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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
External Ids for RPRD1A Gene
- HGNC: 25560
- Entrez Gene: 55197
- Ensembl: ENSG00000141425
- OMIM: 610347
- UniProtKB: Q96P16
Previous GeneCards Identifiers for RPRD1A Gene
- GC18M031824
- GC18M033569
- GC18M030428
Summaries 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
- HGNC(25560)
- Entrez Gene(55197)
- Ensembl(ENSG00000141425)
- OMIM(610347)
- UniProtKB(Q96P16)
- Open Targets Platform(ENSG00000141425)
- Search for RPRD1A at DataMed
- Search for RPRD1A at HumanCyc
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:
-
- 18q12.2 by HGNC
- 18q12.2 by Entrez Gene
- 18q12.2 by Ensembl
RPRD1A Gene in genomic location: bands according to
Ensembl, locations according to GeneLoc
(and/or Entrez Gene and/or Ensembl if different)
Genomic Neighborhood
• Exon Structure
• Gene 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
- 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};
Protein Expression for RPRD1A Gene
Post-translational modifications for RPRD1A Gene
Other Protein References for RPRD1A Gene
Antibody Products
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Protein Products
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- antibodies-online: Show 9 available RPRD1A Proteins ranked by validation data
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Abcam proteins for RPRD1A
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- Family:
-
- Belongs to the UPF0400 (RTT103) family.
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
| GO ID | Qualified GO term | Evidence | PubMed IDs |
|---|---|---|---|
| GO:0000993 | RNA polymerase II complex binding | IBA | 21873635 |
| GO:0005515 | protein binding | IPI | 24997600 |
Phenotypes for RPRD1A Gene
- GenomeRNAi human phenotypes for RPRD1A:
-
- Increased vaccinia virus (VACV) infection
- no effect
- Increased shRNA abundance (Z-score > 2)
- Negative genetic interaction between BLM-/- and BLM+/+
- shRNA abundance <= 25%
- Decreased telomerase activity
- Decreased shRNA abundance (Z-score < -2)
- Increased S DNA content
- Decreased viability in colon lineage
- Negative genetic interaction between PTEN-/- and PTEN+/+
- Decreased focal adhesion (FA) area, decreased FA length, decreased FA mean intensity, increased number of small and round FAs, decreased FA abundance
- Condensed medial Golgi
Animal Model Products
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CRISPR Products
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miRNA for RPRD1A Gene
- miRTarBase miRNAs that target RPRD1A
-
- hsa-miR-155-5p (MIRT020628)
- hsa-miR-30a-5p (MIRT028472)
- hsa-miR-181b-5p (MIRT047242)
- hsa-miR-10a-5p (MIRT047673)
- hsa-miR-20a-5p (MIRT050478)
- mmu-miR-27b-3p (MIRT597405)
- mmu-miR-673-5p (MIRT597406)
- mmu-miR-27a-3p (MIRT597407)
- mmu-miR-3471 (MIRT597408)
- mmu-miR-3110-5p (MIRT597409)
- mmu-miR-5125 (MIRT597410)
- mmu-miR-5127 (MIRT597411)
- mmu-miR-150-5p (MIRT597412)
- mmu-miR-3470b (MIRT603431)
- mmu-miR-139-5p (MIRT603432)
- mmu-miR-1981-5p (MIRT603433)
- mmu-miR-1971 (MIRT603434)
- hsa-miR-140-3p (MIRT762633)
- hsa-miR-1911-5p (MIRT763375)
- hsa-miR-4461 (MIRT769401)
- hsa-miR-4804-3p (MIRT772574)
- hsa-miR-6869-5p (MIRT780686)
miRNA Products
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Clone Products
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Cell Line Products
-
Horizon Cell Lines 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
| Compartment | Confidence |
|---|---|
| nucleus | 5 |
| cytosol | 2 |
| golgi apparatus | 2 |
| plasma membrane | 1 |
| extracellular | 1 |
| cytoskeleton | 1 |
- Nucleoplasm (3)
- Golgi apparatus (2)
| GO ID | Qualified GO term | Evidence | PubMed IDs |
|---|---|---|---|
| GO:0005654 | nucleoplasm | TAS | -- |
| GO:0016591 | RNA polymerase II, holoenzyme | IBA,IDA | 22231121 |
No data available for Subcellular locations from UniProtKB/Swiss-Prot for RPRD1A Gene
Pathways & Interactions for RPRD1A Gene
| SuperPathway | Contained pathways | ||
|---|---|---|---|
| 1 | Gene Expression |
