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P0DJD3 (RBY1A_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 21. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (4) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Alt products·Sequence annotation·Sequences·References·Web links·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
RNA-binding motif protein, Y chromosome, family 1 member A1
Alternative name(s):
RNA-binding motif protein 1
RNA-binding motif protein 2
Y chromosome RNA recognition motif 1
Short name=hRBMY
Gene names
Name:RBMY1A1
Synonyms:RBM1, RBM2, YRRM1, YRRM2
OrganismHomo sapiens (Human) [Reference proteome]
Taxonomic identifier9606 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo

Protein attributes

Sequence length496 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

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. Ref.1 Ref.8

Subunit structure

Interacts with splicing factor proteins SFRS3/SRP20, TRA2B/SFRS10, KHDRBS1/SAM68 and KHDRBS3. Ref.6 Ref.7 Ref.8 Ref.9

Subcellular location

Nucleus Ref.5.

Tissue specificity

Testis-specific. Ref.1

Developmental stage

Expressed in all of the transcriptionally active stages of germ cell development from spermatogonia through spermatocytes to round spermatids. Ref.5

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.

Sequence similarities

Contains 1 RRM (RNA recognition motif) domain.

Ontologies

Keywords
   Biological processmRNA processing
mRNA splicing
   Cellular componentNucleus
   Coding sequence diversityAlternative splicing
   LigandRNA-binding
   Molecular functionActivator
   Technical term3D-structure
Complete proteome
Reference proteome
Gene Ontology (GO)
   Biological_processRNA splicing

Inferred from electronic annotation. Source: UniProtKB-KW

mRNA processing

Inferred from electronic annotation. Source: UniProtKB-KW

regulation of alternative mRNA splicing, via spliceosome

Inferred from direct assay Ref.8. Source: UniProtKB

   Cellular_componentnucleus

Inferred from electronic annotation. Source: UniProtKB-SubCell

   Molecular_functionmRNA binding

Inferred from direct assay Ref.8. Source: UniProtKB

nucleotide binding

Inferred from electronic annotation. Source: InterPro

Complete GO annotation...

Alternative products

This entry describes 3 isoforms produced by alternative splicing. [Align] [Select]
Isoform 1 (identifier: P0DJD3-1)

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.
Isoform 2 (identifier: P0DJD3-2)

The sequence of this isoform differs from the canonical sequence as follows:
     327-363: Missing.
Isoform 3 (identifier: P0DJD3-3)

The sequence of this isoform differs from the canonical sequence as follows:
     1-140: Missing.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 496496RNA-binding motif protein, Y chromosome, family 1 member A1
PRO_0000081899

Regions

Domain8 – 8578RRM
Compositional bias254 – 34087Arg-rich

Natural variations

Alternative sequence1 – 140140Missing in isoform 3.
VSP_042315
Alternative sequence327 – 36337Missing in isoform 2.
VSP_042316

Secondary structure

..................... 496
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
Isoform 1 [UniParc].

Last modified February 22, 2012. Version 1.
Checksum: 3E493C52C7BA9E7E

FASTA49655,784
        10         20         30         40         50         60 
MVEADHPGKL FIGGLNRETN EKMLKAVFGK HGPISEVLLI KDRTSKSRGF AFITFENPAD 

        70         80         90        100        110        120 
AKNAAKDMNG KSLHGKAIKV EQAKKPSFQS GGRRRPPASS RNRSPSGSLR SARGSRGGTR 

       130        140        150        160        170        180 
GWLPSHEGHL DDGGYTPDLK MSYSRGLIPV KRGPSSRSGG PPPKKSAPSA VARSNSWMGS 

       190        200        210        220        230        240 
QGPMSQRREN YGVPPRRATI SSWRNDRMST RHDGYATNDG NHPSCQETRD YAPPSRGYAY 

