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Protein

Y-box-binding protein 2

Gene

YBX2

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: -Experimental evidence at protein leveli

Functioni

Major constituent of messenger ribonucleoprotein particles (mRNPs). Involved in the regulation of the stability and/or translation of germ cell mRNAs. Binds to Y-box consensus promoter element. Binds to full-length mRNA with high affinity in a sequence-independent manner. Binds to short RNA sequences containing the consensus site 5'-UCCAUCA-3' with low affinity and limited sequence specificity. Its binding with maternal mRNAs is necessary for its cytoplasmic retention. May mark specific mRNAs (those transcribed from Y-box promoters) in the nucleus for cytoplasmic storage, thereby linking transcription and mRNA storage/translational delay (By similarity).By similarity

GO - Molecular functioni

GO - Biological processi

  • oocyte development Source: Ensembl
  • positive regulation of cold-induced thermogenesis Source: YuBioLab
  • spermatogenesis Source: ProtInc
  • transcription by RNA polymerase II Source: ProtInc
  • translational attenuation Source: ProtInc

Keywordsi

Molecular functionDNA-binding, RNA-binding

Names & Taxonomyi

Protein namesi
Recommended name:
Y-box-binding protein 2
Alternative name(s):
Contrin
DNA-binding protein C
Short name:
Dbpc
Germ cell-specific Y-box-binding protein
MSY2 homolog
Gene namesi
Name:YBX2
Synonyms:CSDA3, MSY2
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 17

Organism-specific databases

EuPathDBiHostDB:ENSG00000006047.12
HGNCiHGNC:17948 YBX2
MIMi611447 gene
neXtProtiNX_Q9Y2T7

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

Pathology & Biotechi

Organism-specific databases

DisGeNETi51087
OpenTargetsiENSG00000006047
PharmGKBiPA142670560

Polymorphism and mutation databases

BioMutaiYBX2
DMDMi116242847

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001002251 – 364Y-box-binding protein 2Add BLAST364

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei65PhosphothreonineBy similarity1
Modified residuei76PhosphothreonineBy similarity1

Post-translational modificationi

Phosphorylated during oocyte maturation and dephosphorylated following egg activation. Phosphorylated in vitro by a kinase activity associated with testicular mRNPs. Dephosphorylation leads to a decrease in its affinity to bind RNA in vitro (By similarity).By similarity

Keywords - PTMi

Phosphoprotein

Proteomic databases

EPDiQ9Y2T7
MaxQBiQ9Y2T7
PaxDbiQ9Y2T7
PeptideAtlasiQ9Y2T7
PRIDEiQ9Y2T7
ProteomicsDBi85899

PTM databases

iPTMnetiQ9Y2T7
PhosphoSitePlusiQ9Y2T7

Expressioni

Tissue specificityi

Expressed in oocytes and testicular germ cells in the stage of spermatogonia to spermatocyte. Also observed placental trophoblasts, as well as in vascular smooth muscle cells in the pulmonary artery, myocardium, and skeletal muscle. Undetectable in epithelial cells in respiratory, gastrointestinal, and urogenital tracts. Up-regulated in various carcinomas and germ cell tumors (at protein level).2 Publications

Gene expression databases

BgeeiENSG00000006047 Expressed in 118 organ(s), highest expression level in right testis
CleanExiHS_YBX2
ExpressionAtlasiQ9Y2T7 baseline and differential
GenevisibleiQ9Y2T7 HS

Organism-specific databases

HPAiCAB012332
HPA053904
HPA056744

Interactioni

Subunit structurei

Found in a mRNP complex with PABPC1 and YBX3.By similarity

Protein-protein interaction databases

BioGridi119277, 67 interactors
IntActiQ9Y2T7, 3 interactors
STRINGi9606.ENSP00000007699

Structurei

3D structure databases

ProteinModelPortaliQ9Y2T7
SMRiQ9Y2T7
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini93 – 163CSDAdd BLAST71

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni87 – 169Required for cytoplasmic retentionBy similarityAdd BLAST83
Regioni217 – 364Required for mRNA-bindingAdd BLAST148

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi35 – 67Gly-richAdd BLAST33
Compositional biasi185 – 352Pro-richAdd BLAST168

Phylogenomic databases

eggNOGiKOG3070 Eukaryota
COG1278 LUCA
GeneTreeiENSGT00930000150863
HOGENOMiHOG000116439
HOVERGENiHBG079361
InParanoidiQ9Y2T7
KOiK09277
OMAiGPRPSNQ
OrthoDBiEOG091G0W9A
PhylomeDBiQ9Y2T7
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

Sequence (1+)i

Sequence statusi: Complete.

