RIDA

gene
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Also known as UK114P14.5PSP

Summary

RIDA (reactive intermediate imine deaminase A, HGNC:16897) is a protein-coding gene on chromosome 8q22.2, encoding 2-iminobutanoate/2-iminopropanoate deaminase (P52758). Catalyzes the hydrolytic deamination of enamine/imine intermediates that form during the course of normal metabolism.

Enables mRNA binding activity. Involved in mRNA catabolic process and mRNA destabilization. Located in cytoplasm and nucleus.

Source: NCBI Gene 10247 — RefSeq curated summary.

At a glance

  • GWAS associations: 2
  • Clinical variants (ClinVar): 10 total
  • MANE Select transcript: NM_005836

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:16897
Approved symbolRIDA
Namereactive intermediate imine deaminase A
Location8q22.2
Locus typegene with protein product
StatusApproved
AliasesUK114, P14.5, PSP
Ensembl geneENSG00000132541
Ensembl biotypeprotein_coding
OMIM602487
Entrez10247

Gene structure

Transcript identifiers

Ensembl transcripts: 10 — 7 protein_coding, 1 protein_coding_CDS_not_defined, 1 retained_intron, 1 nonsense_mediated_decay

ENST00000254878, ENST00000519155, ENST00000519608, ENST00000520507, ENST00000521560, ENST00000522791, ENST00000883921, ENST00000883922, ENST00000883923, ENST00000883924

RefSeq mRNA: 1 — MANE Select: NM_005836 NM_005836

CCDS: CCDS6276

Canonical transcript exons

ENST00000254878 — 6 exons

ExonStartEnd
ENSE000010267799810234498102904
ENSE000013827199810864698108751
ENSE000021265999811703298117171
ENSE000035344609810448998104544
ENSE000036113009810593898106006
ENSE000036302769810627298106326

Expression profiles

Bgee: expression breadth ubiquitous, 272 present calls, max score 99.56.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 23.3184 / max 1136.7563, expressed in 1765 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter IDTPM avgSamples expressed
9408219.47581755
940813.84261287

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
right lobe of liverUBERON:000111499.56gold quality
liverUBERON:000210799.04gold quality
adult mammalian kidneyUBERON:000008298.42gold quality
adrenal tissueUBERON:001830397.70gold quality
nephron tubuleUBERON:000123197.58gold quality
caudate nucleusUBERON:000187397.20gold quality
nucleus accumbensUBERON:000188297.12gold quality
kidney epitheliumUBERON:000481997.11gold quality
putamenUBERON:000187496.75gold quality
kidneyUBERON:000211396.69gold quality
amygdalaUBERON:000187696.54gold quality
renal glomerulusUBERON:000007496.36gold quality
anterior cingulate cortexUBERON:000983596.23gold quality
cingulate cortexUBERON:000302796.18gold quality
right adrenal gland cortexUBERON:003582796.04gold quality
hypothalamusUBERON:000189895.99gold quality
metanephric glomerulusUBERON:000473695.97gold quality
right adrenal glandUBERON:000123395.89gold quality
cortex of kidneyUBERON:000122595.80gold quality
right frontal lobeUBERON:000281095.67gold quality
left adrenal glandUBERON:000123495.35gold quality
Brodmann (1909) area 9UBERON:001354095.34gold quality
left adrenal gland cortexUBERON:003582595.07gold quality
middle frontal gyrusUBERON:000270294.98gold quality
C1 segment of cervical spinal cordUBERON:000646994.81gold quality
substantia nigraUBERON:000203894.77gold quality
dorsolateral prefrontal cortexUBERON:000983494.74gold quality
metanephrosUBERON:000008194.56gold quality
adrenal cortexUBERON:000123594.45gold quality
adrenal glandUBERON:000236994.27gold quality

Single-cell (SCXA)

Detected in 4 experiment(s), a significant marker in 4.

