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BUD31

gene
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Also known as YCR063WEDG-2EDG2fSAP17Cwc14

Summary

BUD31 (BUD31 spliceosome associated protein, HGNC:29629) is a protein-coding gene on chromosome 7q22.1, encoding Protein BUD31 homolog (P41223). Involved in the pre-mRNA splicing process. It is a common-essential gene (DepMap: required in 100.0% of cancer cell lines).

Enables nuclear receptor binding activity and transcription coactivator activity. Involved in mRNA splicing, via spliceosome. Located in centrosome; chromatin; and nucleoplasm. Part of U2-type catalytic step 2 spliceosome.

Source: NCBI Gene 8896 — RefSeq curated summary.

At a glance

  • GWAS associations: 4
  • Clinical variants (ClinVar): 14 total
  • Cancer dependency (DepMap): dependent in 100.0% of screened cell lines (common-essential)
  • MANE Select transcript: NM_003910

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:29629
Approved symbolBUD31
NameBUD31 spliceosome associated protein
Location7q22.1
Locus typegene with protein product
StatusApproved
AliasesYCR063W, EDG-2, EDG2, fSAP17, Cwc14
Ensembl geneENSG00000106245
Ensembl biotypeprotein_coding
OMIM603477
Entrez8896

Gene structure

Transcript identifiers

Ensembl transcripts: 35 — 29 protein_coding, 4 retained_intron, 1 nonsense_mediated_decay, 1 protein_coding_CDS_not_defined

ENST00000222969, ENST00000403633, ENST00000427499, ENST00000431419, ENST00000456893, ENST00000466798, ENST00000471813, ENST00000473447, ENST00000496696, ENST00000911008, ENST00000911009, ENST00000911010, ENST00000911011, ENST00000911012, ENST00000911013, ENST00000911014, ENST00000911015, ENST00000911016, ENST00000911017, ENST00000911018, ENST00000927018, ENST00000927019, ENST00000927020, ENST00000927021, ENST00000927022, ENST00000927023, ENST00000927024, ENST00000927025, ENST00000927026, ENST00000927027, ENST00000927028, ENST00000927029, ENST00000927030, ENST00000966322, ENST00000966323

RefSeq mRNA: 3 — MANE Select: NM_003910 NM_001370407, NM_001370410, NM_003910

CCDS: CCDS5663

Canonical transcript exons

ENST00000222969 — 6 exons

ExonStartEnd
ENSE000007080869941742999417595
ENSE000010554499940896999409245
ENSE000010554529941003499410169
ENSE000018492739941939199419616
ENSE000034603969941106499411186
ENSE000035330329941613899416260

Expression profiles

Bgee: expression breadth ubiquitous, 293 present calls, max score 97.78.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 106.2027 / max 2371.0981, expressed in 1826 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter IDTPM avgSamples expressed
7987291.06951825
798716.88821765
798704.53211644
798733.71291462

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
olfactory segment of nasal mucosaUBERON:000538697.78gold quality
left testisUBERON:000453397.62gold quality
right testisUBERON:000453497.52gold quality
cortical plateUBERON:000534397.52gold quality
ganglionic eminenceUBERON:000402397.21gold quality
adenohypophysisUBERON:000219697.04gold quality
stromal cell of endometriumCL:000225596.99gold quality
testisUBERON:000047396.98gold quality
islet of LangerhansUBERON:000000696.95gold quality
granulocyteCL:000009496.83gold quality
calcaneal tendonUBERON:000370196.82gold quality
mucosa of transverse colonUBERON:000499196.71gold quality
ventricular zoneUBERON:000305396.66gold quality
right uterine tubeUBERON:000130296.40gold quality
pituitary glandUBERON:000000796.36gold quality
C1 segment of cervical spinal cordUBERON:000646996.31gold quality
descending thoracic aortaUBERON:000234596.26gold quality
popliteal arteryUBERON:000225096.25gold quality
tibial arteryUBERON:000761096.25gold quality
left coronary arteryUBERON:000162696.23gold quality
prefrontal cortexUBERON:000045196.22gold quality
monocyteCL:000057696.18gold quality
ascending aortaUBERON:000149696.18gold quality
aortaUBERON:000094796.17gold quality
thoracic aortaUBERON:000151596.16gold quality
tendon of biceps brachiiUBERON:000818896.15gold quality
tibial nerveUBERON:000132396.14gold quality
caudate nucleusUBERON:000187396.10gold quality
right lobe of thyroid glandUBERON:000111996.09gold quality
leukocyteCL:000073896.05gold quality

Single-cell (SCXA)

Detected in 5 experiment(s), a significant marker in 3.

