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RBMY1A1 Gene

protein-coding   GIFtS: 50
GCID: GC0YP023680

RNA Binding Motif Protein, Y-Linked, Family 1, Member A1

(Previous names: RNA binding motif protein, Y chromosome, family 1, member...)
(Previous symbols: RBM1, RBM2)
  See RBMY1A1-related diseases
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 A11 2     RNA-Binding Motif Protein 22 3
RBM11 2 3 5     RBM2
RBM21 2 3 5     RBMY2
YRRM12 3 5     RBMY1C2
RNA Binding Motif Protein, Y Chromosome, Family 1, Member A11 2     RNA Binding Protein2
Y Chromosome RNA Recognition Motif 12 3     RNA-Binding Motif Protein, Y Chromosome, Family 1 Member A12
YRRM22 3     RNA-Binding Motif Protein, Y Chromosome, Family 1 Member A1/C2
RNA-Binding Motif Protein 12 3     hRBMY3

External Ids:    HGNC: 99121   Entrez Gene: 59402   Ensembl: ENSG000002344147   OMIM: 4000065   UniProtKB: P0DJD33   

Export aliases for RBMY1A1 gene to outside databases

Previous GC identifers: GC0YP022851 GC0YP022518 GC0YP022541 GC0YP022012 GC0YP022084 GC0YP023675


(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 RBMY1A1 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 RBMY1A1 Gene:
RBMY1A1 (RNA binding motif protein, Y-linked, family 1, member A1) is a protein-coding gene. Diseases associated with RBMY1A1 include spermatogenic failure, y-linked, 2, and azoospermia. GO annotations related to this gene include mRNA binding and nucleotide binding. An important paralog of this gene is RBMY1J.

UniProtKB/Swiss-Prot: RBY1A_HUMAN, P0DJD3
Function: RNA-binding protein involved in pre-mRNA splicing. Required for sperm development. Acts additively with
TRA2B to promote exon 7 inclusion of the survival motor neuron SMN. Binds non-specifically to mRNAs

Gene Wiki entry for RBMY1A1 (RNA binding motif protein, Y-linked, family 1, member A1) Gene


(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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RefSeq DNA sequence:
NC_000024.10  NT_011875.13  
Regulatory elements:
   Regulatory transcription factor binding sites in the RBMY1A1 gene promoter:
         POU2F1   POU2F1b   POU2F1a   POU2F1c   CUTL1   GATA-1   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidRBMY1A1 promoter sequence
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Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat RBMY1A1


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: Yq11.23

RBMY1A1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
RBMY1A1 gene location

GeneLoc information about chromosome Y         GeneLoc Exon Structure

GeneLoc location for GC0YP023680:  view genomic region     (about GC identifiers)

Start:
23,673,258 bp from pter      End:
23,711,212 bp from pter
Size:
37,955 bases      Orientation:
plus 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: RBY1A_HUMAN, P0DJD3 (See protein sequence)
Recommended Name: RNA-binding motif protein, Y chromosome, family 1 member A1  
Size: 496 amino acids; 55784 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
1 PDB 3D structure from and Proteopedia for RBMY1A1:
2FY1 (3D)    
Secondary accessions: Q15376 Q15377 Q15414 Q6NSB5 Q86VU6 Q8NHR0
Alternative splicing: 3 isoforms:  P0DJD3-1   P0DJD3-2   P0DJD3-3   

Explore the universe of human proteins at neXtProt for RBMY1A1: NX_P0DJD3

Explore proteomics data for RBMY1A1 at MOPED


See RBMY1A1 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

REFSEQ proteins: NP_005049.1  
ENSEMBL proteins: 
 ENSP00000372154   ENSP00000354329   ENSP00000303712   ENSP00000388006  

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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 P0DJD3

ProtoNet protein and cluster: P0DJD3

UniProtKB/Swiss-Prot: RBY1A_HUMAN, P0DJD3
Similarity: Contains 1 RRM (RNA recognition motif) domain


Find genes that share domains with RBMY1A1           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: RBY1A_HUMAN, P0DJD3
Function: RNA-binding protein involved in pre-mRNA splicing. Required for sperm development. Acts additively with
TRA2B to promote exon 7 inclusion of the survival motor neuron SMN. Binds non-specifically to mRNAs