       250        260        270        280        290        300 
RDNGHSNRDE HSSRGYRNHR SSRETRDYAP PSRGHAYRDY GHSRRDESYS RGYRNRRSSR 

       310        320        330        340        350        360 
ETREYAPPSR GHGYRDYGHS RRHESYSRGY RNHPSSRETR DYAPPHRDYA YRDYGHSSWD 

       370        380        390        400        410        420 
EHSSRGYSYH DGYGEALGRD HSEHLSGSSY RDALQRYGTS HGAPPARGPR MSYGGSTCHA 

       430        440        450        460        470        480 
YSNTRDRYGR SWESYSSCGD FHYCDREHVC RKDQRNPPSL GRVLPDPREA CGSSSYVASI 

       490 
VDGGESRSEK GDSSRY 

« Hide

Isoform 2 [UniParc].

Checksum: F3C0267BBEF99E55
Show »

FASTA45951,292
Isoform 3 [UniParc].

Checksum: 96D4EAB0E82A3C1C
Show »

FASTA35640,651

References

« Hide 'large scale' references
[1]"A Y chromosome gene family with RNA-binding protein homology: candidates for the azoospermia factor AZF controlling human spermatogenesis."
Ma K., Inglis J.D., Sharkey A., Bickmore W.A., Hill R.E., Prosser E.J., Speedson R.M., Thomson E.J., Jobling M.
Cell 75:1287-1295(1993) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), FUNCTION, TISSUE SPECIFICITY.
Tissue: Testis.
[2]"The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
The MGC Project Team
Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 2 AND 3).
Tissue: Brain and Testis.
[3]"The male-specific region of the human Y chromosome is a mosaic of discrete sequence classes."
Skaletsky H., Kuroda-Kawaguchi T., Minx P.J., Cordum H.S., Hillier L.W., Brown L.G., Repping S., Pyntikova T., Ali J., Bieri T., Chinwalla A., Delehaunty A., Delehaunty K., Du H., Fewell G., Fulton L., Fulton R., Graves T.A. expand/collapse author list , Hou S.-F., Latrielle P., Leonard S., Mardis E., Maupin R., McPherson J., Miner T., Nash W., Nguyen C., Ozersky P., Pepin K., Rock S., Rohlfing T., Scott K., Schultz B., Strong C., Tin-Wollam A., Yang S.-P., Waterston R.H., Wilson R.K., Rozen S., Page D.C.
Nature 423:825-837(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[4]"Structure and organization of the RBMY genes on the human Y chromosome: transposition and amplification of an ancestral autosomal hnRNPG gene."
Chai N.-N., Zhou H., Hernandez J., Najmabadi H., Bhasin S., Yen P.H.
Genomics 49:283-289(1998) [PubMed] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION.
[5]"Expression of RBM in the nuclei of human germ cells is dependent on a critical region of the Y chromosome long arm."
Elliott D.J., Millar M.R., Oghene K., Ross A., Kiesewetter F., Pryor J., McIntyre M., Hargreave T.B., Saunders P.T.K., Vogt P.H., Chandley A.C., Cooke H.
Proc. Natl. Acad. Sci. U.S.A. 94:3848-3853(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: SUBCELLULAR LOCATION, DEVELOPMENTAL STAGE.
[6]"T-STAR/ETOILE: a novel relative of SAM68 that interacts with an RNA-binding protein implicated in spermatogenesis."
Venables J.P., Vernet C., Chew S.L., Elliott D.J., Cowmeadow R.B., Wu J., Cooke H.J., Artzt K., Eperon I.C.
Hum. Mol. Genet. 8:959-969(1999) [PubMed] [Europe PMC] [Abstract]
Cited for: INTERACTION WITH KHDRBS3.
[7]"RBMY, a probable human spermatogenesis factor, and other hnRNP G proteins interact with Tra2beta and affect splicing."
Venables J.P., Elliott D.J., Makarova O.V., Makarov E.M., Cooke H.J., Eperon E.C.
Hum. Mol. Genet. 9:685-694(2000) [PubMed] [Europe PMC] [Abstract]
Cited for: INTERACTION WITH TRA2B.
Tissue: Testis.
[8]"hnRNP-G promotes exon 7 inclusion of survival motor neuron (SMN) via direct interaction with Htra2-beta1."
Hofmann Y., Wirth B.
Hum. Mol. Genet. 11:2037-2049(2002) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION, INTERACTION WITH TRA2B, RNA-BINDING.
[9]"The role of potential splicing factors including RBMY, RBMX, hnRNPG-T and STAR proteins in spermatogenesis."
Elliott D.J.
Int. J. Androl. 27:328-334(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: INTERACTION WITH KHDRBS1.
[10]"The testis-specific human protein RBMY recognizes RNA through a novel mode of interaction."
Skrisovska L., Bourgeois C.F., Stefl R., Grellscheid S.-N., Kister L., Wenter P., Elliott D.J., Stevenin J., Allain F.H.-T.
EMBO Rep. 8:372-379(2007) [PubMed] [Europe PMC] [Abstract]
Cited for: STRUCTURE BY NMR OF 1-109 IN COMPLEX WITH RNA.

