Human Gene RBMY1A1 (ENST00000439108.6) Description and Page Index
  Description: 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. (from UniProt P0DJD3)
RefSeq Summary (NM_001006121): 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. [provided by RefSeq, Mar 2016]. Sequence Note: The RefSeq transcript and protein were derived from genomic sequence to make the sequence consistent with the reference genome assembly. The genomic coordinates used for the transcript record were based on alignments. ##Evidence-Data-START## Transcript exon combination :: SRR5189667.274280.1 [ECO:0000332] RNAseq introns :: single sample supports all introns SAMEA1968968, SAMEA2148093 [ECO:0000348] ##Evidence-Data-END## ##RefSeq-Attributes-START## MANE Ensembl match :: ENST00000383020.7/ ENSP00000372484.3 RefSeq Select criteria :: based on conservation, expression, longest protein ##RefSeq-Attributes-END##
Gencode Transcript: ENST00000439108.6
Gencode Gene: ENSG00000234414.7
Transcript (Including UTRs)
   Position: hg38 chrY:21,511,372-21,549,318 Size: 37,947 Total Exon Count: 12 Strand: +
Coding Region
   Position: hg38 chrY:21,513,351-21,549,048 Size: 35,698 Coding Exon Count: 11 

Page IndexSequence and LinksUniProtKB CommentsMalaCardsRNA-Seq ExpressionMicroarray Expression
RNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA DescriptionsOther Names
Methods
Data last updated: 2019-09-04

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chrY:21,511,372-21,549,318)mRNA (may differ from genome)Protein (496 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaBioGPS
CGAPEnsemblExonPrimerGeneCardsHGNCLynx
MGIneXtProtPubMedStanford SOURCEUniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: RBY1A_HUMAN
DESCRIPTION: RecName: Full=RNA-binding motif protein, Y chromosome, family 1 member A1; AltName: Full=RNA-binding motif protein 1; AltName: Full=RNA-binding motif protein 2; AltName: Full=Y chromosome RNA recognition motif 1; Short=hRBMY;
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.
SUBUNIT: Interacts with splicing factor proteins SFRS3/SRP20, TRA2B/SFRS10, KHDRBS1/SAM68 and KHDRBS3.
SUBCELLULAR LOCATION: Nucleus.
TISSUE SPECIFICITY: Testis-specific.
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.
SIMILARITY: Contains 1 RRM (RNA recognition motif) domain.
WEB RESOURCE: Name=GeneReviews; URL="http://www.ncbi.nlm.nih.gov/sites/GeneTests/lab/gene/RBMY1A1";

-  MalaCards Disease Associations
  MalaCards Gene Search: RBMY1A1
Diseases sorted by gene-association score: partial deletion of y* (25), azoospermia (9), male infertility (5), phelan-mcdermid syndrome (3), haemophilus meningitis (2), male reproductive system disease (2), reproductive system disease (1)
* = Manually curated disease association

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 0.61 RPKM in Testis
Total median expression: 0.61 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -42.50118-0.360 Picture PostScript Text
3' UTR -51.40270-0.190 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR012677 - Nucleotide-bd_a/b_plait
IPR012604 - RBM1CTR
IPR000504 - RRM_dom

Pfam Domains:
PF08081 - RBM1CTR (NUC064) family
PF00076 - RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain)

Protein Data Bank (PDB) 3-D Structure
MuPIT help

2FY1
- NMR MuPIT


ModBase Predicted Comparative 3D Structure on P0DJD3
FrontTopSide
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-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
Genome BrowserNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
MGI     
Protein Sequence     
Alignment     

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003676 nucleic acid binding
GO:0003723 RNA binding
GO:0003729 mRNA binding
GO:0005515 protein binding

Biological Process:
GO:0000381 regulation of alternative mRNA splicing, via spliceosome
GO:0006397 mRNA processing
GO:0008380 RNA splicing

