RBMY1E

gene
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Summary

RBMY1E (RNA binding motif protein Y-linked family 1 member E, HGNC:23916) is a protein-coding gene on chromosome Yq11.223, encoding RNA-binding motif protein, Y chromosome, family 1 member E (A6NEQ0). 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 378950 — RefSeq curated summary.

At a glance

  • Clinical variants (ClinVar): 1 total — 1 pathogenic
  • MANE Select transcript: NM_001006118

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:23916
Approved symbolRBMY1E
NameRNA binding motif protein Y-linked family 1 member E
LocationYq11.223
Locus typegene with protein product
StatusApproved
Ensembl geneENSG00000242389
Ensembl biotypeprotein_coding
Entrez378950

Gene structure

Transcript identifiers

Ensembl transcripts: 3 — 2 protein_coding, 1 nonsense_mediated_decay

ENST00000358944, ENST00000382658, ENST00000382659

RefSeq mRNA: 1 — MANE Select: NM_001006118 NM_001006118

CCDS: CCDS35481

Canonical transcript exons

ENST00000382659 — 12 exons

ExonStartEnd
ENSE000016193752191216921912346
ENSE000016355052191594621916058
ENSE000018026442191536621915469
ENSE000034685562191010121910253
ENSE000034801742190691021907020
ENSE000034825212190581321905923
ENSE000035285062190797621908090
ENSE000035476472190460621904694
ENSE000035598502190478121904891
ENSE000035775062190635821906468
ENSE000036135692190362221904194
ENSE000037217122191792021918032

Expression profiles

Bgee: expression breadth tissue_specific, 8 present calls, max score 83.65.

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047383.65gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099179.09gold quality
right testisUBERON:000453462.28gold quality
testisUBERON:000047359.14gold quality
left testisUBERON:000453357.74gold quality
colonic epitheliumUBERON:000039737.20gold quality
ventricular zoneUBERON:000305336.48gold quality
cortical plateUBERON:000534336.47gold quality
bone marrow cellCL:000209236.16gold quality
ganglionic eminenceUBERON:000402335.49gold quality
skeletal muscle tissueUBERON:000113433.38gold quality
hindlimb stylopod muscleUBERON:000425232.15gold quality
bone marrowUBERON:000237131.74gold quality
muscle tissueUBERON:000238531.06gold quality
sural nerveUBERON:001548830.93gold quality
stromal cell of endometriumCL:000225529.87gold quality
prefrontal cortexUBERON:000045129.04gold quality
liverUBERON:000210728.27gold quality
duodenumUBERON:000211428.14gold quality
lymph nodeUBERON:000002927.57gold quality
tonsilUBERON:000237227.05gold quality
islet of LangerhansUBERON:000000626.88gold quality
bloodUBERON:000017826.62gold quality
vermiform appendixUBERON:000115426.42gold quality
gall bladderUBERON:000211025.98gold quality
olfactory segment of nasal mucosaUBERON:000538625.89gold quality
placentaUBERON:000198725.81gold quality
muscle of legUBERON:000138325.21silver quality
leukocyteCL:000073824.80gold quality
primary visual cortexUBERON:000243624.61gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3no0.23

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

23 targeting RBMY1E, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-3613-3P100.0076.367965
HSA-MIR-428299.9975.366408
HSA-MIR-60799.9773.625593
HSA-MIR-590-3P99.9674.346478
HSA-MIR-548AA99.9670.643753
HSA-MIR-548AP-3P99.9670.643753
HSA-MIR-548T-3P99.9670.643753
HSA-MIR-450B-5P99.9271.483175
HSA-MIR-367199.9073.043897
HSA-MIR-76599.8468.242442
HSA-MIR-7856-5P99.7569.992901
HSA-MIR-11181-3P99.7566.382205
HSA-MIR-766-5P99.4767.912225
HSA-MIR-4777-3P99.1568.92626
HSA-MIR-184398.9766.07838
HSA-MIR-4802-5P98.9766.26833
HSA-MIR-6894-5P98.7063.78809
HSA-MIR-6831-5P98.2667.20990
HSA-MIR-509-3P98.1267.25612
HSA-MIR-3927-3P97.6866.76892
HSA-MIR-7154-3P97.6565.02985
HSA-MIR-490-5P96.7565.81661
HSA-MIR-875-5P96.7466.48579

Cross-species orthologs

11 orthologs

OrganismSymbolGene ID
mus_musculusRbmyf3ENSMUSG00000091987
mus_musculusRbmyf5ENSMUSG00000093918
mus_musculusRbmyf7ENSMUSG00000093987
mus_musculusRbmyf6ENSMUSG00000094511
mus_musculusRbmyENSMUSG00000094658
mus_musculusRbmyf2ENSMUSG00000095852
mus_musculusRbmyf8ENSMUSG00000095948
mus_musculusRbmyf9ENSMUSG00000096520
mus_musculusRbmyf4ENSMUSG00000101667
mus_musculusRbmyf1ENSMUSG00000102053
rattus_norvegicusRbmy1jENSRNOG00000060963

