RBMY1B

Summary

RBMY1B (RNA binding motif protein Y-linked family 1 member B, HGNC:23914) is a protein-coding gene on chromosome Yq11.223, encoding RNA-binding motif protein, Y chromosome, family 1 member B (A6NDE4). RNA-binding protein which may be involved in spermatogenesis.

This gene encodes a protein containing an RNA-binding motif in the N-terminus and four SRGY (serine, arginine, glycine, tyrosine) boxes in the C-terminus. This protein likely functions as a splicing factor during spermatogenesis. Multiple closely related paralogs of this gene are found in a gene cluster in the AZFb azoospermia factor region of chromosome Y. Most of these related copies are thought to be pseudogenes, though several likely encode functional proteins.

Source: NCBI Gene 378948 — RefSeq curated summary.

At a glance

• MANE Select transcript: NM_001006121

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:23914
Approved symbol	RBMY1B
Name	RNA binding motif protein Y-linked family 1 member B
Location	Yq11.223
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000242875
Ensembl biotype	protein_coding
Entrez	378948

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 1 nonsense_mediated_decay, 1 protein_coding

ENST00000382639, ENST00000383020

RefSeq mRNA: 2 — MANE Select: NM_001006121 NM_001006121, NM_001320948

CCDS: CCDS35479

Canonical transcript exons

ENST00000383020 — 12 exons

Exon	Start	End
ENSE00001799218	21517057	21517234
ENSE00001881074	21511338	21511485
ENSE00003464309	21522383	21522493
ENSE00003500350	21513934	21514037
ENSE00003552000	21519150	21519302
ENSE00003564737	21513347	21513459
ENSE00003567291	21524512	21524622
ENSE00003596670	21521313	21521427
ENSE00003617149	21525210	21525786
ENSE00003633721	21522935	21523045
ENSE00003674912	21523480	21523590
ENSE00003679647	21524710	21524798

Expression profiles

Bgee: expression breadth tissue_specific, 7 present calls, max score 81.41.

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	81.41	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	80.53	gold quality
right testis	UBERON:0004534	52.16	gold quality
testis	UBERON:0000473	48.61	gold quality
left testis	UBERON:0004533	46.51	gold quality
colonic epithelium	UBERON:0000397	37.20	gold quality
ventricular zone	UBERON:0003053	36.48	gold quality
cortical plate	UBERON:0005343	36.47	gold quality
bone marrow cell	CL:0002092	36.16	gold quality
ganglionic eminence	UBERON:0004023	35.49	gold quality
skeletal muscle tissue	UBERON:0001134	33.38	gold quality
placenta	UBERON:0001987	33.36	gold quality
hindlimb stylopod muscle	UBERON:0004252	32.15	gold quality
bone marrow	UBERON:0002371	31.74	gold quality
muscle tissue	UBERON:0002385	31.06	gold quality
sural nerve	UBERON:0015488	30.93	gold quality
stromal cell of endometrium	CL:0002255	29.87	gold quality
prefrontal cortex	UBERON:0000451	29.04	gold quality
tonsil	UBERON:0002372	28.65	gold quality
right uterine tube	UBERON:0001302	28.26	gold quality
duodenum	UBERON:0002114	28.14	gold quality
monocyte	CL:0000576	27.90	gold quality
leukocyte	CL:0000738	27.87	gold quality
lymph node	UBERON:0000029	27.57	gold quality
islet of Langerhans	UBERON:0000006	27.54	gold quality
cortex of kidney	UBERON:0001225	27.21	gold quality
blood	UBERON:0000178	26.93	gold quality
vermiform appendix	UBERON:0001154	26.42	gold quality
uterine cervix	UBERON:0000002	26.36	gold quality
gall bladder	UBERON:0002110	25.98	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

Literature-anchored findings (GeneRIF, showing 1)

• Potential dual functional roles of the Y-linked RBMY in hepatocarcinogenesis. (PMID:32473614)

