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Protein

Y-box-binding protein 3

Gene

Ybx3

Organism
Rattus norvegicus (Rat)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Binds to the GM-CSF promoter. Seems to act as a repressor. Binds also to full length mRNA and to short RNA sequences containing the consensus site 5'-UCCAUCA-3'. May have a role in translation repression (By similarity).By similarity

GO - Molecular functioni

  • single-stranded DNA binding Source: RGD

GO - Biological processi

  • animal organ regeneration Source: RGD
  • negative regulation of transcription from RNA polymerase II promoter Source: RGD
  • spermatogenesis Source: RGD
  • transcription, DNA-templated Source: UniProtKB-KW
Complete GO annotation...

Keywords - Molecular functioni

Repressor

Keywords - Biological processi

Transcription, Transcription regulation

Keywords - Ligandi

DNA-binding

Names & Taxonomyi

Protein namesi
Recommended name:
Y-box-binding protein 3
Alternative name(s):
Cold shock domain-containing protein A
DNA-binding protein A
Muscle Y-box protein YB2
RYB-A
Y-box-binding protein A
Gene namesi
Name:Ybx3
Synonyms:Csda, Dbpa, Yb2
OrganismiRattus norvegicus (Rat)
Taxonomic identifieri10116 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeRattus
Proteomesi
  • UP000002494 Componenti: Unplaced

Organism-specific databases

RGDi621056. Ybx3.

Subcellular locationi

GO - Cellular componenti

  • cytoplasm Source: UniProtKB-SubCell
  • gap junction Source: MGI
  • nucleus Source: RGD
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemovedBy similarity
ChainiPRO_00001002162 – 361Y-box-binding protein 3Add BLAST360

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei2N-acetylserineBy similarity1
Modified residuei2PhosphoserineCombined sources1
Modified residuei33PhosphoserineCombined sources1
Modified residuei52PhosphoserineCombined sources1
Modified residuei126PhosphoserineBy similarity1
Modified residuei193PhosphoserineCombined sources1
Modified residuei195PhosphoserineCombined sources1
Modified residuei196PhosphoserineCombined sources1
Modified residuei243Omega-N-methylarginineBy similarity1
Modified residuei313PhosphoserineBy similarity1
Modified residuei315Omega-N-methylarginineBy similarity1
Modified residuei335PhosphoserineCombined sources1
Modified residuei358PhosphoserineCombined sources1
Modified residuei359PhosphoserineCombined sources1

Keywords - PTMi

Acetylation, Methylation, Phosphoprotein

Proteomic databases

PaxDbiQ62764.
PRIDEiQ62764.

PTM databases

iPTMnetiQ62764.
PhosphoSitePlusiQ62764.

Expressioni

Tissue specificityi

Abundant in the skeletal muscle, spleen and fetal liver.

Interactioni

Subunit structurei

Found in a mRNP complex with YBX2.By similarity

Protein-protein interaction databases

BioGridi249842. 1 interactor.
IntActiQ62764. 2 interactors.
STRINGi10116.ENSRNOP00000007427.

Structurei

3D structure databases

ProteinModelPortaliQ62764.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini85 – 149CSDAdd BLAST65

Sequence similaritiesi

Contains 1 CSD (cold-shock) domain.Curated

Phylogenomic databases

eggNOGiKOG3070. Eukaryota.
COG1278. LUCA.
HOGENOMiHOG000116439.
HOVERGENiHBG008757.
InParanoidiQ62764.
KOiK06099.
PhylomeDBiQ62764.

Family and domain databases

CDDicd04458. CSP_CDS. 1 hit.
InterProiIPR019844. Cold-shock_CS.
IPR011129. Cold_shock_prot.
IPR002059. CSP_DNA-bd.
IPR012340. NA-bd_OB-fold.
[Graphical view]
PfamiPF00313. CSD. 1 hit.
[Graphical view]
PRINTSiPR00050. COLDSHOCK.
SMARTiSM00357. CSP. 1 hit.
[Graphical view]
SUPFAMiSSF50249. SSF50249. 1 hit.
PROSITEiPS00352. COLD_SHOCK. 1 hit.
[Graphical view]