     Genatlas biochemistry entry for RBMY1A1:
RNA binding motif protein,Y chromosome,interval 6,family 1,member A1,in a AZF deleted region

     Gene Ontology (GO): 4 molecular function terms:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0000166nucleotide binding IEA--
GO:0003676nucleic acid binding ----
GO:0003729mRNA binding IDA12165565
GO:0005515protein binding IPI12165565
     
Find genes that share ontologies with RBMY1A1           About GenesLikeMe


Animal Models:
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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
RBY1A_HUMAN, P0DJD3: 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--

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(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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    Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for RBMY1A1
Interactions:

    GeneGlobe Interaction Network for RBMY1A1

STRING Interaction Network Preview (showing 5 interactants - click image to see 16)

Selected Interacting proteins for RBMY1A1 (ENSP000003037124) via UniProtKB, MINT, STRING, and/or I2D (see all 16)
InteractantInteraction Details
GeneCardExternal ID(s)
SRSF3ENSP000003628204STRING: ENSP00000362820
SRSF9ENSP000002293904STRING: ENSP00000229390
KHDRBS3ENSP000003481084STRING: ENSP00000348108
TRA2BENSP000004169594STRING: ENSP00000416959
TERF1ENSP000002766034STRING: ENSP00000276603
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Gene Ontology (GO): 3 biological process terms:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0000381regulation of alternative mRNA splicing, via spliceosome IDA12165565
GO:0006397mRNA processing IEA--
GO:0008380RNA splicing IEA--

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(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 RBMY1A1 (RBY1A)



(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 RBMY1A1 gene (2 alternative transcripts): 
NM_005058.2  NM_001007526.1  

Unigene Cluster for RBMY1A1:

RNA binding motif protein, Y-linked, family 1, member A1
Hs.380450  [show with all ESTs]
Unigene Representative Sequence: NM_005058
4 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000382707(uc004fuq.4 uc011nbd.2 uc010nxa.3 uc004fur.4)
ENST00000361046 ENST00000303902 ENST00000439108
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Additional mRNA sequence: 

BC047768.1 BC070298.1 BC136862.1 BC140758.1 BC144422.1 BC144423.1 BC144459.1 BC144577.1 
BC146853.1 X76059.1 

4 DOTS entries:

DT.120653962  DT.102820644  DT.92415864  DT.97826649 

12 AceView cDNA sequences:

CB107177 BX282035 BQ212524 BX119894 BI464610 AI220048 BI462515 X76059 
BU568309 BC070298 BP370066 NM_005058 

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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RBMY1A1 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: TACTGCAAAA
RBMY1A1 Expression
About this image


RBMY1A1 expression in embryonic tissues and stem cells    About this table
Data from LifeMap, the Embryonic Development and Stem Cells Database
 selected tissues (see all 3) fully expand
 
 Testis (Reproductive System)
         XY Germ Cells Testis Cord
 
 Bone (Muscoskeletal System)
         Zeugopod Periosteum
 
 Gonad
         XY Germ Cells Testis Cord
RBMY1A1 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

RBMY1A1 Protein Expression

SOURCE GeneReport for Unigene cluster: Hs.380450

UniProtKB/Swiss-Prot: RBY1A_HUMAN, P0DJD3
Tissue specificity: Testis-specific

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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 RBMY1A1 gene from Selected species (see all 10)    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
mouse
(Mus musculus)
Mammalia Rbmy5 RNA binding motif protein, Y chromosome, family 1, more   --   Y 2830680 
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


ENSEMBL Gene Tree for RBMY1A1 (if available)
TreeFam Gene Tree for RBMY1A1 (if available)

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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Paralogs for RBMY1A1 gene
RBMY1D1 2  RBMY1B1 2  RBMY1E1 2  RBMY1F1 2  RBMY1J1 2  TRA2B2  RBMXL22  RBMXL32  
RBMXL12  CIRBP2  RBM32  RBMX2  TRA2A2  
Selected SIMAP similar genes for RBMY1A1 using alignment to 4 protein entries:     RBY1A_HUMAN (see all proteins) (see all similar genes):
RBMY1C    RBMY1B    RBMY1F    RBMY1E    RBMY1J    RBMY1D
RBM    BOLL    YRRM    DAZAP1    CIRBP    DAZ2
DAZ3    DAZ4    RBMX    DAZL    PABPC4L    MSI2

