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RBMY1E Gene

protein-coding   GIFtS: 29
GCID: GC0YM024027

RNA Binding Motif Protein, Y-Linked, Family 1, Member E

  See RBMY1E-related disease
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
RNA Binding Motif Protein, Y-Linked, Family 1, Member E1 2
RNA-Binding Motif Protein, Y Chromosome, Family 1 Member E2

External Ids:    HGNC: 239161   Entrez Gene: 3789502   Ensembl: ENSG000002423897   UniProtKB: A6NEQ03   

Export aliases for RBMY1E gene to outside databases

Previous GC identifers: GC0YU900272 GC0YM022436


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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Entrez Gene summary for RBMY1E Gene:
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. (provided by RefSeq, Jul 2008)

GeneCards Summary for RBMY1E Gene:
RBMY1E (RNA binding motif protein, Y-linked, family 1, member E) is a protein-coding gene. Diseases associated with RBMY1E include azoospermia. GO annotations related to this gene include RNA binding and nucleotide binding. An important paralog of this gene is RBMY1J.

UniProtKB/Swiss-Prot: RBY1E_HUMAN, A6NEQ0
Function: RNA-binding protein which may be involved in spermatogenesis. Required for sperm development, possibly
by participating in pre-mRNA splicing in the testis




(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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Regulatory elements:
   Regulatory transcription factor binding sites in the RBMY1E gene promoter:
         POU2F1   POU2F1b   POU2F1a   POU2F1c   CUTL1   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
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Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat RBMY1E


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: Yq11.223   Ensembl cytogenetic band:  Yq11.223   HGNC cytogenetic band: Yq11.223

RBMY1E Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
RBMY1E gene location

GeneLoc information about chromosome Y         GeneLoc Exon Structure

GeneLoc location for GC0YM024027:  view genomic region     (about GC identifiers)

Start:
24,026,223 bp from pter      End:
24,064,214 bp from pter
Size:
37,992 bases      Orientation:
minus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, Cloud-Clone Corp., and/or eBioscience,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., and/or eBioscience, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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UniProtKB/Swiss-Prot: RBY1E_HUMAN, A6NEQ0 (See protein sequence)
Recommended Name: RNA-binding motif protein, Y chromosome, family 1 member E  
Size: 496 amino acids; 55759 Da
Subunit: Interacts with splicing factor proteins SFRS3/SRP20, TRA2B/SFRS10, KHDRBS1/SAM68 and KHDRBS3
Developmental stage: Expressed in all of the transcriptionally active stages of germ cell development from
spermatogonia through spermatocytes to round spermatids
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
Secondary accessions: A6NCW6 A6NEG9 A6NKQ5

Explore the universe of human proteins at neXtProt for RBMY1E: NX_A6NEQ0

Explore proteomics data for RBMY1E at MOPED


See RBMY1E Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

REFSEQ proteins: NP_001006118.2  
ENSEMBL proteins: 
 ENSP00000351823   ENSP00000372105   ENSP00000372119   ENSP00000372104  

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(According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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HGNC Gene Families:
RBM: RNA binding motif (RRM) containing

3 InterPro protein domains:
 IPR012604 RBM1CTR
 IPR012677 Nucleotide-bd_a/b_plait
 IPR000504 RRM_dom

Graphical View of Domain Structure for InterPro Entry A6NEQ0

ProtoNet protein and cluster: A6NEQ0

UniProtKB/Swiss-Prot: RBY1E_HUMAN, A6NEQ0
Similarity: Contains 1 RRM (RNA recognition motif) domain


Find genes that share domains with RBMY1E           About GenesLikeMe


(According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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Molecular Function:

     UniProtKB/Swiss-Prot Summary: RBY1E_HUMAN, A6NEQ0
Function: RNA-binding protein which may be involved in spermatogenesis. Required for sperm development, possibly
by participating in pre-mRNA splicing in the testis

     Gene Ontology (GO): 3 molecular function terms:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0000166nucleotide binding IEA--
GO:0003676nucleic acid binding ----
GO:0003723RNA binding IEA--
     
