RBM15B

gene
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Also known as HUMAGCGBOTT3

Summary

RBM15B (RNA binding motif protein 15B, HGNC:24303) is a protein-coding gene on chromosome 3p21.2, encoding Putative RNA-binding protein 15B (Q8NDT2). RNA-binding protein that acts as a key regulator of N6-methyladenosine (m6A) methylation of RNAs, thereby regulating different processes, such as alternative splicing of mRNAs and X chromosome inactivation mediated by Xist RNA.

Members of the SPEN (Split-end) family of proteins, including RBM15B, have repressor function in several signaling pathways and may bind to RNA through interaction with spliceosome components (Hiriart et al., 2005 [PubMed 16129689]).

Source: NCBI Gene 29890 — RefSeq curated summary.

At a glance

  • GWAS associations: 2
  • Clinical variants (ClinVar): 99 total
  • MANE Select transcript: NM_013286

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:24303
Approved symbolRBM15B
NameRNA binding motif protein 15B
Location3p21.2
Locus typegene with protein product
StatusApproved
AliasesHUMAGCGB, OTT3
Ensembl geneENSG00000259956
Ensembl biotypeprotein_coding
OMIM612602
Entrez29890

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000563281

RefSeq mRNA: 1 — MANE Select: NM_013286 NM_013286

CCDS: CCDS33764

Canonical transcript exons

ENST00000563281 — 1 exons

ExonStartEnd
ENSE000025891395139128551397908

Expression profiles

Bgee: expression breadth ubiquitous, 278 present calls, max score 91.61.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 25.7444 / max 280.4106, expressed in 1804 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter IDTPM avgSamples expressed
3676524.96121803
367670.6712407
367660.086927
2027630.02513

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
ganglionic eminenceUBERON:000402391.61gold quality
cortical plateUBERON:000534390.61gold quality
embryoUBERON:000092290.51gold quality
ventricular zoneUBERON:000305389.65gold quality
amniotic fluidUBERON:000017387.71gold quality
endometrium epitheliumUBERON:000481187.65silver quality
stromal cell of endometriumCL:000225586.69gold quality
mammary ductUBERON:000176586.47gold quality
type B pancreatic cellCL:000016985.92gold quality
granulocyteCL:000009485.56gold quality
olfactory bulbUBERON:000226485.52gold quality
paraflocculusUBERON:000535185.47silver quality
frontal poleUBERON:000279585.28silver quality
epithelium of mammary glandUBERON:000324485.26gold quality
olfactory segment of nasal mucosaUBERON:000538685.08gold quality
cartilage tissueUBERON:000241884.95gold quality
gingival epitheliumUBERON:000194984.80gold quality
gingivaUBERON:000182884.69gold quality
islet of LangerhansUBERON:000000684.64gold quality
tongue squamous epitheliumUBERON:000691984.42silver quality
middle frontal gyrusUBERON:000270284.35silver quality
leukocyteCL:000073884.27gold quality
tibialis anteriorUBERON:000138584.13silver quality
mononuclear cellCL:000084284.09gold quality
monocyteCL:000057684.01gold quality
lower esophagus muscularis layerUBERON:003583384.01gold quality
lower esophagusUBERON:001347383.99gold quality
esophagus mucosaUBERON:000246983.79gold quality
esophagusUBERON:000104383.72gold quality
tibial arteryUBERON:000761083.72gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3yes6.58

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

115 targeting RBM15B, 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-188-3P100.0068.761240
HSA-MIR-6758-5P100.0066.211470
HSA-MIR-6856-5P100.0065.471298
HSA-MIR-4533100.0069.482758
HSA-MIR-1252-5P100.0069.802774
HSA-MIR-8485100.0077.574731
HSA-MIR-548C-3P99.9974.017587
HSA-MIR-3667-3P99.9967.171636
HSA-MIR-6888-3P99.9765.951170
HSA-MIR-568899.9673.234504
HSA-MIR-495-3P99.9672.814197
HSA-MIR-6755-5P99.9565.59464
HSA-MIR-3140-3P99.8868.472069
HSA-MIR-548D-3P99.8770.674362
HSA-MIR-548BB-3P99.8670.584354
HSA-MIR-221-5P99.8665.451052
HSA-MIR-807399.8665.211118
HSA-MIR-444799.8567.812900
HSA-MIR-548AC99.8470.774351
HSA-MIR-548H-3P99.8470.804349
HSA-MIR-548Z99.8470.804349
HSA-MIR-473999.8465.251832
HSA-MIR-132199.8465.301811
HSA-MIR-4756-5P99.8464.981809
HSA-MIR-6715A-3P99.8368.051473
HSA-MIR-6875-3P99.8270.262983
HSA-MIR-3121-3P99.8271.963630
HSA-MIR-684499.8270.692423
HSA-MIR-6739-5P99.8067.872806