Find genes that share paralogs with RBMY1A1           About GenesLikeMe


Selected Pseudogenes.org Pseudogenes for RBMY1A1 (see all 12)
PGOHUM00000233681 PGOHUM00000233804 PGOHUM00000233805 PGOHUM00000261027 PGOHUM00000233823


(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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2 SNPs for RBMY1A1    About this table                                 

Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr Y posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs2006143451,2
----23702825(+) GAATGA/GTTGAA 1 -- int10--------

HapMap Linkage Disequilibrium report for RBMY1A1 (23673258 - 23711212 bp)

Structural Variations
     Database of Genomic Variants (DGV) 9 variations for RBMY1A1:    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, Novoseek, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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OMIM gene information: 400006    OMIM disorders: --

3 diseases for RBMY1A1:    
About MalaCards
spermatogenic failure, y-linked, 2    azoospermia    y chromosome infertility

1 disease from the University of Copenhagen DISEASES database for RBMY1A1:
Azoospermia

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4 Novoseek inferred disease relationships for RBMY1A1 gene    About this table

Disease   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
azoospermia 76 3 8978761 (1), 16491274 (1)
oligozoospermia 73.3 1 8940286 (1)
chromosome deletion 73.2 1 17296183 (1)
infertility male 56.4 1 11294825 (1)

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Export disorders for RBMY1A1 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 RBMY1A1 gene, integrated from 10 sources (see all 48):
(articles sorted by number of sources associating them with RBMY1A1)
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  1. 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, 2, 3, 9 Chai N.-N.... Yen P.H. (Genomics 1998)
  2. A Y chromosome gene family with RNA-binding protein homology: candidates for the azoospermia factor AZF controlling human spermatogenesis. (PubMed id 8269511)1, 2, 3 Ma K.... Jobling M. (Cell 1993)
  3. The testis-specific human protein RBMY recognizes RNA through a novel mode of interaction. (PubMed id 17318228)1, 2, 9 Skrisovska L.... Allain F.H.-T. (EMBO Rep. 2007)
  4. RBMY, a probable human spermatogenesis factor, and other hnRNP G proteins interact with Tra2beta and affect splicing. (PubMed id 10749975)1, 2, 9 Venables J.P....Eperon E.C. (Hum. Mol. Genet. 2000)
  5. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S.... Malek J. (Genome Res. 2004)
  6. The male-specific region of the human Y chromosome is a mosaic of discrete sequence classes. (PubMed id 12815422)1, 2 Skaletsky H.... Page D.C. (Nature 2003)
  7. hnRNP-G promotes exon 7 inclusion of survival motor neuron (SMN) via direct interaction with Htra2-beta1. (PubMed id 12165565)1, 2 Hofmann Y. and Wirth B. (Hum. Mol. Genet. 2002)
  8. Cellular ontogeny of RBMY during human spermatogenesis and its role in sperm motility. (PubMed id 23385816)1 Abid S....Modi D. (J. Biosci. 2013)
  9. Global landscape of HIV-human protein complexes. (PubMed id 22190034)1 JAoger S....Krogan N.J. (Nature 2012)
  10. Identifying mRNAs bound by human RBMY protein in the testis. (PubMed id 21422736)1 Zeng M....Ma Y. (J. Reprod. Dev. 2011)

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(According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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Entrez Gene: 5940 HGNC: 9912 AceView: RBMY1A1 Ensembl:ENSG00000234414 euGenes: HUgn5940
ECgene: RBMY1A1 H-InvDB: RBMY1A1

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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 RBMY1A1 Pharmacogenomics, SNPs, Pathways
ATLAS Chromosomes in Cancer entry for RBMY1A1 Genetics and Cytogenetics in Oncology and Haematology
GeneReviewshttp://www.ncbi.nlm.nih.gov/books/NBK1116/?term=RBMY1A1[genesymbol]

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