ExperimentMarker?Max mean expression
E-MTAB-10485yes1101.38
E-GEOD-84465yes22.88
E-MTAB-6379no813.64
E-GEOD-93593no7.69
E-ANND-3no0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

3 targeting BUD31, 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-2681-5P99.7567.641655
HSA-MIR-429798.7766.952013
HSA-MIR-6840-3P98.6865.951923

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 100.0% of screened cell lines, common-essential.

Literature-anchored findings (GeneRIF, showing 3)

  • High BUD31 expression is associated with hepatocellular carcinoma. (PMID:25731616)
  • Downregulation of BUD31 Promotes Prostate Cancer Cell Proliferation and Migration via Activation of p-AKT and Vimentin In Vitro. (PMID:37047027)
  • The role of BUD31 in clear cell renal cell carcinoma: prognostic significance, alternative splicing, and tumor immune environment. (PMID:39136845)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_reriobud31ENSDARG00000017084
mus_musculusBud31ENSMUSG00000038722
rattus_norvegicusBud31ENSRNOG00000000989
drosophila_melanogasterl(1)10BbFBGN0001491
caenorhabditis_elegansWBGENE00007400

Protein

Protein identifiers

Protein BUD31 homolog — P41223 (reviewed: P41223)

Alternative names: Protein EDG-2, Protein G10 homolog

All UniProt accessions (3): P41223, C9JCD9, F8WCN7

UniProt curated annotations — full annotation on UniProt →

Function. Involved in the pre-mRNA splicing process. May play a role as regulator of AR transcriptional activity; may increase AR transcriptional activity.

Subunit / interactions. Identified in the spliceosome C complex. May interact with AR.

Subcellular location. Nucleus.

Tissue specificity. Detected in epithelial and stromal cells in benign prostate hyperplasia tissue (at protein level).

Domain organisation. Contains a short sequence motif (Phe-Xaa-Xaa-Phe-Tyr) that can bind to AR and may modulate AR activity.

Similarity. Belongs to the BUD31 (G10) family.

Isoforms (2)

UniProt IDNamesCanonical?
P41223-11yes
P41223-22

RefSeq proteins (3): NP_001357336, NP_001357339, NP_003901* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR001748BUD31Family
IPR018230BUD31/G10-rel_CSConserved_site

Pfam: PF01125

UniProt features (25 total): helix 9, sequence conflict 7, strand 3, chain 1, region of interest 1, short sequence motif 1, turn 1, modified residue 1, splice variant 1

Structure

Experimental structures (PDB)

38 structures, top 30 by resolution.

PDBMethodResolution (Å)
4OEDX-RAY DIFFRACTION2.79
8C6JELECTRON MICROSCOPY2.8
6ID1ELECTRON MICROSCOPY2.86
6ID0ELECTRON MICROSCOPY2.9
4OKBX-RAY DIFFRACTION2.95
6ICZELECTRON MICROSCOPY3
8I0RELECTRON MICROSCOPY3
8I0TELECTRON MICROSCOPY3
8I0VELECTRON MICROSCOPY3
7QTTELECTRON MICROSCOPY3.1
8Q7NELECTRON MICROSCOPY3.1
9R3DELECTRON MICROSCOPY3.12
6QDVELECTRON MICROSCOPY3.3
8I0UELECTRON MICROSCOPY3.3
9FMDELECTRON MICROSCOPY3.3
6FF4ELECTRON MICROSCOPY3.4
6ZYMELECTRON MICROSCOPY3.4
8I0PELECTRON MICROSCOPY3.4
8I0WELECTRON MICROSCOPY3.4
8RO2ELECTRON MICROSCOPY3.5
4OH6X-RAY DIFFRACTION3.56
5XJCELECTRON MICROSCOPY3.6
7W59ELECTRON MICROSCOPY3.6
7W5AELECTRON MICROSCOPY3.6
7ABFELECTRON MICROSCOPY3.9
5YZGELECTRON MICROSCOPY4.1
7AAVELECTRON MICROSCOPY4.2
8I0SELECTRON MICROSCOPY4.2
7W5BELECTRON MICROSCOPY4.3
6FF7ELECTRON MICROSCOPY4.5