Literature-anchored findings (GeneRIF, showing 4)

  • The RNA-binding motif protein 15B (RBM15B/OTT3) acts as cofactor of the nuclear export receptor NXF1. (PMID:19586903)
  • HHV-8 ORF57 interacts with RBM15 and OTT3 to promote expression of viral intronless genes. (PMID:21106733)
  • BAP1 is highly positively correlated with RBM15B and USP19 expression in invasive breast carcinoma, UM, and colon adenocarcinoma (PMID:30716094)
  • N(6)-Methyladenosine regulator RBM15B acts as an independent prognostic biomarker and its clinical significance in uveal melanoma. (PMID:36003405)

Cross-species orthologs

6 orthologs

OrganismSymbolGene ID
danio_reriorbm15bENSDARG00000078966
mus_musculusRbm15bENSMUSG00000074102
rattus_norvegicusRbm15bENSRNOG00000014161
drosophila_melanogasternonAFBGN0004227
drosophila_melanogasternonA-lFBGN0015520
drosophila_melanogasternitoFBGN0027548

Paralogs (7): SPEN (ENSG00000065526), SFPQ (ENSG00000116560), PSPC1 (ENSG00000121390), NONO (ENSG00000147140), RAVER1 (ENSG00000161847), RAVER2 (ENSG00000162437), RBM15 (ENSG00000162775)

Protein

Protein identifiers

Putative RNA-binding protein 15BQ8NDT2 (reviewed: Q8NDT2)

Alternative names: One-twenty two protein 3, RNA-binding motif protein 15B

All UniProt accessions (1): Q8NDT2

UniProt curated annotations — full annotation on UniProt →

Function. RNA-binding protein that acts as a key regulator of N6-methyladenosine (m6A) methylation of RNAs, thereby regulating different processes, such as alternative splicing of mRNAs and X chromosome inactivation mediated by Xist RNA. Associated component of the WMM complex, a complex that mediates N6-methyladenosine (m6A) methylation of RNAs, a modification that plays a role in the efficiency of mRNA splicing and RNA processing. Plays a key role in m6A methylation, possibly by binding target RNAs and recruiting the WMM complex. Involved in random X inactivation mediated by Xist RNA: acts by binding Xist RNA and recruiting the WMM complex, which mediates m6A methylation, leading to target YTHDC1 reader on Xist RNA and promoting transcription repression activity of Xist. Functions in the regulation of alternative or illicit splicing, possibly by regulating m6A methylation. Inhibits pre-mRNA splicing. Also functions as a mRNA export factor by acting as a cofactor for the nuclear export receptor NXF1.

Subunit / interactions. Component of the WMM complex, a N6-methyltransferase complex composed of a catalytic subcomplex, named MAC, and of an associated subcomplex, named MACOM. The MAC subcomplex is composed of METTL3 and METTL14. The MACOM subcomplex is composed of WTAP, ZC3H13, CBLL1/HAKAI, VIRMA, and, in some cases of RBM15 (RBM15 or RBM15B). May interact with NCOR2. Interacts with NXF1, the interaction is required to promote mRNA export. (Microbial infection) Interacts (via the SPOC domain) with Epstein-Barr virus BMLF1 (via the N-terminus); the interaction is direct.

Subcellular location. Nucleus. Nucleoplasm. Nucleus speckle. Nucleus envelope.

Tissue specificity. Ubiquitously expressed.

Similarity. Belongs to the RRM Spen family.

