RBMY1F

Summary

RBMY1F (RNA binding motif protein Y-linked family 1 member F, HGNC:23974) 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. Multiple copies of this gene are found in the AZFb azoospermia factor region of chromosome Y and the encoded protein is thought to be involved in spermatogenesis. Most copies of this locus are pseudogenes, although six highly similar copies have full-length ORFs and are considered functional. Four functional copies of this gene are found within inverted repeat IR2; two functional copies of this gene are found in palindrome P3, along with two copies of PTPN13-like, Y-linked.

Source: NCBI Gene 159163 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 3 total — 1 pathogenic
• MANE Select transcript: NM_152585

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:23974
Approved symbol	RBMY1F
Name	RNA binding motif protein Y-linked family 1 member F
Location	Yq11.223
Locus type	gene with protein product
Status	Approved
Aliases	MGC33094
Ensembl gene	ENSG00000169800
Ensembl biotype	protein_coding
Entrez	159163

Gene structure

Transcript identifiers

Ensembl transcripts: 3 — 2 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000303766, ENST00000454978, ENST00000481858

RefSeq mRNA: 6 — MANE Select: NM_152585 NM_001303410, NM_001382381, NM_001382382, NM_001382383, NM_001382384, NM_152585

CCDS: CCDS35483, CCDS94717

Canonical transcript exons

ENST00000303766 — 12 exons

Exon	Start	End
ENSE00001703126	22182835	22182923
ENSE00001739138	22177094	22177271
ENSE00003469687	22180861	22180973
ENSE00003531954	22171835	22171945
ENSE00003536546	22180291	22180394
ENSE00003557303	22170739	22170849
ENSE00003568885	22169705	22169815
ENSE00003580283	22168542	22169118
ENSE00003638296	22169530	22169618
ENSE00003661928	22171284	22171394
ENSE00003668781	22172901	22173015
ENSE00003679115	22175026	22175178

Expression profiles

Bgee: expression breadth broad, 11 present calls, max score 80.70.

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	80.70	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	78.99	gold quality
right testis	UBERON:0004534	59.21	gold quality
testis	UBERON:0000473	58.68	gold quality
left testis	UBERON:0004533	57.14	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	35.25	gold quality
muscle tissue	UBERON:0002385	32.43	gold quality
hindlimb stylopod muscle	UBERON:0004252	32.15	gold quality
bone marrow	UBERON:0002371	31.74	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
liver	UBERON:0002107	28.97	gold quality
duodenum	UBERON:0002114	28.14	gold quality
monocyte	CL:0000576	27.70	gold quality
leukocyte	CL:0000738	27.69	gold quality
lymph node	UBERON:0000029	27.57	gold quality
tonsil	UBERON:0002372	27.05	gold quality
blood	UBERON:0000178	26.67	silver quality
urinary bladder	UBERON:0001255	26.62	gold quality
vermiform appendix	UBERON:0001154	26.42	gold quality
right coronary artery	UBERON:0001625	26.28	gold quality
rectum	UBERON:0001052	26.27	gold quality
kidney	UBERON:0002113	26.26	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	0.09

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

14 targeting RBMY1F, 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-4282	99.99	75.36	6408
HSA-MIR-607	99.97	73.62	5593
HSA-MIR-590-3P	99.96	74.34	6478
HSA-MIR-450B-5P	99.92	71.48	3175
HSA-MIR-3671	99.90	73.04	3897
HSA-MIR-7856-5P	99.75	69.99	2901
HSA-MIR-766-5P	99.47	67.91	2225
HSA-MIR-4777-3P	99.15	68.92	626
HSA-MIR-3611	98.76	68.76	1290
HSA-MIR-6831-5P	98.26	67.20	990
HSA-MIR-509-3P	98.12	67.25	612
HSA-MIR-3927-3P	97.68	66.76	892
HSA-MIR-875-5P	96.74	66.48	579

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), 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), 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 (2): Q15415, J3KQ82

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 (6): NP_001290339, NP_001369310, NP_001369311, NP_001369312, NP_001369313, NP_689798* (*=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: 20 (showing top): GOBP_RNA_SPLICING, ACEVEDO_METHYLATED_IN_LIVER_CANCER_DN, GOCC_SPLICEOSOMAL_COMPLEX, GOCC_RIBONUCLEOPROTEIN_COMPLEX, GOMF_MRNA_BINDING, chrYq11, GOBP_MRNA_PROCESSING, MIR7856_5P, MIR766_5P, MIR6817_5P, MIR4769_3P, MIR4686, MIR1843, MIR4802_5P, MIR509_3P

