P0DJD3 (RBY1A_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended 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

Organism

Homo sapiens (Human) [Reference proteome]

Taxonomic identifier

9606 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Opisthokonta › Metazoa › Eumetazoa › Bilateria › Deuterostomia › Chordata › Craniata › Vertebrata › Gnathostomata › Teleostomi › Euteleostomi › Sarcopterygii › Tetrapoda › Amniota › Mammalia › Theria › Eutheria › Euarchontoglires › Primates › Haplorrhini › Simiiformes › Catarrhini › Hominoidea › Hominidae › Homininae › Homo

Protein attributes

Sequence length	496 AA.
Sequence status	Complete.
Protein existence	Evidence 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 process	mRNA processing mRNA splicing
Cellular component	Nucleus
Coding sequence diversity	Alternative splicing
Ligand	RNA-binding
Molecular function	Activator
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	RNA 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_component	nucleus Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular_function	mRNA 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 key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 496

496

RNA-binding motif protein, Y chromosome, family 1 member A1

PRO_0000081899

Regions

Domain

8 – 85

78

RRM

Compositional bias

254 – 340

87

Arg-rich

Natural variations

Alternative sequence

1 – 140

140

Missing in isoform 3.

VSP_042315

Alternative sequence

327 – 363

37

Missing in isoform 2.

VSP_042316

Secondary structure

1

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496

Helix Strand Turn

Details...

Beta strand

9 – 13

5

Turn

16 – 18

3

Helix

21 – 29

9

Beta strand

35 – 40

6

Turn

43 – 45

3

Beta strand

50 – 54

5

Helix

58 – 67

10

Beta strand

74 – 77

4

Beta strand

79 – 82

4

Beta strand

89 – 93

5

Sequences

	Sequence		Length	Mass (Da)
	Isoform 1 [UniParc]. Last modified February 22, 2012. Version 1. Checksum: 3E493C52C7BA9E7E	FASTA	496	55,784
	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
	Isoform 2 [UniParc]. Checksum: F3C0267BBEF99E55	FASTA	459	51,292
	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 SYHDGYGEAL GRDHSEHLSG SSYRDALQRY 370 380 390 400 410 420 GTSHGAPPAR GPRMSYGGST CHAYSNTRDR YGRSWESYSS CGDFHYCDRE HVCRKDQRNP 430 440 450 PSLGRVLPDP REACGSSSYV ASIVDGGESR SEKGDSSRY
	Isoform 3 [UniParc]. Checksum: 96D4EAB0E82A3C1C	FASTA	356	40,651
	10 20 30 40 50 60 MSYSRGLIPV KRGPSSRSGG PPPKKSAPSA VARSNSWMGS QGPMSQRREN YGVPPRRATI 70 80 90 100 110 120 SSWRNDRMST RHDGYATNDG NHPSCQETRD YAPPSRGYAY RDNGHSNRDE HSSRGYRNHR 130 140 150 160 170 180 SSRETRDYAP PSRGHAYRDY GHSRRDESYS RGYRNRRSSR ETREYAPPSR GHGYRDYGHS 190 200 210 220 230 240 RRHESYSRGY RNHPSSRETR DYAPPHRDYA YRDYGHSSWD EHSSRGYSYH DGYGEALGRD 250 260 270 280 290 300 HSEHLSGSSY RDALQRYGTS HGAPPARGPR MSYGGSTCHA YSNTRDRYGR SWESYSSCGD 310 320 330 340 350 FHYCDREHVC RKDQRNPPSL GRVLPDPREA CGSSSYVASI VDGGESRSEK GDSSRY

References

	« Hide 'large scale' referencesShow '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. , 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

GeneReviews

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.

IPI

IPI00332760.
IPI00872545.
IPI00872656.

PIR

A49418.

RefSeq

NP_005049.1. NM_005058.2.

UniGene

Hs.380450.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
2FY1	NMR	-	A	1-109	[»]

ProteinModelPortal

P0DJD3.

ModBase

Search...

Polymorphism databases

DMDM

27805716.

Proteomic databases

PRIDE

P0DJD3.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

Ensembl

ENST00000303902; ENSP00000303712; ENSG00000234414.
ENST00000382707; ENSP00000372154; ENSG00000234414.

GeneID

5940.

KEGG

hsa:5940.

Organism-specific databases

CTD

5940.

GeneCards

GC0YP023675.

HGNC

HGNC:9912. RBMY1A1.

HPA

HPA001534.

MIM

400006. gene.

neXtProt

NX_P0DJD3.

GenAtlas

Search...

Phylogenomic databases

OMA

PREYASE.

PhylomeDB

P0DJD3.

Gene expression databases

ArrayExpress

P0DJD3.

Bgee

P0DJD3.

CleanEx

HS_RBMY1A1.

GermOnline

ENSG00000174622. Homo sapiens.

Family and domain databases

Gene3D

3.30.70.330. 1 hit.

InterPro

IPR012677. Nucleotide-bd_a/b_plait.
IPR012604. RBM1CTR.
IPR000504. RRM_dom.
[Graphical view]

Pfam

PF08081. RBM1CTR. 1 hit.
PF00076. RRM_1. 1 hit.
[Graphical view]

SMART

SM00360. RRM. 1 hit.
[Graphical view]

PROSITE

PS50102. RRM. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

GenomeRNAi

5940.

NextBio

23158.

SOURCE

Search...

Entry information

Entry name

RBY1A_HUMAN

Accession

Primary (citable) accession number: P0DJD3
Secondary accession number(s): Q15376 , Q15377, Q15414, Q6NSB5, Q86VU6, Q8NHR0

Entry history

Integrated into UniProtKB/Swiss-Prot:	February 22, 2012
Last sequence update:	February 22, 2012
Last modified:	May 1, 2013
This is version 13 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Chordata Protein Annotation Program

Disclaimer

Any 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.