RBM34

Summary

RBM34 (RNA binding motif protein 34, HGNC:28965) is a protein-coding gene on chromosome 1q42.3, encoding RNA-binding protein 34 (P42696).

This gene encodes a member of the RNA-binding motif family of RNA recognition motif proteins. The encoded protein contains an RNA-binding domain made up of two RNA recognition motif subdomains referred to as RNA recognition motif-1 and RNA recognition motif-2. Alternative splicing results in multiple transcript variants.

Source: NCBI Gene 23029 — RefSeq curated summary.

At a glance

• GWAS associations: 2
• Clinical variants (ClinVar): 83 total
• MANE Select transcript: NM_015014

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:28965
Approved symbol	RBM34
Name	RNA binding motif protein 34
Location	1q42.3
Locus type	gene with protein product
Status	Approved
Aliases	KIAA0117
Ensembl gene	ENSG00000188739
Ensembl biotype	protein_coding
OMIM	619915
Entrez	23029

Gene structure

Transcript identifiers

Ensembl transcripts: 24 — 17 protein_coding, 4 retained_intron, 2 protein_coding_CDS_not_defined, 1 nonsense_mediated_decay

ENST00000408888, ENST00000429912, ENST00000447801, ENST00000468751, ENST00000474086, ENST00000475960, ENST00000476261, ENST00000485019, ENST00000486751, ENST00000495224, ENST00000888456, ENST00000888457, ENST00000888458, ENST00000888459, ENST00000917370, ENST00000917371, ENST00000917372, ENST00000917373, ENST00000917374, ENST00000966607, ENST00000966608, ENST00000966609, ENST00000966610, ENST00000966611

RefSeq mRNA: 2 — MANE Select: NM_015014 NM_001346738, NM_015014

CCDS: CCDS41477

Canonical transcript exons

ENST00000408888 — 11 exons

Exon	Start	End
ENSE00001956022	235131183	235131997
ENSE00003489901	235135652	235135770
ENSE00003543603	235154881	235155112
ENSE00003546444	235148404	235148447
ENSE00003571384	235161174	235161250
ENSE00003586550	235138091	235138174
ENSE00003623354	235160511	235160647
ENSE00003645520	235152706	235152765
ENSE00003684669	235136034	235136073
ENSE00003685408	235137877	235137940
ENSE00003694326	235160893	235161067

Expression profiles

Bgee: expression breadth ubiquitous, 168 present calls, max score 97.91.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 29.8057 / max 397.2214, expressed in 1808 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter ID	TPM avg	Samples expressed
18127	29.2755	1805
18126	0.3078	128
18128	0.1044	35
18124	0.0712	16
18125	0.0467	10

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
calcaneal tendon	UBERON:0003701	97.91	gold quality
ganglionic eminence	UBERON:0004023	96.29	gold quality
right testis	UBERON:0004534	96.02	gold quality
left testis	UBERON:0004533	95.92	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	95.65	gold quality
cortical plate	UBERON:0005343	95.39	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	95.14	gold quality
monocyte	CL:0000576	95.12	gold quality
granulocyte	CL:0000094	95.02	gold quality
leukocyte	CL:0000738	94.74	gold quality
mononuclear cell	CL:0000842	94.71	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	94.50	gold quality
skin of abdomen	UBERON:0001416	94.16	gold quality
descending thoracic aorta	UBERON:0002345	94.10	gold quality
mucosa of transverse colon	UBERON:0004991	94.03	gold quality
anterior cingulate cortex	UBERON:0009835	93.98	gold quality
adenohypophysis	UBERON:0002196	93.91	gold quality
tibial artery	UBERON:0007610	93.83	gold quality
popliteal artery	UBERON:0002250	93.82	gold quality
cingulate cortex	UBERON:0003027	93.80	gold quality
lower esophagus mucosa	UBERON:0035834	93.72	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	93.68	gold quality
minor salivary gland	UBERON:0001830	93.65	gold quality
skin of leg	UBERON:0001511	93.63	gold quality
lower esophagus	UBERON:0013473	93.63	gold quality
lower esophagus muscularis layer	UBERON:0035833	93.62	gold quality
ascending aorta	UBERON:0001496	93.61	gold quality
thoracic aorta	UBERON:0001515	93.61	gold quality
tibial nerve	UBERON:0001323	93.60	gold quality
left coronary artery	UBERON:0001626	93.60	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	3.96

