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    RPRD2 regulation of nuclear pre-mRNA domain containing 2 [ Homo sapiens (human) ]

    Gene ID: 23248, updated on 28-Oct-2024

    Summary

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    Official Symbol
    RPRD2provided by HGNC
    Official Full Name
    regulation of nuclear pre-mRNA domain containing 2provided by HGNC
    Primary source
    HGNC:HGNC:29039
    See related
    Ensembl:ENSG00000163125 MIM:614695; AllianceGenome:HGNC:29039
    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
    HSPC099; KIAA0460
    Summary
    Predicted to enable RNA polymerase II complex binding activity. Predicted to be involved in mRNA 3'-end processing. Part of transcription preinitiation complex. [provided by Alliance of Genome Resources, Oct 2024]
    Expression
    Ubiquitous expression in thyroid (RPKM 11.1), ovary (RPKM 10.9) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See RPRD2 in Genome Data Viewer
    Location:
    1q21.2
    Exon count:
    13
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (150364147..150476566)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (149489227..149601428)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (150336623..150449042)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1681 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:150269465-150270023 Neighboring gene mitochondrial ribosomal protein S21 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:150293095-150293660 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1682 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1683 Neighboring gene pre-mRNA processing factor 3 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:150334918-150335860 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1685 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1686 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1687 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:150383836-150384059 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:150444960-150445472 Neighboring gene uncharacterized LOC124904416 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:150459720-150460226 Neighboring gene microRNA 6878 Neighboring gene threonyl-tRNA synthetase 2, mitochondrial

    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. HIV-1 Accessory Protein Vpr Interacts with REAF/RPRD2 To Mitigate Its Antiviral Activity. Gibbons JM, et al. J Virol, 2020 Jan 31. PMID 31776272, Free PMC Article
    2. 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
    3. Identification of UHRF1/2 as new N-methylpurine DNA glycosylase-interacting proteins. Liang C, et al. Biochem Biophys Res Commun, 2013 Apr 19. PMID 23537643
    4. Intrinsic BET inhibitor resistance in SPOP-mutated prostate cancer is mediated by BET protein stabilization and AKT-mTORC1 activation. Zhang P, et al. Nat Med, 2017 Sep. PMID 28805822, Free PMC Article
    5. Characterization of cDNA clones in size-fractionated cDNA libraries from human brain. Seki N, et al. DNA Res, 1997 Oct 31. PMID 9455484

    See all (83) citations in PubMed

    GeneRIFs: Gene References Into Functions

    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

    HIV-1 interactions

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    Replication interactions

    Interaction Pubs
    Knockdown of regulation of nuclear pre-mRNA domain containing 2 (RPRD2 ) by siRNA enhances the early stages of HIV-1 replication in HeLa-CD4 cells infected with viral pseudotypes HIV89.6R and HIV8.2N PubMed

    Protein interactions

    Protein Gene Interaction Pubs
    Envelope transmembrane glycoprotein gp41 env A synthetic peptide corresponding to the immunosuppressive domain (amino acids 574-592) of HIV-1 gp41 upregulates the expression of regulation of nuclear pre-mRNA domain containing 2 (RPRD2; KIAA0460) in peptide-treated PBMCs PubMed

    Go to the HIV-1, Human Interaction Database

    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

    • FLJ32145, KIAA0460

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables RNA polymerase II C-terminal domain binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables RNA polymerase II complex binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Process Evidence Code Pubs
    involved_in mRNA 3'-end processing IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
    		  
    part_of transcription preinitiation complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    regulation of nuclear pre-mRNA domain-containing protein 2

    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_001297673.2 → NP_001284602.1  regulation of nuclear pre-mRNA domain-containing protein 2 isoform 2

      See identical proteins and their annotated locations for NP_001284602.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks an alternate in-frame exon in the 5' coding region and lacks an alternate segment in 3' coding region, which results in a frameshift, compared to variant 1. The encoded isoform (2) has a distinct C-terminus and is shorter than isoform 1.
      Source sequence(s)
      AA749025, AK304380, AL356356, BX284695, BX641025, HY021241
      UniProtKB/Swiss-Prot
      Q5VT52
      Conserved Domains (1) summary
      smart00582
      Location:27 → 145
      RPR; domain present in proteins, which are involved in regulation of nuclear pre-mRNA

