RPRD1A

gene
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Also known as P15RSFLJ10656HsT3101

Summary

RPRD1A (regulation of nuclear pre-mRNA domain containing 1A, HGNC:25560) is a protein-coding gene on chromosome 18q12.2, encoding Regulation of nuclear pre-mRNA domain-containing protein 1A (Q96P16). 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.

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.

Source: NCBI Gene 55197 — RefSeq curated summary.

At a glance

  • GWAS associations: 3
  • Clinical variants (ClinVar): 32 total
  • MANE Select transcript: NM_018170

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:25560
Approved symbolRPRD1A
Nameregulation of nuclear pre-mRNA domain containing 1A
Location18q12.2
Locus typegene with protein product
StatusApproved
AliasesP15RS, FLJ10656, HsT3101
Ensembl geneENSG00000141425
Ensembl biotypeprotein_coding
OMIM610347
Entrez55197

Gene structure

Transcript identifiers

Ensembl transcripts: 14 — 8 protein_coding, 3 nonsense_mediated_decay, 1 protein_coding_CDS_not_defined, 1 non_stop_decay, 1 retained_intron

ENST00000357384, ENST00000399022, ENST00000585879, ENST00000585953, ENST00000587563, ENST00000588459, ENST00000588737, ENST00000589050, ENST00000590898, ENST00000591994, ENST00000592674, ENST00000896647, ENST00000916733, ENST00000966876

RefSeq mRNA: 4 — MANE Select: NM_018170 NM_001303411, NM_001303412, NM_001303413, NM_018170

CCDS: CCDS11917, CCDS77178

Canonical transcript exons

ENST00000399022 — 7 exons

ExonStartEnd
ENSE000009484693603370836033837
ENSE000009484703603099136031097
ENSE000009484713603080836030905
ENSE000009484723602718436027310
ENSE000009484733602690036027075
ENSE000015360293598982435993300
ENSE000038414253606725436067559

Expression profiles

Bgee: expression breadth ubiquitous, 282 present calls, max score 98.39.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 41.0382 / max 703.3271, expressed in 1816 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter IDTPM avgSamples expressed
17167139.55051816
1716701.4878931

Top tissues by expression

288 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
Brodmann (1909) area 23UBERON:001355498.39gold quality
endothelial cellCL:000011598.24gold quality
adrenal tissueUBERON:001830397.35gold quality
middle temporal gyrusUBERON:000277196.58gold quality
primary visual cortexUBERON:000243696.36gold quality
secondary oocyteCL:000065596.07gold quality
corpus epididymisUBERON:000435995.93gold quality
ventricular zoneUBERON:000305395.50gold quality
corpus callosumUBERON:000233695.33gold quality
calcaneal tendonUBERON:000370195.25gold quality
entorhinal cortexUBERON:000272895.23gold quality
occipital lobeUBERON:000202195.22gold quality
superior frontal gyrusUBERON:000266195.17gold quality
germinal epithelium of ovaryUBERON:000130495.12gold quality
lateral nuclear group of thalamusUBERON:000273695.05gold quality
cortical plateUBERON:000534394.96gold quality
gingival epitheliumUBERON:000194994.93gold quality
postcentral gyrusUBERON:000258194.92gold quality
ganglionic eminenceUBERON:000402394.89gold quality
parietal lobeUBERON:000187294.88gold quality
prefrontal cortexUBERON:000045194.86gold quality
substantia nigra pars compactaUBERON:000196594.71gold quality
substantia nigra pars reticulataUBERON:000196694.61gold quality
temporal lobeUBERON:000187194.48gold quality
dorsolateral prefrontal cortexUBERON:000983494.38gold quality
neocortexUBERON:000195094.32gold quality
frontal cortexUBERON:000187094.26gold quality
cerebral cortexUBERON:000095694.23gold quality
anterior cingulate cortexUBERON:000983594.19gold quality
visceral pleuraUBERON:000240194.11gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 2.

