiquitous expression in thyroid (RPKM 2.5), endometrium (RPKM 2.0) and 25 other tissues See more
    Orthologs
    mouse all
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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_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (92299059..92402056)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (92143968..92246943)
    RS_2024_09 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 (62) 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)

    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 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 IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    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 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 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 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_2024_08

    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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