.48
|
|
| 2 | HIV Transcription Elongation | ||
Pathways by source for RPRD1A Gene
2 Reactome pathways for RPRD1A Gene
Interacting Proteins for RPRD1A Gene
Selected Interacting proteins:
Q96P16-RPR1A_HUMAN
ENSP00000381984
for RPRD1A Gene via
UniProtKB
MINT
STRING
IID
GPS-Prot Interaction Network for RPRD1A
| 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 |
No data available for SIGNOR curated interactions for RPRD1A Gene
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 :
-
- ENST00000357384 1850 nts (view in UCSC)
- ENST00000399022 4421 nts (view in UCSC)
- ENST00000585879 425 nts (view in UCSC)
- ENST00000585953 2357 nts (view in UCSC)
- ENST00000587563 643 nts (view in UCSC)
CRISPR Products
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-
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-
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miRNA Products
Inhibitory RNA Products
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Clone Products
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| 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
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
- Elite partner
Transcriptomic regulation report from SPP (The Signaling Pathways Project) for RPRD1A
SOURCE GeneReport for Unigene cluster for RPRD1A Gene:
Hs.464912Evidence on tissue expression from TISSUES for RPRD1A Gene
- Nervous system(4.7)
- Eye(4.4)
- Muscle(4.3)
- Liver(4.2)
- Lung(2.1)
Primer Products
-
OriGene qPCR primer pairs for RPRD1A
-
OriGene qPCR primer pairs and template standards for RPRD1A
Gene Expression Assay 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.
| Organism | Taxonomy | Gene | Similarity | Type | Details |
|---|---|---|---|---|---|
| Chimpanzee (Pan troglodytes) |
Mammalia | RPRD1A 30 31 |
|
OneToOne | |
| Dog (Canis familiaris) |
Mammalia | RPRD1A 30 31 |
|
OneToOne | |
| Cow (Bos Taurus) |
Mammalia | RPRD1A 30 31 |
|
OneToOne | |
| Oppossum (Monodelphis domestica) |
Mammalia | RPRD1A 31 |
|
OneToOne | |
| Mouse (Mus musculus) |
Mammalia | Rprd1a 30 17 31 |
|
OneToOne | |
| Rat (Rattus norvegicus) |
Mammalia | Rprd1a 30 |
|
||
| Platypus (Ornithorhynchus anatinus) |
Mammalia | -- 31 |
|
OneToMany | |
| -- 31 |
|
OneToMany | |||
| Chicken (Gallus gallus) |
Aves | RPRD1A 30 31 |
|
OneToOne | |
| Lizard (Anolis carolinensis) |
Reptilia | RPRD1A 31 |
|
OneToOne | |
| Tropical Clawed Frog (Silurana tropicalis) |
Amphibia | rprd1b 30 |
|
||
| Zebrafish (Danio rerio) |
Actinopterygii | RPRD1A 31 |
|
OneToOne | |
| LOC560565 30 |
|
||||
| Fruit Fly (Drosophila melanogaster) |
Insecta | CG9018 31 |
|
OneToMany | |
| Worm (Caenorhabditis elegans) |
Secernentea | cids-1 30 31 |
|
OneToMany | |
| Baker's yeast (Saccharomyces cerevisiae) |
Saccharomycetes | RTT103 31 |
|
OneToMany | |
| Sea Squirt (Ciona savignyi) |
Ascidiacea | CSA.4640 31 |
|
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
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 |
| 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 |
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
SNP Genotyping and Copy Number Assay Products
No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for RPRD1A Gene
Disorders for RPRD1A Gene
| Disorder | Aliases | PubMed IDs |
|---|---|---|
| retroperitoneal leiomyosarcoma |
|
|
| retroperitoneal sarcoma |
|
|
Search RPRD1A in MalaCards
View complete list of genes associated with diseases
Additional Disease Information for RPRD1A
No data available for UniProtKB/Swiss-Prot and Genatlas for RPRD1A Gene
Publications for RPRD1A Gene
- 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
- 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
- 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
- Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4
- A reference map of the human binary protein interactome. (PMID: 32296183) Luck K … Calderwood MA (Nature 2020) 3
ExternalLinks
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Sources for RPRD1A Gene
- (1) GeneCards
- (2) HGNC
- (3) NCBI Entrez Gene
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