ExperimentMarker?Max mean expression
E-HCAD-38yes801.75
E-ANND-3yes8.17
E-MTAB-7303no410.37

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

176 targeting RPRD1A, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-3613-3P100.0076.367965
HSA-LET-7A-3P100.0074.033932
HSA-LET-7B-3P100.0074.083913
HSA-LET-7F-1-3P100.0074.023928
HSA-MIR-98-3P100.0074.083907
HSA-MIR-6873-3P100.0071.422626
HSA-MIR-5692A100.0074.406850
HSA-MIR-3163100.0077.238605
HSA-MIR-3120-5P100.0065.56965
HSA-MIR-30A-5P100.0076.313233
HSA-MIR-30B-5P100.0076.293248
HSA-MIR-30C-5P100.0076.293248
HSA-MIR-30D-5P100.0076.323233
HSA-MIR-30E-5P100.0076.323242
HSA-MIR-6833-3P100.0070.633197
HSA-MIR-126-5P100.0072.713180
HSA-MIR-200B-3P100.0073.312693
HSA-MIR-200C-3P100.0073.352685
HSA-MIR-429100.0073.442698
HSA-MIR-4768-5P100.0069.492861
HSA-MIR-3064-3P100.0070.091254
HSA-MIR-8485100.0077.574731
HSA-MIR-453199.9969.703181
HSA-MIR-428299.9975.366408
HSA-MIR-318599.9968.121959
HSA-MIR-1212199.9966.64255
HSA-MIR-520D-5P99.9873.344883
HSA-MIR-524-5P99.9873.434882
HSA-MIR-548N99.9871.944170
HSA-MIR-477599.9875.006394

Literature-anchored findings (GeneRIF, showing 7)

  • molecular cloning and characterization of P15RS, a novel P15(INK4b) related gene involved in G1/S progression (PMID:12470661)
  • p15RS inhibits Wnt signaling by interrupting beta-catenin.TCF4 complex formation and that Wnt signaling initiates downstream gene expression by removing p15RS from promoters. (PMID:20739273)
  • The p15RS expression specifically downregulates the expression of cathepsin B and MMP-9 at RNA levels, which are known to promote cell invasion through degrading extracellular matrix proteins. (PMID:22580456)
  • RPRD1A and RPRD1B associate directly with RPAP2 phosphatase and coordinate the dephosphorylation of RNAPII phospho-S5 by RPAP2. (PMID:24997600)
  • Data suggest that p15RS (p15INK4b-related sequence) acts as an intrinsic transcriptional repressor for Wnt/beta-catenin-mediated gene transcription through recruiting HDAC2 histone deacetylase. (PMID:25697359)
  • The Wnt/beta-catenin signaling antagonist RPRD1A was downregulated and its upstream regulator miR-454-3p was amplified and overexpressed in metastatic breast cancer, and both were correlated with overall and relapse-free survival in breast cancer patients. (PMID:30809286)
  • RPRD1A stabilizes NRF2 and aggravates HCC progression through competing with p62 for TRIM21 binding. (PMID:34921137)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_reriorprd1aENSDARG00000104861
mus_musculusRprd1aENSMUSG00000040446
rattus_norvegicusRprd1aENSRNOG00000016036
drosophila_melanogasterCG9018FBGN0035318
caenorhabditis_elegansWBGENE00015347

Paralogs (2): RPRD1B (ENSG00000101413), RPRD2 (ENSG00000163125)

Protein

Protein identifiers

Regulation of nuclear pre-mRNA domain-containing protein 1AQ96P16 (reviewed: Q96P16)

Alternative names: Cyclin-dependent kinase inhibitor 2B-related protein, p15INK4B-related protein

All UniProt accessions (5): A0A0C4DGQ6, Q96P16, K7EP82, K7EQR8, K7ER50

UniProt curated annotations — full annotation on UniProt →

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.

Subunit / interactions. May form a heterodimer with RPRD1B. Associates with the RNA polymerase II subunit POLR2A (via CTD phosphorylated at ‘Ser-2’ and ‘Ser-7’ of the heptad repeats).

Subcellular location. Nucleus.

Induction. Up-regulated in cells overexpressing CDKN2B.

Similarity. Belongs to the UPF0400 (RTT103) family.

Isoforms (2)

UniProt IDNamesCanonical?
Q96P16-11yes
Q96P16-32

RefSeq proteins (4): NP_001290340, NP_001290341, NP_001290342, NP_060640* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR006569CID_domDomain
IPR008942ENTH_VHSHomologous_superfamily
IPR032337RPRD1A/B_CDomain
IPR047884RPRD1A_CIDDomain

Pfam: PF04818, PF16566

UniProt features (25 total): helix 9, modified residue 4, mutagenesis site 3, sequence conflict 2, initiator methionine 1, chain 1, domain 1, turn 1, coiled-coil region 1, splice variant 1, sequence variant 1

Structure

Experimental structures (PDB)

2 structures.