Cellular Component:
GO:0005634 nucleus


-  Descriptions from all associated GenBank mRNAs
  BC047768 - Homo sapiens RNA binding motif protein, Y-linked, family 1, member A1, mRNA (cDNA clone MGC:54233 IMAGE:5744153), complete cds.
X76059 - H.sapiens mRNA for YRRM1.
BC070298 - Homo sapiens RNA binding motif protein, Y-linked, family 1, member A1, mRNA (cDNA clone MGC:88295 IMAGE:6615329), complete cds.
JD127104 - Sequence 108128 from Patent EP1572962.
BC136862 - Homo sapiens RNA binding motif protein, Y-linked, family 1, member D, mRNA (cDNA clone MGC:168476 IMAGE:9020853), complete cds.
BC140758 - Homo sapiens cDNA clone MGC:176435 IMAGE:9021626, complete cds.
BC144423 - Homo sapiens cDNA clone IMAGE:9052944.
BC144459 - Homo sapiens cDNA clone MGC:178002 IMAGE:9052985, complete cds.
BC160023 - Synthetic construct Homo sapiens clone IMAGE:100063959, MGC:193138 RNA binding motif protein, Y-linked, family 1, member E (RBMY1E) mRNA, encodes complete protein.
HQ447544 - Synthetic construct Homo sapiens clone IMAGE:100070883; CCSB014935_03 RNA binding motif protein, Y-linked, family 1, member A1 (RBMY1A1) gene, encodes complete protein.
CU687086 - Synthetic construct Homo sapiens gateway clone IMAGE:100023167 5' read RBMY1A1 mRNA.
JD502792 - Sequence 483816 from Patent EP1572962.
BC047768 - Homo sapiens RNA binding motif protein, Y-linked, family 1, member A1, mRNA (cDNA clone MGC:54233 IMAGE:5744153), complete cds.
X76059 - H.sapiens mRNA for YRRM1.
BC070298 - Homo sapiens RNA binding motif protein, Y-linked, family 1, member A1, mRNA (cDNA clone MGC:88295 IMAGE:6615329), complete cds.
BC136862 - Homo sapiens RNA binding motif protein, Y-linked, family 1, member D, mRNA (cDNA clone MGC:168476 IMAGE:9020853), complete cds.
BC140758 - Homo sapiens cDNA clone MGC:176435 IMAGE:9021626, complete cds.
BC144423 - Homo sapiens cDNA clone IMAGE:9052944.
BC144459 - Homo sapiens cDNA clone MGC:178002 IMAGE:9052985, complete cds.
BC144577 - Homo sapiens RNA binding motif protein, Y-linked, family 1, member B, mRNA (cDNA clone MGC:178123 IMAGE:9053106), complete cds.
BC146853 - Homo sapiens RNA binding motif protein, Y-linked, family 1, member A1, mRNA (cDNA clone MGC:181956 IMAGE:9056781), complete cds.
BC160023 - Synthetic construct Homo sapiens clone IMAGE:100063959, MGC:193138 RNA binding motif protein, Y-linked, family 1, member E (RBMY1E) mRNA, encodes complete protein.
HQ447544 - Synthetic construct Homo sapiens clone IMAGE:100070883; CCSB014935_03 RNA binding motif protein, Y-linked, family 1, member A1 (RBMY1A1) gene, encodes complete protein.
CU687086 - Synthetic construct Homo sapiens gateway clone IMAGE:100023167 5' read RBMY1A1 mRNA.
JD309043 - Sequence 290067 from Patent EP1572962.
KJ905893 - Synthetic construct Homo sapiens clone ccsbBroadEn_15563 RBMY1A1 gene, encodes complete protein.
JD036629 - Sequence 17653 from Patent EP1572962.
JD202603 - Sequence 183627 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: P0DJD3, Q15376, Q15377, Q15414, Q6NSB5, Q86VU6, Q8NHR0, RBM1, RBM2, RBY1A_HUMAN, uc065cui.1, X76059, YRRM1, YRRM2
UCSC ID: uc065cui.1
RefSeq Accession: NM_001006121
Protein: P0DJD3 (aka RBY1A_HUMAN or RY1A_HUMAN)

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.