RTCA

gene
On this page

Also known as RPCRTC1

Summary

RTCA (RNA 3’-terminal phosphate cyclase, HGNC:17981) is a protein-coding gene on chromosome 1p21.2, encoding RNA 3’-terminal phosphate cyclase (O00442). Catalyzes the conversion of 3’-phosphate to a 2’,3’-cyclic phosphodiester at the end of RNA.

This gene encodes a member of the RNA 3’-phosphate cyclase family. The encoded protein plays a role in RNA metabolism by catalyzing the ATP-dependent conversion of the 3’-phosphate of RNA substrates to a 2’,3’-cyclic phosphodiester. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene.

Source: NCBI Gene 8634 — RefSeq curated summary.

At a glance

  • GWAS associations: 1
  • Clinical variants (ClinVar): 90 total
  • MANE Select transcript: NM_003729

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:17981
Approved symbolRTCA
NameRNA 3’-terminal phosphate cyclase
Location1p21.2
Locus typegene with protein product
StatusApproved
AliasesRPC, RTC1
Ensembl geneENSG00000137996
Ensembl biotypeprotein_coding
OMIM611286
Entrez8634

Gene structure

Transcript identifiers

Ensembl transcripts: 12 — 10 protein_coding, 2 protein_coding_CDS_not_defined

ENST00000260563, ENST00000370126, ENST00000370128, ENST00000483474, ENST00000498617, ENST00000881959, ENST00000881960, ENST00000927400, ENST00000927401, ENST00000958304, ENST00000958305, ENST00000958306

RefSeq mRNA: 2 — MANE Select: NM_003729 NM_001130841, NM_003729

CCDS: CCDS44178, CCDS768

Canonical transcript exons

ENST00000370128 — 11 exons

ExonStartEnd
ENSE00000831307100274824100274965
ENSE00000831308100275599100275723
ENSE00001166889100287099100287203
ENSE00001166896100285228100285322
ENSE00001166905100277258100277316
ENSE00001167849100266216100266420
ENSE00001196477100291403100292769
ENSE00003514174100268152100268295
ENSE00003537387100266524100266624
ENSE00003607452100273394100273452
ENSE00003618171100270557100270680

Expression profiles

Bgee: expression breadth ubiquitous, 296 present calls, max score 96.44.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 52.2743 / max 487.5155, expressed in 1827 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter IDTPM avgSamples expressed
421948.68061827
42202.35111161
42180.7448488
42210.4978276

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
jejunal mucosaUBERON:000039996.44gold quality
esophagus squamous epitheliumUBERON:000692094.91gold quality
duodenumUBERON:000211494.40gold quality
epithelium of esophagusUBERON:000197694.16gold quality
dorsal root ganglionUBERON:000004493.59gold quality
amniotic fluidUBERON:000017393.49gold quality
heart right ventricleUBERON:000208092.80gold quality
jejunumUBERON:000211592.75gold quality
sural nerveUBERON:001548892.43gold quality
mucosa of sigmoid colonUBERON:000499392.15gold quality
colonic mucosaUBERON:000031792.14gold quality
biceps brachiiUBERON:000150792.11gold quality
body of pancreasUBERON:000115092.03gold quality
corpus epididymisUBERON:000435991.87gold quality
ponsUBERON:000098891.80gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099191.59gold quality
adrenal tissueUBERON:001830391.54gold quality
gastrocnemiusUBERON:000138891.45gold quality
calcaneal tendonUBERON:000370191.43gold quality
nephron tubuleUBERON:000123191.37gold quality
muscle of legUBERON:000138391.29gold quality
oral cavityUBERON:000016791.17gold quality
skeletal muscle tissue of biceps brachiiUBERON:000450290.97gold quality
heart left ventricleUBERON:000208490.93gold quality
cardiac ventricleUBERON:000208290.84gold quality
mucosa of transverse colonUBERON:000499190.80gold quality
cortical plateUBERON:000534390.72gold quality
rectumUBERON:000105290.70gold quality
tibiaUBERON:000097990.68gold quality
tendonUBERON:000004390.64gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 1.

