Human Gene RBMY1D (ENST00000418956.2) Description and Page Index
  Description: RNA-binding protein which may be involved in spermatogenesis. Required for sperm development, possibly by participating in pre-mRNA splicing in the testis. (from UniProt P0C7P1)
RefSeq Summary (NM_001320948): 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]. ##Evidence-Data-START## Transcript exon combination :: BC136862.1 [ECO:0000332] RNAseq introns :: single sample supports all introns SAMEA1968968, SAMEA2148093 [ECO:0000348] ##Evidence-Data-END##
Gencode Transcript: ENST00000418956.2
Gencode Gene: ENSG00000244395.6
Transcript (Including UTRs)
   Position: hg38 chrY:21,880,308-21,894,439 Size: 14,132 Total Exon Count: 11 Strand: -
Coding Region
   Position: hg38 chrY:21,880,354-21,892,513 Size: 12,160 Coding Exon Count: 10 

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:21,880,308-21,894,439)mRNA (may differ from genome)Protein (459 aa)
Gene SorterGenome BrowserOther Species FASTATable SchemaBioGPSCGAP
EnsemblExonPrimerGeneCardsHGNCHPRDLynx
MGIneXtProtPubMedStanford SOURCEUniProtKB

-  Comments and Description Text from UniProtKB
  ID: RBY1D_HUMAN
DESCRIPTION: RecName: Full=RNA-binding motif protein, Y chromosome, family 1 member D;
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: 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.

-  MalaCards Disease Associations
  MalaCards Gene Search: RBMY1D
Diseases sorted by gene-association score: azoospermia (5), male reproductive system disease (1)

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 0.09 RPKM in Testis
Total median expression: 0.09 RPKM



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

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -19.5065-0.300 Picture PostScript Text
3' UTR -6.8046-0.148 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)

ModBase Predicted Comparative 3D Structure on P0C7P1
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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 BrowserGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
MGIRGD    
Protein SequenceProtein Sequence    
AlignmentAlignment    

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

Biological Process:
GO:0006397 mRNA processing
GO:0008380 RNA splicing

Cellular Component:
GO:0005634 nucleus


-  Descriptions from all associated GenBank mRNAs
  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.
BC047768 - Homo sapiens RNA binding motif protein, Y-linked, family 1, member A1, mRNA (cDNA clone MGC:54233 IMAGE:5744153), complete cds.
BC070298 - Homo sapiens RNA binding motif protein, Y-linked, family 1, member A1, mRNA (cDNA clone MGC:88295 IMAGE:6615329), complete cds.
X76059 - H.sapiens mRNA for YRRM1.
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.
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.
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.
CU687086 - Synthetic construct Homo sapiens gateway clone IMAGE:100023167 5' read RBMY1A1 mRNA.
JD036629 - Sequence 17653 from Patent EP1572962.
KJ905893 - Synthetic construct Homo sapiens clone ccsbBroadEn_15563 RBMY1A1 gene, encodes complete protein.
JD309043 - Sequence 290067 from Patent EP1572962.
JD502792 - Sequence 483816 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: BC136862, P0C7P1, RBY1D_HUMAN, uc010nxb.1, uc010nxb.2, uc010nxb.3
UCSC ID: uc010nxb.3
RefSeq Accession: NM_001320948
Protein: P0C7P1 (aka RBY1D_HUMAN)
CCDS: CCDS83521.1

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