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

21 targeting RBM34, 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-3613-3P	100.00	76.36	7965
HSA-MIR-371B-5P	99.99	75.34	4759
HSA-MIR-373-5P	99.98	75.36	4753
HSA-MIR-616-5P	99.98	75.58	4775
HSA-MIR-6124	99.87	69.78	3551
HSA-MIR-4728-5P	99.85	69.39	4718
HSA-MIR-4643	99.49	67.63	1791
HSA-MIR-4251	99.40	69.19	3363
HSA-MIR-4311	99.31	70.47	3041
HSA-MIR-4291	99.20	68.88	2969
HSA-MIR-661	99.09	65.94	2062
HSA-MIR-922	99.02	67.23	1838
HSA-MIR-3619-5P	99.00	68.87	2308
HSA-MIR-214-3P	98.71	68.12	2128
HSA-MIR-761	98.71	68.07	2051
HSA-MIR-7977	98.65	66.18	2590
HSA-MIR-2467-3P	98.65	67.18	1969
HSA-MIR-4257	97.86	68.05	1190
HSA-MIR-512-5P	97.47	66.48	591
HSA-MIR-2278	97.30	66.19	1130
HSA-MIR-6741-5P	93.86	63.06	437

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	rbm34	ENSDARG00000101877
mus_musculus	Rbm34	ENSMUSG00000033931
rattus_norvegicus	Rbm34	ENSRNOG00000020004
rattus_norvegicus	Rbm34-ps1	ENSRNOG00000065550

Paralogs (24): ELAVL1 (ENSG00000066044), PABPC1 (ENSG00000070756), RBMS2 (ENSG00000076067), PABPC4 (ENSG00000090621), PABPC1L (ENSG00000101104), ELAVL2 (ENSG00000107105), RBM24 (ENSG00000112183), TARDBP (ENSG00000120948), HNRNPR (ENSG00000125944), RBM38 (ENSG00000132819), SYNCRIP (ENSG00000135316), SF3B4 (ENSG00000143368), RBMS3 (ENSG00000144642), PABPC3 (ENSG00000151846), RBMS1 (ENSG00000153250), RBM45 (ENSG00000155636), ELAVL4 (ENSG00000162374), PABPC5 (ENSG00000174740), PUF60 (ENSG00000179950), PABPC1L2B (ENSG00000184388), PABPC1L2A (ENSG00000186288), ELAVL3 (ENSG00000196361), RBM14 (ENSG00000239306), PABPC4L (ENSG00000254535)

Protein

Protein identifiers

RNA-binding protein 34 — P42696 (reviewed: P42696)

Alternative names: RNA-binding motif protein 34

All UniProt accessions (4): A2A2V2, P42696, H7C5M1, Q5TCT4

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Nucleus. Nucleolus.

Miscellaneous. May be due to an intron retention.

Similarity. Belongs to the RRM RBM34 family.

Isoforms (2)

UniProt ID	Names	Canonical?
P42696-1	1	yes
P42696-2	2

RefSeq proteins (2): NP_001333667, NP_055829* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000504	RRM_dom	Domain
IPR012677	Nucleotide-bd_a/b_plait_sf	Homologous_superfamily
IPR034221	RBM34_RRM2	Domain
IPR035979	RBD_domain_sf	Homologous_superfamily

Pfam: PF00076

UniProt features (19 total): modified residue 5, region of interest 5, domain 2, splice variant 2, compositionally biased region 2, chain 1, cross-link 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-P42696-F1	69.59	0.31

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 (6): 14, 28, 99, 151, 288, 242

