Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.

Q9JKB3

- YBOX3_MOUSE

UniProt

Q9JKB3 - YBOX3_MOUSE

(max 400 entries)x

Your basket is currently empty.

Select item(s) and click on "Add to basket" to create your own collection here
(400 entries max)

Protein

Y-box-binding protein 3

Gene

Ybx3

Organism
Mus musculus (Mouse)
Status
Reviewed - Annotation score: 5 out of 5- 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

GO - Molecular functioni

  1. DNA binding Source: MGI
  2. mRNA 3'-UTR binding Source: MGI
  3. RNA polymerase II regulatory region sequence-specific DNA binding Source: NTNU_SB
  4. RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription Source: NTNU_SB
  5. single-stranded DNA binding Source: MGI

GO - Biological processi

  1. cellular hyperosmotic response Source: Ensembl
  2. cellular response to tumor necrosis factor Source: Ensembl
  3. fertilization Source: MGI
  4. in utero embryonic development Source: MGI
  5. male gonad development Source: MGI
  6. negative regulation of apoptotic process Source: MGI
  7. negative regulation of intrinsic apoptotic signaling pathway in response to osmotic stress Source: Ensembl
  8. negative regulation of necroptotic process Source: Ensembl
  9. negative regulation of skeletal muscle tissue development Source: MGI
  10. negative regulation of transcription from RNA polymerase II promoter Source: NTNU_SB
  11. positive regulation of organ growth Source: MGI
  12. spermatogenesis Source: MGI
Complete GO annotation...

Keywords - Molecular functioni

Repressor

Keywords - Biological processi

Transcription, Transcription regulation

Keywords - Ligandi

DNA-binding, RNA-binding

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 lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
ProteomesiUP000000589: Chromosome 6

Organism-specific databases

MGIiMGI:2137670. Ybx3.

Subcellular locationi

Cytoplasm 1 Publication. Nucleus By similarity

GO - Cellular componenti

  1. cytoplasm Source: MGI
  2. gap junction Source: MGI
  3. nucleus Source: MGI
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methioninei1 – 11RemovedBy similarity
Chaini2 – 361360Y-box-binding protein 3PRO_0000100215Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei2 – 21N-acetylserineBy similarity
Modified residuei126 – 1261PhosphoserineBy similarity
Modified residuei193 – 1931PhosphoserineBy similarity
Modified residuei195 – 1951PhosphoserineBy similarity
Modified residuei196 – 1961PhosphoserineBy similarity
Modified residuei313 – 3131PhosphoserineBy similarity

Keywords - PTMi

Acetylation, Phosphoprotein

Proteomic databases

MaxQBiQ9JKB3.
PaxDbiQ9JKB3.
PRIDEiQ9JKB3.

PTM databases

PhosphoSiteiQ9JKB3.

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

BgeeiQ9JKB3.
CleanExiMM_CSDA.
GenevestigatoriQ9JKB3.

Interactioni

Subunit structurei

Found in a mRNP complex with YBX2.1 Publication

Protein-protein interaction databases

BioGridi207989. 10 interactions.
DIPiDIP-42746N.
IntActiQ9JKB3. 7 interactions.
MINTiMINT-1891951.
STRINGi10090.ENSMUSP00000032309.

Structurei

3D structure databases

ProteinModelPortaliQ9JKB3.
SMRiQ9JKB3. Positions 76-152.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini82 – 15271CSDAdd
BLAST

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi17 – 6953Ala-richAdd
BLAST
Compositional biasi161 – 329169Arg-richAdd
BLAST

Sequence similaritiesi

Contains 1 CSD (cold-shock) domain.Curated

Phylogenomic databases

eggNOGiCOG1278.
GeneTreeiENSGT00390000009256.
HOGENOMiHOG000116439.
HOVERGENiHBG008757.
InParanoidiQ9JKB3.
KOiK06099.
OMAiLSFNRND.
OrthoDBiEOG7TBC44.
PhylomeDBiQ9JKB3.
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]

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. Align

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)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti237 – 2371T → N in AAG14418. (PubMed:10956549)Curated
Sequence conflicti306 – 3061A → G in AAF61741. (PubMed:10772793)Curated
Sequence conflicti349 – 3491E → A in AAF61741. (PubMed:10772793)Curated

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei184 – 25269Missing in isoform 2. 2 PublicationsVSP_013051Add
BLAST

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

Cross-referencesi

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 .
CCDSi CCDS20605.1. [Q9JKB3-2 ]
CCDS20606.1. [Q9JKB3-1 ]
RefSeqi NP_035863.1. NM_011733.2. [Q9JKB3-2 ]
NP_620817.2. NM_139117.2. [Q9JKB3-1 ]
UniGenei Mm.458000.

