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TRNAU1AP

gene
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Also known as SECP43FLJ20503

Summary

TRNAU1AP (tRNA selenocysteine 1 associated protein 1, HGNC:30813) is a protein-coding gene on chromosome 1p35.3, encoding tRNA selenocysteine 1-associated protein 1 (Q9NX07). Involved in the early steps of selenocysteine biosynthesis and tRNA(Sec) charging to the later steps resulting in the cotranslational incorporation of selenocysteine into selenoproteins. It is a selective cancer dependency (DepMap: 23.6% of cell lines).

Enables RNA binding activity. Predicted to be involved in selenocysteine incorporation. Predicted to be located in cytoplasm. Predicted to be active in nucleus.

Source: NCBI Gene 54952 — RefSeq curated summary.

At a glance

  • Clinical variants (ClinVar): 44 total
  • Cancer dependency (DepMap): dependent in 23.6% of screened cell lines
  • MANE Select transcript: NM_017846

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:30813
Approved symbolTRNAU1AP
NametRNA selenocysteine 1 associated protein 1
Location1p35.3
Locus typegene with protein product
StatusApproved
AliasesSECP43, FLJ20503
Ensembl geneENSG00000180098
Ensembl biotypeprotein_coding
OMIM619597
Entrez54952

Gene structure

Transcript identifiers

Ensembl transcripts: 12 — 9 protein_coding_CDS_not_defined, 3 protein_coding

ENST00000373830, ENST00000411406, ENST00000464093, ENST00000464880, ENST00000480930, ENST00000484775, ENST00000491577, ENST00000495215, ENST00000495995, ENST00000497790, ENST00000870778, ENST00000870779

RefSeq mRNA: 1 — MANE Select: NM_017846 NM_017846

CCDS: CCDS324

Canonical transcript exons

ENST00000373830 — 9 exons

ExonStartEnd
ENSE000014616822857750028578545
ENSE000014616832855308528553137
ENSE000034635322857117628571338
ENSE000034931522856470328564834
ENSE000035273692856134628561398
ENSE000035465162856729428567413
ENSE000035628572855364028553737
ENSE000035634222856063328560732
ENSE000036029862857186728571900

Expression profiles

Bgee: expression breadth ubiquitous, 243 present calls, max score 91.71.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 15.2526 / max 94.3440, expressed in 1799 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter IDTPM avgSamples expressed
181713.58551795
18161.6672962

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
granulocyteCL:000009491.71gold quality
mucosa of stomachUBERON:000119990.54gold quality
lower esophagus mucosaUBERON:003583490.43gold quality
tendon of biceps brachiiUBERON:000818889.86gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099189.30gold quality
olfactory segment of nasal mucosaUBERON:000538689.30gold quality
lower esophagusUBERON:001347389.11gold quality
lower esophagus muscularis layerUBERON:003583389.09gold quality
cortical plateUBERON:000534388.81gold quality
esophagogastric junction muscularis propriaUBERON:003584188.78gold quality
cerebellar hemisphereUBERON:000224588.34gold quality
muscle layer of sigmoid colonUBERON:003580588.33gold quality
cerebellar cortexUBERON:000212988.25gold quality
esophagusUBERON:000104388.12gold quality
descending thoracic aortaUBERON:000234588.01gold quality
left ovaryUBERON:000211988.00gold quality
apex of heartUBERON:000209887.92gold quality
ganglionic eminenceUBERON:000402387.92gold quality
monocyteCL:000057687.91gold quality
leukocyteCL:000073887.84gold quality
right ovaryUBERON:000211887.83gold quality
tibial arteryUBERON:000761087.78gold quality
mononuclear cellCL:000084287.76gold quality
popliteal arteryUBERON:000225087.76gold quality
endocervixUBERON:000045887.53gold quality
aortaUBERON:000094787.53gold quality
left uterine tubeUBERON:000130387.51gold quality
thoracic aortaUBERON:000151587.50gold quality
right hemisphere of cerebellumUBERON:001489087.48gold quality
ascending aortaUBERON:000149687.47gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

