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Atlas / Gene / NBDY

NBDY

gene
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Also known as NoBody

Summary

NBDY (negative regulator of P-body association, HGNC:50713) is a protein-coding gene on chromosome Xp11.21, encoding Negative regulator of P-body association (A0A0U1RRE5). Promotes dispersal of P-body components and is likely to play a role in the mRNA decapping process.

Involved in negative regulation of cytoplasmic mRNA processing body assembly and nuclear-transcribed mRNA catabolic process. Located in P-body.

Source: NCBI Gene 550643 — RefSeq curated summary.

At a glance

  • GWAS associations: 1
  • MANE Select transcript: NM_001348129

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:50713
Approved symbolNBDY
Namenegative regulator of P-body association
LocationXp11.21
Locus typegene with protein product
StatusApproved
AliasesNoBody
Ensembl geneENSG00000204272
Ensembl biotypeprotein_coding
OMIM300992
Entrez550643

Gene structure

Transcript identifiers

Ensembl transcripts: 5 — 4 protein_coding, 1 nonsense_mediated_decay

ENST00000374922, ENST00000423617, ENST00000451583, ENST00000637096, ENST00000897759

RefSeq mRNA: 1 — MANE Select: NM_001348129 NM_001348129

CCDS: CCDS87751

Canonical transcript exons

ENST00000374922 — 3 exons

ExonStartEnd
ENSE000014651245681732056819179
ENSE000014651255673206356732199
ENSE000014651275672924356729589

Expression profiles

Bgee: expression breadth ubiquitous, 254 present calls, max score 96.65.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 105.5003 / max 552.5416, expressed in 1811 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter IDTPM avgSamples expressed
19650298.36671810
1965045.36811632
1965031.76551143

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
kidney epitheliumUBERON:000481996.65gold quality
islet of LangerhansUBERON:000000695.27gold quality
left ventricle myocardiumUBERON:000656695.26gold quality
cardiac muscle of right atriumUBERON:000337995.10gold quality
upper arm skinUBERON:000426394.79gold quality
cartilage tissueUBERON:000241894.51gold quality
corpus epididymisUBERON:000435994.29gold quality
cortical plateUBERON:000534394.19gold quality
stromal cell of endometriumCL:000225594.15gold quality
prefrontal cortexUBERON:000045193.98gold quality
ganglionic eminenceUBERON:000402393.97gold quality
adult organismUBERON:000702393.97gold quality
deciduaUBERON:000245093.96gold quality
myocardiumUBERON:000234993.90gold quality
seminal vesicleUBERON:000099893.87gold quality
thoracic aortaUBERON:000151593.58gold quality
ascending aortaUBERON:000149693.57gold quality
descending thoracic aortaUBERON:000234593.41gold quality
aortaUBERON:000094793.33gold quality
left coronary arteryUBERON:000162693.33gold quality
popliteal arteryUBERON:000225093.21gold quality
tibial arteryUBERON:000761093.21gold quality
adrenal tissueUBERON:001830393.20gold quality
right adrenal glandUBERON:000123393.18gold quality
pituitary glandUBERON:000000793.17gold quality
hypothalamusUBERON:000189893.04gold quality
ventricular zoneUBERON:000305393.01gold quality
adenohypophysisUBERON:000219692.99gold quality
cortex of kidneyUBERON:000122592.97gold quality
coronary arteryUBERON:000162192.91gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3yes9.75
E-GEOD-125970yes4.80
E-MTAB-4850no561.60

Regulation

Is transcription factor: no

Literature-anchored findings (GeneRIF, showing 3)

  • results implicate NoBody as a novel component of the mRNA decapping complex and demonstrate potential functionality of a newly discovered microprotein (PMID:27918561)
  • Long Non-coding RNA LINC01420 Contributes to Pancreatic Cancer Progression Through Targeting KRAS Proto-oncogene. (PMID:31562613)
  • LINC01420 RNA structure and influence on cell physiology (PMID:32039714)

Cross-species orthologs

1 orthologs

OrganismSymbolGene ID
mus_musculusNbdyENSMUSG00000086316

Protein

Protein identifiers

Negative regulator of P-body association — A0A0U1RRE5 (reviewed: A0A0U1RRE5)

Alternative names: P-body dissociating protein, Protein NoBody

All UniProt accessions (3): A0A0U1RRE5, A0A0U1RR68, A0A4P8PLQ7

UniProt curated annotations — full annotation on UniProt →

Function. Promotes dispersal of P-body components and is likely to play a role in the mRNA decapping process.

Subunit / interactions. Interacts with mRNA decapping proteins DCP1A, DCP2 and EDC4.

Subcellular location. Cytoplasm. P-body.

