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Protein

Y-box-binding protein 3

Gene

Ybx3

Organism
Rattus norvegicus (Rat)
Status
Reviewed-Annotation score: -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 by RNA polymerase II Source: RGD
  • spermatogenesis Source: RGD
  • transcription, DNA-templated Source: UniProtKB-KW

Keywordsi

Molecular functionDNA-binding, Repressor
Biological processTranscription, Transcription regulation

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 lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaMyomorphaMuroideaMuridaeMurinaeRattus
Proteomesi
  • UP000002494 Componenti: Unplaced

Organism-specific databases

RGDi621056 Ybx3

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

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. Interacts with RRP1B.By similarity

Protein-protein interaction databases

BioGridi249842, 1 interactor
IntActiQ62764, 2 interactors
STRINGi10116.ENSRNOP00000007427

Structurei

3D structure databases

ProteinModelPortaliQ62764
SMRiQ62764
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

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

Phylogenomic databases

eggNOGiKOG3070 Eukaryota
COG1278 LUCA
HOGENOMiHOG000116439
HOVERGENiHBG008757
InParanoidiQ62764
KOiK06099
PhylomeDBiQ62764

Family and domain databases

CDDicd04458 CSP_CDS, 1 hit
InterProiView protein in InterPro
IPR019844 Cold-shock_CS
IPR011129 CSD
IPR002059 CSP_DNA-bd
IPR012340 NA-bd_OB-fold
PfamiView protein in Pfam
PF00313 CSD, 1 hit
PRINTSiPR00050 COLDSHOCK
SMARTiView protein in SMART
SM00357 CSP, 1 hit
SUPFAMiSSF50249 SSF50249, 1 hit
PROSITEiView protein in PROSITE
PS00352 CSD_1, 1 hit
PS51857 CSD_2, 1 hit

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

Similar proteinsi

Entry informationi

Entry nameiYBOX3_RAT
AccessioniPrimary (citable) accession number: Q62764
Secondary accession number(s): Q63748
Entry historyiIntegrated into UniProtKB/Swiss-Prot: July 15, 1999
Last sequence update: November 1, 1996
Last modified: May 23, 2018
This is version 123 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

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