    2. NM_001297674.2 → NP_001284603.1  regulation of nuclear pre-mRNA domain-containing protein 2 isoform 3

      See identical proteins and their annotated locations for NP_001284603.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) lacks an alternate in-frame exon in the 5' coding region, compared to variant 1. The encoded isoform (3) is shorter than isoform 1.
      Source sequence(s)
      AA749025, AL356356, BC045623, BX641025, HY021241
      Consensus CDS
      CCDS72907.1
      UniProtKB/Swiss-Prot
      Q5VT52
      Related
      ENSP00000383785.4, ENST00000401000.8
      Conserved Domains (1) summary
      smart00582
      Location:27 → 145
      RPR; domain present in proteins, which are involved in regulation of nuclear pre-mRNA

    3. NM_001387114.1 → NP_001374043.1  regulation of nuclear pre-mRNA domain-containing protein 2 isoform 4

      Status: VALIDATED

      Source sequence(s)
      AL356356, AL611942, BX284695
      Conserved Domains (3) summary
      pfam05109
      Location:293 → 573
      Herpes_BLLF1; Herpes virus major outer envelope glycoprotein (BLLF1)
      cd17001
      Location:27 → 145
      CID_RPRD2; CID (CTD-Interacting Domain) of Regulation of nuclear pre-mRNA domain-containing protein 2
      NF033930
      Location:96 → 378
      pneumo_PspA; pneumococcal surface protein A

    4. NM_001387115.1 → NP_001374044.1  regulation of nuclear pre-mRNA domain-containing protein 2 isoform 5

      Status: VALIDATED

      Source sequence(s)
      AL356356, AL611942, BX284695
      Conserved Domains (3) summary
      PHA03247
      Location:288 → 561
      PHA03247; large tegument protein UL36; Provisional
      PRK03918
      Location:98 → 292
      PRK03918; DNA double-strand break repair ATPase Rad50
      cd17001
      Location:27 → 145
      CID_RPRD2; CID (CTD-Interacting Domain) of Regulation of nuclear pre-mRNA domain-containing protein 2

    5. NM_001387116.1 → NP_001374045.1  regulation of nuclear pre-mRNA domain-containing protein 2 isoform 6

      Status: VALIDATED

      Source sequence(s)
      AL356356, AL611942, BX284695
      Conserved Domains (3) summary
      PHA03247
      Location:314 → 587
      PHA03247; large tegument protein UL36; Provisional
      PRK03918
      Location:142 → 318
      PRK03918; DNA double-strand break repair ATPase Rad50
      cd17001
      Location:27 → 146
      CID_RPRD2; CID (CTD-Interacting Domain) of Regulation of nuclear pre-mRNA domain-containing protein 2

    6. NM_001387117.1 → NP_001374046.1  regulation of nuclear pre-mRNA domain-containing protein 2 isoform 7

      Status: VALIDATED

      Source sequence(s)
      AL356356, AL611942, BX284695
      Conserved Domains (3) summary
      PRK03918
      Location:142 → 318
      PRK03918; DNA double-strand break repair ATPase Rad50
      pfam05109
      Location:319 → 636
      Herpes_BLLF1; Herpes virus major outer envelope glycoprotein (BLLF1)
      cd17001
      Location:27 → 146
      CID_RPRD2; CID (CTD-Interacting Domain) of Regulation of nuclear pre-mRNA domain-containing protein 2

    7. NM_001387118.1 → NP_001374047.1  regulation of nuclear pre-mRNA domain-containing protein 2 isoform 8

      Status: VALIDATED

      Source sequence(s)
      AL356356, AL611942, BX284695
      Conserved Domains (3) summary
      PRK03918
      Location:98 → 292
      PRK03918; DNA double-strand break repair ATPase Rad50
      pfam05109
      Location:293 → 610
      Herpes_BLLF1; Herpes virus major outer envelope glycoprotein (BLLF1)
      cd17001
      Location:27 → 145
      CID_RPRD2; CID (CTD-Interacting Domain) of Regulation of nuclear pre-mRNA domain-containing protein 2

