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Protein

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

Gene

RBMY1D

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at transcript leveli

Functioni

RNA-binding protein which may be involved in spermatogenesis. Required for sperm development, possibly by participating in pre-mRNA splicing in the testis.

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

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 D
Gene namesi
Name:RBMY1D
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome Y

Organism-specific databases

HGNCiHGNC:23915. RBMY1D.

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Organism-specific databases

PharmGKBiPA134863616.

Polymorphism and mutation databases

BioMutaiRBMY1D.
DMDMi190360153.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 496496RNA-binding motif protein, Y chromosome, family 1 member DPRO_0000341538Add
BLAST

Proteomic databases

EPDiP0C7P1.
PaxDbiP0C7P1.
PRIDEiP0C7P1.

PTM databases

PhosphoSiteiP0C7P1.

Expressioni

Tissue specificityi

Testis-specific.

Developmental stagei

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

Gene expression databases

BgeeiP0C7P1.
ExpressionAtlasiP0C7P1. baseline.
GenevisibleiP0C7P1. HS.

Organism-specific databases

HPAiHPA001534.
HPA053147.

Interactioni

Subunit structurei

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

Structurei

3D structure databases

ProteinModelPortaliP0C7P1.
SMRiP0C7P1. Positions 1-108.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini8 – 8578RRMPROSITE-ProRule annotationAdd
BLAST

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi254 – 34087Arg-richAdd
BLAST

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiENOG410J6JX. Eukaryota.
ENOG4111GI6. LUCA.
GeneTreeiENSGT00710000106295.
HOGENOMiHOG000276235.
HOVERGENiHBG063314.
InParanoidiP0C7P1.
OMAiFIGGFNR.
PhylomeDBiP0C7P1.
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 (2)i

Sequence statusi: Complete.

This entry describes 2 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: P0C7P1-1) [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 GWLPSQEGHL 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):55,775
Last modified:June 10, 2008 - v1
Checksum:i46443ED1F5D72C1B
GO
Isoform 2 (identifier: P0C7P1-2) [UniParc]FASTAAdd to basket

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

Note: No experimental confirmation available.
Show »
Length:459
Mass (Da):51,283
Checksum:i230B6B80FDD26A09
GO

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei327 – 36337Missing in isoform 2. 1 PublicationVSP_056242Add
BLAST

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AC007322 Genomic DNA. No translation available.
BC136862 mRNA. Translation: AAI36863.1.
BC144459 mRNA. Translation: AAI44460.1.
CCDSiCCDS35480.1. [P0C7P1-1]
RefSeqiNP_001006120.2. NM_001006120.3. [P0C7P1-1]
XP_005262642.1. XM_005262585.1. [P0C7P1-2]
XP_011529787.1. XM_011531485.1. [P0C7P1-1]
XP_011529788.1. XM_011531486.1. [P0C7P1-1]
UniGeneiHs.380450.

Genome annotation databases

EnsembliENST00000382680; ENSP00000372127; ENSG00000244395. [P0C7P1-1]
ENST00000418956; ENSP00000399181; ENSG00000244395. [P0C7P1-2]
GeneIDi378949.
KEGGihsa:378949.
UCSCiuc004fuu.3. human. [P0C7P1-1]

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AC007322 Genomic DNA. No translation available.
BC136862 mRNA. Translation: AAI36863.1.
BC144459 mRNA. Translation: AAI44460.1.
CCDSiCCDS35480.1. [P0C7P1-1]
RefSeqiNP_001006120.2. NM_001006120.3. [P0C7P1-1]
XP_005262642.1. XM_005262585.1. [P0C7P1-2]
XP_011529787.1. XM_011531485.1. [P0C7P1-1]
XP_011529788.1. XM_011531486.1. [P0C7P1-1]
UniGeneiHs.380450.

3D structure databases

ProteinModelPortaliP0C7P1.
SMRiP0C7P1. Positions 1-108.
ModBaseiSearch...
MobiDBiSearch...

PTM databases

PhosphoSiteiP0C7P1.

Polymorphism and mutation databases

BioMutaiRBMY1D.
DMDMi190360153.

Proteomic databases

EPDiP0C7P1.
PaxDbiP0C7P1.
PRIDEiP0C7P1.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000382680; ENSP00000372127; ENSG00000244395. [P0C7P1-1]
ENST00000418956; ENSP00000399181; ENSG00000244395. [P0C7P1-2]
GeneIDi378949.
KEGGihsa:378949.
UCSCiuc004fuu.3. human. [P0C7P1-1]

Organism-specific databases

CTDi378949.
GeneCardsiRBMY1D.
HGNCiHGNC:23915. RBMY1D.
HPAiHPA001534.
HPA053147.
neXtProtiNX_P0C7P1.
PharmGKBiPA134863616.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiENOG410J6JX. Eukaryota.
ENOG4111GI6. LUCA.
GeneTreeiENSGT00710000106295.
HOGENOMiHOG000276235.
HOVERGENiHBG063314.
InParanoidiP0C7P1.
OMAiFIGGFNR.
PhylomeDBiP0C7P1.
TreeFamiTF331833.

Miscellaneous databases

GenomeRNAii378949.
NextBioi100875.
PROiP0C7P1.

Gene expression databases

BgeeiP0C7P1.
ExpressionAtlasiP0C7P1. baseline.
GenevisibleiP0C7P1. 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...

Publicationsi

  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  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] (ISOFORM 2).
    Tissue: Testis.

Entry informationi

Entry nameiRBY1D_HUMAN
AccessioniPrimary (citable) accession number: P0C7P1
Secondary accession number(s): B7ZMD9
Entry historyi
Integrated into UniProtKB/Swiss-Prot: June 10, 2008
Last sequence update: June 10, 2008
Last modified: May 11, 2016
This is version 63 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

Complete proteome, Reference proteome

Documents

  1. Human chromosome Y
    Human chromosome Y: entries, gene names and cross-references to MIM
  2. 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.