ExperimentMarker?Max mean expression
E-ANND-3yes5.31
E-MTAB-6142no195.45

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

29 targeting TRNAU1AP, 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-150-5P99.9966.691976
HSA-MIR-22-3P99.9368.13917
HSA-MIR-4713-5P99.7867.801794
HSA-MIR-200A-5P99.7669.10949
HSA-MIR-200B-5P99.7669.05948
HSA-MIR-132-3P99.7370.561424
HSA-MIR-212-3P99.7370.651424
HSA-MIR-141-5P99.5767.86897
HSA-MIR-464399.4967.631791
HSA-MIR-1213199.4868.721673
HSA-MIR-519D-5P99.4169.302057
HSA-MIR-508-5P99.4164.251248
HSA-MIR-372-5P99.4169.112299
HSA-MIR-888-5P99.3070.151855
HSA-MIR-548L99.0670.902560
HSA-MIR-4520-3P98.7566.55963
HSA-MIR-660-5P98.1668.27680
HSA-MIR-1212698.0964.82637
HSA-MIR-446997.9365.811319
HSA-MIR-93897.4168.28656
HSA-MIR-475997.3965.86608
HSA-MIR-3152-5P96.9866.88819
HSA-MIR-127096.9466.65931
HSA-MIR-62096.9466.79888
HSA-MIR-4695-3P96.7167.21836
HSA-MIR-369096.4465.18737
HSA-MIR-316996.4067.58698
HSA-MIR-808395.9367.55694
HSA-MIR-5588-3P94.9665.59500

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 23.6% of screened cell lines.

Literature-anchored findings (GeneRIF, showing 3)

  • our studies delineating the multiple, coordinated protein-nucleic acid interactions between SECp43 and the selenoprotein cotranslational factors. (PMID:16508009)
  • Data confirm interactions among components of the early steps of the selenocysteine biosynthesis pathway (SEPSECS, SECP43, SEPHS1, and SEPHS2); SECP43, which interacts with SEPSECS and SEPHS1, is a globular protein that forms oligomers in vivo. (PMID:28414460)
  • Knockdown of Trnau1ap reduced cell migration and proliferation. Knockdown of Trnau1ap blocked the PI3K/Akt signaling pathway. (PMID:29758194)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_reriotrnau1apaENSDARG00000101323
mus_musculusTrnau1apENSMUSG00000028898
rattus_norvegicusTrnau1apENSRNOG00000055344
drosophila_melanogasterSecp43FBGN0031607
caenorhabditis_elegansWBGENE00011589

Paralogs (36): DAZAP1 (ENSG00000071626), CIRBP (ENSG00000099622), RBM23 (ENSG00000100461), RBM3 (ENSG00000102317), NCL (ENSG00000115053), TIA1 (ENSG00000116001), HNRNPA2B1 (ENSG00000122566), RBM19 (ENSG00000122965), RBM39 (ENSG00000131051), MSI1 (ENSG00000135097), HNRNPA1 (ENSG00000135486), HNRNPD (ENSG00000138668), HNRNPA1L2 (ENSG00000139675), RBMX (ENSG00000147274), A1CF (ENSG00000148584), TIAL1 (ENSG00000151923), RBM46 (ENSG00000151962), HNRNPDL (ENSG00000152795), MSI2 (ENSG00000153944), RBM47 (ENSG00000163694), RBMY1F (ENSG00000169800), HNRNPA3 (ENSG00000170144), RBMXL2 (ENSG00000170748), RBM4B (ENSG00000173914), RBM4 (ENSG00000173933), RBMXL3 (ENSG00000175718), HNRNPA0 (ENSG00000177733), HNRNPAB (ENSG00000197451), RBMXL1 (ENSG00000213516), HNRNPA1L3 (ENSG00000224578), RBMY1J (ENSG00000226941), RBMY1A1 (ENSG00000234414), RBMY1E (ENSG00000242389), RBMY1B (ENSG00000242875), RBMY1D (ENSG00000244395), DND1 (ENSG00000256453)

Protein

Protein identifiers

tRNA selenocysteine 1-associated protein 1 — Q9NX07 (reviewed: Q9NX07)

Alternative names: SECp43, tRNA selenocysteine-associated protein 1

All UniProt accessions (1): Q9NX07

UniProt curated annotations — full annotation on UniProt →

Function. Involved in the early steps of selenocysteine biosynthesis and tRNA(Sec) charging to the later steps resulting in the cotranslational incorporation of selenocysteine into selenoproteins. Stabilizes the SECISBP2, EEFSEC and tRNA(Sec) complex. May be involved in the methylation of tRNA(Sec). Enhances efficiency of selenoproteins synthesis.