RefSeq proteins (1): NP_001335058* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR047852NoBodyFamily

Pfam: PF21949

UniProt features (23 total): mutagenesis site 19, site 2, chain 1, region of interest 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-A0A0U1RRE5-F169.110.00

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 (2): 30 (required for interaction with edc4); 34 (required for interaction with edc4)

Mutagenesis-validated functional residues (19):

PositionPhenotype
28no effect on interaction with edc4.
29no effect on interaction with edc4.
30impaired interaction with edc4.
32no effect on interaction with edc4.
33no effect on interaction with edc4.
34impaired interaction with edc4.
35no effect on interaction with edc4.
36no effect on interaction with edc4.
37no effect on interaction with edc4.
38no effect on interaction with edc4.
39no effect on interaction with edc4.
40no effect on interaction with edc4.
41no effect on interaction with edc4.
22no effect on interaction with edc4.
23no effect on interaction with edc4.
24no effect on interaction with edc4.
25no effect on interaction with edc4.
26no effect on interaction with edc4.
27no effect on interaction with edc4.

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 72 (showing top): WANG_CLIM2_TARGETS_UP, GOBP_P_BODY_ASSEMBLY, GOBP_MACROMOLECULE_CATABOLIC_PROCESS, GOBP_REGULATION_OF_CELLULAR_COMPONENT_BIOGENESIS, GOBP_NEGATIVE_REGULATION_OF_ORGANELLE_ASSEMBLY, GOBP_NEGATIVE_REGULATION_OF_CELLULAR_COMPONENT_ORGANIZATION, CREIGHTON_ENDOCRINE_THERAPY_RESISTANCE_1, GOBP_ORGANELLE_ASSEMBLY, GOBP_REGULATION_OF_ORGANELLE_ASSEMBLY, CERVERA_SDHB_TARGETS_1_UP, GOBP_NEGATIVE_REGULATION_OF_ORGANELLE_ORGANIZATION, GOCC_RIBONUCLEOPROTEIN_GRANULE, KRIGE_RESPONSE_TO_TOSEDOSTAT_24HR_UP, chrXp11, GOBP_NUCLEAR_TRANSCRIBED_MRNA_CATABOLIC_PROCESS

GO Biological Process (3): nuclear-transcribed mRNA catabolic process (GO:0000956), mRNA processing (GO:0006397), negative regulation of cytoplasmic mRNA processing body assembly (GO:0010607)

GO Molecular Function (1): protein binding (GO:0005515)

GO Cellular Component (2): P-body (GO:0000932), cytoplasm (GO:0005737)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
mRNA catabolic process1
RNA processing1
mRNA metabolic process1
regulation of cytoplasmic mRNA processing body assembly1
P-body assembly1
negative regulation of organelle assembly1
binding1
cytoplasmic ribonucleoprotein granule1
intracellular anatomical structure1
cellular anatomical structure1

Protein interactions and networks

STRING

242 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
NBDYSMIM22K7EJ46600
NBDYMTLNQ8NCU8583
NBDYMRLNP0DMT0583
NBDYSMIM30A4D0T7528
NBDYSPAARA0A1B0GVQ0526
NBDYEDC4Q6P2E9523
NBDYPPP1R3FQ6ZSY5514
NBDYSTRIT1P0DN84507
NBDYACAD11Q709F0466
NBDYNPHP3Q7Z494452
NBDYCYRENQ9BWK5447
NBDYCLEC20AQ6ZU45447
NBDYA0A3B3IRQ3A0A3B3IRQ3445
NBDYDDX6P26196425
NBDYMIEF1L0R8F8399

IntAct

13 interactions, top by confidence:

ABTypeScore
EDC4NBDYpsi-mi:“MI:0915”(physical association)0.640
EDC4NBDYpsi-mi:“MI:0407”(direct interaction)0.640
NBDYEDC4psi-mi:“MI:0915”(physical association)0.640
NBDYEDC4psi-mi:“MI:0914”(association)0.640
DCP1ANBDYpsi-mi:“MI:0915”(physical association)0.500
NBDYLSM1psi-mi:“MI:0914”(association)0.350
NBDYDDX6psi-mi:“MI:0914”(association)0.350

ESM2 similar proteins: A0A0U1RRE5, A0A1B0GUV1, A5LFY3, A6NEH8, A6NH13, A8MQ11, B0BND4, B1AUF7, B1PS81, B4RE94, P03163, P03294, P03848, P05671, P06925, P06926, P0CU23, P0DPO2, P0DXO0, P11301, P12064, P16817, P17145, P27070, P92563, P93318, Q03352, Q03831, Q0D252, Q3SY05, Q4G0N7, Q54NK2, Q5RDV1, Q5T6M2, Q5TEZ4, Q64202, Q6PB30, Q6RVD6, Q6ZS52, Q7Z2R9