PDBMethodResolution (Å)
4JXTX-RAY DIFFRACTION1.9
4NACX-RAY DIFFRACTION2

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q96P16-F183.650.56

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Post-translational modifications (4): 2, 153, 156, 285

Mutagenesis-validated functional residues (3):

PositionPhenotype
65partial loss of binding to polr2a ctd in vitro.
106partial loss of binding to polr2a ctd phosphorylated at ‘ser-2’ in the heptad repeats in vitro.
114partial loss of binding to polr2a ctd in vitro.

Function

Pathways and Gene Ontology

Reactome pathways

3 pathways

IDPathway
R-HSA-6807505RNA polymerase II transcribes snRNA genes
R-HSA-73857RNA Polymerase II Transcription
R-HSA-74160Gene expression (Transcription)

MSigDB gene sets: 211 (showing top): ATF_B, RODRIGUES_THYROID_CARCINOMA_POORLY_DIFFERENTIATED_UP, CREBP1_Q2, GGGTGGRR_PAX4_03, YY1_Q6, CREB_Q4, chr18q12, GOBP_MRNA_3_END_PROCESSING, E4F1_Q6, ATF3_Q6, CREB_Q2_01, DODD_NASOPHARYNGEAL_CARCINOMA_UP, ATF_01, DEURIG_T_CELL_PROLYMPHOCYTIC_LEUKEMIA_UP, CREBP1CJUN_01

GO Biological Process (3): RNA polymerase II promoter clearance (GO:0001111), mRNA 3’-end processing (GO:0031124), regulation of transcription by RNA polymerase II (GO:0006357)

GO Molecular Function (5): RNA polymerase II complex binding (GO:0000993), identical protein binding (GO:0042802), RNA polymerase II C-terminal domain binding (GO:0099122), protein binding (GO:0005515), RNA polymerase II CTD heptapeptide repeat phosphatase activity (GO:0008420)

GO Cellular Component (3): nucleus (GO:0005634), nucleoplasm (GO:0005654), transcription preinitiation complex (GO:0097550)

Reactome top-level categories

Rollup of top-2 pathways:

CategoryPathways
RNA Polymerase II Transcription1
Gene expression (Transcription)1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
transcription by RNA polymerase II2
promoter clearance during DNA-templated transcription1
mRNA processing1
RNA 3’-end processing1
regulation of DNA-templated transcription1
RNA polymerase core enzyme binding1
protein binding1
RNA polymerase II complex binding1
binding1
protein serine/threonine phosphatase activity1
RNA polymerase II CTD heptapeptide repeat modifying activity1
intracellular membrane-bounded organelle1
nuclear lumen1
cellular anatomical structure1
protein-DNA complex1

Protein interactions and networks

STRING

1392 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
RPRD1ARPAP2Q8IXW5897
RPRD1ARMP24Q32NC0662
RPRD1ACDKN2BP42772642
RPRD1APOLR2AP24928592
RPRD1APCF11O94913582
RPRD1ARECQL5O94762571
RPRD1ACCNE1P24864549
RPRD1ACDKN3Q16667549
RPRD1ASCAF8Q9UPN6542
RPRD1ARPAP3Q9H6T3495
RPRD1AGPN1Q9HCN4494
RPRD1ASCAF4O95104479
RPRD1ACCND1P24385477
RPRD1AXRN2Q9H0D6477
RPRD1AJAG2Q9Y219466

IntAct

119 interactions, top by confidence:

ABTypeScore
RPRD1BPOLR2Apsi-mi:“MI:0914”(association)0.920
POLR2GPOLR2Dpsi-mi:“MI:0914”(association)0.840
POLR2JPOLR1Cpsi-mi:“MI:0914”(association)0.830
RPRD1BRPRD1Apsi-mi:“MI:0915”(physical association)0.820
RFXANKRFXAPpsi-mi:“MI:0914”(association)0.780
POLR2GRECQL5psi-mi:“MI:0914”(association)0.730
RPRD1BRECQL5psi-mi:“MI:0914”(association)0.730
POLR2DMED19psi-mi:“MI:0914”(association)0.730
POLR2EMED19psi-mi:“MI:0914”(association)0.730
RPRD1BPOLR2Dpsi-mi:“MI:0914”(association)0.730
POLR2JPOLR2Dpsi-mi:“MI:0914”(association)0.730
CFTRESYT2psi-mi:“MI:2364”(proximity)0.710
POLR2ARPAP2psi-mi:“MI:0914”(association)0.640
POLR2DRECQL5psi-mi:“MI:0914”(association)0.640
POLR2LRCCD1psi-mi:“MI:0914”(association)0.640
POLR2FPOLR3Apsi-mi:“MI:0914”(association)0.640
POLR2LPOLR3Apsi-mi:“MI:0914”(association)0.640
POLR2ARPRD1Apsi-mi:“MI:0915”(physical association)0.620
RPRD1AKPNA3psi-mi:“MI:0915”(physical association)0.560
KPNA3RPRD1Apsi-mi:“MI:0915”(physical association)0.560