Web resources

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
X76059 mRNA. Translation: CAA53659.1.
BC047768 mRNA. Translation: AAH47768.1.
BC070298 mRNA. Translation: AAH70298.1.
AC010141 Genomic DNA. No translation available.
PIRA49418.
RefSeqNP_005049.1. NM_005058.2.
XP_005262573.1. XM_005262516.1.
UniGeneHs.380450.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
2FY1NMR-A1-109[»]
ProteinModelPortalP0DJD3.
SMRP0DJD3. Positions 1-108.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

IntActP0DJD3. 1 interaction.

Polymorphism databases

DMDM378522864.

Proteomic databases

PRIDEP0DJD3.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENST00000303902; ENSP00000303712; ENSG00000234414. [P0DJD3-1]
ENST00000382707; ENSP00000372154; ENSG00000234414. [P0DJD3-1]
GeneID5940.
KEGGhsa:5940.
UCSCuc004fur.4. human. [P0DJD3-1]
uc010nxa.3. human. [P0DJD3-2]

Organism-specific databases

CTD5940.
GeneCardsGC0YP023675.
HGNCHGNC:9912. RBMY1A1.
HPAHPA001534.
MIM400006. gene.
neXtProtNX_P0DJD3.
Orphanet1646. Partial chromosome Y deletion.
GenAtlasSearch...

Phylogenomic databases

OrthoDBEOG780RPD.
PhylomeDBP0DJD3.
TreeFamTF331833.

Gene expression databases

BgeeP0DJD3.
CleanExHS_RBMY1A1.

Family and domain databases

Gene3D3.30.70.330. 1 hit.
InterProIPR012677. Nucleotide-bd_a/b_plait.
IPR012604. RBM1CTR.
IPR000504. RRM_dom.
[Graphical view]
PfamPF08081. RBM1CTR. 1 hit.
PF00076. RRM_1. 1 hit.
[Graphical view]
SMARTSM00360. RRM. 1 hit.
[Graphical view]
PROSITEPS50102. RRM. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

GenomeRNAi5940.
NextBio23158.
PROP0DJD3.
SOURCESearch...

Entry information

Entry nameRBY1A_HUMAN
AccessionPrimary (citable) accession number: P0DJD3
Secondary accession number(s): Q15376 expand/collapse secondary AC list , Q15377, Q15414, Q6NSB5, Q86VU6, Q8NHR0
Entry history
Integrated into UniProtKB/Swiss-Prot: February 22, 2012
Last sequence update: February 22, 2012
Last modified: April 16, 2014
This is version 21 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

MIM cross-references

Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot

Human chromosome Y

Human chromosome Y: entries, gene names and cross-references to MIM