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Protein

Y-box-binding protein 3

Gene

YBX3

Organism
Homo sapiens (Human)
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

  • double-stranded DNA binding Source: ProtInc
  • mRNA 3'-UTR binding Source: BHF-UCL
  • poly(A) RNA binding Source: UniProtKB
  • Rho GTPase binding Source: BHF-UCL
  • RNA polymerase II regulatory region sequence-specific DNA binding Source: Ensembl
  • single-stranded DNA binding Source: Ensembl
  • transcriptional repressor activity, RNA polymerase II transcription regulatory region sequence-specific binding Source: Ensembl
  • transcription corepressor activity Source: ProtInc
  • transcription factor activity, sequence-specific DNA binding Source: ProtInc

GO - Biological processi

  • 3'-UTR-mediated mRNA stabilization Source: BHF-UCL
  • cellular hyperosmotic response Source: BHF-UCL
  • cellular response to tumor necrosis factor Source: BHF-UCL
  • fertilization Source: Ensembl
  • in utero embryonic development Source: Ensembl
  • male gonad development Source: Ensembl
  • negative regulation of intrinsic apoptotic signaling pathway in response to osmotic stress Source: BHF-UCL
  • negative regulation of necroptotic process Source: BHF-UCL
  • negative regulation of skeletal muscle tissue development Source: Ensembl
  • negative regulation of transcription from RNA polymerase II promoter Source: ProtInc
  • positive regulation of cytoplasmic translation Source: BHF-UCL
  • positive regulation of organ growth Source: Ensembl
  • response to cold Source: ProtInc
  • spermatogenesis Source: Ensembl
  • transcription, DNA-templated Source: UniProtKB-KW
Complete GO annotation...

Keywords - Molecular functioni

Repressor

Keywords - Biological processi

Transcription, Transcription regulation

Keywords - Ligandi

DNA-binding

Enzyme and pathway databases

BioCyciZFISH:ENSG00000060138-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Y-box-binding protein 3
Alternative name(s):
Cold shock domain-containing protein A
DNA-binding protein A
Single-strand DNA-binding protein NF-GMB
Gene namesi
Name:YBX3
Synonyms:CSDA, DBPA
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 12

Organism-specific databases

HGNCiHGNC:2428. YBX3.

Subcellular locationi

GO - Cellular componenti

  • bicellular tight junction Source: BHF-UCL
  • cytoplasm Source: HPA
  • nucleus Source: BHF-UCL
  • perinuclear region of cytoplasm Source: BHF-UCL
  • polysome Source: Ensembl
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Nucleus

Pathology & Biotechi

Organism-specific databases

DisGeNETi8531.
OpenTargetsiENSG00000060138.
PharmGKBiPA26929.

Polymorphism and mutation databases

BioMutaiYBX3.
DMDMi97536050.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemovedCombined sources
ChainiPRO_00001002142 – 372Y-box-binding protein 3Add BLAST371

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei2N-acetylserineCombined sources1
Modified residuei2PhosphoserineCombined sources1
Modified residuei34PhosphoserineCombined sources1
Modified residuei134PhosphoserineCombined sources1
Modified residuei201PhosphoserineCombined sources1
Modified residuei203PhosphoserineCombined sources1
Modified residuei204PhosphoserineCombined sources1
Modified residuei251Omega-N-methylarginineCombined sources1
Modified residuei324PhosphoserineCombined sources1
Modified residuei326Omega-N-methylarginineCombined sources1
Modified residuei346PhosphoserineBy similarity1
Modified residuei369PhosphoserineBy similarity1
Modified residuei370PhosphoserineBy similarity1

Keywords - PTMi

Acetylation, Methylation, Phosphoprotein

Proteomic databases

EPDiP16989.
MaxQBiP16989.
PaxDbiP16989.
PeptideAtlasiP16989.
PRIDEiP16989.

PTM databases

iPTMnetiP16989.
PhosphoSitePlusiP16989.

Miscellaneous databases

PMAP-CutDBP16989.

Expressioni

Tissue specificityi

Highly expressed in skeletal muscle and heart.

