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

Gene ID: 55197, updated on 21-Dec-2019

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
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

Genomic context

See RPRD1A in Genome Data Viewer
Location:
18q12.2
Exon count:
13
Annotation release Status Assembly Chr Location
109.20191205 current GRCh38.p13 (GCF_000001405.39) 18 NC_000018.10 (35982385..36067594, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 18 NC_000018.9 (33569787..33647538, complement)

Chromosome 18 - NC_000018.10Genomic Context describing neighboring genes Neighboring gene microRNA 3929 Neighboring gene uncharacterized LOC105372066 Neighboring gene Sharpr-MPRA regulatory region 2053 Neighboring gene chromosome 18 open reading frame 21 Neighboring gene solute carrier family 39 member 6 Neighboring gene elongator acetyltransferase complex subunit 2 Neighboring gene uncharacterized LOC101927809

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

NHGRI GWAS Catalog

Description
Genome wide analysis of drug-induced torsades de pointes: lack of common variants with large effect sizes.
NHGRI GWA Catalog

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ10656, MGC19513

Gene Ontology Provided by GOA

Function Evidence Code Pubs
RNA polymerase II complex binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
dephosphorylation of RNA polymerase II C-terminal domain IMP
Inferred from Mutant Phenotype
more info
PubMed 
mRNA 3'-end processing IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
snRNA transcription by RNA polymerase II TAS
Traceable Author Statement
more info
 
Component Evidence Code Pubs
RNA polymerase II, holoenzyme IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
RNA polymerase II, holoenzyme IDA
Inferred from Direct Assay
more info
PubMed 
nucleoplasm TAS
Traceable Author Statement
more info
 

General protein information

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)

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_001303411.2NP_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:2081
    CTD_bind; RNA polymerase II-binding domain
    pfam16566
    Location:129273
    CREPT; Cell-cycle alteration and expression-elevated protein in tumor
  2. NM_001303412.2NP_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:2081
    CTD_bind; RNA polymerase II-binding domain
    pfam16566
    Location:129273
    CREPT; Cell-cycle alteration and expression-elevated protein in tumor
  3. NM_001303413.1NP_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/Swiss-Prot
    Q96P16
    UniProtKB/TrEMBL
    A0A0C4DGQ6
    Related
    ENSP00000468209.1, ENST00000589050.1
    Conserved Domains (2) summary
    smart00582
    Location:8129
    RPR; domain present in proteins, which are involved in regulation of nuclear pre-mRNA
    pfam16566
    Location:165263
    CREPT; Cell-cycle alteration and expression-elevated protein in tumor
  4. NM_018170.5NP_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
    Q96P16
    UniProtKB/TrEMBL
    A0A024RC37
    Related
    ENSP00000381984.3, ENST00000399022.9
    Conserved Domains (2) summary
    pfam16566
    Location:165309
    CREPT; Cell-cycle alteration and expression-elevated protein in tumor
    cd17011
    Location:4131
    CID_RPRD1A; CID (CTD-Interacting Domain) of Regulation of nuclear pre-mRNA domain-containing protein 1A

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20191205

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000018.10 Reference GRCh38.p13 Primary Assembly

    Range
    35982385..36067594 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011526049.1XP_011524351.1  regulation of nuclear pre-mRNA domain-containing protein 1A isoform X2

    See identical proteins and their annotated locations for XP_011524351.1

    UniProtKB/Swiss-Prot
    Q96P16
    Conserved Domains (2) summary
    pfam04818
    Location:2081
    CTD_bind; RNA polymerase II-binding domain
    pfam16566
    Location:129273
    CREPT; Cell-cycle alteration and expression-elevated protein in tumor
  2. XM_011526048.2XP_011524350.1  regulation of nuclear pre-mRNA domain-containing protein 1A isoform X1

    See identical proteins and their annotated locations for XP_011524350.1

    UniProtKB/Swiss-Prot
    Q96P16
    UniProtKB/TrEMBL
    A0A024RC37
    Related
    ENSP00000349955.4, ENST00000357384.8
    Conserved Domains (2) summary
    pfam16566
    Location:165309
    CREPT; Cell-cycle alteration and expression-elevated protein in tumor
    cd17011
    Location:4131
    CID_RPRD1A; CID (CTD-Interacting Domain) of Regulation of nuclear pre-mRNA domain-containing protein 1A
  3. XM_011526050.1XP_011524352.1  regulation of nuclear pre-mRNA domain-containing protein 1A isoform X2

    See identical proteins and their annotated locations for XP_011524352.1

    UniProtKB/Swiss-Prot
    Q96P16
    Conserved Domains (2) summary
    pfam04818
    Location:2081
    CTD_bind; RNA polymerase II-binding domain
    pfam16566
    Location:129273
    CREPT; Cell-cycle alteration and expression-elevated protein in tumor
  4. XM_017025808.2XP_016881297.1  regulation of nuclear pre-mRNA domain-containing protein 1A isoform X3

RNA

  1. XR_001753208.2 RNA Sequence

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