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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: Annotation score: 5 out of 5-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

GO - Molecular functioni

  • mRNA binding Source: UniProtKB
  • nucleotide binding Source: InterPro

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Activator

Keywords - Biological processi

mRNA processing, mRNA splicing

Keywords - Ligandi

RNA-binding

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

HGNCiHGNC:9912. RBMY1A1.

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Organism-specific databases

DisGeNETi5940.
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.

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.
CleanExiHS_RBMY1A1.
ExpressionAtlasiP0DJD3. differential.
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

WithEntry#Exp.IntActNotes
AENQ8WTP83EBI-8638511,EBI-8637627
APOBEC3CQ9NRW33EBI-8638511,EBI-1044593
CBX2Q147813EBI-8638511,EBI-745934
CIRBPQ140113EBI-8638511,EBI-538850
CLK3P497613EBI-8638511,EBI-745579
HNRPKQ6IBN13EBI-8638511,EBI-3440248
LNX1Q8TBB13EBI-8638511,EBI-739832
PCDHB14Q9Y5E93EBI-8638511,EBI-10329013
PRPF31F1T0A53EBI-8638511,EBI-10177194
PRR3P795223EBI-8638511,EBI-2803328
RBM3P981793EBI-8638511,EBI-2949699
RBMXP381594EBI-11994018,EBI-743526
RBMY1JQ154154EBI-11994018,EBI-8642021
TERF1P542742EBI-8638511,EBI-710997
ZNF317Q96PQ64EBI-8638511,EBI-1210473

Protein-protein interaction databases

BioGridi111875. 17 interactors.
IntActiP0DJD3. 22 interactors.
STRINGi9606.ENSP00000303712.

Structurei

Secondary structure

1496
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi9 – 13Combined sources5
Turni16 – 18Combined sources3
Helixi21 – 29Combined sources9
Beta strandi35 – 40Combined sources6
Turni43 – 45Combined sources3
Beta strandi50 – 54Combined sources5
Helixi58 – 67Combined sources10
Beta strandi74 – 77Combined sources4
Beta strandi79 – 82Combined sources4
Beta strandi89 – 93Combined sources5

3D structure databases

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

Sequence similaritiesi

Contains 1 RRM (RNA recognition motif) domain.PROSITE-ProRule annotation

Phylogenomic databases

eggNOGiENOG410J6JX. Eukaryota.
ENOG4111GI6. LUCA.
GeneTreeiENSGT00710000106295.
InParanoidiP0DJD3.
OMAiYRMSERG.
OrthoDBiEOG091G13K0.
PhylomeDBiP0DJD3.
TreeFamiTF331833.

Family and domain databases

Gene3Di3.30.70.330. 1 hit.
InterProiIPR012677. Nucleotide-bd_a/b_plait.
IPR012604. RBM1CTR.
IPR000504. RRM_dom.
[Graphical view]
PfamiPF08081. RBM1CTR. 1 hit.
PF00076. RRM_1. 1 hit.
[Graphical view]
SMARTiSM00360. RRM. 1 hit.
[Graphical view]
SUPFAMiSSF54928. SSF54928. 1 hit.
PROSITEiPS50102. RRM. 1 hit.
[Graphical view]

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

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. 22 interactors.
STRINGi9606.ENSP00000303712.

PTM databases

iPTMnetiP0DJD3.
PhosphoSitePlusiP0DJD3.

Polymorphism and mutation databases

BioMutaiRBMY1A1.
DMDMi378522864.

Proteomic databases

PaxDbiP0DJD3.
PeptideAtlasiP0DJD3.
PRIDEiP0DJD3.

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.
DisGeNETi5940.
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.
OMAiYRMSERG.
OrthoDBiEOG091G13K0.
PhylomeDBiP0DJD3.
TreeFamiTF331833.

Miscellaneous databases

PROiP0DJD3.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000234414.
CleanExiHS_RBMY1A1.
ExpressionAtlasiP0DJD3. differential.
GenevisibleiP0DJD3. HS.

Family and domain databases

Gene3Di3.30.70.330. 1 hit.
InterProiIPR012677. Nucleotide-bd_a/b_plait.
IPR012604. RBM1CTR.
IPR000504. RRM_dom.
[Graphical view]
PfamiPF08081. RBM1CTR. 1 hit.
PF00076. RRM_1. 1 hit.
[Graphical view]
SMARTiSM00360. RRM. 1 hit.
[Graphical view]
SUPFAMiSSF54928. SSF54928. 1 hit.
PROSITEiPS50102. RRM. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiRBY1A_HUMAN
AccessioniPrimary (citable) accession number: P0DJD3
Secondary accession number(s): Q15376
, Q15377, Q15414, Q6NSB5, Q86VU6, Q8NHR0
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 22, 2012
Last sequence update: February 22, 2012
Last modified: November 30, 2016
This is version 47 of the entry and version 1 of the sequence. [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

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.

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

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

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.