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), RBMY1B (ENSG00000242875), RBMY1D (ENSG00000244395), DND1 (ENSG00000256453)

Protein

Protein identifiers

RNA-binding motif protein, Y chromosome, family 1 member EA6NEQ0 (reviewed: A6NEQ0)

All UniProt accessions (3): A6NEQ0, F2Z2U1, J3KPK3

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 (1): NP_001006118* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR000504RRM_domDomain
IPR012604RBM1CTRDomain
IPR012677Nucleotide-bd_a/b_plait_sfHomologous_superfamily
IPR035979RBD_domain_sfHomologous_superfamily
IPR050441RBMFamily

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)

ModelpLDDTFraction very-high
AF-A6NEQ0-F150.090.08

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 17 (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, MIR1843, MIR4802_5P, MIR509_3P, GOCC_NUCLEAR_PROTEIN_CONTAINING_COMPLEX, FOURATI_BLOOD_TWINRIX_AGE_25_83YO_RESPONDERS_VS_POOR_RESPONDERS_0DY_DN, GOBP_MRNA_METABOLIC_PROCESS

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

GO Molecular Function (3): RNA binding (GO:0003723), 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:

CategoryTerms
RNA processing2
binding2
nuclear lumen2
mRNA metabolic process1
mRNA splicing, via spliceosome1
positive regulation of RNA splicing1
regulation of mRNA splicing, via spliceosome1
positive regulation of mRNA processing1
nucleic acid binding1
cellular anatomical structure1
nuclear protein-containing complex1
ribonucleoprotein complex1
intracellular membraneless organelle1
intracellular membrane-bounded organelle1

Protein interactions and networks

STRING

1180 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
RBMY1EA6NGL4A6NGL4717
RBMY1EA6NEC3A6NEC3584
RBMY1EA6NGT6A6NGT6577
RBMY1ERPS4Y2Q8TD47501
RBMY1EAMELYQ99218447
RBMY1ERC3H2Q9HBD1394
RBMY1EEIF1AYO14602389
RBMY1ERPS4Y1P22090371
RBMY1ESPRY3O43610371
RBMY1ETSPY1P09002350
RBMY1EZFYP08048347
RBMY1ENLGN4YQ8NFZ3315
RBMY1EUTYO14607307
RBMY1ERC3H1Q5TC82302
RBMY1EZFXP17010294

IntAct

7 interactions, top by confidence:

ABTypeScore
RBMY1ERBMXpsi-mi:“MI:0915”(physical association)0.560
RBMY1ERBMY1Fpsi-mi:“MI:0915”(physical association)0.560
RBMY1ERBMXpsi-mi:“MI:0915”(physical association)0.000
RBMY1ERBMY1Fpsi-mi:“MI:0915”(physical association)0.000

BioGRID (3): RBMY1E (Two-hybrid), RBMY1E (Two-hybrid), RBMY1E (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: 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

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

ClassificationCount (floor)
Pathogenic1
Likely pathogenic0
Uncertain significance0
Likely benign0
Benign0

Top pathogenic / likely-pathogenic (1)

Variant IDHGVSClassification
870515GRCh37/hg19 Yq11.223-11.23(chrY:23887108-28799937)x0Pathogenic

SpliceAI

1458 predictions. Top by Δscore:

VariantEffectΔscore
Y:21904599:CCCTT:Cdonor_loss1.0000
Y:21904600:CCTTA:Cdonor_loss1.0000
Y:21904601:CTTA:Cdonor_loss1.0000
Y:21904602:TTA:Tdonor_loss1.0000
Y:21904603:T:TGdonor_loss1.0000
Y:21904604:A:ACdonor_gain1.0000
Y:21904604:A:ATdonor_loss1.0000
Y:21904605:C:CCdonor_gain1.0000
Y:21904690:GATAA:Gacceptor_gain1.0000
Y:21904691:ATAA:Aacceptor_gain1.0000
Y:21904692:TAA:Tacceptor_gain1.0000
Y:21904693:AA:Aacceptor_gain1.0000
Y:21904693:AACT:Aacceptor_loss1.0000
Y:21904694:ACTA:Aacceptor_loss1.0000
Y:21904695:C:CCacceptor_gain1.0000
Y:21904695:CT:Cacceptor_loss1.0000
Y:21904700:T:Cacceptor_gain1.0000
Y:21904700:T:TCacceptor_gain1.0000
Y:21904783:ATAT:Adonor_gain1.0000
Y:21905809:GTACC:Gdonor_loss1.0000
Y:21905810:TACCT:Tdonor_loss1.0000
Y:21905815:ATAT:Adonor_gain1.0000
Y:21905921:TTT:Tacceptor_gain1.0000
Y:21905921:TTTC:Tacceptor_loss1.0000
Y:21905922:TT:Tacceptor_gain1.0000
Y:21905923:TCTG:Tacceptor_loss1.0000
Y:21905924:C:CCacceptor_gain1.0000
Y:21905928:A:ACacceptor_gain1.0000
Y:21905928:A:Cacceptor_gain1.0000
Y:21905931:C:CTacceptor_gain1.0000