ExperimentMarker?Max mean expression
E-ANND-3yes6.73

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

62 targeting RTCA, 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-MIR-3163100.0077.238605
HSA-MIR-3646100.0073.565283
HSA-MIR-371B-5P99.9975.344759
HSA-MIR-186-5P99.9970.833707
HSA-MIR-366299.9973.825684
HSA-MIR-450099.9972.722367
HSA-MIR-373-5P99.9875.364753
HSA-MIR-616-5P99.9875.584775
HSA-MIR-569699.9872.364487
HSA-MIR-545-3P99.9570.742783
HSA-MIR-3682-5P99.9367.971163
HSA-MIR-454-3P99.9174.011925
HSA-MIR-130A-3P99.9073.311861
HSA-MIR-130B-3P99.9073.271850
HSA-MIR-301A-3P99.9073.151839
HSA-MIR-301B-3P99.9073.191836
HSA-MIR-366699.9073.241833
HSA-MIR-429599.9073.111838
HSA-MIR-367199.9073.043897
HSA-MIR-4671-3P99.8872.461045
HSA-MIR-6780A-5P99.8866.692776
HSA-MIR-202-3P99.8471.411290
HSA-MIR-1273H-5P99.7766.322471
HSA-MIR-3680-3P99.7572.513095
HSA-MIR-4699-3P99.7170.153142
HSA-MIR-30B-3P99.7065.762325
HSA-MIR-3689A-3P99.7065.732306
HSA-MIR-3689B-3P99.7065.712311
HSA-MIR-3689C99.7065.712311

Literature-anchored findings (GeneRIF, showing 2)

  • Rtc1 forms a stable binary complex with a 3’-phosphate terminated RNA, but not with an identical 3’-OH terminated RNA (PMID:19690099)
  • CNP and RtcA fine-tune XBP1 output during ER stress (PMID:30355738)

Cross-species orthologs

4 orthologs

OrganismSymbolGene ID
danio_reriortcaENSDARG00000002215
mus_musculusRtcaENSMUSG00000000339
rattus_norvegicusRtcaENSRNOG00000014575
drosophila_melanogasterRtcaFBGN0025630

Paralogs (1): RCL1 (ENSG00000120158)

Protein

Protein identifiers

RNA 3’-terminal phosphate cyclaseO00442 (reviewed: O00442)

Alternative names: RNA terminal phosphate cyclase domain-containing protein 1

All UniProt accessions (2): A6NIC1, O00442

UniProt curated annotations — full annotation on UniProt →

Function. Catalyzes the conversion of 3’-phosphate to a 2’,3’-cyclic phosphodiester at the end of RNA. The mechanism of action of the enzyme occurs in 3 steps: (A) adenylation of the enzyme by ATP; (B) transfer of adenylate to an RNA-N3’P to produce RNA-N3’PP5’A; (C) and attack of the adjacent 2’-hydroxyl on the 3’-phosphorus in the diester linkage to produce the cyclic end product. Likely functions in some aspects of cellular RNA processing. Function plays an important role in regulating axon regeneration by inhibiting central nervous system (CNS) axon regeneration following optic nerve injury.

Subcellular location. Nucleus. Nucleoplasm.

Tissue specificity. Ubiquitous.

Similarity. Belongs to the RNA 3’-terminal cyclase family. Type 1 subfamily.

Isoforms (2)

UniProt IDNamesCanonical?
O00442-11yes
O00442-22

RefSeq proteins (2): NP_001124313, NP_003720* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR000228RNA3’_term_phos_cycFamily
IPR013791RNA3’-term_phos_cycl_insertDomain
IPR013792RNA3’P_cycl/enolpyr_Trfase_a/bHomologous_superfamily
IPR017770RNA3’_term_phos_cyc_type_1Family
IPR020719RNA3’_term_phos_cycl-like_CSConserved_site
IPR023797RNA3’_phos_cyclase_domDomain
IPR036553RPTC_insertHomologous_superfamily
IPR037136RNA3’_phos_cyclase_dom_sfHomologous_superfamily

Pfam: PF01137, PF05189

Enzyme classification (BRENDA):

  • EC 6.5.1.4 — RNA 3’-terminal-phosphate cyclase (ATP) (BRENDA: 25 organisms, 55 substrates, 8 inhibitors, 9 Km, 1 kcat entries)

Substrate kinetics (BRENDA)

3 substrates with measured Km, best-characterized 3. Km ranges are aggregated across organisms/conditions.

