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Protein

Y-box-binding protein 2

Gene

YBX2

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-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

  1. chromatin binding Source: Ensembl
  2. DNA binding Source: UniProtKB-KW
  3. lipid binding Source: Ensembl
  4. mRNA 3'-UTR binding Source: Ensembl
  5. ribonucleoprotein complex binding Source: Ensembl
  6. translation regulator activity Source: Ensembl

GO - Biological processi

  1. mRNA stabilization Source: Ensembl
  2. negative regulation of binding Source: Ensembl
  3. negative regulation of translation Source: Ensembl
  4. oocyte development Source: Ensembl
  5. regulation of transcription, DNA-templated Source: InterPro
  6. spermatid development Source: Ensembl
  7. spermatogenesis Source: ProtInc
  8. transcription from RNA polymerase II promoter Source: ProtInc
  9. translational attenuation Source: ProtInc
Complete GO annotation...

Keywords - Ligandi

DNA-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
ProteomesiUP000005640: Chromosome 17

Organism-specific databases

HGNCiHGNC:17948. YBX2.

Subcellular locationi

Cytoplasm 1 Publication. Nucleus 1 Publication

GO - Cellular componenti

  1. cytoplasm Source: ProtInc
  2. nucleolus Source: HPA
  3. nucleus Source: ProtInc
  4. polysome Source: Ensembl
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Nucleus

Pathology & Biotechi

Organism-specific databases

PharmGKBiPA142670560.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 364364Y-box-binding protein 2PRO_0000100225Add
BLAST

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

MaxQBiQ9Y2T7.
PaxDbiQ9Y2T7.
PRIDEiQ9Y2T7.

PTM databases

PhosphoSiteiQ9Y2T7.

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

BgeeiQ9Y2T7.
CleanExiHS_YBX2.
GenevestigatoriQ9Y2T7.

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. 7 interactions.
IntActiQ9Y2T7. 2 interactions.
STRINGi9606.ENSP00000007699.

Structurei

3D structure databases

ProteinModelPortaliQ9Y2T7.
SMRiQ9Y2T7. Positions 87-164.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini93 – 16371CSDAdd
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni87 – 16983Required for cytoplasmic retentionBy similarityAdd
BLAST
Regioni217 – 364148Required for mRNA-bindingAdd
BLAST

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi35 – 6733Gly-richAdd
BLAST
Compositional biasi185 – 352168Pro-richAdd
BLAST

Sequence similaritiesi

Contains 1 CSD (cold-shock) domain.Curated

Phylogenomic databases

eggNOGiCOG1278.
GeneTreeiENSGT00390000009256.
HOGENOMiHOG000116439.
HOVERGENiHBG079361.
InParanoidiQ9Y2T7.
KOiK09277.
OMAiGPRPSNQ.
OrthoDBiEOG7TBC44.
PhylomeDBiQ9Y2T7.
TreeFamiTF317306.

Family and domain databases

Gene3Di2.40.50.140. 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]

Sequencei

Sequence statusi: Complete.

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

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti9 – 91G → V.3 Publications
Corresponds to variant rs222859 [ dbSNP | Ensembl ].
VAR_027916
Natural varianti63 – 631S → P.
Corresponds to variant rs8069533 [ dbSNP | Ensembl ].
VAR_027917

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.2. human.

Polymorphism databases

DMDMi116242847.

Keywords - Coding sequence diversityi

Polymorphism

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. Positions 87-164.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi119277. 7 interactions.
IntActiQ9Y2T7. 2 interactions.
STRINGi9606.ENSP00000007699.

PTM databases

PhosphoSiteiQ9Y2T7.

Polymorphism databases

DMDMi116242847.

Proteomic databases

MaxQBiQ9Y2T7.
PaxDbiQ9Y2T7.
PRIDEiQ9Y2T7.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000007699; ENSP00000007699; ENSG00000006047.
GeneIDi51087.
KEGGihsa:51087.
UCSCiuc002gfq.2. human.

Organism-specific databases

CTDi51087.
GeneCardsiGC17M007191.
HGNCiHGNC:17948. YBX2.
HPAiCAB012332.
HPA053904.
HPA056744.
MIMi611447. gene.
neXtProtiNX_Q9Y2T7.
PharmGKBiPA142670560.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiCOG1278.
GeneTreeiENSGT00390000009256.
HOGENOMiHOG000116439.
HOVERGENiHBG079361.
InParanoidiQ9Y2T7.
KOiK09277.
OMAiGPRPSNQ.
OrthoDBiEOG7TBC44.
PhylomeDBiQ9Y2T7.
TreeFamiTF317306.

Miscellaneous databases

ChiTaRSiYBX2. human.
GeneWikiiYBX2.
GenomeRNAii51087.
NextBioi53755.
PROiQ9Y2T7.
SOURCEiSearch...

Gene expression databases

BgeeiQ9Y2T7.
CleanExiHS_YBX2.
GenevestigatoriQ9Y2T7.

Family and domain databases

Gene3Di2.40.50.140. 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...

Publicationsi

« Hide 'large scale' publications
  1. "Contrin, the human homologue of a germ-cell Y-box-binding protein: cloning, expression, and chromosomal localization."
    Tekur S., Pawlak A., Guellaen G., Hecht N.B.
    J. Androl. 20:135-144(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA], TISSUE SPECIFICITY, VARIANT VAL-9.
  2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA], VARIANT VAL-9.
  3. "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], VARIANT VAL-9.
    Tissue: Brain.
  4. "Expression of Y-box-binding protein dbpC/contrin, a potentially new cancer/testis antigen."
    Kohno Y., Matsuki Y., Tanimoto A., Izumi H., Uchiumi T., Kohno K., Shimajiri S., Sasaguri Y.
    Br. J. Cancer 94:710-716(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: TISSUE SPECIFICITY, SUBCELLULAR LOCATION.

Entry informationi

Entry nameiYBOX2_HUMAN
AccessioniPrimary (citable) accession number: Q9Y2T7
Secondary accession number(s): D3DTP1, Q8N4P0
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 15, 2005
Last sequence update: October 17, 2006
Last modified: February 4, 2015
This is version 110 of the entry and version 2 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

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Human chromosome 17
    Human chromosome 17: entries, gene names and cross-references to MIM
  2. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  3. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  4. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  5. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

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 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.