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 110 (showing top): GOBP_RIBOSOME_BIOGENESIS, RODRIGUES_THYROID_CARCINOMA_ANAPLASTIC_UP, PUJANA_CHEK2_PCC_NETWORK, RICKMAN_METASTASIS_DN, MILI_PSEUDOPODIA_HAPTOTAXIS_UP, GOBP_MATURATION_OF_LSU_RRNA, SCHLOSSER_SERUM_RESPONSE_DN, DODD_NASOPHARYNGEAL_CARCINOMA_UP, CAIRO_HEPATOBLASTOMA_UP, TIEN_INTESTINE_PROBIOTICS_24HR_UP, BOYAULT_LIVER_CANCER_SUBCLASS_G12_UP, ACEVEDO_LIVER_CANCER_UP, GOBP_RIBONUCLEOPROTEIN_COMPLEX_BIOGENESIS, GOBP_RIBOSOMAL_LARGE_SUBUNIT_BIOGENESIS, KAYO_AGING_MUSCLE_UP

GO Biological Process (1): maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000463)

GO Molecular Function (2): RNA binding (GO:0003723), nucleic acid binding (GO:0003676)

GO Cellular Component (4): nucleoplasm (GO:0005654), chromosome (GO:0005694), nucleolus (GO:0005730), nucleus (GO:0005634)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
nuclear lumen	2
intracellular membraneless organelle	2
maturation of LSU-rRNA	1
nucleic acid binding	1
binding	1
cellular anatomical structure	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

2556 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
RBM34	URB1	O60287	618
RBM34	NOL10	Q9BSC4	597
RBM34	NOL9	Q5SY16	565
RBM34	DDX51	Q8N8A6	517
RBM34	UTP14A	Q9BVJ6	511
RBM34	ZCRB1	Q8TBF4	497
RBM34	WDR36	Q8NI36	467
RBM34	PDCD11	Q14690	441
RBM34	VWA5B2	Q8N398	437
RBM34	CEP126	Q9P2H0	415
RBM34	DQX1	Q8TE96	396
RBM34	RBM28	Q9NW13	389
RBM34	MITD1	Q8WV92	388
RBM34	KATNIP	O60303	383
RBM34	SRRM1	Q8IYB3	368

IntAct

201 interactions, top by confidence:

A	B	Type	Score
PTK2	TGFB1I1	psi-mi:“MI:0914”(association)	0.680
RPL10A	RRP8	psi-mi:“MI:0914”(association)	0.640
RPL14	RRP8	psi-mi:“MI:0914”(association)	0.640
H1-1	RRP8	psi-mi:“MI:0914”(association)	0.640
NOL12	RRP8	psi-mi:“MI:0914”(association)	0.640
LIN28A	IGF2BP3	psi-mi:“MI:0914”(association)	0.640
RBM34	RRP8	psi-mi:“MI:0914”(association)	0.640
NPM1	NVL	psi-mi:“MI:0914”(association)	0.610
NSA2	TYW5	psi-mi:“MI:0914”(association)	0.530
RBM34	NVL	psi-mi:“MI:0914”(association)	0.530
H1-4	IGF2BP3	psi-mi:“MI:0914”(association)	0.530
RPL37A	MPHOSPH10	psi-mi:“MI:0914”(association)	0.530
ZNF2	MPHOSPH10	psi-mi:“MI:0914”(association)	0.530
RPL18	NOP56	psi-mi:“MI:0914”(association)	0.530
RSBN1	SETD1A	psi-mi:“MI:0914”(association)	0.530
MACROH2A2	PPM1G	psi-mi:“MI:0914”(association)	0.530
PRR11	NVL	psi-mi:“MI:0914”(association)	0.530
MAK16	NVL	psi-mi:“MI:0914”(association)	0.530
RPL8	RRP8	psi-mi:“MI:0914”(association)	0.530
RPL18A	RRP8	psi-mi:“MI:0914”(association)	0.530
ZBTB48	ZBTB24	psi-mi:“MI:0914”(association)	0.530
RPL6	MRPS14	psi-mi:“MI:0914”(association)	0.530
PDGFB	DKC1	psi-mi:“MI:0914”(association)	0.530
H1-6	ZNF724	psi-mi:“MI:0914”(association)	0.530
MAGEB2	POLRMT	psi-mi:“MI:0914”(association)	0.530