Diamond homologs: A0A0U1RRE5, Q5RDV1

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

0 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

1210 predictions. Top by Δscore:

VariantEffectΔscore
X:56732061:A:AGacceptor_gain1.0000
X:56732062:G:GGacceptor_gain1.0000
X:56817318:A:AGacceptor_gain1.0000
X:56817319:G:GGacceptor_gain1.0000
X:56817319:GTCTT:Gacceptor_gain1.0000
X:56729481:G:GTdonor_gain0.9900
X:56729554:G:GTdonor_gain0.9900
X:56732182:G:GTdonor_gain0.9900
X:56817319:GT:Gacceptor_gain0.9900
X:56817319:GTC:Gacceptor_gain0.9900
X:56817319:GTCT:Gacceptor_gain0.9900
X:56729465:G:GTdonor_gain0.9800
X:56729557:G:GGdonor_gain0.9800
X:56817315:TTCA:Tacceptor_loss0.9800
X:56817316:TCA:Tacceptor_loss0.9800
X:56817318:AGTC:Aacceptor_loss0.9800
X:56729556:A:AGdonor_gain0.9700
X:56798813:GACCT:Gdonor_gain0.9700
X:56798818:G:GGdonor_gain0.9700
X:56816821:A:AGacceptor_gain0.9700
X:56816822:G:GGacceptor_gain0.9700
X:56732062:GT:Gacceptor_gain0.9600
X:56729411:G:Tdonor_gain0.9500
X:56729559:AG:Adonor_gain0.9500
X:56732062:GTCTT:Gacceptor_gain0.9500
X:56798830:G:GAdonor_gain0.9500
X:56729558:T:TAdonor_gain0.9400
X:56798769:A:AGdonor_gain0.9300
X:56798770:G:GGdonor_gain0.9300
X:56729554:GAA:Gdonor_gain0.9100

AlphaMissense

416 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
X:56729455:G:CW34C0.943
X:56729455:G:TW34C0.943
X:56729435:T:CC28R0.839
X:56729453:T:AW34R0.839
X:56729453:T:CW34R0.839
X:56729437:C:GC28W0.825
X:56729435:T:AC28S0.795
X:56729436:G:CC28S0.795
X:56729456:G:CD35H0.763
X:56729450:C:AR33S0.758
X:56729454:G:TW34L0.748
X:56729445:C:AA31D0.734
X:56729454:G:CW34S0.723
X:56729371:T:GC6W0.710
X:56729431:G:CK26N0.657
X:56729431:G:TK26N0.657
X:56729435:T:GC28G0.647
X:56729447:C:AP32T0.633
X:56729436:G:AC28Y0.630
X:56729448:C:AP32Q0.625
X:56729451:G:CR33P0.623
X:56729428:A:CK25N0.622
X:56729428:A:TK25N0.622
X:56729457:A:CD35A0.616
X:56729369:T:CC6R0.610
X:56729457:A:GD35G0.603
X:56729457:A:TD35V0.594
X:56729460:A:GY36C0.593
X:56729447:C:TP32S0.567
X:56729448:C:TP32L0.567

dbSNP variants (sampled 300 via entrez): RS1000056284 (X:56798872 T>C,G), RS1000081165 (X:56727421 A>C), RS1000193511 (X:56799277 G>A), RS1000206498 (X:56761688 G>A), RS1000360368 (X:56784183 C>G,T), RS1000411381 (X:56784480 A>T), RS1000510715 (X:56750607 C>G,T), RS1000671746 (X:56757698 C>A,G,T), RS1000695098 (X:56790843 G>A), RS1000795544 (X:56783006 A>G), RS1000872481 (X:56811947 G>A,C), RS1000879097 (X:56788499 C>G,T), RS1000990987 (X:56798630 GGAA>G), RS1001061880 (X:56739270 A>G), RS1001101165 (X:56767651 G>A)

Disease associations

OMIM: gene MIM:300992 | 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
GCST011956_123Systemic lupus erythematosus7.000000e-09

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

14 total (human), top 14 by PubMed support.

ChemicalActions (top 5)PubMed papers
Benzo(a)pyreneaffects methylation, decreases methylation2
Phenylmercuric Acetateaffects cotreatment, decreases expression2
Valproic Acidincreases expression2
benzo(e)pyrenedecreases methylation1
chloropicrinincreases expression1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, decreases expression1
dorsomorphinaffects cotreatment, decreases expression1
Temozolomideincreases expression1
Methapyrilenedecreases methylation1
Smokedecreases expression1
Zincaffects abundance1
Aflatoxin B1decreases methylation, increases expression1
Cadmium Chlorideincreases expression1
Lactic Aciddecreases 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