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-P41223-F191.030.72

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 (1): 125

Function

Pathways and Gene Ontology

Reactome pathways

5 pathways

IDPathway
R-HSA-72163mRNA Splicing - Major Pathway
R-HSA-9918481Dengue Virus-Host Interactions
R-HSA-72172mRNA Splicing
R-HSA-72203Processing of Capped Intron-Containing Pre-mRNA
R-HSA-8953854Metabolism of RNA

MSigDB gene sets: 179 (showing top): AP1_01, MORF_MBD4, MORF_RAB5A, BASSO_B_LYMPHOCYTE_NETWORK, ENK_UV_RESPONSE_KERATINOCYTE_UP, STARK_PREFRONTAL_CORTEX_22Q11_DELETION_DN, MORF_RAD21, HSIAO_HOUSEKEEPING_GENES, MORF_PSMC2, CEBPB_01, MORF_SKP1A, CEBP_Q2, MORF_ATOX1, SHETH_LIVER_CANCER_VS_TXNIP_LOSS_PAM5, GGAANCGGAANY_UNKNOWN

GO Biological Process (4): mRNA splicing, via spliceosome (GO:0000398), mRNA processing (GO:0006397), RNA splicing (GO:0008380), positive regulation of DNA-templated transcription (GO:0045893)

GO Molecular Function (3): transcription coactivator activity (GO:0003713), nuclear receptor binding (GO:0016922), protein binding (GO:0005515)

GO Cellular Component (7): chromatin (GO:0000785), nucleus (GO:0005634), nucleoplasm (GO:0005654), spliceosomal complex (GO:0005681), centrosome (GO:0005813), microtubule cytoskeleton (GO:0015630), U2-type catalytic step 2 spliceosome (GO:0071007)

Reactome top-level categories

Rollup of top-4 pathways:

CategoryPathways
mRNA Splicing1
Dengue Virus Infection1
Processing of Capped Intron-Containing Pre-mRNA1
Metabolism of RNA1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
RNA processing2
cellular anatomical structure2
RNA splicing, via transesterification reactions with bulged adenosine as nucleophile1
mRNA processing1
mRNA metabolic process1
DNA-templated transcription1
regulation of DNA-templated transcription1
positive regulation of RNA biosynthetic process1
transcription coregulator activity1
positive regulation of DNA-templated transcription1
RNA polymerase II-specific DNA-binding transcription factor binding1
binding1
chromosome1
intracellular membrane-bounded organelle1
nuclear lumen1
nuclear protein-containing complex1
ribonucleoprotein complex1
centriole1
microtubule organizing center1
cytoskeleton1
U2-type spliceosomal complex1
U2 snRNP1
U6 snRNP1
catalytic step 2 spliceosome1

Protein interactions and networks

STRING

2087 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
BUD31RBM22Q9NW64856
BUD31ECM2O94769776
BUD31CDC5LQ99459775
BUD31PLRG1O43660760
BUD31SNW1Q13573759
BUD31CWC15Q9P013745
BUD31XAB2Q9HCS7743
BUD31CWC22Q9HCG8743
BUD31EFTUD2Q15029742
BUD31DHX8Q14562678
BUD31YJU2Q9BW85647
BUD31PRPF19Q9UMS4613
BUD31CDC40O60508599
BUD31CRNKL1Q9BZJ0595
BUD31SYF2O95926590

IntAct

92 interactions, top by confidence:

ABTypeScore
RNASE1RNH1psi-mi:“MI:0914”(association)0.850
PRPF19AQRpsi-mi:“MI:0914”(association)0.790
KRTAP10-7BUD31psi-mi:“MI:0915”(physical association)0.720
BUD31KRTAP10-7psi-mi:“MI:0915”(physical association)0.720
SNRPA1HTATSF1psi-mi:“MI:0914”(association)0.640
BUD31psi-mi:“MI:0915”(physical association)0.560
BEND5BUD31psi-mi:“MI:0915”(physical association)0.560
BUD31psi-mi:“MI:0915”(physical association)0.560
BUD31MEOX2psi-mi:“MI:0915”(physical association)0.560
BUD31PICK1psi-mi:“MI:0915”(physical association)0.560
BUD31HOXA1psi-mi:“MI:0915”(physical association)0.560
KSR2POLR3Apsi-mi:“MI:0914”(association)0.530
AKIRIN2RGPD3psi-mi:“MI:0914”(association)0.530
SNRPNPRMT5psi-mi:“MI:0914”(association)0.530
SNIP1CASC3psi-mi:“MI:0914”(association)0.530
PRPF19STRNpsi-mi:“MI:0914”(association)0.530
KIAA1143AQRpsi-mi:“MI:0914”(association)0.530
WDR83SH2B2psi-mi:“MI:0914”(association)0.530
PPIL1AQRpsi-mi:“MI:0914”(association)0.530
H3C1SMCHD1psi-mi:“MI:2364”(proximity)0.410