ExperimentMarker?Max mean expression
E-GEOD-124472yes531.99
E-HCAD-10yes439.78
E-MTAB-10553yes37.66
E-ANND-3no0.00

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): MYC

miRNA regulators (miRDB)

29 targeting RIDA, 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-477599.9875.006394
HSA-MIR-548N99.9871.944170
HSA-MIR-590-3P99.9674.346478
HSA-MIR-314399.9371.963104
HSA-MIR-6809-3P99.9171.453814
HSA-MIR-4753-3P99.9071.033786
HSA-MIR-132399.8369.892471
HSA-MIR-130B-5P99.8368.501888
HSA-MIR-548O-3P99.7469.302228
HSA-MIR-3913-3P99.7466.53938
HSA-MIR-3934-5P99.6764.04846
HSA-MIR-58799.6470.862611
HSA-MIR-368599.6268.831621
HSA-MIR-372-5P99.4169.112299
HSA-MIR-942-5P99.4168.401977
HSA-MIR-130A-5P99.3370.262623
HSA-MIR-410-3P99.2769.982457
HSA-MIR-1213598.9970.261814
HSA-MIR-5001-3P98.9167.281394
HSA-MIR-607498.8969.642187
HSA-MIR-320A-5P98.8866.751248
HSA-MIR-3124-3P98.8768.952123
HSA-MIR-6868-3P98.6369.642259
HSA-MIR-451898.1266.821030
HSA-MIR-337-3P97.9069.371052
HSA-MIR-3664-3P97.8567.621452
HSA-MIR-6750-3P96.7967.50740
HSA-MIR-4695-3P96.7167.21836
HSA-MIR-6760-3P96.3568.311001

Literature-anchored findings (GeneRIF, showing 5)

  • x-ray crystallography study of p14.5 (PMID:14997576)
  • analysis of ligand binding sites of protein p14.5 (PMID:16198412)
  • We also find that a subset of m(6)A-containing circular RNAs associates with YTHDF2 in an HRSP12-dependent manner and is selectively downregulated by RNase P/MRP. (PMID:30930054)
  • The new findings regarding the biological significance of enamine and imine production and outline the importance of RidA in controlling the accumulation of reactive metabolites. (PMID:31103411)
  • P14.5 functions to inhibit cell migration and can be used as a prognostic marker in hepatocellular carcinoma. (PMID:36434386)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_rerioridaENSDARG00000035882
mus_musculusRidaENSMUSG00000022323
rattus_norvegicusRidaENSRNOG00000005437
drosophila_melanogasterUK114FBGN0086691
caenorhabditis_elegansWBGENE00016011

Protein

Protein identifiers

2-iminobutanoate/2-iminopropanoate deaminaseP52758 (reviewed: P52758)

Alternative names: 14.5 kDa translational inhibitor protein, Heat-responsive protein 12, Reactive intermediate imine deaminase A homolog, Translation inhibitor L-PSP ribonuclease, UK114 antigen homolog

All UniProt accessions (4): P52758, E5RIP8, H0YB34, H0YBX3

UniProt curated annotations — full annotation on UniProt →

Function. Catalyzes the hydrolytic deamination of enamine/imine intermediates that form during the course of normal metabolism. May facilitate the release of ammonia from these potentially toxic reactive metabolites, reducing their impact on cellular components. It may act on enamine/imine intermediates formed by several types of pyridoxal-5’-phosphate-dependent dehydratases including L-threonine dehydratase. Also promotes endoribonucleolytic cleavage of some transcripts by promoting recruitment of the ribonuclease P/MRP complex. Acts by bridging YTHDF2 and the ribonuclease P/MRP complex. RIDA/HRSP12 binds to N6-methyladenosine (m6A)-containing mRNAs containing a 5’-GGUUC-3’ motif: cooperative binding of RIDA/HRSP12 and YTHDF2 to such transcripts lead to recruitment of the ribonuclease P/MRP complex and subsequent endoribonucleolytic cleavage.

Subunit / interactions. Homotrimer. Interacts with YTHDF2.

Subcellular location. Cytoplasm. Nucleus. Peroxisome. Mitochondrion.

Tissue specificity. Expressed predominantly in liver and kidney. Lower levels in lung and brain.

Similarity. Belongs to the RutC family.

RefSeq proteins (1): NP_005827* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR006056RidAFamily
IPR006175YjgF/YER057c/UK114Family
IPR019897RidA_CSConserved_site
IPR035959RutC-like_sfHomologous_superfamily

Pfam: PF01042

Catalyzed reactions (Rhea), 2 shown:

  • 2-iminobutanoate + H2O = 2-oxobutanoate + NH4(+) (RHEA:39975)
  • 2-iminopropanoate + H2O = pyruvate + NH4(+) (RHEA:40671)

UniProt features (23 total): strand 8, modified residue 6, helix 5, initiator methionine 1, chain 1, turn 1, sequence conflict 1

Structure

Experimental structures (PDB)

2 structures.

