RBMY1J

Summary

RBMY1J (RNA binding motif protein Y-linked family 1 member J, HGNC:23917) is a protein-coding gene on chromosome Yq11.223, encoding RNA-binding motif protein, Y chromosome, family 1 member F/J (Q15415). 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 378951 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 1 total
• MANE Select transcript: NM_001006117

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:23917
Approved symbol	RBMY1J
Name	RNA binding motif protein Y-linked family 1 member J
Location	Yq11.223
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000226941
Ensembl biotype	protein_coding
Entrez	378951

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 1 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000250831, ENST00000470460

RefSeq mRNA: 1 — MANE Select: NM_001006117 NM_001006117

CCDS: CCDS35484

Canonical transcript exons

ENST00000250831 — 12 exons

Exon	Start	End
ENSE00001663738	22409152	22409329
ENSE00003478187	22414478	22414588
ENSE00003481268	22411245	22411397
ENSE00003509588	22417305	22417881
ENSE00003515241	22415029	22415139
ENSE00003518190	22415574	22415684
ENSE00003560118	22406025	22406128
ENSE00003566008	22416608	22416718
ENSE00003571276	22405444	22405556
ENSE00003643053	22413408	22413522
ENSE00003680149	22416805	22416893
ENSE00003978223	22403410	22403582

Expression profiles

Bgee: expression breadth broad, 11 present calls, max score 84.75.

Top tissues by expression

130 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	84.75	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	79.92	gold quality
right testis	UBERON:0004534	52.64	gold quality
testis	UBERON:0000473	52.52	gold quality
left testis	UBERON:0004533	51.05	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
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
liver	UBERON:0002107	29.13	gold quality
prefrontal cortex	UBERON:0000451	29.04	gold quality
islet of Langerhans	UBERON:0000006	28.77	gold quality
adult mammalian kidney	UBERON:0000082	28.57	gold quality
kidney	UBERON:0002113	28.55	gold quality
duodenum	UBERON:0002114	28.14	gold quality
urinary bladder	UBERON:0001255	28.05	gold quality
monocyte	CL:0000576	27.86	gold quality
leukocyte	CL:0000738	27.83	gold quality
right coronary artery	UBERON:0001625	27.77	gold quality
lymph node	UBERON:0000029	27.57	gold quality
tonsil	UBERON:0002372	27.05	gold quality
vermiform appendix	UBERON:0001154	26.42	gold quality
blood	UBERON:0000178	26.11	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	0.35

Regulation

Is transcription factor: no

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), RBMY1A1 (ENSG00000234414), RBMY1E (ENSG00000242389), RBMY1B (ENSG00000242875), RBMY1D (ENSG00000244395), DND1 (ENSG00000256453)

Protein

Protein identifiers

RNA-binding motif protein, Y chromosome, family 1 member F/J — Q15415 (reviewed: Q15415)

Alternative names: Y chromosome RNA recognition motif 2

All UniProt accessions (1): Q15415

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.

Isoforms (2)

UniProt ID	Names	Canonical?
Q15415-1	1	yes
Q15415-2	2

RefSeq proteins (1): NP_001006117* (*=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 (16 total): compositionally biased region 9, splice variant 2, region of interest 2, chain 1, domain 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q15415-F1	49.40	0.09

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 11 (showing top): GOBP_RNA_SPLICING, ACEVEDO_METHYLATED_IN_LIVER_CANCER_DN, GOCC_SPLICEOSOMAL_COMPLEX, GOCC_RIBONUCLEOPROTEIN_COMPLEX, GOMF_MRNA_BINDING, chrYq11, GOBP_MRNA_PROCESSING, GOCC_NUCLEAR_PROTEIN_CONTAINING_COMPLEX, GOBP_MRNA_METABOLIC_PROCESS, GOBP_RNA_SPLICING_VIA_TRANSESTERIFICATION_REACTIONS, GOBP_RNA_PROCESSING

GO Biological Process (3): mRNA processing (GO:0006397), RNA splicing (GO:0008380), positive regulation of mRNA splicing, via spliceosome (GO:0048026)

GO Molecular Function (4): RNA binding (GO:0003723), identical protein binding (GO:0042802), nucleic acid binding (GO:0003676), protein binding (GO:0005515)

