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RPRD1A regulation of nuclear pre-mRNA domain containing 1A [ Homo sapiens (human) ]

Gene ID: 55197, updated on 3-Nov-2024

Summary

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Official Symbol
RPRD1Aprovided by HGNC
Official Full Name
regulation of nuclear pre-mRNA domain containing 1Aprovided by HGNC
Primary source
HGNC:HGNC:25560
See related
Ensembl:ENSG00000141425 MIM:610347; AllianceGenome:HGNC:25560
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
P15RS; HsT3101
Summary
This gene encodes a cell-cycle and transcription regulatory protein. The encoded protein interacts with the cell cycle inhibitor cyclin-dependent kinase 4 inhibitor B and may function as a negative regulator of G(1)/S phase progression. This protein also forms homo- and hetrodimers with the protein, regulation of nuclear pre-mRNA domain-containing protein 1B, to form a scaffold that interacts with the C-terminal domain of RNA polymerase II subunit B1 and regulates several aspects of transcription. Alternate splicing results in multiple transcript variants. A pseudogene of this gene is found on chromosome 16. [provided by RefSeq, Dec 2014]
Expression
Ubiquitous expression in brain (RPKM 13.6), adrenal (RPKM 9.9) and 25 other tissues See more
Orthologs
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Genomic context

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See RPRD1A in Genome Data Viewer
Location:
18q12.2
Exon count:
10
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 18 NC_000018.10 (35989824..36067559, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 18 NC_060942.1 (36181320..36259091, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 18 NC_000018.9 (33569787..33647522, complement)

Chromosome 18 - NC_000018.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105372066 Neighboring gene Sharpr-MPRA regulatory region 2053 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:33552432-33553324 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr18:33564018-33565217 Neighboring gene chromosome 18 open reading frame 21 Neighboring gene Sharpr-MPRA regulatory region 15530 Neighboring gene H3K27ac hESC enhancer GRCh37_chr18:33647245-33647760 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:33664612-33665166 Neighboring gene H3K27ac hESC enhancer GRCh37_chr18:33666275-33666828 Neighboring gene ReSE screen-validated silencer GRCh37_chr18:33678780-33678940 Neighboring gene solute carrier family 39 member 6 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:33709101-33709606 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:33709607-33710112 Neighboring gene elongator acetyltransferase complex subunit 2 Neighboring gene MPRA-validated peak3116 silencer Neighboring gene cell fate and sterol metabolism associated divergent transcript of MOCOS

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. Identification and characterization of P15RS, a novel P15(INK4b) related gene on G1/S progression. Liu J, et al. Biochem Biophys Res Commun, 2002 Dec 20. PMID 12470661
  2. Cellular and molecular evidence for malignancy-inhibitory functions of p15RS. Zhang X, et al. Cell Cycle, 2012 May 15. PMID 22580456
  3. p15RS attenuates Wnt/{beta}-catenin signaling by disrupting {beta}-catenin·TCF4 Interaction. Wu Y, et al. J Biol Chem, 2010 Nov 5. PMID 20739273, Free PMC Article
  4. MiR-454-3p-Mediated Wnt/β-catenin Signaling Antagonists Suppression Promotes Breast Cancer Metastasis. Ren L, et al. Theranostics, 2019. PMID 30809286, Free PMC Article
  5. p15RS/RPRD1A (p15INK4b-related sequence/regulation of nuclear pre-mRNA domain-containing protein 1A) interacts with HDAC2 in inhibition of the Wnt/β-catenin signaling pathway. Liu C, et al. J Biol Chem, 2015 Apr 10. PMID 25697359, Free PMC Article

See all (53) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. RPRD1A stabilizes NRF2 and aggravates HCC progression through competing with p62 for TRIM21 binding.
    Title: RPRD1A stabilizes NRF2 and aggravates HCC progression through competing with p62 for TRIM21 binding.
  2. The Wnt/beta-catenin signaling antagonist RPRD1A was downregulated and its upstream regulator miR-454-3p was amplified and overexpressed in metastatic breast cancer, and both were correlated with overall and relapse-free survival in breast cancer patients.
    Title: MiR-454-3p-Mediated Wnt/β-catenin Signaling Antagonists Suppression Promotes Breast Cancer Metastasis.
  3. Data suggest that p15RS (p15INK4b-related sequence) acts as an intrinsic transcriptional repressor for Wnt/beta-catenin-mediated gene transcription through recruiting HDAC2 histone deacetylase.
    Title: p15RS/RPRD1A (p15INK4b-related sequence/regulation of nuclear pre-mRNA domain-containing protein 1A) interacts with HDAC2 in inhibition of the Wnt/β-catenin signaling pathway.
  4. RPRD1A and RPRD1B associate directly with RPAP2 phosphatase and coordinate the dephosphorylation of RNAPII phospho-S5 by RPAP2.
    Title: RPRD1A and RPRD1B are human RNA polymerase II C-terminal domain scaffolds for Ser5 dephosphorylation.
  5. The p15RS expression specifically downregulates the expression of cathepsin B and MMP-9 at RNA levels, which are known to promote cell invasion through degrading extracellular matrix proteins.
    Title: Cellular and molecular evidence for malignancy-inhibitory functions of p15RS.
  6. p15RS inhibits Wnt signaling by interrupting beta-catenin.TCF4 complex formation and that Wnt signaling initiates downstream gene expression by removing p15RS from promoters.
    Title: p15RS attenuates Wnt/{beta}-catenin signaling by disrupting {beta}-catenin·TCF4 Interaction.
  7. molecular cloning and characterization of P15RS, a novel P15(INK4b) related gene involved in G1/S progression
    Title: Identification and characterization of P15RS, a novel P15(INK4b) related gene on G1/S progression.
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
Genome wide analysis of drug-induced torsades de pointes: lack of common variants with large effect sizes.
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

