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... See more...

Aliases for RPRD1A Gene

Aliases for RPRD1A Gene

  • Regulation Of Nuclear Pre-MRNA Domain Containing 1A 2 3 5
  • P15RS 2 3 4
  • Cyclin-Dependent Kinase Inhibitor 2B-Related Protein (P15INK4B-Related Protein) 2 3
  • Regulation Of Nuclear Pre-MRNA Domain-Containing Protein 1A 3 4
  • Cyclin-Dependent Kinase 2B-Inhibitor-Related Protein 2 3
  • P15INK4B-Related Protein 3 4
  • HsT3101 2 3
  • Cyclin-Dependent Kinase Inhibitor 2B-Related Protein 4
  • CDKN2B-Related Protein 3
  • FLJ10656 2
  • RPRD1A 5

External Ids for RPRD1A Gene

Previous GeneCards Identifiers for RPRD1A Gene

  • GC18M031824
  • GC18M033569
  • GC18M030428

Summaries for RPRD1A Gene

Entrez Gene Summary for RPRD1A Gene

  • 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]

GeneCards Summary for RPRD1A Gene

RPRD1A (Regulation Of Nuclear Pre-MRNA Domain Containing 1A) is a Protein Coding gene. Diseases associated with RPRD1A include Retroperitoneal Leiomyosarcoma and Retroperitoneal Sarcoma. Among its related pathways are Gene Expression and HIV Transcription Elongation. An important paralog of this gene is RPRD1B.

UniProtKB/Swiss-Prot Summary for RPRD1A Gene

  • Interacts with phosphorylated C-terminal heptapeptide repeat domain (CTD) of the largest RNA polymerase II subunit POLR2A, and participates in dephosphorylation of the CTD by RPAP2. May act as a negative regulator of cyclin-D1 (CCND1) and cyclin-E (CCNE1) in the cell cycle.

Additional gene information for RPRD1A Gene

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for RPRD1A Gene

Genomics for RPRD1A Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for RPRD1A Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around RPRD1A on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for RPRD1A

Top Transcription factor binding sites by QIAGEN in the RPRD1A gene promoter:
  • AhR
  • Arnt
  • ATF
  • HTF
  • Pax-3
  • POU2F1
  • POU2F1a
  • POU2F1b
  • POU2F1c
  • Sp1

Genomic Locations for RPRD1A Gene

Genomic Locations for RPRD1A Gene
chr18:35,982,385-36,067,594
(GRCh38/hg38)
Size:
85,210 bases
Orientation:
Minus strand
chr18:33,564,350-33,647,539
(GRCh37/hg19)
Size:
83,190 bases
Orientation:
Minus strand

Genomic View for RPRD1A Gene

Genes around RPRD1A on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
RPRD1A Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for RPRD1A Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for RPRD1A Gene

Proteins for RPRD1A Gene

  • Protein details for RPRD1A Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q96P16-RPR1A_HUMAN
    Recommended name:
    Regulation of nuclear pre-mRNA domain-containing protein 1A
    Protein Accession:
    Q96P16
    Secondary Accessions:
    • A8KA42
    • B2RBA3
    • Q7Z5G8
    • Q96FY9
    • Q9NVL4

    Protein attributes for RPRD1A Gene

    Size:
    312 amino acids
    Molecular mass:
    35720 Da
    Quaternary structure:
    • May form a heterodimer with RPRD1B (PubMed:24997600). Associates with the RNA polymerase II subunit POLR2A (via CTD phosphorylated at 'Ser-2' and 'Ser-7' of the heptad repeats) (PubMed:22231121, PubMed:24997600, PubMed:24399136).
    SequenceCaution:
    • Sequence=AAH10136.1; Type=Miscellaneous discrepancy; Note=Probable cloning artifact.; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for RPRD1A Gene

    Alternative splice isoforms for RPRD1A Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for RPRD1A Gene

Post-translational modifications for RPRD1A Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for RPRD1A Gene

Domains & Families for RPRD1A Gene

Gene Families for RPRD1A Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for RPRD1A Gene

InterPro:
Blocks:
  • Regulation of nuclear pre-mRNA protein
ProtoNet:

Suggested Antigen Peptide Sequences for RPRD1A Gene

GenScript: Design optimal peptide antigens:
  • p15INK4B-related protein (RPR1A_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q96P16