BioGRID (151): BEND5 (Two-hybrid), KRTAP10-7 (Two-hybrid), KRTAP10-3 (Two-hybrid), BUD31 (Affinity Capture-MS), BUD31 (Affinity Capture-MS), BUD31 (Affinity Capture-MS), BUD31 (Affinity Capture-MS), BUD31 (Affinity Capture-MS), BUD31 (Affinity Capture-MS), BUD31 (Affinity Capture-MS), BUD31 (Co-fractionation), BUD31 (Co-fractionation), BUD31 (Co-fractionation), CCDC101 (Co-fractionation), CCDC12 (Co-fractionation)

ESM2 similar proteins: A1RV74, A1RWQ5, A2BMB3, A3DNB1, A3MTT6, A4WIZ3, A8AA18, A9A5J1, B1L708, B1YD00, B6YSL7, B9K890, C5A282, C6A163, G1U0Q2, O26114, O28358, O29789, O59422, O65059, O66435, O70454, P20342, P38520, P41223, P42078, P54018, P62841, P62842, P62843, P62844, P62845, P62846, Q0W1Y5, Q2NKU3, Q4JB44, Q56K10, Q5JDH3, Q5RDI7, Q6PGH1

Diamond homologs: O70454, O74772, P12805, P25337, P34313, P35682, P41223, Q2NKU3, Q567Z7, Q65WT0, Q6PGH1, Q94DE2, Q962X9

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 86 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
mRNA Splicing1220.6×5e-11
mRNA Splicing - Major Pathway2218.8×3e-20
Processing of Capped Intron-Containing Pre-mRNA1418.0×5e-12
mRNA Polyadenylation1013.7×2e-07
Dengue Virus-Host Interactions1510.7×5e-10
Metabolism of RNA159.8×2e-09

GO biological processes:

GO termPartnersFoldFDR
mRNA splicing, via spliceosome2024.4×6e-20
RNA splicing1011.8×4e-06

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance8
Likely benign0
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

943 predictions. Top by Δscore:

VariantEffectΔscore
7:99410165:CTAAG:Cdonor_loss1.0000
7:99410166:TAAG:Tdonor_loss1.0000
7:99410167:AAG:Adonor_loss1.0000
7:99410168:AGG:Adonor_loss1.0000
7:99410170:G:Tdonor_loss1.0000
7:99410171:T:Gdonor_loss1.0000
7:99411062:A:AGacceptor_gain1.0000
7:99411063:G:GCacceptor_gain1.0000
7:99411063:GA:Gacceptor_gain1.0000
7:99411063:GAT:Gacceptor_gain1.0000
7:99411063:GATC:Gacceptor_gain1.0000
7:99411063:GATCT:Gacceptor_gain1.0000
7:99411183:GAAG:Gdonor_gain1.0000
7:99411184:AAG:Adonor_gain1.0000
7:99411185:AG:Adonor_gain1.0000
7:99411186:GG:Gdonor_gain1.0000
7:99411186:GGTG:Gdonor_loss1.0000
7:99411187:G:GGdonor_gain1.0000
7:99411187:GTGA:Gdonor_loss1.0000
7:99416136:A:AGacceptor_gain1.0000
7:99416136:AGCT:Aacceptor_gain1.0000
7:99416137:G:GTacceptor_gain1.0000
7:99416137:GC:Gacceptor_gain1.0000
7:99416137:GCT:Gacceptor_gain1.0000
7:99416137:GCTG:Gacceptor_gain1.0000
7:99416137:GCTGA:Gacceptor_gain1.0000
7:99416258:GAG:Gdonor_gain1.0000
7:99416259:AGGTA:Adonor_loss1.0000
7:99416260:GG:Gdonor_loss1.0000
7:99416261:G:GGdonor_gain1.0000