Subunit / interactions. Component of the tRNA(Sec) complex composed at least of EEFSEC, SECISBP2, SEPHS1, SEPHS2, SEPSECS, TRNAU1AP and tRNA(Sec). Associates with mRNP and/or polysomes.

Subcellular location. Nucleus. Cytoplasm.

Similarity. Belongs to the RRM TRSPAP family.

Isoforms (2)

UniProt IDNamesCanonical?
Q9NX07-11yes
Q9NX07-22

RefSeq proteins (1): NP_060316* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR000504RRM_domDomain
IPR012677Nucleotide-bd_a/b_plait_sfHomologous_superfamily
IPR034510SECp43_RRM2Domain
IPR035979RBD_domain_sfHomologous_superfamily
IPR040434TSAP1Family
IPR041085TSAP1_CDomain

Pfam: PF00076, PF17654

UniProt features (20 total): strand 10, helix 4, domain 2, turn 2, chain 1, splice variant 1

Structure

Experimental structures (PDB)

2 structures.

PDBMethodResolution (Å)
2DHGSOLUTION NMR
2DIVSOLUTION NMR

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9NX07-F174.760.49

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 95 (showing top): GOBP_TRANSLATION, GOBP_POST_TRANSCRIPTIONAL_REGULATION_OF_GENE_EXPRESSION, GOBP_TRANSLATIONAL_ELONGATION, LASTOWSKA_NEUROBLASTOMA_COPY_NUMBER_DN, GOBP_REGULATION_OF_TRANSLATION, chr1p35, GOMF_TRNA_BINDING, MEISSNER_NPC_HCP_WITH_H3K4ME2, GOBP_REGULATION_OF_PROTEIN_METABOLIC_PROCESS, MARTENS_TRETINOIN_RESPONSE_DN, GOBP_TRANSLATIONAL_READTHROUGH, MYC_UP.V1_UP, GSE14415_ACT_VS_CTRL_NATURAL_TREG_DN, HES4_TARGET_GENES, HMG20B_TARGET_GENES

GO Biological Process (2): selenocysteine incorporation (GO:0001514), translation (GO:0006412)

GO Molecular Function (4): tRNA binding (GO:0000049), RNA binding (GO:0003723), nucleic acid binding (GO:0003676), protein binding (GO:0005515)

GO Cellular Component (2): nucleus (GO:0005634), cytoplasm (GO:0005737)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
binding2
translational readthrough1
peptidyltransferase activity1
translational initiation1
translational elongation1
translational termination1
macromolecule biosynthetic process1
protein metabolic process1
protein biosynthetic process1
RNA binding1
nucleic acid binding1
intracellular membrane-bounded organelle1
intracellular anatomical structure1
cellular anatomical structure1

Protein interactions and networks

STRING

2024 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
TRNAU1APPSTKQ8IV42935
TRNAU1APSEPSECSQ9HD40925
TRNAU1APEEFSECP57772901
TRNAU1APSECISBP2Q96T21881
TRNAU1APSEPHS2Q99611858
TRNAU1APSEPHS1P49903689
TRNAU1APSARS1P49591551
TRNAU1APRPL30P04645521
TRNAU1APM0R2C6M0R2C6519
TRNAU1APSARS2Q9NP81519
TRNAU1APSELENOKQ9Y6D0516
TRNAU1APSCLYQ96I15506
TRNAU1APSELENOTP62341490
TRNAU1APSELENOMQ8WWX9486
TRNAU1APSELENOPP49908477
TRNAU1APSELENOSQ9BQE4477

IntAct

28 interactions, top by confidence:

ABTypeScore
CALRTRNAU1APpsi-mi:“MI:0915”(physical association)0.560
DLSTTRNAU1APpsi-mi:“MI:0915”(physical association)0.560
TRNAU1APKLK6psi-mi:“MI:0915”(physical association)0.560
TRNAU1APpsi-mi:“MI:0915”(physical association)0.560
TRNAU1APNEK7psi-mi:“MI:0915”(physical association)0.560
TRNAU1APPRPF39psi-mi:“MI:0915”(physical association)0.400
TRNAU1APE6psi-mi:“MI:0915”(physical association)0.370
NS1HAX1psi-mi:“MI:0914”(association)0.350
NS1ESYT2psi-mi:“MI:0914”(association)0.350
CAND1GTPBP10psi-mi:“MI:0914”(association)0.350
IRAK1ILVBLpsi-mi:“MI:0914”(association)0.350
TRNAU1APSLC25A4psi-mi:“MI:0914”(association)0.350
CER1PCpsi-mi:“MI:0914”(association)0.350
NXPH3NXPH4psi-mi:“MI:0914”(association)0.350
RHBGPEDS1psi-mi:“MI:0914”(association)0.350