AlphaMissense

3226 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
Y:21915423:A:CF52L1.000
Y:21915423:A:TF52L1.000
Y:21915425:A:GF52L1.000
Y:21915429:A:CF50L1.000
Y:21915429:A:TF50L1.000
Y:21915431:A:GF50L1.000
Y:21916022:G:CF11L1.000
Y:21916022:G:TF11L1.000
Y:21916024:A:GF11L1.000
Y:21915414:A:CF55L0.999
Y:21915414:A:TF55L0.999
Y:21915416:A:GF55L0.999
Y:21915424:A:GF52S0.999
Y:21915430:A:GF50S0.999
Y:21915435:T:AR48S0.999
Y:21915435:T:GR48S0.999
Y:21915971:A:CF28L0.999
Y:21915971:A:TF28L0.999
Y:21915973:A:GF28L0.999
Y:21916023:A:GF11S0.999
Y:21915436:C:GR48T0.998
Y:21915984:A:TL24H0.998
Y:21916020:A:TI12N0.998
Y:21916023:A:CF11C0.998
Y:21915415:A:GF55S0.997
Y:21915421:A:TI53N0.997
Y:21915427:G:TA51E0.997
Y:21915972:A:GF28S0.997
Y:21916026:A:GL10P0.997
Y:21915424:A:CF52C0.996

dbSNP variants (sampled 113 via entrez): RS1160419817 (Y:21904100 G>A), RS1164519279 (Y:21906357 C>T), RS1175616459 (Y:21906334 C>T), RS1180219298 (Y:21904702 GA>G), RS1189660077 (Y:21906342 G>C), RS1194098937 (Y:21904019 A>C), RS1197406025 (Y:21906451 C>T), RS1202321544 (Y:21906473 A>G), RS1214396324 (Y:21903975 C>T), RS1233316015 (Y:21906401 A>T), RS1233391775 (Y:21904737 A>G), RS1240013790 (Y:21903984 C>T), RS1272169212 (Y:21906416 G>A), RS1273430528 (Y:21906454 G>C), RS1280668224 (Y:21904188 G>A)

Disease associations

OMIM: gene `` | disease phenotypes:

GenCC curated gene-disease

Mondo (1): male infertility (MONDO:0005372)

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

0 associations (top):

MeSH disease descriptors (1)

DescriptorNameTree numbers
D007248Infertility, MaleC12.100.500.430; C12.100.750.700; C12.200.294.430

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

1 total (human), top 1 by PubMed support.

ChemicalActions (top 5)PubMed papers
Temozolomideincreases expression1

Clinical trials (associated diseases)