Gene expression databases

BgeeiENSG00000060138.
CleanExiHS_CSDA.
ExpressionAtlasiP16989. baseline and differential.
GenevisibleiP16989. HS.

Organism-specific databases

HPAiHPA034838.

Interactioni

Subunit structurei

Found in a mRNP complex with YBX2.By similarity

GO - Molecular functioni

Protein-protein interaction databases

BioGridi114101. 97 interactors.
DIPiDIP-42489N.
IntActiP16989. 43 interactors.
MINTiMINT-1152000.
STRINGi9606.ENSP00000228251.

Structurei

3D structure databases

ProteinModelPortaliP16989.
SMRiP16989.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini93 – 157CSDAdd BLAST65

Sequence similaritiesi

Contains 1 CSD (cold-shock) domain.Curated

Phylogenomic databases

eggNOGiKOG3070. Eukaryota.
COG1278. LUCA.
GeneTreeiENSGT00860000133704.
HOGENOMiHOG000116439.
HOVERGENiHBG008757.
InParanoidiP16989.
KOiK06099.
OMAiLSFNRND.
OrthoDBiEOG091G0W9A.
PhylomeDBiP16989.
TreeFamiTF317306.

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 (3)i

Sequence statusi: Complete.

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

This entry describes 3 isoformsi produced by alternative splicing. AlignAdd to basket

Note: Additional isoforms seem to exist.
Isoform 1 (identifier: P16989-1) [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
MSEAGEATTT TTTTLPQAPT EAAAAAPQDP APKSPVGSGA PQAAAPAPAA
60 70 80 90 100
HVAGNPGGDA APAATGTAAA ASLATAAGSE DAEKKVLATK VLGTVKWFNV
110 120 130 140 150
RNGYGFINRN DTKEDVFVHQ TAIKKNNPRK YLRSVGDGET VEFDVVEGEK
160 170 180 190 200
GAEAANVTGP DGVPVEGSRY AADRRRYRRG YYGRRRGPPR NYAGEEEEEG
210 220 230 240 250
SGSSEGFDPP ATDRQFSGAR NQLRRPQYRP QYRQRRFPPY HVGQTFDRRS
260 270 280 290 300
RVLPHPNRIQ AGEIGEMKDG VPEGAQLQGP VHRNPTYRPR YRSRGPPRPR
310 320 330 340 350
PAPAVGEAED KENQQATSGP NQPSVRRGYR RPYNYRRRPR PPNAPSQDGK
360 370
EAKAGEAPTE NPAPPTQQSS AE
Length:372
Mass (Da):40,090
Last modified:May 16, 2006 - v4
Checksum:iAA8517AC3B7D35CC
GO
Isoform 2 (identifier: P16989-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     192-260: Missing.

Show »
Length:303
Mass (Da):31,947
Checksum:i29E708D6FCB442CD
GO
Isoform 3 (identifier: P16989-3) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     340-372: RPPNAPSQDGKEAKAGEAPTENPAPPTQQSSAE → PSS

Show »
Length:342
Mass (Da):37,021
Checksum:i255258C4B4E80A4F
GO

Sequence cautioni

The sequence AAA35749 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.Curated

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_01311475T → A.3 PublicationsCorresponds to variant rs1126501dbSNPEnsembl.1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_001135192 – 260Missing in isoform 2. 1 PublicationAdd BLAST69
Alternative sequenceiVSP_001136340 – 372RPPNA…QSSAE → PSS in isoform 3. 1 PublicationAdd BLAST33

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M24069 mRNA. Translation: AAA35749.1. Different initiation.
L29071
, L29064, L29065, L29066, L29067, L29068, L29069, L29070 Genomic DNA. Translation: AAA79243.1.
X95325 mRNA. Translation: CAA64631.1.
X72712 mRNA. Translation: CAA51261.1.
AK314846 mRNA. Translation: BAG37363.1.
CH471094 Genomic DNA. Translation: EAW96201.1.
CH471094 Genomic DNA. Translation: EAW96203.1.
BC008801 mRNA. Translation: AAH08801.1.
BC015564 mRNA. Translation: AAH15564.1.
BC015913 mRNA. Translation: AAH15913.1.
BC021926 mRNA. Translation: AAH21926.1.
CCDSiCCDS44831.1. [P16989-2]
CCDS8630.1. [P16989-1]
PIRiI53354.
S69501.
RefSeqiNP_001138898.1. NM_001145426.1. [P16989-2]
NP_003642.3. NM_003651.4. [P16989-1]
UniGeneiHs.221889.