BioGRID (441): RBM34 (Affinity Capture-MS), RBM34 (Affinity Capture-MS), RBM34 (Affinity Capture-MS), RBM34 (Affinity Capture-MS), RBM34 (Affinity Capture-MS), RBM34 (Affinity Capture-MS), RBM34 (Affinity Capture-MS), RBM34 (Affinity Capture-MS), RBM34 (Affinity Capture-MS), RBM34 (Affinity Capture-MS), RBM34 (Affinity Capture-MS), RBM34 (Affinity Capture-MS), ALYREF (Co-fractionation), PWP1 (Co-fractionation), RBBP6 (Co-fractionation)

ESM2 similar proteins: A3LVD5, A7EAY2, O13620, O13741, O74362, O74400, O74978, P37838, P42696, P53743, P53883, P53927, Q01491, Q06106, Q07623, Q08208, Q09100, Q1E7Y4, Q2GZQ4, Q3SZM1, Q4PC17, Q4WCH5, Q5AHI7, Q5AJS6, Q5BDC8, Q5M9F1, Q5RJM0, Q6BTS9, Q6C007, Q6C2Q7, Q6CEW9, Q6CFT1, Q6CKV6, Q6CQR6, Q6FUS6, Q6FWS2, Q6FXP4, Q6GL69, Q757I6, Q75A83

Diamond homologs: A0A0D1C8Z4, A2Q848, A6NDY0, A8WLV5, B0BNE4, B3LYP1, B3P0D7, B4JUT1, B4KCD5, B4LZ88, O13620, O13741, O13845, O14327, O80678, P19683, P19684, P20397, P33240, P38922, P40561, P42696, P49313, P49314, Q00916, Q05AT9, Q05CL8, Q06106, Q08208, Q08937, Q09295, Q09301, Q10B98, Q1PEP5, Q28165, Q28ZX3, Q44554, Q44556, Q44560, Q4G0J3

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 211 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:

Pathway	Partners	Fold	FDR
Peptide chain elongation	20	19.2×	1e-18
Viral mRNA Translation	20	19.2×	1e-18
PELO:HBS1L and ABCE1 dissociate a ribosome on a non-stop mRNA	20	19.0×	1e-18
Selenocysteine synthesis	20	18.2×	3e-18
Eukaryotic Translation Termination	20	18.2×	3e-18
Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC)	20	17.8×	3e-18
ZNF598 and the Ribosome-associated Quality Trigger (RQT) complex dissociate a ribosome stalled on a no-go mRNA	20	17.8×	3e-18
Formation of a pool of free 40S subunits	20	17.0×	7e-18

GO biological processes:

GO term	Partners	Fold	FDR
cytoplasmic translation	22	21.6×	1e-20
ribosomal large subunit biogenesis	9	21.1×	7e-08
ribosomal small subunit biogenesis	11	13.2×	1e-07
translation	23	12.5×	3e-16
rRNA processing	16	12.0×	1e-10
negative regulation of viral genome replication	6	11.9×	1e-03
regulation of alternative mRNA splicing, via spliceosome	7	9.1×	1e-03
negative regulation of translation	7	7.3×	4e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	59
Likely benign	2
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1740 predictions. Top by Δscore:

Variant	Effect	Δscore
1:235131996:TT:T	acceptor_gain	1.0000
1:235131998:C:CC	acceptor_gain	1.0000
1:235131998:CT:C	acceptor_loss	1.0000
1:235135647:CATAC:C	donor_loss	1.0000
1:235135648:ATAC:A	donor_loss	1.0000
1:235135649:TACC:T	donor_loss	1.0000
1:235135650:A:C	donor_loss	1.0000
1:235135651:C:A	donor_loss	1.0000
1:235135685:G:A	donor_gain	1.0000
1:235135768:CTT:C	acceptor_gain	1.0000
1:235135769:TT:T	acceptor_gain	1.0000
1:235135771:C:CC	acceptor_gain	1.0000
1:235135778:C:CT	acceptor_gain	1.0000
1:235135779:A:T	acceptor_gain	1.0000
1:235136032:A:AC	donor_gain	1.0000
1:235136033:C:CC	donor_gain	1.0000
1:235137869:CTACT:C	donor_loss	1.0000
1:235137870:TACTT:T	donor_loss	1.0000
1:235137871:ACTTA:A	donor_loss	1.0000
1:235137873:TTA:T	donor_loss	1.0000
1:235137874:T:TG	donor_loss	1.0000
1:235137875:A:AC	donor_gain	1.0000
1:235137875:A:AG	donor_loss	1.0000
1:235137876:C:CG	donor_gain	1.0000
1:235137876:CA:C	donor_gain	1.0000
1:235137876:CAG:C	donor_gain	1.0000
1:235137936:CATTT:C	acceptor_gain	1.0000
1:235137938:TTT:T	acceptor_gain	1.0000
1:235137939:TT:T	acceptor_gain	1.0000
1:235137939:TTCTG:T	acceptor_loss	1.0000