This entry has 1 described isoform and 1 potential isoform that is computationally mapped.Show allAlign All

Q9Y2T7-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MSEVEAAAGA TAVPAATVPA TAAGVVAVVV PVPAGEPQKG GGAGGGGGAA
60 70 80 90 100
SGPAAGTPSA PGSRTPGNPA TAVSGTPAPP ARSQADKPVL AIQVLGTVKW
110 120 130 140 150
FNVRNGYGFI NRNDTKEDVF VHQTAIKRNN PRKFLRSVGD GETVEFDVVE
160 170 180 190 200
GEKGAEATNV TGPGGVPVKG SRYAPNRRKS RRFIPRPPSV APPPMVAEIP
210 220 230 240 250
SAGTGPGSKG ERAEDSGQRP RRWCPPPFFY RRRFVRGPRP PNQQQPIEGT
260 270 280 290 300
DRVEPKETAP LEGHQQQGDE RVPPPRFRPR YRRPFRPRPR QQPTTEGGDG
310 320 330 340 350
ETKPSQGPAD GSRPEPQRPR NRPYFQRRRQ QAPGPQQAPG PRQPAAPETS
360
APVNSGDPTT TILE
Length:364
Mass (Da):38,518
Last modified:October 17, 2006 - v2
Checksum:i0B16DEF46F4634FA
GO

Computationally mapped potential isoform sequencesi

There is 1 potential isoform mapped to this entry.BLASTAlignShow allAdd to basket
EntryEntry nameProtein names
Gene namesLengthAnnotation
I3L2D6I3L2D6_HUMAN
Y-box-binding protein 2
YBX2
164Annotation score:

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_0279169G → V3 PublicationsCorresponds to variant dbSNP:rs222859Ensembl.1
Natural variantiVAR_02791763S → P. Corresponds to variant dbSNP:rs8069533Ensembl.1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF096834 mRNA Translation: AAD30662.1
CH471108 Genomic DNA Translation: EAW90223.1
CH471108 Genomic DNA Translation: EAW90224.1
BC033800 mRNA Translation: AAH33800.1
BC047760 mRNA Translation: AAH47760.1
CCDSiCCDS11098.1
RefSeqiNP_057066.2, NM_015982.3
UniGeneiHs.567494

Genome annotation databases

EnsembliENST00000007699; ENSP00000007699; ENSG00000006047
GeneIDi51087
KEGGihsa:51087
UCSCiuc002gfq.3 human

Keywords - Coding sequence diversityi

Polymorphism

Similar proteinsi

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF096834 mRNA Translation: AAD30662.1
CH471108 Genomic DNA Translation: EAW90223.1
CH471108 Genomic DNA Translation: EAW90224.1
BC033800 mRNA Translation: AAH33800.1
BC047760 mRNA Translation: AAH47760.1
CCDSiCCDS11098.1
RefSeqiNP_057066.2, NM_015982.3
UniGeneiHs.567494

3D structure databases

ProteinModelPortaliQ9Y2T7
SMRiQ9Y2T7
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi119277, 67 interactors
IntActiQ9Y2T7, 3 interactors
STRINGi9606.ENSP00000007699

PTM databases

iPTMnetiQ9Y2T7
PhosphoSitePlusiQ9Y2T7

Polymorphism and mutation databases

BioMutaiYBX2
DMDMi116242847

Proteomic databases

EPDiQ9Y2T7
MaxQBiQ9Y2T7
PaxDbiQ9Y2T7
PeptideAtlasiQ9Y2T7
PRIDEiQ9Y2T7
ProteomicsDBi85899

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000007699; ENSP00000007699; ENSG00000006047
GeneIDi51087
KEGGihsa:51087
UCSCiuc002gfq.3 human

Organism-specific databases

CTDi51087
DisGeNETi51087
EuPathDBiHostDB:ENSG00000006047.12
GeneCardsiYBX2
HGNCiHGNC:17948 YBX2
HPAiCAB012332
HPA053904
HPA056744
MIMi611447 gene
neXtProtiNX_Q9Y2T7
OpenTargetsiENSG00000006047
PharmGKBiPA142670560
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG3070 Eukaryota
COG1278 LUCA
GeneTreeiENSGT00930000150863
HOGENOMiHOG000116439
HOVERGENiHBG079361
InParanoidiQ9Y2T7
KOiK09277
OMAiGPRPSNQ
OrthoDBiEOG091G0W9A
PhylomeDBiQ9Y2T7
TreeFamiTF317306

Miscellaneous databases

ChiTaRSiYBX2 human
GeneWikiiYBX2
GenomeRNAii51087
PROiPR:Q9Y2T7
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000006047 Expressed in 118 organ(s), highest expression level in right testis
CleanExiHS_YBX2
ExpressionAtlasiQ9Y2T7 baseline and differential
GenevisibleiQ9Y2T7 HS

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
ProtoNetiSearch...

Entry informationi

Entry nameiYBOX2_HUMAN
AccessioniPrimary (citable) accession number: Q9Y2T7
Secondary accession number(s): D3DTP1, Q8N4P0
Entry historyiIntegrated into UniProtKB/Swiss-Prot: March 15, 2005
Last sequence update: October 17, 2006
Last modified: November 7, 2018
This is version 138 of the entry and version 2 of the sequence. See 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

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  2. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  3. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  4. Human chromosome 17
    Human chromosome 17: entries, gene names and cross-references to MIM
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Main funding by: National Institutes of Health

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