Genome annotation databases

EnsembliENST00000228251; ENSP00000228251; ENSG00000060138. [P16989-1]
ENST00000279550; ENSP00000279550; ENSG00000060138. [P16989-2]
GeneIDi8531.
KEGGihsa:8531.
UCSCiuc001qyt.4. human. [P16989-1]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M24069 mRNA. Translation: AAA35749.1. Different initiation.
L29071
, L29064, L29065, L29066, L29067, L29068, L29069, L29070 Genomic DNA. Translation: AAA79243.1.
X95325 mRNA. Translation: CAA64631.1.
X72712 mRNA. Translation: CAA51261.1.
AK314846 mRNA. Translation: BAG37363.1.
CH471094 Genomic DNA. Translation: EAW96201.1.
CH471094 Genomic DNA. Translation: EAW96203.1.
BC008801 mRNA. Translation: AAH08801.1.
BC015564 mRNA. Translation: AAH15564.1.
BC015913 mRNA. Translation: AAH15913.1.
BC021926 mRNA. Translation: AAH21926.1.
CCDSiCCDS44831.1. [P16989-2]
CCDS8630.1. [P16989-1]
PIRiI53354.
S69501.
RefSeqiNP_001138898.1. NM_001145426.1. [P16989-2]
NP_003642.3. NM_003651.4. [P16989-1]
UniGeneiHs.221889.

3D structure databases

ProteinModelPortaliP16989.
SMRiP16989.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi114101. 97 interactors.
DIPiDIP-42489N.
IntActiP16989. 43 interactors.
MINTiMINT-1152000.
STRINGi9606.ENSP00000228251.

PTM databases

iPTMnetiP16989.
PhosphoSitePlusiP16989.

Polymorphism and mutation databases

BioMutaiYBX3.
DMDMi97536050.

Proteomic databases

EPDiP16989.
MaxQBiP16989.
PaxDbiP16989.
PeptideAtlasiP16989.
PRIDEiP16989.

Protocols and materials databases

DNASUi8531.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000228251; ENSP00000228251; ENSG00000060138. [P16989-1]
ENST00000279550; ENSP00000279550; ENSG00000060138. [P16989-2]
GeneIDi8531.
KEGGihsa:8531.
UCSCiuc001qyt.4. human. [P16989-1]

Organism-specific databases

CTDi8531.
DisGeNETi8531.
GeneCardsiYBX3.
HGNCiHGNC:2428. YBX3.
HPAiHPA034838.
MIMi603437. gene.
neXtProtiNX_P16989.
OpenTargetsiENSG00000060138.
PharmGKBiPA26929.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG3070. Eukaryota.
COG1278. LUCA.
GeneTreeiENSGT00860000133704.
HOGENOMiHOG000116439.
HOVERGENiHBG008757.
InParanoidiP16989.
KOiK06099.
OMAiLSFNRND.
OrthoDBiEOG091G0W9A.
PhylomeDBiP16989.
TreeFamiTF317306.

Enzyme and pathway databases

BioCyciZFISH:ENSG00000060138-MONOMER.

Miscellaneous databases

GeneWikiiCSDA_(gene).
GenomeRNAii8531.
PMAP-CutDBP16989.
PROiP16989.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000060138.
CleanExiHS_CSDA.
ExpressionAtlasiP16989. baseline and differential.
GenevisibleiP16989. HS.

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_HUMAN
AccessioniPrimary (citable) accession number: P16989
Secondary accession number(s): B2RBW6
, Q14121, Q969N6, Q96B76
Entry historyi
Integrated into UniProtKB/Swiss-Prot: August 1, 1990
Last sequence update: May 16, 2006
Last modified: November 30, 2016
This is version 178 of the entry and version 4 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 12
    Human chromosome 12: 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

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.