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Protein

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

Gene

RBMY1A1

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: -Experimental evidence at protein leveli

Functioni

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.2 Publications

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.

GO - Molecular functioni

  • mRNA binding Source: UniProtKB

GO - Biological processi

Keywordsi

Molecular functionActivator, RNA-binding
Biological processmRNA processing, mRNA splicing

Names & Taxonomyi

Protein namesi
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 namesi
Name:RBMY1A1
Synonyms:RBM1, RBM2, YRRM1, YRRM2
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome Y

Organism-specific databases

EuPathDBiHostDB:ENSG00000234414.7
HGNCiHGNC:9912 RBMY1A1
MIMi400006 gene
neXtProtiNX_P0DJD3

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Organism-specific databases

DisGeNETi378949
5940
GeneReviewsiRBMY1A1
MalaCardsiRBMY1A1
OpenTargetsiENSG00000234414
Orphaneti1646 Partial chromosome Y deletion

Polymorphism and mutation databases

BioMutaiRBMY1A1
DMDMi378522864

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000818991 – 496RNA-binding motif protein, Y chromosome, family 1 member A1Add BLAST496

Proteomic databases

PaxDbiP0DJD3
PeptideAtlasiP0DJD3
PRIDEiP0DJD3
ProteomicsDBi52540
52541 [P0DJD3-2]
52542 [P0DJD3-3]

PTM databases

iPTMnetiP0DJD3
PhosphoSitePlusiP0DJD3

Expressioni

Tissue specificityi

Testis-specific.1 Publication

Developmental stagei

Expressed in all of the transcriptionally active stages of germ cell development from spermatogonia through spermatocytes to round spermatids.1 Publication

Gene expression databases

BgeeiENSG00000234414 Expressed in 12 organ(s), highest expression level in right testis
CleanExiHS_RBMY1A1
ExpressionAtlasiP0DJD3 baseline
GenevisibleiP0DJD3 HS

Organism-specific databases

HPAiHPA001534
HPA053147

Interactioni

Subunit structurei

Interacts with splicing factor proteins SFRS3/SRP20, TRA2B/SFRS10, KHDRBS1/SAM68 and KHDRBS3.5 Publications

Binary interactionsi

Protein-protein interaction databases

BioGridi111875, 17 interactors
IntActiP0DJD3, 24 interactors
MINTiP0DJD3
STRINGi9606.ENSP00000303712

Structurei

Secondary structure

1496
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

ProteinModelPortaliP0DJD3
SMRiP0DJD3
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini8 – 85RRMPROSITE-ProRule annotationAdd BLAST78

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi254 – 340Arg-richAdd BLAST87

Phylogenomic databases

eggNOGiENOG410J6JX Eukaryota
ENOG4111GI6 LUCA
GeneTreeiENSGT00710000106295
InParanoidiP0DJD3
OMAiADINEPE
OrthoDBiEOG091G13K0
PhylomeDBiP0DJD3
TreeFamiTF331833

Family and domain databases

Gene3Di3.30.70.330, 1 hit
InterProiView protein in InterPro
IPR012677 Nucleotide-bd_a/b_plait_sf
IPR035979 RBD_domain_sf
IPR012604 RBM1CTR
IPR000504 RRM_dom
PfamiView protein in Pfam
PF08081 RBM1CTR, 1 hit
PF00076 RRM_1, 1 hit
SMARTiView protein in SMART
SM00360 RRM, 1 hit
SUPFAMiSSF54928 SSF54928, 1 hit
PROSITEiView protein in PROSITE
PS50102 RRM, 1 hit

Sequences (3)i

Sequence statusi: Complete.

This entry describes 3 isoformsi produced by alternative splicing. AlignAdd to basket
Isoform 1 (identifier: P0DJD3-1) [UniParc]FASTAAdd to basket

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.

« Hide
        10         20         30         40         50
MVEADHPGKL FIGGLNRETN EKMLKAVFGK HGPISEVLLI KDRTSKSRGF
60 70 80 90 100
AFITFENPAD AKNAAKDMNG KSLHGKAIKV EQAKKPSFQS GGRRRPPASS
110 120 130 140 150
RNRSPSGSLR SARGSRGGTR GWLPSHEGHL DDGGYTPDLK MSYSRGLIPV
160 170 180 190 200
KRGPSSRSGG PPPKKSAPSA VARSNSWMGS QGPMSQRREN YGVPPRRATI
210 220 230 240 250
SSWRNDRMST RHDGYATNDG NHPSCQETRD YAPPSRGYAY RDNGHSNRDE
260 270 280 290 300
HSSRGYRNHR SSRETRDYAP PSRGHAYRDY GHSRRDESYS RGYRNRRSSR
310 320 330 340 350
ETREYAPPSR GHGYRDYGHS RRHESYSRGY RNHPSSRETR DYAPPHRDYA
360 370 380 390 400
YRDYGHSSWD EHSSRGYSYH DGYGEALGRD HSEHLSGSSY RDALQRYGTS
410 420 430 440 450
HGAPPARGPR MSYGGSTCHA YSNTRDRYGR SWESYSSCGD FHYCDREHVC
460 470 480 490
RKDQRNPPSL GRVLPDPREA CGSSSYVASI VDGGESRSEK GDSSRY
Length:496
Mass (Da):55,784
Last modified:February 22, 2012 - v1
Checksum:i3E493C52C7BA9E7E
GO
Isoform 2 (identifier: P0DJD3-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     327-363: Missing.