Cross-species orthologs

11 orthologs

Organism	Symbol	Gene ID
mus_musculus	Rbmyf3	ENSMUSG00000091987
mus_musculus	Rbmyf5	ENSMUSG00000093918
mus_musculus	Rbmyf7	ENSMUSG00000093987
mus_musculus	Rbmyf6	ENSMUSG00000094511
mus_musculus	Rbmy	ENSMUSG00000094658
mus_musculus	Rbmyf2	ENSMUSG00000095852
mus_musculus	Rbmyf8	ENSMUSG00000095948
mus_musculus	Rbmyf9	ENSMUSG00000096520
mus_musculus	Rbmyf4	ENSMUSG00000101667
mus_musculus	Rbmyf1	ENSMUSG00000102053
rattus_norvegicus	Rbmy1j	ENSRNOG00000060963

Paralogs (36): DAZAP1 (ENSG00000071626), CIRBP (ENSG00000099622), RBM23 (ENSG00000100461), RBM3 (ENSG00000102317), NCL (ENSG00000115053), TIA1 (ENSG00000116001), HNRNPA2B1 (ENSG00000122566), RBM19 (ENSG00000122965), RBM39 (ENSG00000131051), MSI1 (ENSG00000135097), HNRNPA1 (ENSG00000135486), HNRNPD (ENSG00000138668), HNRNPA1L2 (ENSG00000139675), RBMX (ENSG00000147274), A1CF (ENSG00000148584), TIAL1 (ENSG00000151923), RBM46 (ENSG00000151962), HNRNPDL (ENSG00000152795), MSI2 (ENSG00000153944), RBM47 (ENSG00000163694), RBMY1F (ENSG00000169800), HNRNPA3 (ENSG00000170144), RBMXL2 (ENSG00000170748), RBM4B (ENSG00000173914), RBM4 (ENSG00000173933), RBMXL3 (ENSG00000175718), HNRNPA0 (ENSG00000177733), TRNAU1AP (ENSG00000180098), HNRNPAB (ENSG00000197451), RBMXL1 (ENSG00000213516), HNRNPA1L3 (ENSG00000224578), RBMY1J (ENSG00000226941), RBMY1A1 (ENSG00000234414), RBMY1E (ENSG00000242389), RBMY1D (ENSG00000244395), DND1 (ENSG00000256453)

Protein

Protein identifiers

RNA-binding motif protein, Y chromosome, family 1 member B — A6NDE4 (reviewed: A6NDE4)

All UniProt accessions (2): A6NDE4, F2Z2U1

UniProt curated annotations — full annotation on UniProt →

Function. RNA-binding protein which may be involved in spermatogenesis. Required for sperm development, possibly by participating in pre-mRNA splicing in the testis.

Subunit / interactions. Interacts with splicing factor proteins SFRS3/SRP20, TRA2B/SFRS10, KHDRBS1/SAM68 and KHDRBS3.

Subcellular location. Nucleus.

Tissue specificity. Testis-specific.

Miscellaneous. The RBMY1 proteins are encoded by repeated regions of the Y chromosome, mostly within the AZFb region. The exact number of functional copies is unclear and may vary between individuals, and some of them may represent pseudogenes. The proteins are very similar, which makes the characterization of each protein difficult. Thus, most experiments do not discriminate between the different members. One can therefore suppose that reported interactions with a RBMY1 protein involve all the proteins.

RefSeq proteins (2): NP_001006121, NP_001307877 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000504	RRM_dom	Domain
IPR012604	RBM1CTR	Domain
IPR012677	Nucleotide-bd_a/b_plait_sf	Homologous_superfamily
IPR035979	RBD_domain_sf	Homologous_superfamily
IPR050441	RBM	Family

Pfam: PF00076, PF08081

UniProt features (13 total): compositionally biased region 9, region of interest 2, chain 1, domain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-A6NDE4-F1	49.54	0.09