SubstrateKm (mM)Measurements
ATP0.0017–0.025
ATPGAMMAS0.0062
GTP0.1–0.22

Catalyzed reactions (Rhea), 1 shown:

  • a 3’-end 3’-phospho-ribonucleotide-RNA + ATP = a 3’-end 2’,3’-cyclophospho-ribonucleotide-RNA + AMP + diphosphate (RHEA:23976)

UniProt features (10 total): binding site 6, chain 1, active site 1, splice variant 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-O00442-F195.900.95

Functional residue map

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

Catalytic / active sites (1): 320 (tele-amp-histidine intermediate)

Ligand- & substrate-binding residues (6): 104; 131; 294; 297; 298; 320

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 169 (showing top): GSE45365_NK_CELL_VS_CD8_TCELL_UP, RODRIGUES_THYROID_CARCINOMA_ANAPLASTIC_UP, RODRIGUES_THYROID_CARCINOMA_POORLY_DIFFERENTIATED_UP, GOBP_REGENERATION, GOBP_NEUROGENESIS, GOBP_RESPONSE_TO_AXON_INJURY, GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_BLUE_UP, PATIL_LIVER_CANCER, GOBP_NEGATIVE_REGULATION_OF_CELLULAR_COMPONENT_ORGANIZATION, GOBP_REGULATION_OF_CELL_PROJECTION_ORGANIZATION, GOBP_REGULATION_OF_RESPONSE_TO_WOUNDING, GNF2_XRCC5, GOBP_REGULATION_OF_RESPONSE_TO_STRESS, GOBP_REGULATION_OF_NEURON_PROJECTION_REGENERATION, GOBP_NEGATIVE_REGULATION_OF_CELL_PROJECTION_ORGANIZATION

GO Biological Process (2): RNA processing (GO:0006396), negative regulation of optical nerve axon regeneration (GO:1905592)

GO Molecular Function (7): RNA binding (GO:0003723), RNA-3’-phosphate cyclase activity (GO:0003963), ATP binding (GO:0005524), nucleotide binding (GO:0000166), catalytic activity (GO:0003824), protein binding (GO:0005515), ligase activity (GO:0016874)

GO Cellular Component (2): nucleus (GO:0005634), nucleoplasm (GO:0005654)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
gene expression1
RNA biosynthetic process1
primary metabolic process1
negative regulation of axon regeneration1
optical nerve axon regeneration1
regulation of optical nerve axon regeneration1
nucleic acid binding1
cyclase activity1
ligase activity, forming phosphoric ester bonds1
catalytic activity, acting on RNA1
adenyl ribonucleotide binding1
purine ribonucleoside triphosphate binding1
nucleoside phosphate binding1
heterocyclic compound binding1
molecular_function1
binding1
catalytic activity1
intracellular membrane-bounded organelle1
nuclear lumen1
cellular anatomical structure1

Protein interactions and networks

STRING

2519 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
RTCABMS1Q14692853
RTCARTCBQ9Y3I0851
RTCADPH5Q9H2P9614
RTCALRRC39Q96DD0609
RTCATRPT1Q86TN4605
RTCADBTP11182557
RTCAZBTB8OSQ8IWT0547
RTCATRMT13Q9NUP7512
RTCAFCF1Q9Y324478
RTCASLC35H1Q9NQQ7457
RTCASLC30A7Q8NEW0455
RTCARO60P10155446
RTCAFAM98BQ52LJ0430
RTCAGGNQ86UU5425
RTCAFPGTO14772423
RTCAGPR88Q9GZN0423

IntAct

80 interactions, top by confidence:

ABTypeScore
CFTRESYT2psi-mi:“MI:2364”(proximity)0.710
LAMP3METTL15psi-mi:“MI:0914”(association)0.530
Sass6MACF1psi-mi:“MI:0914”(association)0.350
FOXL2RTCApsi-mi:“MI:0914”(association)0.350
FOXQ1ARHGAP10psi-mi:“MI:0914”(association)0.350
FOXS1DDX39Apsi-mi:“MI:0914”(association)0.350
JUNpsi-mi:“MI:0914”(association)0.350
JUNTPM3psi-mi:“MI:0914”(association)0.350
HSCBRBP5psi-mi:“MI:0914”(association)0.350
CAND1GTPBP10psi-mi:“MI:0914”(association)0.350
USP45RTCApsi-mi:“MI:0914”(association)0.350
PRKD1MYO1Cpsi-mi:“MI:0914”(association)0.350
ZDHHC5HACD3psi-mi:“MI:0914”(association)0.350
TAGLNLOC392647psi-mi:“MI:0914”(association)0.350
ARID1BRTCApsi-mi:“MI:0914”(association)0.350
ITM2BILVBLpsi-mi:“MI:0914”(association)0.350
OSTM1ILVBLpsi-mi:“MI:0914”(association)0.350
PRKYMETTL15psi-mi:“MI:0914”(association)0.350
HOXC5PDLIM1psi-mi:“MI:0914”(association)0.350
GORASP1RTCApsi-mi:“MI:0914”(association)0.350
CNTN2RTCApsi-mi:“MI:0914”(association)0.350
ZNF695RTCApsi-mi:“MI:0914”(association)0.350
PAEPRTCApsi-mi:“MI:0914”(association)0.350
HNRNPCL2SMCHD1psi-mi:“MI:0914”(association)0.350
RTCANDUFA4psi-mi:“MI:0914”(association)0.350
RTCApsi-mi:“MI:0914”(association)0.350
POLRMTpsi-mi:“MI:0914”(association)0.350