UniProtKB/Swiss-Prot:

RPR1A_HUMAN :
  • Belongs to the UPF0400 (RTT103) family.
Family:
  • Belongs to the UPF0400 (RTT103) family.
genes like me logo Genes that share domains with RPRD1A: view

Function for RPRD1A Gene

Molecular function for RPRD1A Gene

UniProtKB/Swiss-Prot Function:
Interacts with phosphorylated C-terminal heptapeptide repeat domain (CTD) of the largest RNA polymerase II subunit POLR2A, and participates in dephosphorylation of the CTD by RPAP2. May act as a negative regulator of cyclin-D1 (CCND1) and cyclin-E (CCNE1) in the cell cycle.
UniProtKB/Swiss-Prot Induction:
Up-regulated in cells overexpressing CDKN2B.

Phenotypes From GWAS Catalog for RPRD1A Gene

Gene Ontology (GO) - Molecular Function for RPRD1A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000993 RNA polymerase II complex binding IBA 21873635
GO:0005515 protein binding IPI 24997600
genes like me logo Genes that share ontologies with RPRD1A: view
genes like me logo Genes that share phenotypes with RPRD1A: view

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for RPRD1A

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for RPRD1A Gene

Localization for RPRD1A Gene

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for RPRD1A gene
Compartment Confidence
nucleus 5
cytosol 2
golgi apparatus 2
plasma membrane 1
extracellular 1
cytoskeleton 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleoplasm (3)
  • Golgi apparatus (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for RPRD1A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005654 nucleoplasm TAS --
GO:0016591 RNA polymerase II, holoenzyme IBA,IDA 22231121
genes like me logo Genes that share ontologies with RPRD1A: view

No data available for Subcellular locations from UniProtKB/Swiss-Prot for RPRD1A Gene

Pathways & Interactions for RPRD1A Gene

PathCards logo

SuperPathways for RPRD1A Gene

genes like me logo Genes that share pathways with RPRD1A: view

Pathways by source for RPRD1A Gene

2 Reactome pathways for RPRD1A Gene

Gene Ontology (GO) - Biological Process for RPRD1A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0031124 mRNA 3'-end processing IBA 21873635
GO:0042795 snRNA transcription by RNA polymerase II TAS --
GO:0070940 dephosphorylation of RNA polymerase II C-terminal domain IMP 22231121
genes like me logo Genes that share ontologies with RPRD1A: view

No data available for SIGNOR curated interactions for RPRD1A Gene

Drugs & Compounds for RPRD1A Gene

No Compound Related Data Available

Transcripts for RPRD1A Gene

mRNA/cDNA for RPRD1A Gene

4 REFSEQ mRNAs :
11 NCBI additional mRNA sequence :
11 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for RPRD1A

Alternative Splicing Database (ASD) splice patterns (SP) for RPRD1A Gene

ExUns: 1a · 1b · 1c · 1d ^ 2 ^ 3 ^ 4 ^ 5 ^ 6a · 6b ^ 7 ^ 8 ^ 9a · 9b ^ 10a · 10b · 10c ^ 11 ^ 12a · 12b · 12c ^ 13
SP1: - - - - - - - -
SP2: - - - - - - -
SP3: - - - - - -
SP4: - - - - - - -
SP5: - -
SP6:
SP7: - - - - - - - - - - - - - -
SP8:

Relevant External Links for RPRD1A Gene

GeneLoc Exon Structure for
RPRD1A

Expression for RPRD1A Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for RPRD1A Gene

Protein differential expression in normal tissues from HIPED for RPRD1A Gene

This gene is overexpressed in Breast (20.2).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for RPRD1A Gene



Protein tissue co-expression partners for RPRD1A Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for RPRD1A

SOURCE GeneReport for Unigene cluster for RPRD1A Gene:

Hs.464912

Evidence on tissue expression from TISSUES for RPRD1A Gene

  • Nervous system(4.7)
  • Eye(4.4)
  • Muscle(4.3)
  • Liver(4.2)
  • Lung(2.1)
genes like me logo Genes that share expression patterns with RPRD1A: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for RPRD1A Gene