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

TrialPhaseStatusTitle
NCT02202382PHASE4COMPLETEDEffects of Korean Red Ginseng on Male Infertility
NCT02204826PHASE4COMPLETEDEffects of Korean Red Ginseng on Semen Parameters in Male Infertility Patients: a Randomized, Placebo-controlled, Double-blind Clinical Study
NCT03802864PHASE4COMPLETEDPost-operative Pain Control of Testicular Sperm Extraction Using Liposomal Bupivacaine
NCT06100432PHASE4ACTIVE_NOT_RECRUITINGEffect of Eurycoma Longifolia (DLBS5055) and Multivitamins (Vitamin C+Vitamin E+ β-carotene) for Infertile Males
NCT07523022PHASE4ENROLLING_BY_INVITATIONComparison of the Effect of Gonadotropin and Clomiphene Citrate Treatment on Sperm Parameters and the Outcome of Assisted Reproductive Procedures in Subfertile Men Based on the APHRODITE Groups
NCT00975117PHASE3COMPLETEDSpermotrend in the Treatment of Male Infertility
NCT01407432PHASE3COMPLETEDImpact of Folates in the Care of the Male Infertility
NCT01895816PHASE3COMPLETEDHerbal Tonic Fertile Supplement(ZO2C5)
NCT02605070PHASE3TERMINATEDPilot Study on the Effects of FSH Treatment on the Epigenetic Characteristics of Spermatozoa in Infertile Patients With Severe Oligozoospermia
NCT07402759PHASE3ACTIVE_NOT_RECRUITINGImpact of tdrd9 Gene Mutations in the Therapeutic Response to L-carnitine in Oligoasthenozoospermic Men
NCT01880086PHASE2COMPLETEDClomiphene Citrate for the Treatment of Low Testosterone Associated With Chronic Opioid Pain Medication Administration
NCT02061384PHASE2COMPLETEDRA-2 13-cis Retinoic Acid (Isotretinoin)
NCT02421887PHASE2COMPLETEDMales, Antioxidants, and Infertility Trial
NCT05200663PHASE2UNKNOWNEfficacy Comparison of Tamoxifen and Tamoxifen With Antioxidants on Semen Quality of Male With Idiopathic Infertility
NCT05290558PHASE2ACTIVE_NOT_RECRUITINGThe Therapeutic Effects of Bu Shen Yi Jing Pill on Semen Quality in Sub Fertile Males: a Randomized Controlled Trial
NCT06091969PHASE2NOT_YET_RECRUITINGSupplementation for Male Subfertility
NCT01595308PHASE1COMPLETEDA Pilot Study to Evaluate the Effect of Pomegranate Juice on Semen Parameters in Healthy Male Volunteers
NCT02122211PHASE1COMPLETEDCholine Dehydrogenase and Sperm Function: Effects of Betaine
NCT02575924PHASE1UNKNOWNInfluence of Culture Media on Clinical Outcomes in Poor Responders or Severe Male Infertility
NCT01304927PHASE2/PHASE3COMPLETEDVitamin D Supplementation and Male Infertility: The CBG-study a Randomized Clinical Trial
NCT02349945PHASE2/PHASE3COMPLETEDFSH Receptor Polymorphism p.N680S and Efficacy of FSH Therapy
NCT05222841PHASE2/PHASE3COMPLETEDThe Effectiveness of Spermotrend Food Supplement in the Treatment of Male Infertility
NCT05616598PHASE2/PHASE3COMPLETEDEffect of New Oral Treatment for Hepatitis C Virus on Seminal Parameters
NCT02025270PHASE1/PHASE2COMPLETEDMSCs For Treatment of Azoospermic Patients
NCT04541459EARLY_PHASE1UNKNOWNValidation of New Devices Against Ambient Electromagnetic Radiation
NCT05792813EARLY_PHASE1UNKNOWNEfficacy and Safety of Linggui Yangyuan Paste in Patients With Male Infertility
NCT06188936EARLY_PHASE1COMPLETEDHome Semen Analysis Tests As a Screening Tool for Fertility Patients
NCT00012480Not specifiedCOMPLETEDEffect of Environmental Exposures on the Egg Fertilizing Ability of Human Sperm
NCT00044369Not specifiedCOMPLETEDRole of the Toxic Metal Cadmium in the Mechanism Producing Infertility With a Varicocele
NCT00119925Not specifiedUNKNOWN‘SPRING’-Study: Subfertility Guidelines: Patient Related Implementation in the Netherlands Among Gynaecologists
NCT00178516Not specifiedCOMPLETEDVitamin E and Male Infertility
NCT00315029Not specifiedCOMPLETEDPatient-Centered Implementation Trial for Single Embryo Transfer
NCT00341120Not specifiedCOMPLETEDGenetic Causes of Male Infertility
NCT00481403Not specifiedCOMPLETEDStudy of Sperm Molecular Factors Implicated in Male Fertility
NCT00548977Not specifiedCOMPLETEDGenetic Studies Spermatogenic Failure
NCT00596739Not specifiedCOMPLETEDA Study of the Pre- and Post-operative Semen Analyses and Reproductive Hormone Levels of Men Undergoing Weight-reduction Surgery
NCT00756561Not specifiedCOMPLETEDHOP-2A - Intratesticular Hormone Levels
NCT00961558Not specifiedTERMINATEDCanadian Varicocelectomy Initiative (CVI): Effects on Male Fertility and Testicular Function of Varicocelectomy
NCT01075334Not specifiedUNKNOWNIs a Carnitine Based Food Supplement (PorimoreTM) for Infertile Men Superior to Folate and Zinc With Regard to Pregnancy Rates in Intrauterine Insemination Cycles?
NCT01178463Not specifiedUNKNOWNSpermatogonial Stem Cells in Azoospermic Patients: a Comparison Between Obstructive and Non-obstructive Azoospermia
  • Disease cohort memberships (association, not causation — diseases whose associated-gene cohort lists this gene; a subset are also under Associated diseases): male infertility