BioGRID (47): LMNB2 (Affinity Capture-MS), PRPF39 (Affinity Capture-MS), ZG16B (Affinity Capture-MS), PRPF39 (Affinity Capture-MS), TRNAU1AP (Affinity Capture-MS), TRNAU1AP (Negative Genetic), TRNAU1AP (Negative Genetic), TRNAU1AP (Negative Genetic), TRNAU1AP (Negative Genetic), TRNAU1AP (Negative Genetic), TRNAU1AP (Negative Genetic), TRNAU1AP (Negative Genetic), TRNAU1AP (Affinity Capture-MS), TRNAU1AP (Positive Genetic), TRNAU1AP (Affinity Capture-MS)

ESM2 similar proteins: A0A0R4IEW8, A0JM51, A4QNI8, O09032, O57406, P26378, P29558, Q08E07, Q0V9L3, Q14576, Q15434, Q1RMJ7, Q28GD4, Q3ZBP3, Q3ZC34, Q4R535, Q5NVC8, Q5PQP1, Q5R995, Q5RBD3, Q5SZQ8, Q60899, Q60900, Q61701, Q62176, Q6DGV1, Q6DIV4, Q6XE24, Q6YZW2, Q7SZT7, Q7T3I7, Q7TN33, Q7TSY6, Q7ZWM3, Q8BWL5, Q8CH84, Q8CIN6, Q8N6W0, Q8VC70, Q8VXZ9

Diamond homologs: A0A0A0LLY1, A2A5N3, A2VDB3, A5A6M3, A6NDE4, A6NEQ0, D4AE41, F1QB54, F4I3B3, O60176, O64380, O75526, O93235, P0C7P1, P0C8Z4, P0CB38, P0CP46, P0CP47, P0DJD3, P0DJD4, P10979, P11940, P20965, P21187, P29341, P31483, P32588, P38159, P38760, P39684, P49310, P49311, P52912, P60824, P60825, P60826, P61286, P70318, P84586, Q00539

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance34
Likely benign0
Benign1

Top pathogenic / likely-pathogenic (0)

SpliceAI

1433 predictions. Top by Δscore:

VariantEffectΔscore
1:28553174:G:GTdonor_gain1.0000
1:28553199:G:GTdonor_gain1.0000
1:28553200:A:Tdonor_gain1.0000
1:28553635:C:CAacceptor_gain1.0000
1:28553638:AGCT:Aacceptor_gain1.0000
1:28553639:GCTG:Gacceptor_gain1.0000
1:28553733:ACTGG:Adonor_gain1.0000
1:28553734:CTGG:Cdonor_gain1.0000
1:28553735:TGG:Tdonor_gain1.0000
1:28553736:GG:Gdonor_gain1.0000
1:28553736:GGG:Gdonor_gain1.0000
1:28553737:GG:Gdonor_gain1.0000
1:28553738:G:GGdonor_gain1.0000
1:28553739:T:Gdonor_loss1.0000
1:28560733:G:GGdonor_gain1.0000
1:28561322:GTTT:Gacceptor_gain1.0000
1:28564698:CTCA:Cacceptor_loss1.0000
1:28564699:TCAGC:Tacceptor_loss1.0000
1:28564700:CAGCC:Cacceptor_loss1.0000
1:28564701:A:AGacceptor_gain1.0000
1:28564701:A:ATacceptor_loss1.0000
1:28564702:G:GAacceptor_gain1.0000
1:28564702:GCC:Gacceptor_gain1.0000
1:28564702:GCCC:Gacceptor_gain1.0000
1:28564702:GCCCT:Gacceptor_gain1.0000
1:28564802:C:Tdonor_gain1.0000
1:28564827:GTGTC:Gdonor_gain1.0000
1:28564828:TGTCT:Tdonor_gain1.0000
1:28564829:GTC:Gdonor_gain1.0000
1:28564830:TCT:Tdonor_gain1.0000