  • FLJ10656, MGC19513

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
  
enables identical protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in RNA polymerase II promoter clearance IMP
Inferred from Mutant Phenotype
more info
 PubMed 
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
  
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
regulation of nuclear pre-mRNA domain-containing protein 1A
Names
CDKN2B-related protein
Cyclin-dependent kinase inhibitor 2B-related protein (p15INK4B-related protein)
cyclin-dependent kinase 2B-inhibitor-related protein
p15INK4B-related protein

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_001303411.2 → NP_001290340.1  regulation of nuclear pre-mRNA domain-containing protein 1A isoform 2

    See identical proteins and their annotated locations for NP_001290340.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses an alternate exon in the 5' UTR and 5' coding region which results in the use of an alternate start codon compare to variant 1. The encoded isoform (2) is shorter and has a distinct N-terminus compared to isoform 1.
    Source sequence(s)
    AC091060, AF419845, AK292907, BC000225, DB444937
    Consensus CDS
    CCDS77178.1
    UniProtKB/Swiss-Prot
    Q96P16
    Related
    ENSP00000465444.1, ENST00000588737.5
    Conserved Domains (2) summary
    pfam04818
    Location:20 → 81
    CTD_bind; RNA polymerase II-binding domain
    pfam16566
    Location:129 → 273
    CREPT; Cell-cycle alteration and expression-elevated protein in tumor

  2. NM_001303412.2 → NP_001290341.1  regulation of nuclear pre-mRNA domain-containing protein 1A isoform 2

    See identical proteins and their annotated locations for NP_001290341.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) uses an alternate exon in the 5' UTR and 5' coding region uses an alternate splice site in the 3' UTR. These differences result in the use of an alternate start codon compared to variant 1. The encoded isoform (2) is shorter and has a distinct N_terminus compared to isoform 1. Variant 2 and 3 encode the same isoform (2).
    Source sequence(s)
    BC000225, BG325568, DB444937
    Consensus CDS
    CCDS77178.1
    UniProtKB/Swiss-Prot
    Q96P16
    Related
    ENSP00000467991.1, ENST00000590898.5
    Conserved Domains (2) summary
    pfam04818
    Location:20 → 81
    CTD_bind; RNA polymerase II-binding domain
    pfam16566
    Location:129 → 273
    CREPT; Cell-cycle alteration and expression-elevated protein in tumor

  3. NM_001303413.2 → NP_001290342.1  regulation of nuclear pre-mRNA domain-containing protein 1A isoform 3

    See identical proteins and their annotated locations for NP_001290342.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) uses an alternate 3' terminal exon compared to variant 1. The encoded isoform (3) is shorter and has a distinct C-terminus compared to isoform 1.
    Source sequence(s)
    AC091060, BC010136, CA944610, DB444937
    UniProtKB/TrEMBL
    A0A0C4DGQ6
    Related
    ENSP00000468209.1, ENST00000589050.1
    Conserved Domains (2) summary
    cd17011
    Location:4 → 131
    CID_RPRD1A; CID (CTD-Interacting Domain) of Regulation of nuclear pre-mRNA domain-containing protein 1A
    pfam16566
    Location:165 → 263
    CREPT; Cell-cycle alteration and expression-elevated protein in tumor

  4. NM_018170.5 → NP_060640.2  regulation of nuclear pre-mRNA domain-containing protein 1A isoform 1

    See identical proteins and their annotated locations for NP_060640.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
    Source sequence(s)
    AF419845, AK001518, AW409855, BC000225
    Consensus CDS
    CCDS11917.1
    UniProtKB/Swiss-Prot
    A8KA42, B2RBA3, Q7Z5G8, Q96FY9, Q96P16, Q9NVL4
    Related
    ENSP00000381984.3, ENST00000399022.9
    Conserved Domains (2) summary
    cd17011
    Location:4 → 131
    CID_RPRD1A; CID (CTD-Interacting Domain) of Regulation of nuclear pre-mRNA domain-containing protein 1A
    pfam16566
    Location:165 → 310
    CREPT; Cell-cycle alteration and expression-elevated protein in tumor

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_000018.10 Reference GRCh38.p14 Primary Assembly

    Range
    35989824..36067559 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060942.1 Alternate T2T-CHM13v2.0

    Range
    36181320..36259091 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q96P16.1 GenPept UniProtKB/Swiss-Prot:Q96P16

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