BioGRID (211): RPRD1A (Two-hybrid), RPRD1A (Affinity Capture-RNA), RPRD1A (Affinity Capture-RNA), RPRD1A (Affinity Capture-MS), RPRD1A (Affinity Capture-MS), RPRD1A (Affinity Capture-MS), RPRD1A (Affinity Capture-MS), RPRD1A (Affinity Capture-MS), RPRD1A (Affinity Capture-MS), DPH2 (Co-fractionation), DXO (Co-fractionation), MITD1 (Co-fractionation), RPRD1A (Co-fractionation), RPRD1A (Co-fractionation), VPS37B (Co-fractionation)

ESM2 similar proteins: A0JMA8, A4UUI3, A8WLG6, A8WZU5, A8XEZ1, A8XY47, F4ICD9, F4JIN3, G5EDN3, O13745, O43150, O59668, O74737, O74749, O93436, P32744, P34281, P38753, P90740, Q03609, Q07872, Q0P5J9, Q10410, Q17423, Q20977, Q21444, Q23088, Q4VBT2, Q5R8Y3, Q5SPP5, Q5U245, Q61D31, Q61J98, Q61QN4, Q641A2, Q756C5, Q7SIG6, Q7XPJ0, Q8IGJ0, Q8STE5

Diamond homologs: Q0P5J9, Q5R8Y3, Q5ZM30, Q8VDS4, Q96P16, Q9CSU0, Q9NQG5, Q05543, Q5VT52, Q6NXI6

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 123 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

PathwayPartnersFoldFDR
FGFR2 mutant receptor activation872.5×2e-12
Signaling by FGFR2 IIIa TM964.4×1e-12
Abortive elongation of HIV-1 transcript in the absence of Tat953.2×2e-12
MicroRNA (miRNA) biogenesis948.9×4e-12
Activation of HOX genes during differentiation947.1×5e-12
FGFR2 alternative splicing945.3×7e-12
RNA Polymerase III Chain Elongation645.3×2e-08
Pausing and recovery of Tat-mediated HIV elongation1043.9×1e-12

GO biological processes:

GO termPartnersFoldFDR
transcription by RNA polymerase II106.1×2e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

32 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance22
Likely benign0
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1885 predictions. Top by Δscore:

VariantEffectΔscore
18:36026895:CGCA:Cdonor_gain1.0000
18:36026896:GCA:Gdonor_loss1.0000
18:36026897:CACTT:Cdonor_loss1.0000
18:36026898:A:ACdonor_gain1.0000
18:36026898:ACTT:Adonor_gain1.0000
18:36026898:ACTTC:Adonor_gain1.0000
18:36026899:C:CAdonor_gain1.0000
18:36026899:CTT:Cdonor_gain1.0000
18:36026899:CTTC:Cdonor_gain1.0000
18:36026899:CTTCC:Cdonor_gain1.0000
18:36026901:T:TAdonor_gain1.0000
18:36026902:C:Adonor_gain1.0000
18:36026931:T:TAdonor_gain1.0000
18:36027076:C:CCacceptor_gain1.0000
18:36027076:C:CGacceptor_loss1.0000
18:36027178:TCTTA:Tdonor_loss1.0000
18:36027179:CTTA:Cdonor_loss1.0000
18:36027180:TTA:Tdonor_loss1.0000
18:36027181:TA:Tdonor_loss1.0000
18:36027182:A:AGdonor_loss1.0000
18:36027183:C:CTdonor_loss1.0000
18:36027309:GT:Gacceptor_gain1.0000
18:36027310:TCT:Tacceptor_loss1.0000
18:36030637:C:CTdonor_gain1.0000
18:36030638:T:TTdonor_gain1.0000
18:36030802:TTCTA:Tdonor_loss1.0000
18:36030803:TCTA:Tdonor_loss1.0000
18:36030804:CTA:Cdonor_loss1.0000
18:36030805:TA:Tdonor_loss1.0000
18:36030807:C:Tdonor_loss1.0000