PDBMethodResolution (Å)
9N80X-RAY DIFFRACTION1.39
1ONIX-RAY DIFFRACTION1.9

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-P52758-F197.120.96

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 (6): 2, 13, 60, 67, 74, 136

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

IDPathway
R-HSA-8849175Threonine catabolism

MSigDB gene sets: 210 (showing top): GSE45365_CD8A_DC_VS_CD11B_DC_IFNAR_KO_DN, GSE18804_SPLEEN_MACROPHAGE_VS_BRAIN_TUMORAL_MACROPHAGE_DN, GSE18804_BRAIN_VS_COLON_TUMORAL_MACROPHAGE_DN, GSE18804_SPLEEN_MACROPHAGE_VS_TUMORAL_MACROPHAGE_DN, GSE45365_CTRL_VS_MCMV_INFECTION_NK_CELL_DN, GOMF_ENDONUCLEASE_ACTIVITY, GOMF_RNA_NUCLEASE_ACTIVITY, BUYTAERT_PHOTODYNAMIC_THERAPY_STRESS_DN, GOBP_REGULATION_OF_MRNA_CATABOLIC_PROCESS, GOMF_NUCLEASE_ACTIVITY, GOBP_ALPHA_AMINO_ACID_METABOLIC_PROCESS, GOBP_SERINE_FAMILY_AMINO_ACID_BIOSYNTHETIC_PROCESS, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_UP, GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_UP, GOBP_MACROMOLECULE_CATABOLIC_PROCESS

GO Biological Process (8): mRNA catabolic process (GO:0006402), lipid metabolic process (GO:0006629), negative regulation of translation (GO:0017148), obsolete L-threonine catabolic process to glycine (GO:0019518), mRNA destabilization (GO:0061157), post-transcriptional regulation of gene expression (GO:0010608), negative regulation of gene expression (GO:0010629), regulation of primary metabolic process (GO:0080090)

GO Molecular Function (9): RNA binding (GO:0003723), mRNA binding (GO:0003729), RNA endonuclease activity producing 3’-phosphomonoesters, hydrolytic mechanism (GO:0016892), deaminase activity (GO:0019239), 2-iminobutanoate deaminase activity (GO:0120242), 2-iminopropanoate deaminase activity (GO:0120243), protein binding (GO:0005515), hydrolase activity (GO:0016787), 2-iminobutanoate/2-iminopropanoate deaminase activity (GO:0120241)

GO Cellular Component (7): nucleus (GO:0005634), cytoplasm (GO:0005737), mitochondrion (GO:0005739), mitochondrial matrix (GO:0005759), peroxisome (GO:0005777), cytosol (GO:0005829), extracellular exosome (GO:0070062)

Reactome top-level categories

Rollup of top-1 pathways:

CategoryPathways
Metabolism of amino acids and derivatives1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
negative regulation of gene expression3
primary metabolic process2
regulation of gene expression2
2-iminobutanoate/2-iminopropanoate deaminase activity2
intracellular membrane-bounded organelle2
cellular anatomical structure2
cytoplasm2
RNA catabolic process1
mRNA metabolic process1
translation1
regulation of translation1
negative regulation of protein metabolic process1
regulation of mRNA stability1
RNA destabilization1
positive regulation of mRNA catabolic process1
gene expression1
negative regulation of macromolecule biosynthetic process1
regulation of metabolic process1
nucleic acid binding1
RNA binding1
RNA endonuclease activity1
hydrolase activity, acting on ester bonds1
hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds1
binding1
catalytic activity1
deaminase activity1
intracellular anatomical structure1
mitochondrion1
intracellular organelle lumen1
microbody1
extracellular vesicle1

Protein interactions and networks

STRING

1805 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
RIDAYTHDF2Q9Y5A9989
RIDACNOT1A5YKK6554
RIDAYTHDC1Q96MU7542
RIDAYTHDF3Q7Z739516
RIDADPH3Q96FX2506
RIDADPH6Q7L8W6499
RIDADPH5Q9H2P9493
RIDAUPF1Q92900492
RIDADPH7Q9BTV6490
RIDAYTHDF1Q9BYJ9490
RIDAYTHDC2Q9H6S0489
RIDAMETTL3Q86U44488
RIDAPNRC2Q9NPJ4462
RIDADPH2Q9BQC3459
RIDADPH1Q9BZG8459

IntAct

22 interactions, top by confidence:

ABTypeScore
RIDABANPpsi-mi:“MI:0915”(physical association)0.560
RIDARIDApsi-mi:“MI:0915”(physical association)0.370
DEAF1RIDApsi-mi:“MI:0915”(physical association)0.370
RIDAHIVEP1psi-mi:“MI:0915”(physical association)0.370
HPDRIDApsi-mi:“MI:0915”(physical association)0.370
MDM2RIDApsi-mi:“MI:0915”(physical association)0.370
RIDAMT-CO2psi-mi:“MI:0915”(physical association)0.370
RIDASERPINA5psi-mi:“MI:0915”(physical association)0.370
SPENRIDApsi-mi:“MI:0915”(physical association)0.370
RIDATMEM176Apsi-mi:“MI:0915”(physical association)0.370
PRNPSYNJ1psi-mi:“MI:0914”(association)0.350
PRNPMBPpsi-mi:“MI:0914”(association)0.350
RIDAOGApsi-mi:“MI:0914”(association)0.350
NDUFS3ACOT7psi-mi:“MI:0914”(association)0.350
SHTN1psi-mi:“MI:0914”(association)0.350
FTSJ1RIDApsi-mi:“MI:0915”(physical association)0.000
TRAF6RIDApsi-mi:“MI:0915”(physical association)0.000
RIDABANPpsi-mi:“MI:0915”(physical association)0.000
RIDAalrpsi-mi:“MI:0915”(physical association)0.000

BioGRID (47): HRSP12 (Two-hybrid), BROX (Co-fractionation), TPI1 (Co-fractionation), ACOX1 (Affinity Capture-MS), CARM1 (Affinity Capture-MS), UBB (Affinity Capture-MS), MGEA5 (Affinity Capture-MS), BANP (Two-hybrid), HRSP12 (Proximity Label-MS), HRSP12 (Proximity Label-MS), ACOX1 (Affinity Capture-MS), MGEA5 (Affinity Capture-MS), CARM1 (Affinity Capture-MS), UBB (Affinity Capture-MS), HRSP12 (Two-hybrid)

ESM2 similar proteins: A0A1J1DL12, A4W923, A6T7A0, A8GCT4, B0SW61, B5XXN2, B6I986, B7N3G6, B8H1Q2, B9JLT7, C5B0U7, C5CN81, C9Y0S5, D0LI57, D3QPK3, D3RKL2, D4GEU6, D5CE34, D5VGV2, O25598, O34133, O52178, P0AF93, P0AF94, P0AF95, P0AFQ5, P0AGL2, P0AGL3, P0AGL4, P40037, P40185, P40431, P44839, P52758, P52759, P52760, P55654, P80601, Q3T114, Q48MQ6

Diamond homologs: A0A1J1DL12, A6T7A0, A8IAD2, B0SW61, B1M5I6, B1ZB17, B5XXN2, D0LI57, D3RKL2, O25598, O34133, O43003, O52178, O58584, O66689, P0AF93, P0AF94, P0AF95, P0AGL2, P0AGL3, P0AGL4, P37552, P40037, P40185, P40431, P44839, P52758, P52759, P52760, P52761, P55654, P57452, P80601, P97117, Q10121, Q3T114, Q6FFZ5, Q7CP78, Q89AG0, Q8K9H7

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance0
Likely benign0
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

685 predictions. Top by Δscore:

VariantEffectΔscore
8:98102903:CCCTG:Cacceptor_loss1.0000
8:98102905:C:Aacceptor_loss1.0000
8:98105932:A:ACdonor_gain1.0000
8:98105932:ACTT:Adonor_loss1.0000
8:98105933:C:CCdonor_gain1.0000
8:98105934:TTACA:Tdonor_loss1.0000
8:98105935:TA:Tdonor_loss1.0000
8:98105936:A:ACdonor_gain1.0000
8:98105936:ACAC:Adonor_loss1.0000
8:98105937:C:CAdonor_gain1.0000
8:98105937:CA:Cdonor_gain1.0000
8:98105937:CACT:Cdonor_gain1.0000
8:98105937:CACTG:Cdonor_gain1.0000
8:98106002:CACCA:Cacceptor_gain1.0000
8:98106003:ACCA:Aacceptor_gain1.0000
8:98106004:CCA:Cacceptor_gain1.0000
8:98106004:CCAC:Cacceptor_gain1.0000
8:98106005:CA:Cacceptor_gain1.0000
8:98106005:CAC:Cacceptor_gain1.0000
8:98106006:ACTAG:Aacceptor_loss1.0000
8:98106007:C:CCacceptor_gain1.0000
8:98106007:CT:Cacceptor_loss1.0000
8:98106008:T:Cacceptor_loss1.0000
8:98106267:CTCA:Cdonor_loss1.0000
8:98106268:TCA:Tdonor_loss1.0000
8:98106269:CAC:Cdonor_loss1.0000
8:98106270:ACCG:Adonor_loss1.0000
8:98108644:A:ACdonor_gain1.0000
8:98108645:C:CCdonor_gain1.0000
8:98102900:CTGCC:Cacceptor_gain0.9900