Find genes that share ontologies with RBMY1E           About GenesLikeMe


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(According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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Subcellular locations from UniProtKB/Swiss-Prot
RBY1E_HUMAN, A6NEQ0: Nucleus
Subcellular locations from COMPARTMENTS: 

CompartmentConfidence
nucleus5

Gene Ontology (GO): 1 cellular component term:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0005634nucleus IEA--

Find genes that share ontologies with RBMY1E           About GenesLikeMe


(SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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Interactions:

    Search GeneGlobe Interaction Network for RBMY1E

STRING Interaction Network Preview (showing 5 interactants - click image to see 7)

Selected Interacting proteins for RBMY1E (ENSP000003721044) via UniProtKB, MINT, STRING, and/or I2D (see all 7)
InteractantInteraction Details
GeneCardExternal ID(s)
CRNKL1ENSP000003665574STRING: ENSP00000366557
ISY1ENSP000003769734STRING: ENSP00000376973
PLRG1ENSP000003031914STRING: ENSP00000303191
SF3A3ENSP000003621104STRING: ENSP00000362110
SF3B1ENSP000003353214STRING: ENSP00000335321
About this table

Gene Ontology (GO): 2 biological process terms:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0006397mRNA processing IEA--
GO:0008380RNA splicing IEA--

Find genes that share ontologies with RBMY1E           About GenesLikeMe



(Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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Browse Tocris compounds for RBMY1E (RBY1E)



(Secondary structures according to fRNAdb,
GenBank/EMBL/DDBJ Accessions according to
Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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REFSEQ mRNAs for RBMY1E gene: 
NM_001006118.2  

4 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000358944(uc011nbg.2) ENST00000382659(uc010nxd.3 uc004fux.4 uc004fuw.4 uc011nbf.2)
ENST00000382673 ENST00000382658
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GeneLoc Exon Structure


(RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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RBMY1E expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: --
RBMY1E Expression
About this image

RBMY1E Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

RBMY1E Protein Expression

UniProtKB/Swiss-Prot: RBY1E_HUMAN, A6NEQ0
Tissue specificity: Testis-specific

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In Situ
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(Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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This gene was present in the common ancestor of animals.

Orthologs for RBMY1E gene from Selected species (see all 10)    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
chicken
(Gallus gallus)
Aves RBMX6
Gallus gallus RNA binding motif protein, X-linked ...
61(a)
1 → many
4(4390057-4400409)
lizard
(Anolis carolinensis)
Reptilia --
Uncharacterized protein
57(a)
1 → many
GL343562.1(327293-337930)
zebrafish
(Danio rerio)
Actinopterygii rbmx6
RNA binding motif protein, X-linked
51(a)
1 → many
14(32725471-32732600) ENSDARG00000014244
fruit fly
(Drosophila melanogaster)
Insecta tra26
transformer 2
15(a)
1 → many
2R(10489509-10491857)
worm
(Caenorhabditis elegans)
Secernentea rsp-86
Protein RSP-8, isoform a
18(a)
1 → many
III(11826215-11831475) WBGene00004705
        Species with no ortholog for RBMY1E

ENSEMBL Gene Tree for RBMY1E (if available)
TreeFam Gene Tree for RBMY1E (if available)

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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Paralogs for RBMY1E gene
RBMY1D1 2  RBMY1A11 2  RBMY1B1 2  RBMY1F1 2  RBMY1J1 2  TRA2B2  RBMXL22  RBMXL32  
RBMXL12  CIRBP2  RBM32  RBMX2  TRA2A2  
Selected SIMAP similar genes for RBMY1E using alignment to 2 protein entries:     RBY1E_HUMAN (see all proteins) (see all similar genes):
RBMY1C    RBMY1D    RBMY1B    RBMY1A1    RBMY1F    RBMY1J
RBM    BOLL    YRRM    HNRNPD    RBMX    PABPC4
PABPC1    CIRBP    RBMXL2    RBM38    RBMXL1    RBM3