Isoforms (2)

UniProt IDNamesCanonical?
Q8NDT2-11yes
Q8NDT2-22

RefSeq proteins (1): NP_037418* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR000504RRM_domDomain
IPR010912SPOC_metDomain
IPR012677Nucleotide-bd_a/b_plait_sfHomologous_superfamily
IPR012921SPOC_CDomain
IPR016194SPOC-like_C_dom_sfHomologous_superfamily
IPR034475RBM15B_RRM1Domain
IPR034535RBM15B_RRM2Domain
IPR034536RBM15B_RRM3Domain
IPR035979RBD_domain_sfHomologous_superfamily

Pfam: PF00076, PF07744

UniProt features (33 total): compositionally biased region 11, modified residue 8, domain 4, region of interest 4, cross-link 2, chain 1, splice variant 1, sequence conflict 1, short sequence motif 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q8NDT2-F162.050.26

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 (10): 109, 113, 265, 267, 532, 552, 556, 562, 213, 702

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 155 (showing top): YAGI_AML_WITH_INV_16_TRANSLOCATION, GCANCTGNY_MYOD_Q6, GOBP_ALTERNATIVE_MRNA_SPLICING_VIA_SPLICEOSOME, CAGCTG_AP4_Q5, YY1_Q6, GOBP_RNA_METHYLATION, GOBP_NUCLEAR_TRANSPORT, BROWNE_HCMV_INFECTION_48HR_DN, GOBP_NEGATIVE_REGULATION_OF_GENE_EXPRESSION_EPIGENETIC, GOBP_RNA_MODIFICATION, YY1_02, TGCTGAY_UNKNOWN, USF_01, GOBP_NUCLEOBASE_CONTAINING_COMPOUND_TRANSPORT, AAAGACA_MIR511

GO Biological Process (6): regulation of alternative mRNA splicing, via spliceosome (GO:0000381), RNA methylation (GO:0001510), mRNA processing (GO:0006397), mRNA export from nucleus (GO:0006406), RNA splicing (GO:0008380), dosage compensation by inactivation of X chromosome (GO:0009048)

GO Molecular Function (4): RNA binding (GO:0003723), mRNA binding (GO:0003729), nucleic acid binding (GO:0003676), protein binding (GO:0005515)

GO Cellular Component (5): nucleus (GO:0005634), nuclear envelope (GO:0005635), nucleoplasm (GO:0005654), nuclear speck (GO:0016607), RNA N6-methyladenosine methyltransferase complex (GO:0036396)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
RNA processing2
binding2
alternative mRNA splicing, via spliceosome1
regulation of mRNA splicing, via spliceosome1
RNA modification1
macromolecule methylation1
mRNA metabolic process1
RNA export from nucleus1
gene expression1
mRNA transport1
sex-chromosome dosage compensation1
heterochromatin formation1
nucleic acid binding1
RNA binding1
intracellular membrane-bounded organelle1
nucleus1
endomembrane system1
organelle envelope1
nuclear lumen1
cellular anatomical structure1
nuclear ribonucleoprotein granule1
methyltransferase complex1

Protein interactions and networks

STRING

804 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
RBM15BZC3H13Q5T200998
RBM15BVIRMAQ69YN4998
RBM15BWTAPQ15007998
RBM15BMETTL14Q9HCE5998
RBM15BMETTL3Q86U44997
RBM15BCBLL1Q75N03990
RBM15BRBM15Q96T37983
RBM15BMETTL16Q86W50966
RBM15BMAPRE2Q15555903
RBM15BRAE1P78406891
RBM15BYTHDC1Q96MU7842
RBM15BYTHDC2Q9H6S0829
RBM15BYTHDF3Q7Z739827
RBM15BYTHDF1Q9BYJ9823
RBM15BALKBH5Q6P6C2823

IntAct

76 interactions, top by confidence:

ABTypeScore
ASH2LKMT2Dpsi-mi:“MI:0914”(association)0.890
P4HA3FAM171A2psi-mi:“MI:0914”(association)0.640
YWHAHPLEKHG3psi-mi:“MI:0914”(association)0.610
RBM15BNAV2psi-mi:“MI:0915”(physical association)0.560
NAV2RBM15Bpsi-mi:“MI:0915”(physical association)0.560
METTL3WTAPpsi-mi:“MI:0914”(association)0.530
IL13RA2METTL15psi-mi:“MI:0914”(association)0.530
TRIM23POTEB3psi-mi:“MI:0914”(association)0.530
ZC3H18AQRpsi-mi:“MI:0914”(association)0.530
RBM15BKLHL22psi-mi:“MI:0914”(association)0.530
NRBM47psi-mi:“MI:0914”(association)0.530
WDR83SH2B2psi-mi:“MI:0914”(association)0.530
RBM15BYWHAHpsi-mi:“MI:0914”(association)0.530
EZH1EPOPpsi-mi:“MI:0914”(association)0.530
RPL13RRP8psi-mi:“MI:0914”(association)0.530
ERBB2RBM15Bpsi-mi:“MI:0915”(physical association)0.370
RBM15BPApsi-mi:“MI:0915”(physical association)0.370
RBM15BPB1psi-mi:“MI:0915”(physical association)0.370
RBM15BPB2psi-mi:“MI:0915”(physical association)0.370
RBM15BEGR2psi-mi:“MI:0915”(physical association)0.370
TNNC1RBM15Bpsi-mi:“MI:0915”(physical association)0.370
ATP6V0D2RBM15Bpsi-mi:“MI:0915”(physical association)0.370
NCAPHSCAMP2psi-mi:“MI:0914”(association)0.350
CEP170P1PCYT1Apsi-mi:“MI:0914”(association)0.350
THOC1TARS3psi-mi:“MI:0914”(association)0.350
MATR3BCLAF3psi-mi:“MI:0914”(association)0.350

BioGRID (122): RBM15B (Two-hybrid), NAV2 (Two-hybrid), RBM15B (Affinity Capture-MS), RBM15B (Affinity Capture-MS), RBM15B (Affinity Capture-MS), DDX47 (Co-fractionation), RBM15B (Co-fractionation), RBM15B (Biochemical Activity), RBM15B (Affinity Capture-MS), RBM15B (Affinity Capture-MS), RBM15B (Affinity Capture-MS), RBM15B (Affinity Capture-MS), RBM15B (Affinity Capture-MS), RBM15B (Affinity Capture-MS), RBM15B (Affinity Capture-MS)

ESM2 similar proteins: D3YXK2, F4IS91, F4JCU0, O13845, O88453, P18615, P19426, P51116, Q05519, Q08CF3, Q08DZ2, Q0P5D2, Q0V898, Q0VBL3, Q14151, Q15424, Q16630, Q2QKB3, Q5NVH8, Q5R452, Q5RKH1, Q5TYQ8, Q5VUA4, Q5XI29, Q5ZL34, Q61136, Q62504, Q641G3, Q68UI8, Q6DDW4, Q6NVF9, Q6NWC6, Q6PHZ5, Q7KMJ6, Q803E1, Q86U06, Q8BTV2, Q8N684, Q8NDT2, Q91W39

Diamond homologs: F4I3B3, O15042, O64380, O93235, Q0VBL3, Q1LZD9, Q4KLH4, Q5R7X2, Q5ZK88, Q62504, Q6NV83, Q6PHZ5, Q7KMJ6, Q8NDT2, Q8R326, Q8SX83, Q8WXF1, Q96T37, Q96T58, Q9SX79, A2A5N3, A4F5G6, A6NFN3, B3LYP1, B4JUT1, B4KCD5, B4LZ88, B4NB54, C0H859, O74400, O75494, P19682, P19683, P23246, P28644, P30352, P60824, P60825, P60826, Q01130

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 88 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
Processing of Capped Intron-Containing Pre-mRNA812.6×8e-05

GO biological processes:

GO termPartnersFoldFDR
RNA splicing78.3×9e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance97
Likely benign2
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

107 predictions. Top by Δscore:

VariantEffectΔscore
3:51393756:G:Tdonor_gain0.9800
3:51394046:A:AGdonor_gain0.9600
3:51394045:GAT:Gdonor_gain0.9200
3:51393795:C:Tdonor_gain0.8500
3:51393908:A:AGdonor_gain0.8300
3:51395912:CTTG:Cacceptor_gain0.8200
3:51393756:G:GTdonor_gain0.8000
3:51394098:T:Gdonor_gain0.7700
3:51394118:T:Gdonor_gain0.7700
3:51396193:T:TCacceptor_gain0.7400
3:51396207:C:CTacceptor_gain0.7300
3:51396193:T:Cacceptor_gain0.7200
3:51396208:A:Tacceptor_gain0.7100
3:51396864:T:TAacceptor_gain0.6800
3:51396225:C:Tacceptor_gain0.6700
3:51395915:G:GCacceptor_gain0.6600
3:51393889:G:GTdonor_gain0.6300
3:51396195:G:Cacceptor_gain0.6300
3:51396185:TCCCA:Tacceptor_gain0.5900
3:51396223:TGC:Tacceptor_gain0.5800
3:51393768:GC:Gdonor_gain0.5700
3:51396191:CTT:Cacceptor_gain0.5500
3:51396192:TTT:Tacceptor_gain0.5500
3:51396193:T:Gacceptor_gain0.5500
3:51393865:G:GTdonor_gain0.5400
3:51393736:C:Adonor_gain0.5300
3:51393735:TCAC:Tdonor_gain0.5200
3:51393536:GA:Gdonor_gain0.5100
3:51393866:A:Tdonor_gain0.5000
3:51396195:G:GCacceptor_gain0.4900