AlphaMissense

876 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
8:98108747:C:GA24P0.987
8:98102883:C:GA125P0.986
8:98105991:A:TV81D0.983
8:98104512:A:CY110D0.979
8:98106000:T:AK78I0.979
8:98104523:G:TA106D0.978
8:98104519:T:AR107S0.976
8:98104519:T:GR107S0.976
8:98102876:G:TA127D0.975
8:98105988:A:GL82P0.975
8:98102882:G:TA125E0.974
8:98104496:A:GL115S0.974
8:98108654:C:GA55P0.973
8:98105958:A:TV92D0.972
8:98108713:C:TG35E0.972
8:98106301:A:GL66P0.970
8:98102890:T:AE122D0.969
8:98102890:T:GE122D0.969
8:98105966:G:CF89L0.969
8:98105966:G:TF89L0.969
8:98105968:A:GF89L0.969
8:98108746:G:TA24D0.969
8:98104518:C:GA108P0.967
8:98105999:T:AK78N0.967
8:98105999:T:GK78N0.967
8:98108704:C:TG38D0.967
8:98104514:G:TA109D0.965
8:98104526:G:TP105H0.964
8:98108713:C:AG35V0.964
8:98105954:A:CN93K0.963

dbSNP variants (sampled 300 via entrez): RS1000187597 (8:98111423 C>T), RS1000344019 (8:98118097 C>T), RS1000662520 (8:98109325 T>C), RS1000676032 (8:98116743 C>A,G), RS1000725587 (8:98111102 T>C), RS1000928429 (8:98109634 C>T), RS1001017629 (8:98118630 T>C), RS1001257510 (8:98103737 T>C,G), RS1001448124 (8:98110551 C>T), RS1001575364 (8:98117721 C>A), RS1001825853 (8:98108493 A>G), RS1002053667 (8:98117408 G>A), RS1002244119 (8:98106442 T>A), RS1002248399 (8:98116339 C>T), RS1002394458 (8:98113421 T>C)

Disease associations

OMIM: gene MIM:602487 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

2 associations (top):

StudyTraitp-value
GCST001762_746Obesity-related traits6.000000e-07
GCST006585_1707Blood protein levels6.000000e-10

EFO canonical traits (1, from GWAS)

EFO IDTrait name
EFO:0003939energy intake

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
Tretinoindecreases expression3
Cyclosporinedecreases expression3
Aflatoxin B1decreases methylation, affects expression, decreases expression3
bisphenol Aaffects expression, decreases expression2
Benzo(a)pyrenedecreases expression, increases expression2
Cadmium Chloridedecreases expression, increases expression2
aristolochic acid Iincreases expression1
Esketaminedecreases expression1
dicrotophosdecreases expression1
methyleugenoldecreases expression1
arseniteincreases reaction, affects binding1
tris(1,3-dichloro-2-propyl)phosphatedecreases expression1
sodium arsenitedecreases expression1
potassium chromate(VI)affects cotreatment, decreases expression1
beta-methylcholineaffects expression1
epigallocatechin gallatedecreases expression, affects cotreatment1
di-n-butylphosphoric acidaffects expression1
perfluorooctane sulfonic aciddecreases expression1
K 7174decreases expression1
bisphenol Bincreases expression1
abrinedecreases expression1
bisphenol Sincreases expression1
MT19c compoundincreases expression1
bisphenol AFincreases expression1
Resveratrolaffects cotreatment, increases expression1
Sunitinibdecreases expression1
Acetaminophendecreases expression1
Air Pollutantsincreases abundance, decreases expression1
Azathioprinedecreases expression1
Oxygendecreases expression1

Cellosaurus cell lines

3 cell lines: 3 cancer cell line

First 10 cell lines (id-ordered, not curated):

CellosaurusNameCategorySex
CVCL_SR66HAP1 HRSP12 (-) 1Cancer cell lineMale
CVCL_SR67HAP1 HRSP12 (-) 2Cancer cell lineMale
CVCL_SR68HAP1 HRSP12 (-) 3Cancer cell lineMale

Clinical trials (associated diseases)

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

No linked Atlas pages yet — the cross-entity mesh grows as the corpus expands.