AlphaMissense

951 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
7:99411135:T:AW15R1.000
7:99411135:T:CW15R1.000
7:99411137:G:CW15C1.000
7:99411137:G:TW15C1.000
7:99416165:G:TR41M1.000
7:99416182:T:AW47R1.000
7:99416182:T:CW47R1.000
7:99416216:G:CR58P1.000
7:99416231:T:CL63P1.000
7:99417443:T:CC78R1.000
7:99417444:G:AC78Y1.000
7:99417445:T:GC78W1.000
7:99417474:T:CL88P1.000
7:99417485:T:AW92R1.000
7:99417485:T:CW92R1.000
7:99417487:G:CW92C1.000
7:99417487:G:TW92C1.000
7:99417497:G:AG96R1.000
7:99417497:G:CG96R1.000
7:99417498:G:AG96E1.000
7:99417510:T:GL100W1.000
7:99417512:T:AC101S1.000
7:99417512:T:CC101R1.000
7:99417513:G:AC101Y1.000
7:99417513:G:CC101S1.000
7:99417514:C:GC101W1.000
7:99417515:T:CC102R1.000
7:99417516:G:AC102Y1.000
7:99417516:G:TC102F1.000
7:99417517:C:GC102W1.000

dbSNP variants (sampled 300 via entrez): RS1000026358 (7:99416421 T>C,G), RS1000087151 (7:99410930 A>G), RS1000375588 (7:99410460 G>A), RS1000698508 (7:99409159 C>G,T), RS1000819053 (7:99414187 T>C), RS1000854654 (7:99412512 T>G), RS1001362260 (7:99417983 C>G,T), RS1001426958 (7:99419279 T>C), RS1001435506 (7:99417746 A>G), RS1001863380 (7:99407704 C>A), RS1002051364 (7:99413504 G>A), RS1002096658 (7:99413672 A>G,T), RS1002304270 (7:99418766 C>T), RS1002329777 (7:99408489 C>A,G,T), RS1002835162 (7:99411886 T>C)

Disease associations

OMIM: gene MIM:603477 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

4 associations (top):

StudyTraitp-value
GCST004730_2Facial emotion recognition (sad faces)3.000000e-06
GCST006249_21Serum metabolite levels4.000000e-11
GCST006249_22Serum metabolite levels2.000000e-12
GCST006249_46Serum metabolite levels4.000000e-21

EFO canonical traits (1, from GWAS)

EFO IDTrait name
EFO:0008329facial emotion recognition measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
sodium arseniteaffects cotreatment, decreases expression, increases abundance, increases expression3
methacrylaldehydeincreases abundance, affects cotreatment, increases oxidation2
Acroleinaffects cotreatment, increases oxidation, increases abundance2
Ozoneincreases oxidation, increases abundance, affects cotreatment2
Cyclosporineincreases expression2
triphenyl phosphateaffects expression1
alpha-pineneaffects cotreatment, increases oxidation, increases abundance1
bisphenol Aaffects expression1
trichostatin Aaffects expression1
beta-lapachoneincreases expression1
mono-(2-ethylhexyl)phthalatedecreases methylation, increases abundance1
butyraldehydeincreases expression1
manganese chlorideaffects cotreatment, increases abundance, increases expression1
potassium chromate(VI)affects cotreatment, increases expression1
epigallocatechin gallateaffects cotreatment, increases expression1
yessotoxindecreases expression1
CGP 52608increases reaction, affects binding1
chloropicrinincreases expression1
2-palmitoylglycerolincreases expression1
ICG 001increases expression1
abrineincreases expression1
2,2’,4,4’-tetrabromodiphenyl etherincreases expression1
(4-amino-1,4-dihydro-3-(2-pyridyl)-5-thioxo-1,2,4-triazole)copper(II)increases expression1
PP242increases expression1
Sunitinibincreases expression1
Acetaminophenincreases expression1
Air Pollutantsincreases oxidation, affects cotreatment, increases abundance1
Arsenicincreases abundance, increases expression, affects cotreatment1
Benzo(a)pyreneaffects methylation1
Diethylhexyl Phthalatedecreases methylation, increases abundance1

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 75

This page pulls from 75 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_assaypubmedreactomereactomeparentrefseqrhearnacentralscxa_expressionscxa_gene_experimentsignorspliceaistring_interactiontranscriptufeatureuniprot