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

Gene ID: 23248, updated on 3-Nov-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, Nov 2024]
Expression
Ubiquitous expression in thyroid (RPKM 11.1), ovary (RPKM 10.9) and 25 other tissues See more
Orthologs
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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 (84) citations in PubMed

GeneRIFs: Gene References Into Functions

Phenotypes

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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)

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

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