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Aliases for RPRD1A Gene

Aliases for RPRD1A Gene

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

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. Among its related pathways are Gene Expression and RNA polymerase II transcribes snRNA genes. An important paralog of this gene is RPRD1B.

UniProtKB/Swiss-Prot 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.

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for RPRD1A Gene

Genomics for RPRD1A Gene

Regulatory Elements for RPRD1A Gene

Enhancers for RPRD1A Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH18G036075 1.2 Ensembl ENCODE 13.2 -8.5 -8512 1.3 ELF3 PKNOX1 FOXA2 NFRKB SIN3A RELB FOS IKZF2 THAP11 SMARCC1 RPRD1A MOCOS FHOD3 C18orf21 GC18P036078
GH18G036065 1.1 ENCODE 12.7 +0.8 848 2.9 HDGF PKNOX1 FOXA2 MLX ARID4B SIN3A DMAP1 FEZF1 YY1 ZNF143 RPRD1A C18orf21 LOC105372066 GC18M035972
GH18G036096 0.8 dbSUPER 13.2 -29.9 -29857 2.6 TBP ZFP64 RAD21 RFX5 FOS ZNF654 ZBTB11 ZNF426 REST ZNF781 RPRD1A ZSCAN30 ZNF397 MOCOS FHOD3 ZNF271P ELP2 GC18M036078
GH18G036098 0.7 dbSUPER 13.1 -32.2 -32206 1.9 TAL1 CEBPB DPF2 RAD21 MBD2 ZNF579 ZNF217 GATA3 GATA2 TARDBP RPRD1A MOCOS FHOD3 LOC105372066 ELP2 GC18M036078
GH18G035825 1.4 FANTOM5 ENCODE dbSUPER 4.8 +239.8 239773 3.7 SOX13 CTCF LEF1 TAL1 CHD7 TCF12 NCOR1 NFE2 NR2F6 MAFK ZNF396 RPRD1A C18orf21 ZNF24 INO80C NRBF2P1 ENSG00000267397
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around RPRD1A on UCSC Golden Path with GeneCards custom track

Promoters for RPRD1A Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000102274 594 2000 HDGF PKNOX1 MLX ARID4B SIN3A DMAP1 FEZF1 YY1 ZNF143 ZNF207

Genomic Location for RPRD1A Gene

Chromosome:
18
Start:
35,984,387 bp from pter
End:
36,067,594 bp from pter
Size:
83,208 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

Protein Domains for RPRD1A Gene

Suggested Antigen Peptide Sequences for RPRD1A Gene

GenScript: Design optimal peptide antigens:

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

No data available for Gene Families for RPRD1A Gene

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.
genes like me logo Genes that share phenotypes with RPRD1A: view

Animal Model Products

CRISPR Products

Inhibitory RNA Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , 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

Gene Ontology (GO) - Cellular Components for RPRD1A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005654 nucleoplasm TAS --
GO:0016591 DNA-directed RNA polymerase II, holoenzyme 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

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:0042795 snRNA transcription from RNA polymerase II promoter 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

Unigene Clusters for RPRD1A Gene

Regulation of nuclear pre-mRNA domain containing 1A:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

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
ECgene alternative splicing isoforms for
RPRD1A

Expression for RPRD1A Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP 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, PaxDb, MaxQB, and MOPED for RPRD1A Gene



Protein tissue co-expression partners for RPRD1A Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of RPRD1A Gene:

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

Primer Products

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 34 35
  • 99.68 (n)
dog
(Canis familiaris)
Mammalia RPRD1A 34 35
  • 95.62 (n)
cow
(Bos Taurus)
Mammalia RPRD1A 34 35
  • 94.93 (n)
oppossum
(Monodelphis domestica)
Mammalia RPRD1A 35
  • 93 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Rprd1a 34 16 35
  • 91.24 (n)
rat
(Rattus norvegicus)
Mammalia Rprd1a 34
  • 90.92 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia -- 35
  • 87 (a)
OneToMany
-- 35
  • 71 (a)
OneToMany
chicken
(Gallus gallus)
Aves RPRD1A 34 35
  • 84.86 (n)
lizard
(Anolis carolinensis)
Reptilia RPRD1A 35
  • 86 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia rprd1b 34
  • 75.53 (n)
zebrafish
(Danio rerio)
Actinopterygii RPRD1A 35
  • 73 (a)
OneToOne
LOC560565 34
  • 68.18 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG9018 35
  • 39 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea cids-1 34 35
  • 41.7 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes RTT103 35
  • 14 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea CSA.4640 35
  • 48 (a)
OneToMany
Species where no ortholog for RPRD1A was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya 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 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)

Paralogs for RPRD1A Gene

Paralogs for RPRD1A Gene

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

Pseudogenes.org Pseudogenes for RPRD1A Gene

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

Variants for RPRD1A Gene

Sequence variations from dbSNP and Humsavar for RPRD1A Gene

SNP ID Clin Chr 18 pos Sequence Context AA Info Type
VAR_037229 A breast cancer sample
rs1000005328 -- 36,042,740(+) TTTTC(A/C)ACCTA intron-variant
rs1000017776 -- 36,059,264(+) TCCCA(A/C)GTAGC intron-variant
rs1000054492 -- 36,064,508(+) CACCA(A/G)TCAGT intron-variant, upstream-variant-2KB
rs1000191925 -- 36,063,317(+) CCTGC(A/G)CCATC intron-variant

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)

Relevant External Links 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

Relevant External Links for RPRD1A

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
RPRD1A

No disorders were found for RPRD1A Gene.

No data available for MalaCards , 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. (Biochem. Biophys. Res. Commun. 2002) 2 3 4 22 64
  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 J.F. (Transcription 2011) 2 3 4 64
  3. RPRD1A and RPRD1B are human RNA polymerase II C-terminal domain scaffolds for Ser5 dephosphorylation. (PMID: 24997600) Ni Z. … Greenblatt J.F. (Nat. Struct. Mol. Biol. 2014) 3 4 64
  4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T. … Sugano S. (Nat. Genet. 2004) 3 4 64
  5. The BioPlex Network: A Systematic Exploration of the Human Interactome. (PMID: 26186194) Huttlin E.L. … Gygi S.P. (Cell 2015) 3 64

Products for RPRD1A Gene

Sources for RPRD1A Gene

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