Human Gene RBMY1J (ENST00000250831.6_5) from GENCODE V47lift37
  Description: RNA binding motif protein Y-linked family 1 member J (from RefSeq NM_001006117.4)
Gencode Transcript: ENST00000250831.6_5
Gencode Gene: ENSG00000226941.9_11
Transcript (Including UTRs)
   Position: hg19 chrY:24,549,557-24,564,028 Size: 14,472 Total Exon Count: 12 Strand: +
Coding Region
   Position: hg19 chrY:24,551,595-24,563,750 Size: 12,156 Coding Exon Count: 11 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chrY:24,549,557-24,564,028)mRNA (may differ from genome)Protein (496 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsHGNC
MalacardsMGIPubMedUniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: RBY1F_HUMAN
DESCRIPTION: RecName: Full=RNA-binding motif protein, Y chromosome, family 1 member F/J; AltName: Full=Y chromosome RNA recognition motif 2;
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.

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: RBMY1J
Diseases sorted by gene-association score: azoospermia (5)

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 0.07 RPKM in Testis
Total median expression: 0.07 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 -65.50177-0.370 Picture PostScript Text
3' UTR -54.20278-0.195 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:
PF00076 - RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain)
PF08081 - RBM1CTR (NUC064) family
PF13893 - RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain)

SCOP Domains:
54928 - RNA-binding domain, RBD

ModBase Predicted Comparative 3D Structure on Q15415
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  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
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGD    
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003676 nucleic acid binding
GO:0003723 RNA binding
GO:0005515 protein binding
GO:0042802 identical protein binding

Biological Process:
GO:0006397 mRNA processing
GO:0007283 spermatogenesis
GO:0008380 RNA splicing

Cellular Component:
GO:0005575 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.
BC030018 - Homo sapiens RNA binding motif protein, Y-linked, family 1, member F, mRNA (cDNA clone MGC:33094 IMAGE:5269012), complete cds.
X76060 - H.sapiens mRNA for YRRM2.
BC140758 - Homo sapiens cDNA clone MGC:176435 IMAGE:9021626, complete cds.
BC144422 - Homo sapiens cDNA clone MGC:177960 IMAGE:9052943, 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.
AK313597 - Homo sapiens cDNA, FLJ94166, highly similar to Homo sapiens RNA binding motif protein, Y-linked, family 1, memberA1 (RBMY1A1), mRNA.
JD127104 - Sequence 108128 from Patent EP1572962.
BC148576 - Synthetic construct Homo sapiens clone IMAGE:100015526, MGC:183078 RNA binding motif protein, Y-linked, family 1, member J (RBMY1J) mRNA, encodes complete protein.
DQ894382 - Synthetic construct Homo sapiens clone IMAGE:100008842; FLH170092.01L; RZPDo839B0997D RNA binding motif protein, Y-linked, family 1, member F (RBMY1F) gene, encodes complete protein.
BC152392 - Homo sapiens RNA binding motif protein, Y-linked, family 1, member F, mRNA (cDNA clone MGC:166957 IMAGE:8860211), complete cds.
DQ891199 - Synthetic construct clone IMAGE:100003829; FLH170096.01X; RZPDo839B0998D RNA binding motif protein, Y-linked, family 1, member F (RBMY1F) gene, encodes complete protein.
CU687086 - Synthetic construct Homo sapiens gateway clone IMAGE:100023167 5' read RBMY1A1 mRNA.
AB464182 - Synthetic construct DNA, clone: pF1KB7444, Homo sapiens RBMY1F gene for RNA binding motif protein, Y-linked, family 1, member F, without stop codon, in Flexi system.
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.
KJ895709 - Synthetic construct Homo sapiens clone ccsbBroadEn_05103 RBMY1F gene, encodes complete protein.
JD502792 - Sequence 483816 from Patent EP1572962.
JD260288 - Sequence 241312 from Patent EP1572962.
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: B2R916, ENST00000250831.1, ENST00000250831.2, ENST00000250831.3, ENST00000250831.4, ENST00000250831.5, NM_001006117, Q15415, RBMY1F, RBY1F_HUMAN, uc317fcj.1, uc317fcj.2, YRRM2
UCSC ID: ENST00000250831.6_5
RefSeq Accession: NM_001006117.4
Protein: Q15415 (aka RBY1F_HUMAN)

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

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