Sequences (2)i

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

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

Note: Additional isoforms seem to exist.
Isoform 1 (identifier: Q62764-1) [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
MSEAGEATTG GTTLPQAAAD APAAAPPDPA PKSPAASGAP QAPAPAALLA
60 70 80 90 100
GSPGGDAAPG PAPASSAPAG SEDAEKKVLA TKVLGTVKWF NVRNGYGFIN
110 120 130 140 150
RNDTKEDVFV HQTAIKKNNP RKYLRSVGDG ETVEFDVVEG EKGAEAANVT
160 170 180 190 200
GPDGVPVEGS RYAADRRRYR RGYYGRRRGP PRNYAGEEEE EGSGSSEGFE
210 220 230 240 250
PPAADGQFSG ARNQLRRPQY RPPYRQRRFP PYHVGQTFDR RSRVFPHPNR
260 270 280 290 300
MQAGEIGEMK DGVPEGAQLQ VHRNPTYRPR FRRGPARPRP APAIGEAEDK
310 320 330 340 350
ENQQAANGPN QPSARRGFRR PYNYRRRPRP LNAVSQDGKE TKAGEAPTEN
360
PAPATEQSSA E
Length:361
Mass (Da):38,852
Last modified:November 1, 1996 - v1
Checksum:iC6799D5A3DA5C3F3
GO
Isoform 2 (identifier: Q62764-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     184-252: Missing.

Show »
Length:292
Mass (Da):30,803
Checksum:iBD0F683586047A1B
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti14L → H in BAA05907 (PubMed:8029009).Curated1
Sequence conflicti52 – 74SPGGD…GSEDA → APARASPRARPGLISPRGKR GR in BAA05907 (PubMed:8029009).CuratedAdd BLAST23
Sequence conflicti120 – 121PR → HV in BAA05907 (PubMed:8029009).Curated2

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_001137184 – 252Missing in isoform 2. CuratedAdd BLAST69

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U22893 mRNA. Translation: AAB60520.1.
D28557 mRNA. Translation: BAA05907.1.
PIRiS51608.
RefSeqiNP_114185.3. NM_031979.3. [Q62764-1]
UniGeneiRn.3306.

Genome annotation databases

GeneIDi83807.
KEGGirno:83807.
UCSCiRGD:621056. rat. [Q62764-1]

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U22893 mRNA. Translation: AAB60520.1.
D28557 mRNA. Translation: BAA05907.1.
PIRiS51608.
RefSeqiNP_114185.3. NM_031979.3. [Q62764-1]
UniGeneiRn.3306.

3D structure databases

ProteinModelPortaliQ62764.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi249842. 1 interactor.
IntActiQ62764. 2 interactors.
STRINGi10116.ENSRNOP00000007427.

PTM databases

iPTMnetiQ62764.
PhosphoSitePlusiQ62764.

Proteomic databases

PaxDbiQ62764.
PRIDEiQ62764.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

GeneIDi83807.
KEGGirno:83807.
UCSCiRGD:621056. rat. [Q62764-1]

Organism-specific databases

CTDi8531.
RGDi621056. Ybx3.

Phylogenomic databases

eggNOGiKOG3070. Eukaryota.
COG1278. LUCA.
HOGENOMiHOG000116439.
HOVERGENiHBG008757.
InParanoidiQ62764.
KOiK06099.
PhylomeDBiQ62764.

Miscellaneous databases

PROiQ62764.

Family and domain databases

CDDicd04458. CSP_CDS. 1 hit.
InterProiIPR019844. Cold-shock_CS.
IPR011129. Cold_shock_prot.
IPR002059. CSP_DNA-bd.
IPR012340. NA-bd_OB-fold.
[Graphical view]
PfamiPF00313. CSD. 1 hit.
[Graphical view]
PRINTSiPR00050. COLDSHOCK.
SMARTiSM00357. CSP. 1 hit.
[Graphical view]
SUPFAMiSSF50249. SSF50249. 1 hit.
PROSITEiPS00352. COLD_SHOCK. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiYBOX3_RAT
AccessioniPrimary (citable) accession number: Q62764
Secondary accession number(s): Q63748
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 15, 1999
Last sequence update: November 1, 1996
Last modified: November 2, 2016
This is version 115 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. 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.