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

    Gene ID: 55197, updated on 9-Dec-2024

    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
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    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

    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

    EBI GWAS Catalog

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

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    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

    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)

    NEW Try the new Transcript table

    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_001303413.2NP_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:4131
      CID_RPRD1A; CID (CTD-Interacting Domain) of Regulation of nuclear pre-mRNA domain-containing protein 1A
      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
      A8KA42, B2RBA3, Q7Z5G8, Q96FY9, Q96P16, Q9NVL4
      Related
      ENSP00000381984.3, ENST00000399022.9
      Conserved Domains (2) summary
      cd17011
      Location:4131
      CID_RPRD1A; CID (CTD-Interacting Domain) of Regulation of nuclear pre-mRNA domain-containing protein 1A
      pfam16566
      Location:165310
      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)