RBM11

Summary

RBM11 (RNA binding motif protein 11, HGNC:9897) is a protein-coding gene on chromosome 21q11.2, encoding Splicing regulator RBM11 (P57052). Tissue-specific splicing factor with potential implication in the regulation of alternative splicing during neuron and germ cell differentiation.

Enables poly(U) RNA binding activity and protein homodimerization activity. Acts upstream of or within cellular response to oxidative stress and regulation of alternative mRNA splicing, via spliceosome. Located in nuclear speck.

Source: NCBI Gene 54033 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 51 total
• MANE Select transcript: NM_144770

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:9897
Approved symbol	RBM11
Name	RNA binding motif protein 11
Location	21q11.2
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000185272
Ensembl biotype	protein_coding
OMIM	617937
Entrez	54033

Gene structure

Transcript identifiers

Ensembl transcripts: 7 — 4 protein_coding_CDS_not_defined, 2 protein_coding, 1 retained_intron

ENST00000400577, ENST00000461088, ENST00000468643, ENST00000468788, ENST00000475864, ENST00000495055, ENST00000900829

RefSeq mRNA: 2 — MANE Select: NM_144770 NM_001320602, NM_144770

CCDS: CCDS46635

Canonical transcript exons

ENST00000400577 — 5 exons

Exon	Start	End
ENSE00001939246	14216157	14216282
ENSE00003485052	14224438	14224537
ENSE00003529564	14226880	14228372
ENSE00003546298	14219563	14219725
ENSE00003560060	14221097	14221169

Expression profiles

Bgee: expression breadth ubiquitous, 194 present calls, max score 97.62.

FANTOM5 (CAGE): breadth broad, TPM avg 4.3325 / max 598.0450, expressed in 728 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
188483	4.0660	720
188484	0.2664	77

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
corpus epididymis	UBERON:0004359	97.62	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	90.47	gold quality
spinal cord	UBERON:0002240	89.37	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	88.37	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	88.01	gold quality
oocyte	CL:0000023	87.51	gold quality
tibial nerve	UBERON:0001323	84.65	gold quality
left ovary	UBERON:0002119	80.97	gold quality
Brodmann (1909) area 9	UBERON:0013540	80.81	gold quality
prefrontal cortex	UBERON:0000451	80.52	gold quality
secondary oocyte	CL:0000655	79.81	gold quality
adenohypophysis	UBERON:0002196	79.78	gold quality
cortical plate	UBERON:0005343	79.26	gold quality
hypothalamus	UBERON:0001898	78.72	gold quality
islet of Langerhans	UBERON:0000006	78.54	gold quality
right ovary	UBERON:0002118	78.26	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	77.89	gold quality
anterior cingulate cortex	UBERON:0009835	77.77	gold quality
lower esophagus mucosa	UBERON:0035834	77.54	gold quality
left lobe of thyroid gland	UBERON:0001120	77.49	gold quality
pituitary gland	UBERON:0000007	77.27	gold quality
ovary	UBERON:0000992	76.72	gold quality
right frontal lobe	UBERON:0002810	76.63	gold quality
frontal cortex	UBERON:0001870	76.53	gold quality
thyroid gland	UBERON:0002046	76.44	gold quality
neocortex	UBERON:0001950	76.38	gold quality
substantia nigra	UBERON:0002038	76.27	gold quality
right lobe of thyroid gland	UBERON:0001119	76.05	gold quality
cerebral cortex	UBERON:0000956	74.92	gold quality
caput epididymis	UBERON:0004358	74.30	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-ANND-3	no	2.81