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
RBMY1F	A6NGT6	A6NGT6	670
RBMY1F	TSPY4	P0CV99	668
RBMY1F	A6NEC3	A6NEC3	579
RBMY1F	TSPY1	P09002	516
RBMY1F	VCY	O14598	505
RBMY1F	SPATA31A1	Q5TZJ5	475
RBMY1F	EIF1AY	O14602	466
RBMY1F	PRY	O14603	446
RBMY1F	CDY2A	Q9Y6F7	435
RBMY1F	RPS4Y1	P22090	408
RBMY1F	BTBD19	C9JJ37	397
RBMY1F	DDX3Y	O15523	382
RBMY1F	MAGEB16	A2A368	378
RBMY1F	ANKRD36B	Q8N2N9	372
RBMY1F	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 36 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	136.8×	7e-09
positive regulation of mRNA splicing, via spliceosome	6	116.5×	5e-10
regulation of alternative mRNA splicing, via spliceosome	5	43.6×	2e-06
mRNA splicing, via spliceosome	9	29.4×	5e-10

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	1
Likely pathogenic	0
Uncertain significance	0
Likely benign	0
Benign	2

Top pathogenic / likely-pathogenic (1)

Variant ID	HGVS	Classification
145989	GRCh38/hg38 Yq11.223(chrY:21927773-22494369)x0	Pathogenic

SpliceAI

1409 predictions. Top by Δscore:

Variant	Effect	Δscore
Y:22169534:CCT:C	donor_gain	1.0000
Y:22169614:GATAA:G	acceptor_gain	1.0000
Y:22169616:TAA:T	acceptor_gain	1.0000
Y:22169616:TAAC:T	acceptor_loss	1.0000
Y:22169617:AA:A	acceptor_gain	1.0000
Y:22169617:AACT:A	acceptor_loss	1.0000
Y:22169618:AC:A	acceptor_loss	1.0000
Y:22169619:C:CC	acceptor_gain	1.0000
Y:22169619:CT:C	acceptor_loss	1.0000
Y:22169620:T:A	acceptor_loss	1.0000
Y:22169624:T:TC	acceptor_gain	1.0000
Y:22169707:ATAT:A	donor_gain	1.0000
Y:22170741:ATAT:A	donor_gain	1.0000
Y:22170760:T:A	donor_gain	1.0000
Y:22170847:TTT:T	acceptor_gain	1.0000
Y:22170847:TTTC:T	acceptor_loss	1.0000
Y:22170848:TT:T	acceptor_gain	1.0000
Y:22170848:TTC:T	acceptor_loss	1.0000
Y:22170850:C:CC	acceptor_gain	1.0000
Y:22170854:A:AC	acceptor_gain	1.0000
Y:22170854:A:C	acceptor_gain	1.0000
Y:22171279:AGTAC:A	donor_loss	1.0000
Y:22171280:GTA:G	donor_loss	1.0000
Y:22171281:TA:T	donor_loss	1.0000
Y:22171282:ACC:A	donor_loss	1.0000
Y:22171283:C:CT	donor_loss	1.0000
Y:22171390:GATTT:G	acceptor_gain	1.0000
Y:22171391:ATTT:A	acceptor_gain	1.0000
Y:22171392:TTT:T	acceptor_gain	1.0000
Y:22171392:TTTCT:T	acceptor_loss	1.0000

AlphaMissense

3230 scored. Top likely-pathogenic:

dbSNP variants (sampled 185 via entrez): RS1003449 (Y:22167682 T>C), RS112554694 (Y:22171848 A>T), RS112936698 (Y:22173339 C>T), RS1168910271 (Y:22180301 A>T), RS1174098750 (Y:22178716 A>C), RS1187238352 (Y:22169543 T>G), RS1230022085 (Y:22180469 G>A), RS1269194802 (Y:22182685 T>G), RS1297685843 (Y:22180518 A>G), RS1336747582 (Y:22181002 T>G), RS1361756132 (Y:22183103 C>T), RS1373556062 (Y:22169436 T>C), RS1396193502 (Y:22180309 C>G), RS1408751859 (Y:22180349 A>C), RS1415960532 (Y:22169626 GA>G)

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
arsenite	increases methylation	1
Benzo(a)pyrene	affects methylation	1

Clinical trials (associated diseases)

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