    8. NM_001387119.1 → NP_001374048.1  regulation of nuclear pre-mRNA domain-containing protein 2 isoform 9

      Status: VALIDATED

      Source sequence(s)
      AL356356, AL611942, BX284695
      Conserved Domains (3) summary
      PRK03918
      Location:142 → 318
      PRK03918; DNA double-strand break repair ATPase Rad50
      pfam05109
      Location:319 → 636
      Herpes_BLLF1; Herpes virus major outer envelope glycoprotein (BLLF1)
      cd17001
      Location:27 → 146
      CID_RPRD2; CID (CTD-Interacting Domain) of Regulation of nuclear pre-mRNA domain-containing protein 2

    9. NM_001387120.1 → NP_001374049.1  regulation of nuclear pre-mRNA domain-containing protein 2 isoform 10

      Status: VALIDATED

      Source sequence(s)
      AL356356, AL611942, BX284695
      Conserved Domains (3) summary
      PHA03247
      Location:314 → 587
      PHA03247; large tegument protein UL36; Provisional
      PRK03918
      Location:142 → 318
      PRK03918; DNA double-strand break repair ATPase Rad50
      cd17001
      Location:27 → 146
      CID_RPRD2; CID (CTD-Interacting Domain) of Regulation of nuclear pre-mRNA domain-containing protein 2

    10. NM_001387121.1 → NP_001374050.1  regulation of nuclear pre-mRNA domain-containing protein 2 isoform 11

      Status: VALIDATED

      Source sequence(s)
      AL356356, AL611942, BX284695
      Conserved Domains (1) summary
      pfam05109
      Location:103 → 420
      Herpes_BLLF1; Herpes virus major outer envelope glycoprotein (BLLF1)

    11. NM_001387122.1 → NP_001374051.1  regulation of nuclear pre-mRNA domain-containing protein 2 isoform 12

      Status: VALIDATED

      Source sequence(s)
      AL356356, AL611942, BX284695
      Conserved Domains (2) summary
      PHA03247
      Location:178 → 451
      PHA03247; large tegument protein UL36; Provisional
      PRK03918
      Location:6 → 182
      PRK03918; DNA double-strand break repair ATPase Rad50

    12. NM_001387123.1 → NP_001374052.1  regulation of nuclear pre-mRNA domain-containing protein 2 isoform 13

      Status: VALIDATED

      Source sequence(s)
      AL356356, AL611942, BX284695
      Conserved Domains (2) summary
      PHA03247
      Location:178 → 451
      PHA03247; large tegument protein UL36; Provisional
      PRK03918
      Location:6 → 182
      PRK03918; DNA double-strand break repair ATPase Rad50

    13. NM_001387124.1 → NP_001374053.1  regulation of nuclear pre-mRNA domain-containing protein 2 isoform 13

      Status: VALIDATED

      Source sequence(s)
      AL356356, AL611942, BX284695
      Conserved Domains (2) summary
      PHA03247
      Location:178 → 451
      PHA03247; large tegument protein UL36; Provisional
      PRK03918
      Location:6 → 182
      PRK03918; DNA double-strand break repair ATPase Rad50

    14. NM_015203.5 → NP_056018.2  regulation of nuclear pre-mRNA domain-containing protein 2 isoform 1

      See identical proteins and their annotated locations for NP_056018.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      AA749025, AK291703, AL356356, BC045623, DB455925, HY021241
      Consensus CDS
      CCDS44216.1
      UniProtKB/Swiss-Prot
      A8K6N8, B3KPT1, B4E2Q6, O75048, Q5VT51, Q5VT52, Q5VT53, Q6MZL4, Q86XD2, Q9P0D7
      Related
      ENSP00000358064.4, ENST00000369068.5
      Conserved Domains (1) summary
      smart00582
      Location:27 → 145
      RPR; domain present in proteins, which are involved in regulation of nuclear pre-mRNA

    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
      150364147..150476566
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047415788.1 → XP_047271744.1  regulation of nuclear pre-mRNA domain-containing protein 2 isoform X2

    2. XM_047415787.1 → XP_047271743.1  regulation of nuclear pre-mRNA domain-containing protein 2 isoform X1

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      149489227..149601428
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054335395.1 → XP_054191370.1  regulation of nuclear pre-mRNA domain-containing protein 2 isoform X2

    2. XM_054335394.1 → XP_054191369.1  regulation of nuclear pre-mRNA domain-containing protein 2 isoform X1

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q5VT52.1 GenPept UniProtKB/Swiss-Prot:Q5VT52

    Gene LinkOut

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

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