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

69 targeting RBM11, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-5692A	100.00	74.40	6850
HSA-MIR-5011-5P	100.00	83.46	5820
HSA-MIR-190A-3P	100.00	80.35	5520
HSA-MIR-1277-5P	100.00	73.95	5056
HSA-MIR-3662	99.99	73.82	5684
HSA-MIR-3185	99.99	68.12	1959
HSA-MIR-433-3P	99.98	69.37	1203
HSA-MIR-568	99.98	69.86	2084
HSA-MIR-548P	99.98	72.25	3784
HSA-MIR-485-3P	99.98	70.68	1585
HSA-MIR-539-3P	99.98	70.74	1616
HSA-MIR-1250-3P	99.96	70.04	4038
HSA-MIR-590-3P	99.96	74.34	6478
HSA-MIR-146A-5P	99.96	68.93	988
HSA-MIR-146B-5P	99.96	69.13	977
HSA-MIR-7153-5P	99.94	68.89	1006
HSA-MIR-335-3P	99.93	73.36	4958
HSA-MIR-3119	99.92	71.34	2390
HSA-MIR-4496	99.88	68.89	2236
HSA-MIR-4659A-3P	99.80	72.62	4248
HSA-MIR-4659B-3P	99.80	72.62	4248
HSA-MIR-548AJ-5P	99.78	71.12	3085
HSA-MIR-548F-5P	99.78	71.02	3093
HSA-MIR-548G-5P	99.78	71.12	3085
HSA-MIR-548X-5P	99.78	71.12	3085
HSA-MIR-4658	99.77	64.94	514
HSA-MIR-6790-5P	99.77	65.24	505
HSA-MIR-3659	99.70	67.97	694
HSA-MIR-29B-2-5P	99.67	68.98	1726

Literature-anchored findings (GeneRIF, showing 2)

• RBM11 is a representative splicing factor that is upregulated in glioblastoma tumors after therapy and shed in extracellular vesicles upon induction of apoptosis. Once internalized in recipient cells, exogenous RBM11 switches splicing of MDM4 and Cyclin D1 toward the expression of more oncogenic isoforms. (PMID:29937354)
• RNA-Binding Motif Protein 11 (RBM11) Serves as a Prognostic Biomarker and Promotes Ovarian Cancer Progression. (PMID:34434291)

Cross-species orthologs

6 orthologs

Organism	Symbol	Gene ID
danio_rerio	rbm11	ENSDARG00000090202
mus_musculus	Rbm11	ENSMUSG00000032940
rattus_norvegicus	Rbm11	ENSRNOG00000029147
drosophila_melanogaster	CG11454	FBGN0031224
caenorhabditis_elegans		WBGENE00012558
caenorhabditis_elegans	rnp-8	WBGENE00020091

Paralogs (1): RBM7 (ENSG00000076053)

Protein

Protein identifiers

Splicing regulator RBM11 — P57052 (reviewed: P57052)

Alternative names: RNA-binding motif protein 11

All UniProt accessions (1): P57052

UniProt curated annotations — full annotation on UniProt →

Function. Tissue-specific splicing factor with potential implication in the regulation of alternative splicing during neuron and germ cell differentiation. Antagonizes SRSF1-mediated BCL-X splicing. May affect the choice of alternative 5’ splice sites by binding to specific sequences in exons and antagonizing the SR protein SRSF1.

Subunit / interactions. Homodimer.

Subcellular location. Nucleus. Nucleoplasm. Nucleus speckle.

Tissue specificity. Expressed in brain, hippocampus, prefrontal cortex, cerebellum, spinal cord, testis, mammary gland, spleen and kidney. Also expressed in fetal brain.

Miscellaneous. May be produced at very low levels due to a premature stop CC codon in the mRNA, leading to nonsense-mediated mRNA decay.

Isoforms (2)

UniProt ID	Names	Canonical?
P57052-1	1	yes
P57052-3	3

RefSeq proteins (2): NP_001307531, NP_658983* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000504	RRM_dom	Domain
IPR012677	Nucleotide-bd_a/b_plait_sf	Homologous_superfamily
IPR034501	RBM11_RRM	Domain
IPR035979	RBD_domain_sf	Homologous_superfamily
IPR052285	NEXT_complex_subunit	Family

Pfam: PF00076

UniProt features (18 total): helix 4, strand 3, compositionally biased region 3, splice variant 2, chain 1, domain 1, sequence conflict 1, region of interest 1, short sequence motif 1, sequence variant 1

Structure

Experimental structures (PDB)

1 structures.