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 23 (showing top): GOBP_MALE_GAMETE_GENERATION, GOBP_REPRODUCTIVE_SYSTEM_DEVELOPMENT, GOBP_RNA_SPLICING, GOBP_SEX_DIFFERENTIATION, GOBP_DEVELOPMENTAL_PROCESS_INVOLVED_IN_REPRODUCTION, ACEVEDO_METHYLATED_IN_LIVER_CANCER_DN, CHEN_ETV5_TARGETS_TESTIS, GOBP_MALE_SEX_DIFFERENTIATION, GOBP_DEVELOPMENT_OF_PRIMARY_SEXUAL_CHARACTERISTICS, GOCC_SPLICEOSOMAL_COMPLEX, GOCC_RIBONUCLEOPROTEIN_COMPLEX, ZHENG_IL22_SIGNALING_DN, GOMF_MRNA_BINDING, chrYq11, GOBP_MRNA_PROCESSING

GO Biological Process (5): mRNA processing (GO:0006397), spermatogenesis (GO:0007283), RNA splicing (GO:0008380), male gonad development (GO:0008584), positive regulation of mRNA splicing, via spliceosome (GO:0048026)

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

GO Cellular Component (4): nucleus (GO:0005634), nucleoplasm (GO:0005654), spliceosomal complex (GO:0005681), nucleolus (GO:0005730)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
RNA processing	2
nuclear lumen	2
mRNA metabolic process	1
developmental process involved in reproduction	1
male gamete generation	1
gonad development	1
development of primary male sexual characteristics	1
mRNA splicing, via spliceosome	1
positive regulation of RNA splicing	1
regulation of mRNA splicing, via spliceosome	1
positive regulation of mRNA processing	1
nucleic acid binding	1
binding	1
intracellular membrane-bounded organelle	1
cellular anatomical structure	1
nuclear protein-containing complex	1
ribonucleoprotein complex	1
intracellular membraneless organelle	1

Protein interactions and networks

STRING

1228 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
RBMY1B	TSPY4	P0CV99	721
RBMY1B	A6NEC3	A6NEC3	716
RBMY1B	A6NGT6	A6NGT6	697
RBMY1B	A6NGL4	A6NGL4	577
RBMY1B	VCY	O14598	571
RBMY1B	EIF1AY	O14602	524
RBMY1B	RPS4Y2	Q8TD47	506
RBMY1B	ZFY	P08048	496
RBMY1B	TGIF2LY	Q8IUE0	491
RBMY1B	TSPY1	P09002	482
RBMY1B	RPS4Y1	P22090	464
RBMY1B	AMELY	Q99218	444
RBMY1B	CDY2A	Q9Y6F7	433
RBMY1B	UTY	O14607	425
RBMY1B	TMSB4Y	O14604	423

IntAct

2 interactions, top by confidence:

A	B	Type	Score
NT5C3B	RBMY1B	psi-mi:“MI:0915”(physical association)	0.400

BioGRID (1): RBMY1B (Affinity Capture-MS)

ESM2 similar proteins: A0A1I8MUL8, A1YFA7, A2T806, A6NDE4, A6NEQ0, E9Q5K9, E9Q784, F4JCU0, O22703, O23372, O35698, O60828, O74418, O75526, P0C7P1, P0DJD3, P0DJD4, P11596, P78332, Q10B98, Q15415, Q1ECZ9, Q23935, Q24669, Q24761, Q2HJC9, Q3MHY8, Q3UC65, Q3URU2, Q3V0C1, Q4PB36, Q4R626, Q4R813, Q4R881, Q5R840, Q5T200, Q5U2S0, Q60990, Q62504, Q80Y39

Diamond homologs: A0A0A0LLY1, A2A5N3, A2VDB3, A5A6M3, A6NDE4, A6NEQ0, D4AE41, F1QB54, F4I3B3, O60176, O64380, O75526, O93235, P0C7P1, P0C8Z4, P0CB38, P0CP46, P0CP47, P0DJD3, P0DJD4, P10979, P11940, P20965, P21187, P29341, P31483, P32588, P38159, P38760, P39684, P49310, P49311, P52912, P60824, P60825, P60826, P61286, P70318, P84586, Q00539

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

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

Top pathogenic / likely-pathogenic (0)

SpliceAI

1432 predictions. Top by Δscore:

Variant	Effect	Δscore
Y:21513339:A:AG	acceptor_gain	1.0000
Y:21513340:T:G	acceptor_gain	1.0000
Y:21513342:TACA:T	acceptor_loss	1.0000
Y:21513344:C:G	acceptor_gain	1.0000
Y:21513344:CAGC:C	acceptor_loss	1.0000
Y:21513345:A:AG	acceptor_gain	1.0000
Y:21513345:AG:A	acceptor_loss	1.0000
Y:21513346:G:GA	acceptor_gain	1.0000
Y:21513346:GC:G	acceptor_gain	1.0000
Y:21513346:GCA:G	acceptor_gain	1.0000
Y:21513346:GCAC:G	acceptor_gain	1.0000
Y:21513346:GCACA:G	acceptor_gain	1.0000
Y:21513455:AGAAG:A	donor_loss	1.0000
Y:21513456:GAAG:G	donor_gain	1.0000
Y:21513456:GAAGG:G	donor_loss	1.0000
Y:21513461:T:G	donor_loss	1.0000
Y:21513932:A:AG	acceptor_gain	1.0000
Y:21513933:G:GC	acceptor_gain	1.0000
Y:21513933:GT:G	acceptor_gain	1.0000
Y:21513933:GTT:G	acceptor_gain	1.0000
Y:21513933:GTTC:G	acceptor_gain	1.0000
Y:21513933:GTTCT:G	acceptor_gain	1.0000
Y:21514033:GAAAG:G	donor_gain	1.0000
Y:21514036:AG:A	donor_gain	1.0000
Y:21514037:GG:G	donor_gain	1.0000
Y:21514038:G:GA	donor_loss	1.0000
Y:21514038:G:GG	donor_gain	1.0000
Y:21514039:T:G	donor_loss	1.0000
Y:21517055:A:AG	acceptor_gain	1.0000
Y:21517056:G:GG	acceptor_gain	1.0000

AlphaMissense

3225 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
Y:21513972:T:C	F50L	1.000
Y:21513974:T:A	F50L	1.000
Y:21513974:T:G	F50L	1.000
Y:21513978:T:C	F52L	1.000
Y:21513980:T:A	F52L	1.000
Y:21513980:T:G	F52L	1.000
Y:21513381:T:C	F11L	0.999
Y:21513383:C:A	F11L	0.999
Y:21513383:C:G	F11L	0.999
Y:21513421:T:A	L24H	0.999
Y:21513432:T:C	F28L	0.999
Y:21513434:T:A	F28L	0.999
Y:21513434:T:G	F28L	0.999
Y:21513979:T:C	F52S	0.999
Y:21513982:T:A	I53N	0.999
Y:21513987:T:C	F55L	0.999
Y:21513989:T:A	F55L	0.999
Y:21513989:T:G	F55L	0.999
Y:21513379:T:C	L10P	0.998
Y:21513382:T:C	F11S	0.998
Y:21513385:T:A	I12N	0.998
Y:21513421:T:C	L24P	0.998
Y:21513973:T:C	F50S	0.998
Y:21513988:T:C	F55S	0.998
Y:21513379:T:A	L10H	0.997
Y:21513394:T:A	L15H	0.997
Y:21513433:T:C	F28S	0.997
Y:21513982:T:G	I53S	0.997
Y:21514015:C:A	A64D	0.997
Y:21513394:T:C	L15P	0.996

dbSNP variants (sampled 23 via entrez): RS1165147189 (Y:21510427 A>C), RS1367954918 (Y:21510410 CACCCCA>C), RS1458619016 (Y:21510424 G>C), RS1556246210 (Y:21516141 A>G), RS1556246219 (Y:21519310 C>A), RS1556246226 (Y:21525215 T>G), RS1556246240 (Y:21525549 G>C), RS1556246251 (Y:21526945 C>T), RS1603588592 (Y:21510251 C>G), RS1603588593 (Y:21510411 A>C), RS1603588594 (Y:21510416 A>C), RS1603588595 (Y:21510431 G>C), RS1603588596 (Y:21510432 T>G), RS1603588597 (Y:21510434 A>C), RS1603588598 (Y:21510437 T>C)

Disease associations

OMIM: gene `` | 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

2 total (human), top 2 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Endosulfan	decreases expression	1
Aflatoxin B1	increases methylation	1

Clinical trials (associated diseases)

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