BioGRID (146): HNRNPH1 (Co-fractionation), RTCA (Affinity Capture-MS), RTCA (Affinity Capture-MS), RTCA (Affinity Capture-MS), RTCA (Affinity Capture-MS), RTCA (Affinity Capture-MS), RTCA (Affinity Capture-MS), RTCA (Affinity Capture-MS), RTCA (Affinity Capture-MS), RPL21 (Affinity Capture-MS), FBL (Affinity Capture-MS), RPL23A (Affinity Capture-MS), RPL18A (Affinity Capture-MS), DDX21 (Affinity Capture-MS), RTCA (Affinity Capture-MS)

ESM2 similar proteins: A2RVK7, A2X0Q3, A6QLJ3, O00442, O23617, O81147, O81852, P0CT46, P31754, P37142, P48605, P49080, P49368, P80318, Q01415, Q06265, Q14181, Q2HJ88, Q2KHU3, Q3SWZ4, Q3T0K2, Q4QR75, Q4R3J0, Q4R963, Q5NVF9, Q5R6J8, Q5R7P3, Q5RCW2, Q5RGJ5, Q5XJQ5, Q69LE7, Q6P502, Q6STH5, Q6YXZ7, Q7YRA3, Q84T68, Q8C3X4, Q8GZQ3, Q8K1R3, Q8N442

Diamond homologs: A0B532, A1AGU3, A1RSJ7, A2BN21, A3DN24, A3MXQ7, A4XRJ0, A4YEC3, A7ZSU9, A8A5M8, A8A9W2, A8MAV7, B0R414, B1IP46, B1L6E9, B1LI80, B1X765, B1YDJ1, B2IWJ8, B2U3M8, B4TKU5, B5F8N4, B5R378, B5R7J6, B5YTX2, B6YSJ5, B7KCF3, B7L4U9, B7LSC2, B7M2I0, B7MDP5, B7N1J7, B7NE24, B7NMI4, B7UKC4, B7V0C8, B8D680, C0Q0J3, C3MKC1, C3MU91

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 80 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
Peptide chain elongation1023.5×1e-09
Viral mRNA Translation1023.5×1e-09
PELO:HBS1L and ABCE1 dissociate a ribosome on a non-stop mRNA1023.2×1e-09
Selenocysteine synthesis1022.3×1e-09
Eukaryotic Translation Termination1022.3×1e-09
Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC)1021.8×1e-09
ZNF598 and the Ribosome-associated Quality Trigger (RQT) complex dissociate a ribosome stalled on a no-go mRNA1021.8×1e-09
Formation of a pool of free 40S subunits1020.7×1e-09

GO biological processes:

GO termPartnersFoldFDR
cytoplasmic translation1128.3×6e-11
translation1014.3×4e-07

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance63
Likely benign2
Benign1

Top pathogenic / likely-pathogenic (0)

SpliceAI

1801 predictions. Top by Δscore:

VariantEffectΔscore
1:100266417:AGGGG:Adonor_loss1.0000
1:100266418:GGG:Gdonor_gain1.0000
1:100266419:GG:Gdonor_gain1.0000
1:100266419:GGG:Gdonor_gain1.0000
1:100266420:GG:Gdonor_gain1.0000
1:100266420:GGT:Gdonor_loss1.0000
1:100266421:G:GAdonor_loss1.0000
1:100266421:G:GGdonor_gain1.0000
1:100266422:T:Adonor_loss1.0000
1:100266618:GCC:Gdonor_gain1.0000
1:100266621:TGAGG:Tdonor_loss1.0000
1:100266623:AGGT:Adonor_loss1.0000
1:100266624:GGTAA:Gdonor_loss1.0000
1:100266625:G:Adonor_loss1.0000
1:100266626:T:Adonor_loss1.0000
1:100268135:A:AGacceptor_gain1.0000
1:100268136:G:GGacceptor_gain1.0000
1:100268167:T:TAacceptor_gain1.0000
1:100270556:GGA:Gacceptor_gain1.0000
1:100270556:GGAGT:Gacceptor_gain1.0000
1:100270605:T:Aacceptor_gain1.0000
1:100273388:TTTCA:Tacceptor_loss1.0000
1:100273389:TTCA:Tacceptor_loss1.0000
1:100273391:CA:Cacceptor_loss1.0000
1:100273392:A:AGacceptor_gain1.0000
1:100273392:A:Tacceptor_loss1.0000
1:100273393:G:GGacceptor_gain1.0000
1:100274820:ATAGG:Aacceptor_gain1.0000
1:100275592:A:AGacceptor_gain1.0000
1:100275596:TA:Tacceptor_loss1.0000