PDB	Method	Resolution (Å)
2YWK	X-RAY DIFFRACTION	1.54

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-P57052-F1	61.85	0.28

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 90 (showing top): GOBP_ALTERNATIVE_MRNA_SPLICING_VIA_SPLICEOSOME, GOBP_RNA_SPLICING, GOBP_REGULATION_OF_MRNA_SPLICING_VIA_SPLICEOSOME, GOBP_REGULATION_OF_RNA_SPLICING, GOCC_NUCLEAR_SPECK, GOCC_NUCLEAR_BODY, TAKEDA_TARGETS_OF_NUP98_HOXA9_FUSION_8D_UP, GOCC_RIBONUCLEOPROTEIN_GRANULE, GOMF_PROTEIN_DIMERIZATION_ACTIVITY, GOMF_PROTEIN_HOMODIMERIZATION_ACTIVITY, GOMF_POLY_PYRIMIDINE_TRACT_BINDING, GOMF_SINGLE_STRANDED_RNA_BINDING, GOBP_REGULATION_OF_MRNA_PROCESSING, GOBP_MRNA_PROCESSING, GOCC_SUPRAMOLECULAR_COMPLEX

GO Biological Process (5): regulation of alternative mRNA splicing, via spliceosome (GO:0000381), mRNA processing (GO:0006397), RNA splicing (GO:0008380), cell differentiation (GO:0030154), cellular response to oxidative stress (GO:0034599)

GO Molecular Function (6): single-stranded RNA binding (GO:0003727), poly(U) RNA binding (GO:0008266), protein homodimerization activity (GO:0042803), nucleic acid binding (GO:0003676), RNA binding (GO:0003723), protein binding (GO:0005515)

GO Cellular Component (3): nucleus (GO:0005634), nucleoplasm (GO:0005654), nuclear speck (GO:0016607)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
RNA processing	2
binding	2
alternative mRNA splicing, via spliceosome	1
regulation of mRNA splicing, via spliceosome	1
mRNA metabolic process	1
cellular developmental process	1
response to oxidative stress	1
cellular response to chemical stress	1
RNA binding	1
poly-pyrimidine tract binding	1
identical protein binding	1
protein dimerization activity	1
nucleic acid binding	1
intracellular membrane-bounded organelle	1
nuclear lumen	1
cellular anatomical structure	1
nuclear ribonucleoprotein granule	1

Protein interactions and networks

STRING

1049 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
RBM11	RBM25	P49756	652
RBM11	RBM4	Q9BWF3	616
RBM11	KHDRBS1	Q07666	595
RBM11	RBM10	P98175	594
RBM11	MDM4	O15151	559
RBM11	SRSF1	Q07955	527
RBM11	ZCCHC8	Q6NZY4	517
RBM11	HSPA13	P48723	490
RBM11	LIPI	Q6XZB0	489
RBM11	RBM19	Q9Y4C8	487
RBM11	FBF1	Q8TES7	478
RBM11	RBM17	Q96I25	476
RBM11	TRA2B	P62995	474
RBM11	PCBP3	P57721	473
RBM11	SF3B2	Q13435	454

IntAct

178 interactions, top by confidence:

A	B	Type	Score
MED4	MED19	psi-mi:“MI:2364”(proximity)	0.900
RBM11	ZCCHC8	psi-mi:“MI:0914”(association)	0.740
QKI	RBM11	psi-mi:“MI:0915”(physical association)	0.560
GABPB1	RBM11	psi-mi:“MI:0915”(physical association)	0.560
RBM11	SNRPC	psi-mi:“MI:0915”(physical association)	0.560
ZNF774	RBM11	psi-mi:“MI:0915”(physical association)	0.560
RBM11	QKI	psi-mi:“MI:0915”(physical association)	0.560
SNRPC	RBM11	psi-mi:“MI:0915”(physical association)	0.560
PIBF1	RBM11	psi-mi:“MI:0915”(physical association)	0.560
U2AF2	RBM11	psi-mi:“MI:0915”(physical association)	0.560
RBM11	ATOSB	psi-mi:“MI:0915”(physical association)	0.560
RBM11	GPATCH2L	psi-mi:“MI:0915”(physical association)	0.560
SNRPA	RBM11	psi-mi:“MI:0915”(physical association)	0.560
RBM11	PIBF1	psi-mi:“MI:0915”(physical association)	0.560
RBM11	SCNM1	psi-mi:“MI:0915”(physical association)	0.560
RBM11	GLIS2	psi-mi:“MI:0915”(physical association)	0.560
DDX6	RBM11	psi-mi:“MI:0915”(physical association)	0.560
RBM11	ZFHX3	psi-mi:“MI:0915”(physical association)	0.560
RBM11	DTX2	psi-mi:“MI:0915”(physical association)	0.560
RBM11	SAXO4	psi-mi:“MI:0915”(physical association)	0.560
RBM11	ZNF414	psi-mi:“MI:0915”(physical association)	0.560
RBM11	GADD45GIP1	psi-mi:“MI:0915”(physical association)	0.560
RBM11	ENKD1	psi-mi:“MI:0915”(physical association)	0.560

BioGRID (194): RBM11 (Two-hybrid), RBM11 (Two-hybrid), RBM11 (Two-hybrid), ZNF774 (Two-hybrid), SF3B2 (Affinity Capture-MS), SKIV2L2 (Affinity Capture-MS), USP7 (Affinity Capture-MS), SLC4A1AP (Affinity Capture-MS), ZCCHC8 (Affinity Capture-MS), TTC33 (Affinity Capture-MS), RHOXF2 (Two-hybrid), RBM11 (Reconstituted Complex), RBM11 (Proximity Label-MS), DAZAP2 (Two-hybrid), SLC4A1AP (Affinity Capture-MS)

ESM2 similar proteins: A0A087WUL8, A0A0J9YWL9, A0A0J9YY54, A0A1L8G2K9, A6NJ88, A6QL64, B4DH59, B5DUH6, B7SY83, B9G9L9, F4HXQ7, O04492, O77733, P0DKJ7, P0DKJ8, P0DKL2, P0DPF3, P17772, P48785, P48786, P53353, P57052, Q0DVU4, Q15361, Q3BBV0, Q3BBV2, Q4ZJY7, Q4ZJZ0, Q4ZJZ1, Q4ZJZ3, Q5JPF3, Q5TAG4, Q5TI25, Q5XHX6, Q5ZCC5, Q6P3W6, Q6P902, Q6PGQ1, Q6ZQX7, Q86T75

Diamond homologs: A0A0D1DZT6, A3LXL0, B1WC40, B5FXN8, B5G279, F4HT49, O08583, O22173, O35698, O64380, O75821, O93235, P04147, P19683, P19684, P27476, P29341, P42731, P49313, P49314, P52298, P57052, P60824, P60825, P60826, Q06106, Q08935, Q08937, Q09330, Q10355, Q13595, Q14011, Q1ZXC2, Q28CY2, Q28FB9, Q28IQ9, Q29RT0, Q2GSX8, Q3T0I4, Q3ZBJ1

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	41
Likely benign	4
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1094 predictions. Top by Δscore:

Variant	Effect	Δscore
21:14221093:A:AG	acceptor_gain	1.0000
21:14221093:AAAG:A	acceptor_gain	1.0000
21:14221093:AAAGG:A	acceptor_gain	1.0000
21:14221094:A:G	acceptor_gain	1.0000
21:14221096:GGGA:G	acceptor_gain	1.0000
21:14216253:G:GT	donor_gain	0.9900
21:14216278:TTCAG:T	donor_loss	0.9900
21:14216280:CAG:C	donor_loss	0.9900
21:14216281:AGG:A	donor_loss	0.9900
21:14216282:GGTAC:G	donor_loss	0.9900
21:14216283:G:A	donor_loss	0.9900
21:14216284:T:G	donor_loss	0.9900
21:14219712:GC:G	donor_gain	0.9900
21:14221091:TCAAA:T	acceptor_loss	0.9900
21:14221092:CAAA:C	acceptor_loss	0.9900
21:14221094:AAG:A	acceptor_gain	0.9900
21:14221095:A:G	acceptor_gain	0.9900
21:14221095:AG:A	acceptor_gain	0.9900
21:14221095:AGGG:A	acceptor_loss	0.9900
21:14221096:G:GG	acceptor_gain	0.9900
21:14221096:GG:G	acceptor_gain	0.9900
21:14221166:ACAG:A	donor_loss	0.9900
21:14221167:CAG:C	donor_loss	0.9900
21:14221169:GG:G	donor_loss	0.9900
21:14221170:GTAAT:G	donor_loss	0.9900
21:14221171:TAATT:T	donor_loss	0.9900
21:14216253:G:T	donor_gain	0.9800
21:14218103:C:CG	donor_gain	0.9800
21:14218103:C:G	donor_gain	0.9800
21:14219723:TTGGT:T	donor_loss	0.9800

AlphaMissense

1857 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
21:14216227:T:A	V14D	1.000
21:14219624:G:A	G53E	1.000
21:14219630:T:A	V55D	1.000
21:14219675:T:C	L70P	1.000
21:14216223:T:C	F13L	0.999
21:14216225:T:A	F13L	0.999
21:14216225:T:G	F13L	0.999
21:14216236:T:C	L17S	0.999
21:14216263:T:A	L26Q	0.999
21:14216263:T:C	L26P	0.999
21:14216272:T:C	L29P	0.999
21:14216274:T:C	F30L	0.999
21:14216276:C:A	F30L	0.999
21:14216276:C:G	F30L	0.999
21:14219566:G:A	G34R	0.999
21:14219566:G:C	G34R	0.999
21:14219566:G:T	G34W	0.999
21:14219567:G:A	G34E	0.999
21:14219620:T:C	F52L	0.999
21:14219622:T:A	F52L	0.999
21:14219622:T:G	F52L	0.999
21:14219623:G:A	G53R	0.999
21:14219623:G:C	G53R	0.999
21:14219626:T:C	F54L	0.999
21:14219628:T:A	F54L	0.999
21:14219628:T:G	F54L	0.999
21:14219635:T:C	F57L	0.999
21:14219636:T:C	F57S	0.999
21:14219637:T:A	F57L	0.999
21:14219637:T:G	F57L	0.999

dbSNP variants (sampled 300 via entrez): RS1000085994 (21:14223859 C>A), RS1000444485 (21:14228005 C>G), RS1000531068 (21:14222234 C>A,T), RS1000583269 (21:14221954 A>G), RS1001160195 (21:14216209 C>G), RS1001291083 (21:14228592 A>G,T), RS1001487211 (21:14223750 G>C), RS1001950015 (21:14227598 T>C), RS1002358880 (21:14227862 A>G), RS1002482192 (21:14215499 C>T), RS1002486732 (21:14222575 C>T), RS1002540903 (21:14222396 T>C), RS1002967726 (21:14226121 C>T), RS1002975359 (21:14216365 G>A,C,T), RS1003088434 (21:14220402 C>T)

Disease associations

OMIM: gene MIM:617937 | 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

11 total (human), top 11 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	increases expression	3
trichostatin A	affects expression, increases expression	2
p-Chloromercuribenzoic Acid	affects cotreatment, increases expression	2
potassium chromate(VI)	increases expression	1
entinostat	increases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	increases expression, affects cotreatment	1
dorsomorphin	affects cotreatment, increases expression	1
Vorinostat	increases expression	1
Benzo(a)pyrene	increases methylation	1
Cadmium Chloride	decreases expression	1
S-Nitrosoglutathione	increases expression	1

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.