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

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
RNA processing	2
binding	2
nuclear lumen	2
mRNA metabolic process	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
protein binding	1
cellular anatomical structure	1
nuclear protein-containing complex	1
ribonucleoprotein complex	1
intracellular membraneless organelle	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

1286 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
RBMY1J	A6NGT6	A6NGT6	670
RBMY1J	TSPY4	P0CV99	668
RBMY1J	A6NEC3	A6NEC3	579
RBMY1J	TSPY1	P09002	516
RBMY1J	VCY	O14598	505
RBMY1J	SPATA31A1	Q5TZJ5	475
RBMY1J	EIF1AY	O14602	466
RBMY1J	PRY	O14603	446
RBMY1J	CDY2A	Q9Y6F7	435
RBMY1J	RPS4Y1	P22090	408
RBMY1J	BTBD19	C9JJ37	397
RBMY1J	DDX3Y	O15523	382
RBMY1J	MAGEB16	A2A368	378
RBMY1J	ANKRD36B	Q8N2N9	372
RBMY1J	BPY2	O14599	359

IntAct

154 interactions, top by confidence:

A	B	Type	Score
PRPF31	RBMY1F	psi-mi:“MI:0915”(physical association)	0.810
RBMY1F	PRPF31	psi-mi:“MI:0915”(physical association)	0.810
RBMY1F	PRR3	psi-mi:“MI:0915”(physical association)	0.780
PRR3	RBMY1F	psi-mi:“MI:0915”(physical association)	0.780
RBMY1F	RBMX	psi-mi:“MI:0915”(physical association)	0.720
RBM3	RBMY1F	psi-mi:“MI:0915”(physical association)	0.720
YTHDC1	RBMY1F	psi-mi:“MI:0915”(physical association)	0.720
APOBEC3C	RBMY1F	psi-mi:“MI:0915”(physical association)	0.720
RBMY1F	RASD1	psi-mi:“MI:0915”(physical association)	0.720
PCDHB14	RBMY1F	psi-mi:“MI:0915”(physical association)	0.720
RBMX	RBMY1F	psi-mi:“MI:0915”(physical association)	0.720
RBMY1F	YTHDC1	psi-mi:“MI:0915”(physical association)	0.720
RBMY1F	APOBEC3C	psi-mi:“MI:0915”(physical association)	0.720
RASD1	RBMY1F	psi-mi:“MI:0915”(physical association)	0.720
RBMY1F	RBM3	psi-mi:“MI:0915”(physical association)	0.720
RBMY1F	PCDHB14	psi-mi:“MI:0915”(physical association)	0.720

BioGRID (80): RBMY1F (Two-hybrid), RBMY1F (Two-hybrid), RBMY1F (Two-hybrid), RBMY1F (Two-hybrid), RBMY1F (Two-hybrid), RBMY1F (Two-hybrid), RBMY1F (Two-hybrid), RBMY1F (Two-hybrid), RBMY1F (Two-hybrid), RBMY1F (Two-hybrid), RBMY1F (Two-hybrid), RBMY1F (Two-hybrid), RBMY1F (Two-hybrid), RBMY1F (Two-hybrid), RBMY1F (Two-hybrid)

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: A0A0D1C8Z4, A1A5R1, A2A5N3, A3LXL0, A4F5G6, A5A6M3, A5DW14, A6NFN3, A6QPR6, F1QB54, F4HT49, O04319, O13845, O35698, O43251, O93235, P0CB38, P11940, P19682, P19683, P19684, P20965, P28644, P29341, P38159, P42731, P49313, P49314, P60824, P60825, P60826, P61286, P62995, P62996, P62997, Q04836, Q08935, Q08937, Q09511, Q0VD23

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 37 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
mRNA Polyadenylation	6	32.9×	4e-07
Processing of Capped Intron-Containing Pre-mRNA	6	30.8×	4e-07
mRNA Splicing - Major Pathway	8	27.3×	8e-09

GO biological processes:

GO term	Partners	Fold	FDR
negative regulation of mRNA splicing, via spliceosome	5	132.1×	9e-09
positive regulation of mRNA splicing, via spliceosome	7	131.2×	5e-12
regulation of alternative mRNA splicing, via spliceosome	5	42.1×	3e-06
mRNA splicing, via spliceosome	9	28.4×	7e-10

Disease & clinical

Clinical variants and AI predictions

ClinVar

1 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	1

Top pathogenic / likely-pathogenic (0)