Orthologs for RPRD1A Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for RPRD1A Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia RPRD1A 30 31
  • 99.68 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia RPRD1A 30 31
  • 95.62 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia RPRD1A 30 31
  • 94.93 (n)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia RPRD1A 31
  • 93 (a)
OneToOne
Mouse
(Mus musculus)
Mammalia Rprd1a 30 17 31
  • 91.24 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Rprd1a 30
  • 90.92 (n)
Platypus
(Ornithorhynchus anatinus)
Mammalia -- 31
  • 87 (a)
OneToMany
-- 31
  • 71 (a)
OneToMany
Chicken
(Gallus gallus)
Aves RPRD1A 30 31
  • 84.86 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia RPRD1A 31
  • 86 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia rprd1b 30
  • 75.53 (n)
Zebrafish
(Danio rerio)
Actinopterygii RPRD1A 31
  • 73 (a)
OneToOne
LOC560565 30
  • 68.18 (n)
Fruit Fly
(Drosophila melanogaster)
Insecta CG9018 31
  • 39 (a)
OneToMany
Worm
(Caenorhabditis elegans)
Secernentea cids-1 30 31
  • 41.7 (n)
OneToMany
Baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes RTT103 31
  • 14 (a)
OneToMany
Sea Squirt
(Ciona savignyi)
Ascidiacea CSA.4640 31
  • 48 (a)
OneToMany
Species where no ortholog for RPRD1A was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Wheat (Triticum aestivum)

Evolution for RPRD1A Gene

ENSEMBL:
Gene Tree for RPRD1A (if available)
TreeFam:
Gene Tree for RPRD1A (if available)
Aminode:
Evolutionary constrained regions (ECRs) for RPRD1A: view image

Paralogs for RPRD1A Gene

Paralogs for RPRD1A Gene

(1) SIMAP similar genes for RPRD1A Gene using alignment to 4 proteins:

  • RPR1A_HUMAN
  • K7EP82_HUMAN
  • K7EQR8_HUMAN
  • K7ER50_HUMAN

Pseudogenes.org Pseudogenes for RPRD1A Gene

genes like me logo Genes that share paralogs with RPRD1A: view

Variants for RPRD1A Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for RPRD1A Gene

SNP ID Clinical significance and condition Chr 18 pos Variation AA Info Type
VAR_037229 A breast cancer sample p.Gln21His

Additional dbSNP identifiers (rs#s) for RPRD1A Gene

Structural Variations from Database of Genomic Variants (DGV) for RPRD1A Gene

Variant ID Type Subtype PubMed ID
dgv978e212 CNV loss 25503493
esv1506593 CNV insertion 17803354
esv25678 CNV loss 19812545
esv275291 CNV loss 21479260
esv3642213 CNV loss 21293372
esv3642214 CNV loss 21293372
nsv1065113 CNV loss 25217958
nsv522157 CNV loss 19592680
nsv576651 CNV loss 21841781
nsv7303 OTHER inversion 18451855

Variation tolerance for RPRD1A Gene

Residual Variation Intolerance Score: 23.8% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.05; 1.17% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for RPRD1A Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
RPRD1A

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for RPRD1A Gene

Disorders for RPRD1A Gene

MalaCards: The human disease database

(2) MalaCards diseases for RPRD1A Gene - From: DISEASES

- elite association - COSMIC cancer census association via MalaCards
genes like me logo Genes that share disorders with RPRD1A: view

No data available for UniProtKB/Swiss-Prot and Genatlas for RPRD1A Gene

Publications for RPRD1A Gene

  1. Identification and characterization of P15RS, a novel P15(INK4b) related gene on G1/S progression. (PMID: 12470661) Liu J … Hu Z (Biochemical and biophysical research communications 2002) 2 3 4 23
  2. Control of the RNA polymerase II phosphorylation state in promoter regions by CTD interaction domain-containing proteins RPRD1A and RPRD1B. (PMID: 22231121) Ni Z … Greenblatt JF (Transcription 2011) 2 3 4
  3. RPRD1A and RPRD1B are human RNA polymerase II C-terminal domain scaffolds for Ser5 dephosphorylation. (PMID: 24997600) Ni Z … Greenblatt JF (Nature structural & molecular biology 2014) 3 4
  4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4
  5. A reference map of the human binary protein interactome. (PMID: 32296183) Luck K … Calderwood MA (Nature 2020) 3

Products for RPRD1A Gene

Sources for RPRD1A Gene