AlphaMissense

2039 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
18:36031005:A:GL125P1.000
18:36031032:A:TV116D1.000
18:36031037:C:AR114S1.000
18:36031037:C:GR114S1.000
18:36031038:C:AR114M1.000
18:36031038:C:GR114T1.000
18:36031046:C:AW111C1.000
18:36031046:C:GW111C1.000
18:36031047:C:GW111S1.000
18:36031048:A:GW111R1.000
18:36031048:A:TW111R1.000
18:36031050:A:CI110S1.000
18:36031050:A:GI110T1.000
18:36031050:A:TI110N1.000
18:36031061:T:AR106S1.000
18:36031061:T:GR106S1.000
18:36031062:C:GR106T1.000
18:36033746:A:CF81L1.000
18:36033746:A:TF81L1.000
18:36033747:A:GF81S1.000
18:36033748:A:GF81L1.000
18:36033758:A:CF77L1.000
18:36033758:A:TF77L1.000
18:36033759:A:CF77C1.000
18:36033759:A:GF77S1.000
18:36033760:A:GF77L1.000
18:36033768:C:TG74E1.000
18:36033769:C:GG74R1.000
18:36033769:C:TG74R1.000
18:36033776:C:AK71N1.000

dbSNP variants (sampled 300 via entrez): RS1000005328 (18:36042740 A>C), RS1000017776 (18:36059264 A>C,G), RS1000054492 (18:36064508 A>G), RS1000191925 (18:36063317 G>A), RS1000323673 (18:35992964 TAAGTC>T), RS1000334916 (18:36036945 C>T), RS1000365667 (18:36067754 C>A), RS1000379695 (18:36044125 A>G), RS1000426987 (18:35999154 C>T), RS1000451826 (18:36064291 T>A,G), RS1000473815 (18:36023941 T>C), RS1000479200 (18:36025542 C>A,G,T), RS1000491014 (18:36026067 C>A,T), RS1000504190 (18:36003653 T>C), RS1000561443 (18:36017108 G>A)

Disease associations

OMIM: gene MIM:610347 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

3 associations (top):

StudyTraitp-value
GCST002269_1Drug-induced torsades de pointes4.000000e-07
GCST90002390_550Mean corpuscular hemoglobin1.000000e-11
GCST90002392_29Mean corpuscular volume1.000000e-11

EFO canonical traits (1, from GWAS)

EFO IDTrait name
EFO:0004527mean corpuscular hemoglobin

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

40 total (human), top 30 by PubMed support.

ChemicalActions (top 5)PubMed papers
Valproic Acidincreases expression, affects cotreatment, decreases expression, affects expression7
bisphenol Adecreases expression, affects cotreatment, affects expression, increases abundance2
sodium arseniteaffects expression, decreases expression2
Phenylmercuric Acetateaffects cotreatment, decreases expression2
FR900359increases phosphorylation1
ginger extractaffects cotreatment, affects expression, increases abundance1
dicrotophosdecreases expression1
methylmercuric chloridedecreases expression1
triphenyl phosphateaffects expression1
tris(1,3-dichloro-2-propyl)phosphatedecreases expression1
ochratoxin Aincreases expression1
coumarinincreases phosphorylation1
beta-methylcholineaffects expression1
di-n-butylphosphoric acidaffects expression1
2,3,5-(triglutathion-S-yl)hydroquinoneincreases ADP-ribosylation1
chloropicrindecreases expression1
entinostatdecreases expression1
monomethylarsonous aciddecreases expression1
K 7174increases expression1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamidedecreases expression, affects cotreatment1
dorsomorphinaffects cotreatment, decreases expression1
jinfukangdecreases expression1
Sunitinibincreases expression1
Vorinostatincreases expression1
Benzo(a)pyreneincreases mutagenesis1
Doxorubicindecreases expression1
Enzyme Inhibitorsdecreases activity, increases O-linked glycosylation1
Ethyl Methanesulfonatedecreases expression1
Formaldehydedecreases expression1
Ivermectindecreases expression1

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.

  • Disease cohort memberships (association, not causation — diseases whose associated-gene cohort lists this gene; a subset are also under Associated diseases): torsades de pointes