AlphaMissense

2376 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
1:100274826:G:AG159E0.999
1:100275623:G:CA214P0.998
1:100285248:G:AG274R0.998
1:100285248:G:CG274R0.998
1:100285249:G:AG274E0.998
1:100285260:G:CA278P0.998
1:100285318:A:CD297A0.998
1:100285318:A:TD297V0.998
1:100287162:C:GH320D0.998
1:100268158:A:CQ51H0.997
1:100268158:A:TQ51H0.997
1:100268292:C:AA96E0.997
1:100270558:A:CS98R0.997
1:100270560:T:AS98R0.997
1:100270560:T:GS98R0.997
1:100270568:T:CL101P0.997
1:100270637:G:AG124E0.997
1:100270644:T:AN126K0.997
1:100270644:T:GN126K0.997
1:100274825:G:AG159R0.997
1:100274825:G:CG159R0.997
1:100274847:G:AG166D0.997
1:100275717:G:AG245E0.997
1:100277266:C:AA250D0.997
1:100285261:C:AA278D0.997
1:100285317:G:CD297H0.997
1:100287164:T:AH320Q0.997
1:100287164:T:GH320Q0.997
1:100266540:G:CR21T0.996
1:100270633:G:CG123R0.996

dbSNP variants (sampled 300 via entrez): RS1000150682 (1:100280849 A>G), RS1000162035 (1:100281423 A>G), RS1000171084 (1:100270214 T>G), RS1000487267 (1:100282517 T>G), RS1000541523 (1:100268926 C>T), RS1000594813 (1:100275143 C>A,T), RS1000912896 (1:100269049 A>C,G), RS1000929471 (1:100287801 T>C), RS1000961809 (1:100264338 T>C), RS1001128756 (1:100270155 C>T), RS1001163737 (1:100279762 A>T), RS1001165586 (1:100281307 G>A), RS1001420737 (1:100276381 T>C), RS1001484497 (1:100281558 A>G), RS1001501670 (1:100265121 T>C)

Disease associations

OMIM: gene MIM:611286 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

1 associations (top):

StudyTraitp-value
GCST002337_70Amyotrophic lateral sclerosis (sporadic)9.000000e-06

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
sodium arseniteincreases expression, decreases expression, increases abundance3
Valproic Acidincreases expression, affects expression3
cobaltous chlorideincreases expression2
Air Pollutantsdecreases expression, increases abundance, increases expression2
Arsenicaffects methylation, increases abundance, increases expression2
Cyclosporineincreases expression2
Particulate Matterdecreases expression, increases abundance, increases expression2
dicrotophosdecreases expression1
bisphenol Aaffects expression1
sodium arsenatedecreases expression1
tris(1,3-dichloro-2-propyl)phosphateincreases expression1
beta-methylcholineaffects expression1
di-n-butylphosphoric acidaffects expression1
nutlin 3increases secretion, affects cotreatment1
ICG 001increases expression1
bisphenol Bincreases expression1
abrinedecreases expression1
pentabrominated diphenyl ether 100decreases expression1
hexabrominated diphenyl ether 153decreases expression1
NSC 689534increases expression, affects binding1
Resveratrolaffects cotreatment, increases expression1
Copperaffects binding, increases expression1
Dactinomycinaffects cotreatment, increases secretion1
Doxorubicindecreases expression1
Enzyme Inhibitorsdecreases activity, increases O-linked glycosylation1
Ivermectindecreases expression1
Plant Extractsaffects cotreatment, increases expression1
Quercetindecreases expression1
Rotenonedecreases expression1
Thiramincreases 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): sporadic amyotrophic lateral sclerosis