SpliceAI

1271 predictions. Top by Δscore:

Variant	Effect	Δscore
Y:22405436:A:AG	acceptor_gain	1.0000
Y:22405440:ACAG:A	acceptor_loss	1.0000
Y:22405441:CA:C	acceptor_loss	1.0000
Y:22405442:A:AG	acceptor_gain	1.0000
Y:22405443:G:GA	acceptor_gain	1.0000
Y:22405443:G:GT	acceptor_loss	1.0000
Y:22405443:GC:G	acceptor_gain	1.0000
Y:22405443:GCAC:G	acceptor_gain	1.0000
Y:22405443:GCACA:G	acceptor_gain	1.0000
Y:22405552:AGAAG:A	donor_loss	1.0000
Y:22405553:GAAG:G	donor_gain	1.0000
Y:22405554:AAGGT:A	donor_loss	1.0000
Y:22405555:AGG:A	donor_loss	1.0000
Y:22405556:GGTA:G	donor_loss	1.0000
Y:22405557:GT:G	donor_loss	1.0000
Y:22405558:T:G	donor_loss	1.0000
Y:22406021:TTAGT:T	acceptor_loss	1.0000
Y:22406023:A:AG	acceptor_gain	1.0000
Y:22406024:G:GA	acceptor_gain	1.0000
Y:22406024:GT:G	acceptor_gain	1.0000
Y:22406024:GTT:G	acceptor_gain	1.0000
Y:22406024:GTTC:G	acceptor_gain	1.0000
Y:22406024:GTTCT:G	acceptor_gain	1.0000
Y:22406124:GAACG:G	donor_gain	1.0000
Y:22406127:CGG:C	donor_loss	1.0000
Y:22406128:GGTAA:G	donor_loss	1.0000
Y:22406129:G:GG	donor_gain	1.0000
Y:22406130:T:G	donor_loss	1.0000
Y:22409150:A:AG	acceptor_gain	1.0000
Y:22409151:G:GG	acceptor_gain	1.0000

AlphaMissense

3229 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
Y:22405478:T:C	F11L	0.999
Y:22405480:C:A	F11L	0.999
Y:22405480:C:G	F11L	0.999
Y:22405529:T:C	F28L	0.999
Y:22405531:T:A	F28L	0.999
Y:22405531:T:G	F28L	0.999
Y:22406063:T:C	F50L	0.999
Y:22406065:T:A	F50L	0.999
Y:22406065:T:G	F50L	0.999
Y:22406069:T:C	F52L	0.999
Y:22406071:T:A	F52L	0.999
Y:22406071:T:G	F52L	0.999
Y:22406078:T:C	F55L	0.999
Y:22406080:T:A	F55L	0.999
Y:22406080:T:G	F55L	0.999
Y:22405479:T:C	F11S	0.998
Y:22405518:T:A	L24H	0.998
Y:22406070:T:C	F52S	0.998
Y:22406073:T:A	I53N	0.998
Y:22405476:T:C	L10P	0.997
Y:22405482:T:A	I12N	0.997
Y:22405530:T:C	F28S	0.997
Y:22406067:C:A	A51E	0.997
Y:22406079:T:C	F55S	0.997
Y:22405479:T:G	F11C	0.996
Y:22405518:T:C	L24P	0.996
Y:22405542:G:A	G32D	0.996
Y:22406031:T:C	L39S	0.996
Y:22406064:T:C	F50S	0.996
Y:22406073:T:G	I53S	0.996

dbSNP variants (sampled 173 via entrez): RS112431691 (Y:22407876 G>T), RS112686876 (Y:22406178 T>A), RS113148937 (Y:22420287 C>T), RS113218204 (Y:22423034 A>G), RS113307592 (Y:22418335 G>A), RS1176116223 (Y:22405239 C>G), RS1195699969 (Y:22406127 C>A), RS1212505894 (Y:22403532 C>CG), RS1290865957 (Y:22418269 A>G), RS1294829928 (Y:22405950 C>T), RS1334354896 (Y:22405577 T>TGC), RS1344750866 (Y:22416695 T>A), RS1365693581 (Y:22418467 G>A), RS1381667492 (Y:22405901 T>C), RS1431485253 (Y:22416820 C>T)

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
Temozolomide	increases expression	1
Benzo(a)pyrene	affects methylation	1

Clinical trials (associated diseases)

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