Find genes that share paralogs with RBMY1E           About GenesLikeMe


Selected Pseudogenes.org Pseudogenes for RBMY1E (see all 8)
PGOHUM00000249967 PGOHUM00000249970 PGOHUM00000261042 PGOHUM00000233916 PGOHUM00000234009


(SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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6 SNPs for RBMY1E    About this table                                 

Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr Y posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs2013689411,2
C--24052303(+) CATGAC/TGAGTT 1 -- int10--------
rs3763069051,2
----24052771(+) GGACAC/GTACTC 1 -- int10--------
rs2019645791,2
----24050298(+) CCATAA/GGACAT 2 S syn10--------

HapMap Linkage Disequilibrium report for RBMY1E (24026223 - 24064214 bp)

Structural Variations
     Database of Genomic Variants (DGV) 9 variations for RBMY1E:    About this table    
Variant IDTypeSubtypePubMed ID
nsv819669CNV Insertion19587683
nsv469635CNV Loss16826518
nsv10026CNV Gain18304495
nsv471611CNV Gain+Loss15918152
essv23856CNV CNV17122850
nsv469695CNV Complex16826518
dgv2503e1CNV Complex17122850
dgv2502e1CNV Complex17122850
dgv2501e1CNV Complex17122850

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(in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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1 disease for RBMY1E:    
About MalaCards
azoospermia


Find genes that share disorders with RBMY1E           About GenesLikeMe


Export disorders for RBMY1E gene to outside databases

(in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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PubMed articles for RBMY1E gene integrated from 10 sources:
(articles sorted by number of sources associating them with RBMY1E)
    Utopia: connect your pdf to the dynamic
world of online information

  1. The male-specific region of the human Y chromosome is a mosaic of discrete sequence classes. (PubMed id 12815422)1, 2, 3 Skaletsky H.... Page D.C. (Nature 2003)
  2. RBMY, a male germ cell-specific RNA-binding protein, activated in human liver cancers and transforms rodent fibroblasts. (PubMed id 15184870)1 Tsuei D.J....Chang M.H. (Oncogene 2004)
  3. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1 Strausberg R.L....Marra M.A. (Proc. Natl. Acad. Sci. U.S.A. 2002)
  4. Structure and organization of the RBMY genes on the human Y chromosome: transposition and amplification of an ancestral autosomal hnRNPG gene. (PubMed id 9598316)1 Chai N.-N.... Yen P.H. (Genomics 1998)
  5. Degeneracy in human multicopy RBM (YRRM), a candidate spermatogenesis gene. (PubMed id 8875892)1 Prosser J.... Cooke H.J. (Mamm. Genome 1996)
  6. A Y chromosome gene family with RNA-binding protein homology: candidates for the azoospermia factor AZF controlling human spermatogenesis. (PubMed id 8269511)1 Ma K.... Jobling M. (Cell 1993)

(in PubMed, OMIM, and NCBI Bookshelf)
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 ANDOR
Aliases
Free Text  

  Query String
PubMed
OMIM
NCBI Bookshelf
  (Note: In FireFox, select the above section and copy using Ctrl-C)

(According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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Entrez Gene: 378950 HGNC: 23916 Ensembl:ENSG00000242389 euGenes: HUgn378950 ECgene: RBMY1E
H-InvDB: RBMY1E

(According to HUGE)
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  --

(According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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NameDescription
PharmGKB entry for RBMY1E Pharmacogenomics, SNPs, Pathways

(Patent information from GeneIP,
Licensable technologies from WIS Yeda, Salk, Tufts,
IP news from LifeMap Sciences, Inc.)
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Patent Information for RBMY1E gene:
Search GeneIP for patents involving RBMY1E

GeneCards and IP:
Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



(Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, eBioscience, and/or others, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Addgene, Cell lines from GenScript, and ESI BIO, Flow cytometery from eBioscience, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
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GeneCards Homepage - Last full update: 7 May 2014 - Incrementals: 9 May 2014 , 2 Jun 2014 , 26 Jun 2014 , 30 Jun 2014 , 21 Aug 2014 , 8 Sep 2014

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