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

Summary

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: mouse all
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Genomic context

Location:: 18q12.2

Exon count:: 10

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	18	NC_000018.10 (35989824..36067559, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	18	NC_060942.1 (36181320..36259091, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	18	NC_000018.9 (33569787..33647522, complement)

Chromosome 18 - NC_000018.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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.
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.
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.
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.
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.
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.

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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 EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH80213 (e-PCR)
- UniSTS:90411

P15RS_1703 (e-PCR)
- UniSTS:277549

RH99173 (e-PCR)
- UniSTS:93053

SGC38081 (e-PCR)
- UniSTS:67455

WIAF-1571 (e-PCR)
- UniSTS:42404

RH47092 (e-PCR)
- UniSTS:79096

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 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)

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
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
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
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