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    RPAP3 RNA polymerase II associated protein 3 [ Homo sapiens (human) ]

    Gene ID: 79657, updated on 3-Nov-2024

    Summary

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    Official Symbol
    RPAP3provided by HGNC
    Official Full Name
    RNA polymerase II associated protein 3provided by HGNC
    Primary source
    HGNC:HGNC:26151
    See related
    Ensembl:ENSG00000005175 MIM:611477; AllianceGenome:HGNC:26151
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    Tah1; hSpagh
    Summary
    This gene encodes an RNA polymerase II-associated protein. The encoded protein may function in transcriptional regulation and may also regulate apoptosis. Alternatively spliced transcript variants have been described. [provided by RefSeq, Mar 2009]
    Expression
    Ubiquitous expression in lymph node (RPKM 11.2), appendix (RPKM 8.8) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See RPAP3 in Genome Data Viewer
    Location:
    12q13.11
    Exon count:
    17
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (47661249..47706030, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (47622569..47667355, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (48055032..48099813, complement)

    Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene acireductone dioxygenase 1 pseudogene 3 Neighboring gene STBD1 pseudogene 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:48030175-48030714 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6256 Neighboring gene H3K27ac hESC enhancers GRCh37_chr12:48099027-48099528 and GRCh37_chr12:48099529-48100028 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6258 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6259 Neighboring gene RPAP3 divergent transcript Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4394 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4395 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr12:48131928-48133127 Neighboring gene endonuclease, poly(U) specific Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6260 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6261 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:48146243-48146784 Neighboring gene Sharpr-MPRA regulatory region 8178 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6262 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6263 Neighboring gene Rap guanine nucleotide exchange factor 3 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:48151874-48152542 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:48152543-48153211 Neighboring gene solute carrier family 48 member 1

    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 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. Deep Structural Analysis of RPAP3 and PIH1D1, Two Components of the HSP90 Co-chaperone R2TP Complex. Henri J, et al. Structure, 2018 Sep 4. PMID 30033218
    2. RPAP3 enhances cytotoxicity of doxorubicin by impairing NF-kappa B pathway. Shimada K, et al. Biochem Biophys Res Commun, 2011 Jan 28. PMID 21184742
    3. Molecular cloning of novel Monad binding protein containing tetratricopeptide repeat domains. Itsuki Y, et al. FEBS Lett, 2008 Jul 9. PMID 18538670
    4. RPAP3 splicing variant isoform 1 interacts with PIH1D1 to compose R2TP complex for cell survival. Yoshida M, et al. Biochem Biophys Res Commun, 2013 Jan 4. PMID 23159623
    5. HSP90 and its R2TP/Prefoldin-like cochaperone are involved in the cytoplasmic assembly of RNA polymerase II. Boulon S, et al. Mol Cell, 2010 Sep 24. PMID 20864038, Free PMC Article

    See all (112) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Results show the TPR2 domain in RPAP3 is responsible for the recruitment of HSP90, its N-terminal domain participates to the positive regulation of HSP90.
      Title: Deep Structural Analysis of RPAP3 and PIH1D1, Two Components of the HSP90 Co-chaperone R2TP Complex.
    2. RPAP3 provides a flexible scaffold for coupling HSP90 to the human R2TP co-chaperone complex.
      Title: RPAP3 provides a flexible scaffold for coupling HSP90 to the human R2TP co-chaperone complex.
    3. this study investigated the interaction between RPAP3 and PIH1D1.
      Title: RPAP3 splicing variant isoform 1 interacts with PIH1D1 to compose R2TP complex for cell survival.
    4. These results indicate that RPAP3 may be a novel modulator of NF-kappaB pathway in apoptosis induced by anti-cancer chemotherapeutic agents.
      Title: RPAP3 enhances cytotoxicity of doxorubicin by impairing NF-kappa B pathway.
    5. Data indicate that RNA polymerase II is built in the cytoplasm and reveal quality-control mechanisms that link HSP90 and its cochaperone hSpagh (RPAP3) to the nuclear import of fully assembled enzymes.
      Title: HSP90 and its R2TP/Prefoldin-like cochaperone are involved in the cytoplasmic assembly of RNA polymerase II.
    6. Is part of an RNA polymerase II-associated complex with possible chaperone activity.
      Title: High-resolution mapping of the protein interaction network for the human transcription machinery and affinity purification of RNA polymerase II-associated complexes.
    7. RPAP3 interacts with Reptin to modulate UV-induced DNA damage by regulating H2AX phosphorylation
      Title: RPAP3 interacts with Reptin to regulate UV-induced phosphorylation of H2AX and DNA damage.
    8. Overexpression of RPAP3 in HEK 293 cells potentiated caspase-3 activation and apoptosis.
      Title: Molecular cloning of novel Monad binding protein containing tetratricopeptide repeat domains.
    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