3D structure databases

ProteinModelPortali Q9JKB3.
SMRi Q9JKB3. Positions 76-152.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

BioGridi 207989. 10 interactions.
DIPi DIP-42746N.
IntActi Q9JKB3. 7 interactions.
MINTi MINT-1891951.
STRINGi 10090.ENSMUSP00000032309.

PTM databases

PhosphoSitei Q9JKB3.

Proteomic databases

MaxQBi Q9JKB3.
PaxDbi Q9JKB3.
PRIDEi Q9JKB3.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

Ensembli ENSMUST00000032309 ; ENSMUSP00000032309 ; ENSMUSG00000030189 . [Q9JKB3-1 ]
ENSMUST00000087865 ; ENSMUSP00000085172 ; ENSMUSG00000030189 . [Q9JKB3-2 ]
GeneIDi 56449.
KEGGi mmu:56449.
UCSCi uc009eis.1. mouse. [Q9JKB3-1 ]
uc009eit.1. mouse. [Q9JKB3-2 ]

Organism-specific databases

CTDi 8531.
MGIi MGI:2137670. Ybx3.

Phylogenomic databases

eggNOGi COG1278.
GeneTreei ENSGT00390000009256.
HOGENOMi HOG000116439.
HOVERGENi HBG008757.
InParanoidi Q9JKB3.
KOi K06099.
OMAi LSFNRND.
OrthoDBi EOG7TBC44.
PhylomeDBi Q9JKB3.
TreeFami TF317306.

Miscellaneous databases

NextBioi 312662.
PROi Q9JKB3.
SOURCEi Search...

Gene expression databases

Bgeei Q9JKB3.
CleanExi MM_CSDA.
Genevestigatori Q9JKB3.

Family and domain databases

Gene3Di 2.40.50.140. 1 hit.
InterProi IPR019844. Cold-shock_CS.
IPR011129. Cold_shock_prot.
IPR002059. CSP_DNA-bd.
IPR012340. NA-bd_OB-fold.
[Graphical view ]
Pfami PF00313. CSD. 1 hit.
[Graphical view ]
PRINTSi PR00050. COLDSHOCK.
SMARTi SM00357. CSP. 1 hit.
[Graphical view ]
SUPFAMi SSF50249. SSF50249. 1 hit.
PROSITEi PS00352. COLD_SHOCK. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  1. "A sequence-specific RNA binding complex expressed in murine germ cells contains MSY2 and MSY4."
    Davies H.G., Giorgini F., Fajardo M.A., Braun R.E.
    Dev. Biol. 221:87-100(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), IDENTIFICATION IN A MRNP COMPLEX WITH YBX2, RNA-BINDING, SUBCELLULAR LOCATION, TISSUE SPECIFICITY.
    Tissue: Testis.
  2. "Developmental expression of Y-box protein 1 mRNA and alternatively spliced Y-box protein 3 mRNAs in spermatogenic cells in mice."
    Mastrangelo M.-A., Kleene K.C.
    Mol. Hum. Reprod. 6:779-788(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORMS 1 AND 2), TISSUE SPECIFICITY.
    Strain: CD-1.
    Tissue: Testis.
  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] (ISOFORMS 1 AND 2).
    Strain: FVB/N.
    Tissue: Colon and Eye.
  4. "MSY2 and MSY4 bind a conserved sequence in the 3' untranslated region of protamine 1 mRNA in vitro and in vivo."
    Giorgini F., Davies H.G., Braun R.E.
    Mol. Cell. Biol. 21:7010-7019(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: RNA-BINDING.
  5. "Translational repression by MSY4 inhibits spermatid differentiation in mice."
    Giorgini F., Davies H.G., Braun R.E.
    Development 129:3669-3679(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION IN TRANSLATIONAL REPRESSION, TISSUE SPECIFICITY.

Entry informationi

Entry nameiYBOX3_MOUSE
AccessioniPrimary (citable) accession number: Q9JKB3
Secondary accession number(s): Q80WG4, Q9EQF7, Q9EQF8
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 15, 2005
Last sequence update: March 15, 2005
Last modified: November 26, 2014
This is version 103 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Miscellaneous

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

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. MGD cross-references
    Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot
  2. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3