Show »
Length:459
Mass (Da):51,292
Checksum:iF3C0267BBEF99E55
GO
Isoform 3 (identifier: P0DJD3-3) [UniParc]FASTAAdd to basket

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

Show »
Length:356
Mass (Da):40,651
Checksum:i96D4EAB0E82A3C1C
GO

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_0423151 – 140Missing in isoform 3. 1 PublicationAdd BLAST140
Alternative sequenceiVSP_042316327 – 363Missing in isoform 2. 1 PublicationAdd BLAST37

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X76059 mRNA Translation: CAA53659.1
BC047768 mRNA Translation: AAH47768.1
BC070298 mRNA Translation: AAH70298.1
AC010141 Genomic DNA No translation available.
CCDSiCCDS14796.1 [P0DJD3-1]
PIRiA49418
RefSeqiNP_001307873.1, NM_001320944.1 [P0DJD3-2]
NP_001307874.1, NM_001320945.1 [P0DJD3-3]
NP_005049.1, NM_005058.3 [P0DJD3-1]
XP_011529792.1, XM_011531490.1 [P0DJD3-3]
UniGeneiHs.380450
Hs.725744

Genome annotation databases

EnsembliENST00000303902; ENSP00000303712; ENSG00000234414 [P0DJD3-2]
ENST00000382707; ENSP00000372154; ENSG00000234414 [P0DJD3-1]
ENST00000439108; ENSP00000388006; ENSG00000234414 [P0DJD3-1]
GeneIDi378949
5940
KEGGihsa:5940
UCSCiuc004fuq.4 human [P0DJD3-1]

Keywords - Coding sequence diversityi

Alternative splicing

Similar proteinsi

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X76059 mRNA Translation: CAA53659.1
BC047768 mRNA Translation: AAH47768.1
BC070298 mRNA Translation: AAH70298.1
AC010141 Genomic DNA No translation available.
CCDSiCCDS14796.1 [P0DJD3-1]
PIRiA49418
RefSeqiNP_001307873.1, NM_001320944.1 [P0DJD3-2]
NP_001307874.1, NM_001320945.1 [P0DJD3-3]
NP_005049.1, NM_005058.3 [P0DJD3-1]
XP_011529792.1, XM_011531490.1 [P0DJD3-3]
UniGeneiHs.380450
Hs.725744

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2FY1NMR-A1-109[»]
ProteinModelPortaliP0DJD3
SMRiP0DJD3
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi111875, 17 interactors
IntActiP0DJD3, 24 interactors
MINTiP0DJD3
STRINGi9606.ENSP00000303712

PTM databases

iPTMnetiP0DJD3
PhosphoSitePlusiP0DJD3

Polymorphism and mutation databases

BioMutaiRBMY1A1
DMDMi378522864

Proteomic databases

PaxDbiP0DJD3
PeptideAtlasiP0DJD3
PRIDEiP0DJD3
ProteomicsDBi52540
52541 [P0DJD3-2]
52542 [P0DJD3-3]

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000303902; ENSP00000303712; ENSG00000234414 [P0DJD3-2]
ENST00000382707; ENSP00000372154; ENSG00000234414 [P0DJD3-1]
ENST00000439108; ENSP00000388006; ENSG00000234414 [P0DJD3-1]
GeneIDi378949
5940
KEGGihsa:5940
UCSCiuc004fuq.4 human [P0DJD3-1]

Organism-specific databases

CTDi378949
5940
DisGeNETi378949
5940
EuPathDBiHostDB:ENSG00000234414.7
GeneCardsiRBMY1A1
GeneReviewsiRBMY1A1
HGNCiHGNC:9912 RBMY1A1
HPAiHPA001534
HPA053147
MalaCardsiRBMY1A1
MIMi400006 gene
neXtProtiNX_P0DJD3
OpenTargetsiENSG00000234414
Orphaneti1646 Partial chromosome Y deletion
GenAtlasiSearch...

Phylogenomic databases

eggNOGiENOG410J6JX Eukaryota
ENOG4111GI6 LUCA
GeneTreeiENSGT00710000106295
InParanoidiP0DJD3
OMAiADINEPE
OrthoDBiEOG091G13K0
PhylomeDBiP0DJD3
TreeFamiTF331833

Miscellaneous databases

PROiPR:P0DJD3
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000234414 Expressed in 12 organ(s), highest expression level in right testis
CleanExiHS_RBMY1A1
ExpressionAtlasiP0DJD3 baseline
GenevisibleiP0DJD3 HS

Family and domain databases

Gene3Di3.30.70.330, 1 hit
InterProiView protein in InterPro
IPR012677 Nucleotide-bd_a/b_plait_sf
IPR035979 RBD_domain_sf
IPR012604 RBM1CTR
IPR000504 RRM_dom
PfamiView protein in Pfam
PF08081 RBM1CTR, 1 hit
PF00076 RRM_1, 1 hit
SMARTiView protein in SMART
SM00360 RRM, 1 hit
SUPFAMiSSF54928 SSF54928, 1 hit
PROSITEiView protein in PROSITE
PS50102 RRM, 1 hit
ProtoNetiSearch...

Entry informationi

Entry nameiRBY1A_HUMAN
AccessioniPrimary (citable) accession number: P0DJD3
Secondary accession number(s): Q15376
, Q15377, Q15414, Q6NSB5, Q86VU6, Q8NHR0
Entry historyiIntegrated into UniProtKB/Swiss-Prot: February 22, 2012
Last sequence update: February 22, 2012
Last modified: September 12, 2018
This is version 59 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (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.

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. Human chromosome Y
    Human chromosome Y: entries, gene names and cross-references to MIM
  3. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
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