    EBI GWAS Catalog

    Description
    Meta-analysis of genome-wide association studies identifies novel loci that influence cupping and the glaucomatous process.
    EBI GWAS Catalog

    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

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ21908

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in protein stabilization NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    Component Evidence Code Pubs
    part_of R2TP complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of R2TP complex IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    part_of RPAP3/R2TP/prefoldin-like complex IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    		  
    part_of protein folding chaperone complex IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    RNA polymerase II-associated protein 3

    NCBI Reference Sequences (RefSeq)

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    NEW Try the new Transcript table

    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_001146075.2 → NP_001139547.1  RNA polymerase II-associated protein 3 isoform 2

      See identical proteins and their annotated locations for NP_001139547.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an in-frame exon in the 3' coding region compared to variant 1. The encoded isoform (2) is shorter than isoform 1.
      Source sequence(s)
      AC004241, BC056415, DA096405, N39593
      Consensus CDS
      CCDS53783.1
      UniProtKB/Swiss-Prot
      Q9H6T3
      Related
      ENSP00000370024.4, ENST00000380650.4
      Conserved Domains (3) summary
      sd00006
      Location:133 → 161
      TPR; TPR repeat [structural motif]
      pfam13877
      Location:512 → 599
      RPAP3_C; Potential Monad-binding region of RPAP3
      cl26005
      Location:136 → 267
      PLN03088; SGT1, suppressor of G2 allele of SKP1; Provisional

    2. NM_001146076.2 → NP_001139548.1  RNA polymerase II-associated protein 3 isoform 3

      See identical proteins and their annotated locations for NP_001139548.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR, lacks a segment of the 5' coding region, and uses a downstream start codon compared to variant 1. The encoded isoform (3) has a shorter N-terminus than isoform 1.
      Source sequence(s)
      AC004241, AK299465, BC056415, DA096405, N39593
      Consensus CDS
      CCDS53782.1
      UniProtKB/Swiss-Prot
      Q9H6T3
      Related
      ENSP00000401823.3, ENST00000432584.7
      Conserved Domains (5) summary
      sd00006
      Location:127 → 151
      TPR; TPR repeat [structural motif]
      pfam00515
      Location:43 → 75
      TPR_1; Tetratricopeptide repeat
      pfam13414
      Location:122 → 187
      TPR_11; TPR repeat
      pfam13432
      Location:14 → 75
      TPR_16; Tetratricopeptide repeat
      pfam13877
      Location:387 → 477
      RPAP3_C; Potential Monad-binding region of RPAP3

    3. NM_024604.3 → NP_078880.2  RNA polymerase II-associated protein 3 isoform 1

      See identical proteins and their annotated locations for NP_078880.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      AC004241, AK025561, BC056415, DA096405, N39593
      Consensus CDS
      CCDS8753.1
      UniProtKB/Swiss-Prot
      B4DRW9, Q6PHR5, Q9H6T3
      Related
      ENSP00000005386.3, ENST00000005386.8
      Conserved Domains (3) summary
      PLN03088
      Location:136 → 267
      PLN03088; SGT1, suppressor of G2 allele of SKP1; Provisional
      sd00006
      Location:133 → 161
      TPR; TPR repeat [structural motif]
      pfam13877
      Location:545 → 633
      RPAP3_C; Potential Monad-binding region of RPAP3

    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_000012.12 Reference GRCh38.p14 Primary Assembly

      Range
      47661249..47706030 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060936.1 Alternate T2T-CHM13v2.0

      Range
      47622569..47667355 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9H6T3.2 GenPept UniProtKB/Swiss-Prot:Q9H6T3

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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