AlphaMissense

5733 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
3:51391821:T:CL141S1.000
3:51391887:T:CF163S1.000
3:51391899:G:TG167V1.000
3:51391947:C:AA183D1.000
3:51391958:T:CF187L1.000
3:51391959:T:CF187S1.000
3:51391960:C:AF187L1.000
3:51391960:C:GF187L1.000
3:51392403:C:AA335D1.000
3:51392415:T:AL339H1.000
3:51392415:T:CL339P1.000
3:51392415:T:GL339R1.000
3:51392417:T:AF340I1.000
3:51392417:T:CF340L1.000
3:51392417:T:GF340V1.000
3:51392418:T:CF340S1.000
3:51392418:T:GF340C1.000
3:51392419:C:AF340L1.000
3:51392419:C:GF340L1.000
3:51392421:T:AI341N1.000
3:51392423:G:CG342R1.000
3:51392423:G:TG342C1.000
3:51392424:G:AG342D1.000
3:51392424:G:TG342V1.000
3:51392428:C:AN343K1.000
3:51392428:C:GN343K1.000
3:51392430:T:AL344Q1.000
3:51392430:T:CL344P1.000
3:51392457:T:CL353P1.000
3:51392468:T:CF357L1.000

dbSNP variants (sampled 300 via entrez): RS1000436457 (3:51390648 C>A,T), RS1000542905 (3:51391111 C>T), RS1000624451 (3:51396109 A>C), RS1000678216 (3:51395841 C>T), RS1001145996 (3:51389899 G>A), RS1002349348 (3:51397445 C>G), RS1003381331 (3:51394238 A>G,T), RS1003905304 (3:51396955 C>T), RS1003931959 (3:51390569 C>T), RS1003957503 (3:51396565 T>C), RS1004282464 (3:51390277 G>A,T), RS1005340086 (3:51389284 C>A,T), RS1005550607 (3:51391944 T>C), RS1005630609 (3:51398161 T>A), RS1006017481 (3:51392263 G>A,T)

Disease associations

OMIM: gene MIM:612602 | 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
GCST007732_15Allergic disease (asthma, hay fever or eczema)1.000000e-07
GCST012232_7Lipoprotein (a) levels3.000000e-10

EFO canonical traits (1, from GWAS)

EFO IDTrait name
EFO:0006925lipoprotein A measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
Cadmium Chlorideincreases expression2
aristolochic acid Idecreases expression1
GSK-J4decreases expression1
FR900359affects phosphorylation1
triphenyl phosphateaffects expression1
bisphenol Adecreases expression1
quercitrinincreases expression1
tris(1,3-dichloro-2-propyl)phosphatedecreases expression1
sodium arseniteincreases expression1
cobaltous chloridedecreases expression1
butyraldehydedecreases expression1
potassium chromate(VI)increases expression, affects cotreatment1
coumarindecreases phosphorylation1
cyclic 3’,5’-uridine monophosphateaffects binding1
epigallocatechin gallateaffects cotreatment, increases expression1
pentanaldecreases expression1
CGP 52608affects binding, increases reaction1
NSC 689534affects binding, decreases expression1
Temozolomidedecreases expression1
Decitabineaffects expression1
Benzo(a)pyreneaffects methylation1
Caffeineaffects phosphorylation1
Cisplatinaffects expression1
Copperaffects binding, decreases expression1
Diazinonincreases methylation1
Dimethyl Sulfoxideincreases expression1
Folic Aciddecreases expression1
Ivermectindecreases expression1
Methyl Methanesulfonatedecreases expression1
Ribonucleotidesaffects binding1

Cellosaurus cell lines

1 cell lines: 1 transformed cell line

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

CellosaurusNameCategorySex
CVCL_D9QCUbigene HEK293 RBM15B KOTransformed cell lineFemale

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.