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Protein

Y-box-binding protein 3

Gene

Ybx3

Organism
Mus musculus (Mouse)
Status
Reviewed-Annotation score: -Experimental evidence at protein leveli

Functioni

Binds to the GM-CSF promoter. Seems to act as a repressor (By similarity). 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 similarity1 Publication

Miscellaneous

Transgenic mice overexpressing Ybx3 exhibit disruption of the normal completion of spermatogenesis, dominant sterility and abnormal translation activation of repressed mRNA.

GO - Molecular functioni

  • DNA binding Source: MGI
  • mRNA 3'-UTR binding Source: MGI
  • RNA polymerase II regulatory region sequence-specific DNA binding Source: NTNU_SB
  • single-stranded DNA binding Source: MGI
  • transcriptional repressor activity, RNA polymerase II transcription regulatory region sequence-specific DNA binding Source: NTNU_SB

GO - Biological processi

  • cellular hyperosmotic response Source: MGI
  • cellular response to tumor necrosis factor Source: MGI
  • fertilization Source: MGI
  • in utero embryonic development Source: MGI
  • male gonad development Source: MGI
  • negative regulation of apoptotic process Source: MGI
  • negative regulation of intrinsic apoptotic signaling pathway in response to osmotic stress Source: MGI
  • negative regulation of necroptotic process Source: MGI
  • negative regulation of skeletal muscle tissue development Source: MGI
  • negative regulation of transcription by RNA polymerase II Source: NTNU_SB
  • positive regulation of organ growth Source: MGI
  • spermatogenesis Source: MGI
  • transcription, DNA-templated Source: UniProtKB-KW

Keywordsi

Molecular functionDNA-binding, Repressor, RNA-binding
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
Y-box protein 3
Gene namesi
Name:Ybx3
Synonyms:Csda, Msy4
OrganismiMus musculus (Mouse)
Taxonomic identifieri10090 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaMyomorphaMuroideaMuridaeMurinaeMusMus
Proteomesi
  • UP000000589 Componenti: Chromosome 6

Organism-specific databases

MGIiMGI:2137670 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_00001002152 – 361Y-box-binding protein 3Add BLAST360

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei2N-acetylserineBy similarity1
Modified residuei2PhosphoserineBy similarity1
Modified residuei33PhosphoserineCombined sources1
Modified residuei52PhosphoserineCombined sources1
Modified residuei126PhosphoserineBy similarity1
Modified residuei193PhosphoserineBy similarity1
Modified residuei195PhosphoserineCombined sources1
Modified residuei196PhosphoserineBy similarity1
Modified residuei243Omega-N-methylarginineBy similarity1
Modified residuei313PhosphoserineBy similarity1
Modified residuei315Omega-N-methylarginineCombined sources1
Modified residuei335PhosphoserineBy similarity1
Modified residuei358PhosphoserineBy similarity1
Modified residuei359PhosphoserineBy similarity1

Keywords - PTMi

Acetylation, Methylation, Phosphoprotein

Proteomic databases

EPDiQ9JKB3
PaxDbiQ9JKB3
PeptideAtlasiQ9JKB3
PRIDEiQ9JKB3

PTM databases

iPTMnetiQ9JKB3
PhosphoSitePlusiQ9JKB3

Expressioni

Tissue specificityi

Expressed in oocytes, spermatocytes and spermatids (at protein level). Expressed in skeletal muscle, kidney, brain, spleen, liver, heart and spermatids. Isoform 2 is preferentially expressed in somatic tissues (PubMed:10956549).3 Publications

Gene expression databases

BgeeiENSMUSG00000030189
CleanExiMM_CSDA
GenevisibleiQ9JKB3 MM

Interactioni

Subunit structurei

Found in a mRNP complex with YBX2 (PubMed:10772793). Interacts with RRP1B (By similarity).By similarity1 Publication

Protein-protein interaction databases

BioGridi207989, 3 interactors
DIPiDIP-42746N
IntActiQ9JKB3, 9 interactors
MINTiQ9JKB3
STRINGi10090.ENSMUSP00000032309

Structurei

3D structure databases

ProteinModelPortaliQ9JKB3
SMRiQ9JKB3
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini82 – 152CSDAdd BLAST71

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi17 – 69Ala-richAdd BLAST53
Compositional biasi161 – 329Arg-richAdd BLAST169

Phylogenomic databases

eggNOGiKOG3070 Eukaryota
COG1278 LUCA
GeneTreeiENSGT00880000137907
HOGENOMiHOG000116439
HOVERGENiHBG008757
InParanoidiQ9JKB3
KOiK06099
OMAiQQVHRNP
OrthoDBiEOG091G0W9A
PhylomeDBiQ9JKB3
TreeFamiTF317306

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

Isoform 1 (identifier: Q9JKB3-1) [UniParc]FASTAAdd to basket
Also known as: Msy3l

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 GEDAEKKVLA 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 DGVPEGTQLQ AHRNPTYRPR FRRGPARPRP APAIGEAEDK
310 320 330 340 350
ENQQAANGPN QPSARRGFRR PYNYRRRSRP LNAVSQDGKE TKAGEAPTEN
360
PAPATEQSSA E
Length:361
Mass (Da):38,814
Last modified:March 15, 2005 - v2
Checksum:i5BAF6A144A127CEC
GO
Isoform 2 (identifier: Q9JKB3-2) [UniParc]FASTAAdd to basket
Also known as: Msy3s

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

Show »
Length:292
Mass (Da):30,765
Checksum:i57B2898DF2D18155
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti237T → N in AAG14418 (PubMed:10956549).Curated1
Sequence conflicti306A → G in AAF61741 (PubMed:10772793).Curated1
Sequence conflicti349E → A in AAF61741 (PubMed:10772793).Curated1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_013051184 – 252Missing in isoform 2. 2 PublicationsAdd BLAST69

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF246224 mRNA Translation: AAF61741.1
AF248546 mRNA Translation: AAG14418.1
AF248547 mRNA Translation: AAG14419.1
BC048242 mRNA Translation: AAH48242.1
BC062377 mRNA Translation: AAH62377.1
CCDSiCCDS20605.1 [Q9JKB3-2]
CCDS20606.1 [Q9JKB3-1]
RefSeqiNP_035863.1, NM_011733.2 [Q9JKB3-2]
NP_620817.2, NM_139117.2 [Q9JKB3-1]
UniGeneiMm.458000

Genome annotation databases

EnsembliENSMUST00000032309; ENSMUSP00000032309; ENSMUSG00000030189 [Q9JKB3-1]
ENSMUST00000087865; ENSMUSP00000085172; ENSMUSG00000030189 [Q9JKB3-2]
GeneIDi56449
KEGGimmu:56449
UCSCiuc009eis.1 mouse [Q9JKB3-1]
uc009eit.1 mouse [Q9JKB3-2]

Keywords - Coding sequence diversityi

Alternative splicing

Similar proteinsi

Entry informationi

Entry nameiYBOX3_MOUSE
AccessioniPrimary (citable) accession number: Q9JKB3
Secondary accession number(s): Q80WG4, Q9EQF7, Q9EQF8
Entry historyiIntegrated into UniProtKB/Swiss-Prot: March 15, 2005
Last sequence update: March 15, 2005
Last modified: May 23, 2018
This is version 135 of the entry and version 2 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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