AlphaMissense

2845 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
1:235136057:A:T	V289D	0.998
1:235138133:A:T	V248D	0.998
1:235154912:A:T	V189D	0.998
1:235131975:G:T	A344D	0.997
1:235135668:C:T	G331D	0.997
1:235138139:G:T	A246D	0.997
1:235138140:C:G	A246P	0.997
1:235131930:A:T	V359D	0.996
1:235135662:A:T	V333E	0.995
1:235137902:A:T	V275D	0.995
1:235136042:A:G	L294P	0.994
1:235136053:A:C	F290L	0.994
1:235136053:A:T	F290L	0.994
1:235136055:A:G	F290L	0.994
1:235154914:A:C	F188L	0.994
1:235154914:A:T	F188L	0.994
1:235154916:A:G	F188L	0.994
1:235135669:C:G	G331R	0.992
1:235135740:A:G	F307S	0.992
1:235136051:A:T	V291E	0.992
1:235131941:T:A	R355S	0.991
1:235131941:T:G	R355S	0.991
1:235131976:C:G	A344P	0.991
1:235154918:A:T	V187E	0.991
1:235135656:A:G	F335S	0.990
1:235138101:C:G	A259P	0.990
1:235152761:A:G	L201P	0.990
1:235154903:A:G	L192S	0.990
1:235136061:A:G	S288P	0.989
1:235152726:A:G	S213P	0.989

dbSNP variants (sampled 300 via entrez): RS1000012324 (1:235144002 C>T), RS1000081775 (1:235145766 G>C), RS1000149368 (1:235144219 T>C), RS1000288295 (1:235133154 A>C), RS1000352419 (1:235134351 G>A,T), RS1000361443 (1:235140765 G>A), RS1000489644 (1:235134593 C>T), RS1000845217 (1:235144572 C>A,T), RS1000965073 (1:235139967 T>C), RS1001005379 (1:235149651 G>A,T), RS1001077314 (1:235150041 C>T), RS1001086718 (1:235144244 T>C), RS1001199637 (1:235135773 G>A), RS1001213353 (1:235150712 A>T), RS1001271627 (1:235135441 C>T)

Disease associations

OMIM: gene MIM:619915 | 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):

Study	Trait	p-value
GCST003542_147	Night sleep phenotypes	8.000000e-07
GCST005212_7	Asthma	3.000000e-06

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	affects methylation, decreases methylation, increases expression	3
trichostatin A	decreases expression, affects cotreatment	2
Cyclosporine	increases expression	2
aristolochic acid I	decreases expression	1
FR900359	affects phosphorylation	1
dicrotophos	decreases expression	1
bisphenol A	increases expression	1
deoxynivalenol	increases expression	1
pyrimidin-2-one beta-ribofuranoside	decreases expression	1
sodium arsenite	increases abundance, increases expression	1
nivalenol	increases expression	1
di-n-butylphosphoric acid	affects expression	1
CGP 52608	affects binding, increases reaction	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression	1
ICG 001	decreases expression	1
abrine	increases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
Resveratrol	affects cotreatment, increases expression	1
Decitabine	decreases expression	1
Adenine	decreases expression	1
Air Pollutants	decreases expression, increases abundance	1
Arsenic	increases abundance, increases expression	1
Caffeine	decreases phosphorylation	1
Cisplatin	decreases expression	1
Coal	decreases expression, increases abundance	1
Colchicine	decreases expression	1
Cytarabine	decreases expression	1
Diazinon	decreases methylation	1
Ethyl Methanesulfonate	decreases expression	1
Etoposide	decreases expression	1

Clinical trials (associated diseases)

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