AlphaMissense

1900 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
1:28553126:T:AW6R1.000
1:28553126:T:CW6R1.000
1:28553128:G:CW6C1.000
1:28553128:G:TW6C1.000
1:28553132:G:CG8R1.000
1:28553132:G:TG8C1.000
1:28553133:G:AG8D1.000
1:28553133:G:TG8V1.000
1:28553641:T:CL10P1.000
1:28553664:T:CF18L1.000
1:28553666:C:AF18L1.000
1:28553666:C:GF18L1.000
1:28553668:T:AI19N1.000
1:28553676:G:CA22P1.000
1:28553677:C:AA22D1.000
1:28553679:T:CF23L1.000
1:28553680:T:CF23S1.000
1:28553681:T:AF23L1.000
1:28553681:T:GF23L1.000
1:28553710:T:AV33D1.000
1:28553712:A:GK34E1.000
1:28553719:T:AI36N1.000
1:28560646:T:CY47H1.000
1:28560649:T:CC48R1.000
1:28560650:G:AC48Y1.000
1:28560651:C:GC48W1.000
1:28560652:T:AF49I1.000
1:28560652:T:CF49L1.000
1:28560652:T:GF49V1.000
1:28560653:T:CF49S1.000

dbSNP variants (sampled 300 via entrez): RS1000011644 (1:28563041 A>C), RS1000106582 (1:28574299 G>C), RS1000177798 (1:28555160 G>A,C), RS1000295474 (1:28571397 T>C,G), RS1000337433 (1:28561430 A>G), RS1000364174 (1:28559209 C>A), RS1000379104 (1:28567755 A>G), RS1000422045 (1:28564586 C>T), RS1000637786 (1:28554796 A>G), RS1000729977 (1:28578120 G>T), RS1000782060 (1:28577880 A>G), RS1000983116 (1:28561125 C>G,T), RS1001060454 (1:28554009 C>G), RS1001084983 (1:28570938 A>G,T), RS1001113045 (1:28573203 T>C)

Disease associations

OMIM: gene MIM:619597 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

24 total (human), top 24 by PubMed support.

ChemicalActions (top 5)PubMed papers
bisphenol Adecreases expression, increases expression2
Valproic Aciddecreases methylation, affects expression2
selenomethylselenocysteineincreases expression1
methylmercuric chloridedecreases expression, increases expression1
sodium arseniteaffects cotreatment, decreases expression, increases abundance1
manganese chlorideaffects cotreatment, decreases expression, increases abundance1
di-n-butylphosphoric acidaffects expression1
pentabromodiphenyl etherincreases expression1
CGP 52608affects binding, increases reaction1
2,2’,4,4’-tetrabromodiphenyl etherincreases expression1
bisphenol Sdecreases methylation1
jinfukangincreases expression1
Leflunomidedecreases expression1
Acetaminophenincreases expression1
Air Pollutantsincreases abundance, increases expression1
Arsenicaffects cotreatment, decreases expression, increases abundance1
Manganeseaffects cotreatment, decreases expression, increases abundance1
Methyl Methanesulfonateincreases expression1
Ribonucleotidesaffects binding1
Rotenonedecreases expression1
Smokedecreases expression1
Asbestos, Serpentinedecreases methylation1
Sodium Seleniteincreases expression1
Particulate Matterincreases abundance, increases expression1

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.

About this page

Generated deterministically by Sugi Atlas from primary biomedical databases via BioBTree. Every record on this page traces to a primary source.

Generated
Atlas version
v1.1.4
BioBTree
v2.0.2

Sources 74

This page pulls from 74 datasets indexed by BioBTree:

alphafoldalphamissenseantibodybgeebgee_evidencebindingdbbiogrid_interactionbrendabrenda_kineticsccdscellosauruschembl_activitychembl_targetciviccivic_evidenceclingen_dosageclingen_gene_validityclinical_trialsclinvarcollectrictd_gene_interactiondbsnpdepmapdiamond_similarityefoensemblentrezesm2_similarityexonfantom5_genefantom5_promotergenccgenerifgogoparentgtopdbgwasgwas_studyhgnchpointactinterprointogenjasparmeshmimmirdbmondomsigdborphanetorthologparalogpdbpfampharmgkb_clinicalpharmgkb_genepharmgkb_guidelinepharmgkb_variantpubchempubchem_activitypubchem_assaypubmedreactomerefseqrhearnacentralscxa_expressionscxa_gene_experimentsignorspliceaistring_interactiontranscriptufeatureuniprot