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Q9JKB3 (YBOX3_MOUSE) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 100. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (2) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Alt products·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Y-box-binding protein 3
Alternative name(s):
Cold shock domain-containing protein A
DNA-binding protein A
Y-box protein 3
Gene names
Name:Ybx3
Synonyms:Csda, Msy4
OrganismMus musculus (Mouse) [Reference proteome]
Taxonomic identifier10090 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus

Protein attributes

Sequence length361 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

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. Ref.5

Subunit structure

Found in a mRNP complex with YBX2. Ref.1

Subcellular location

Cytoplasm. Nucleus By similarity Ref.1.

Tissue specificity

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 (Ref.2). Ref.1 Ref.2 Ref.5

Miscellaneous

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

Sequence similarities

Contains 1 CSD (cold-shock) domain.

Ontologies

Keywords
   Biological processTranscription
Transcription regulation
   Cellular componentCytoplasm
Nucleus
   Coding sequence diversityAlternative splicing
   LigandDNA-binding
RNA-binding
   Molecular functionRepressor
   PTMAcetylation
Phosphoprotein
   Technical termComplete proteome
Reference proteome
Gene Ontology (GO)
   Biological_processcellular hyperosmotic response

Inferred from electronic annotation. Source: Ensembl

cellular response to tumor necrosis factor

Inferred from electronic annotation. Source: Ensembl

fertilization

Inferred from mutant phenotype PubMed 16954378. Source: MGI

in utero embryonic development

Inferred from genetic interaction PubMed 16954378. Source: MGI

male gonad development

Inferred from mutant phenotype PubMed 16954378. Source: MGI

negative regulation of apoptotic process

Inferred from mutant phenotype PubMed 16954378. Source: MGI

negative regulation of intrinsic apoptotic signaling pathway in response to osmotic stress

Inferred from electronic annotation. Source: Ensembl

negative regulation of necrotic cell death

Inferred from electronic annotation. Source: Ensembl

negative regulation of skeletal muscle tissue development

Inferred from direct assay PubMed 18676817. Source: MGI

positive regulation of organ growth

Inferred from mutant phenotype PubMed 16954378. Source: MGI

regulation of transcription, DNA-templated

Inferred from electronic annotation. Source: UniProtKB-KW

spermatogenesis

Inferred from mutant phenotype PubMed 16954378. Source: MGI

transcription, DNA-templated

Inferred from electronic annotation. Source: UniProtKB-KW

   Cellular_componentcytoplasm

Inferred from direct assay Ref.1. Source: MGI

gap junction

Inferred from sequence orthology PubMed 16650609. Source: MGI

nucleus

Inferred from direct assay PubMed 12433987. Source: MGI

   Molecular_functionDNA binding

Inferred from direct assay PubMed 12433987. Source: MGI

mRNA 3'-UTR binding

Inferred from direct assay Ref.1. Source: MGI

protein binding

Inferred from physical interaction PubMed 11591653PubMed 19710015. Source: MGI

single-stranded DNA binding

Inferred from direct assay PubMed 18676817. Source: MGI

Complete GO annotation...

Alternative products

This entry describes 2 isoforms produced by alternative splicing. [Align] [Select]
Isoform 1 (identifier: Q9JKB3-1)

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.
Isoform 2 (identifier: Q9JKB3-2)

Also known as: Msy3s;

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

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Initiator methionine11Removed By similarity
Chain2 – 361360Y-box-binding protein 3
PRO_0000100215

Regions

Domain82 – 15271CSD
Compositional bias17 – 6953Ala-rich
Compositional bias161 – 329169Arg-rich

Amino acid modifications

Modified residue21N-acetylserine By similarity
Modified residue1261Phosphoserine By similarity
Modified residue1931Phosphoserine By similarity
Modified residue1951Phosphoserine By similarity
Modified residue1961Phosphoserine By similarity
Modified residue3131Phosphoserine By similarity

Natural variations

Alternative sequence184 – 25269Missing in isoform 2.
VSP_013051

Experimental info

Sequence conflict2371T → N in AAG14418. Ref.2
Sequence conflict3061A → G in AAF61741. Ref.1
Sequence conflict3491E → A in AAF61741. Ref.1

Sequences

Sequence LengthMass (Da)Tools
Isoform 1 (Msy3l) [UniParc].

Last modified March 15, 2005. Version 2.
Checksum: 5BAF6A144A127CEC

FASTA36138,814
        10         20         30         40         50         60 
MSEAGEATTG GTTLPQAAAD APAAAPPDPA PKSPAASGAP QAPAPAALLA GSPGGDAAPG 

        70         80         90        100        110        120 
PAPASSAPAG GEDAEKKVLA TKVLGTVKWF NVRNGYGFIN RNDTKEDVFV HQTAIKKNNP 

       130        140        150        160        170        180 
RKYLRSVGDG ETVEFDVVEG EKGAEAANVT GPDGVPVEGS RYAADRRRYR RGYYGRRRGP 

       190        200        210        220        230        240 
PRNYAGEEEE EGSGSSEGFE PPAADGQFSG ARNQLRRPQY RPPYRQRRFP PYHVGQTFDR 

       250        260        270        280        290        300 
RSRVFPHPNR MQAGEIGEMK DGVPEGTQLQ AHRNPTYRPR FRRGPARPRP APAIGEAEDK 

       310        320        330        340        350        360 
ENQQAANGPN QPSARRGFRR PYNYRRRSRP LNAVSQDGKE TKAGEAPTEN PAPATEQSSA 


E 

« Hide

Isoform 2 (Msy3s) [UniParc].

Checksum: 57B2898DF2D18155
Show »

FASTA29230,765

References

« Hide 'large scale' references
[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.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
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.
CCDSCCDS20605.1. [Q9JKB3-2]
CCDS20606.1. [Q9JKB3-1]
RefSeqNP_035863.1. NM_011733.2. [Q9JKB3-2]
NP_620817.2. NM_139117.2. [Q9JKB3-1]
UniGeneMm.458000.

3D structure databases

ProteinModelPortalQ9JKB3.
SMRQ9JKB3. Positions 76-152.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid207989. 10 interactions.
DIPDIP-42746N.
IntActQ9JKB3. 7 interactions.
MINTMINT-1891951.
STRING10090.ENSMUSP00000032309.

PTM databases

PhosphoSiteQ9JKB3.

Proteomic databases

MaxQBQ9JKB3.
PaxDbQ9JKB3.
PRIDEQ9JKB3.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENSMUST00000032309; ENSMUSP00000032309; ENSMUSG00000030189. [Q9JKB3-1]
ENSMUST00000087865; ENSMUSP00000085172; ENSMUSG00000030189. [Q9JKB3-2]
GeneID56449.
KEGGmmu:56449.
UCSCuc009eis.1. mouse. [Q9JKB3-1]
uc009eit.1. mouse. [Q9JKB3-2]

Organism-specific databases

CTD8531.
MGIMGI:2137670. Ybx3.

Phylogenomic databases

eggNOGCOG1278.
GeneTreeENSGT00390000009256.
HOGENOMHOG000116439.
HOVERGENHBG008757.
InParanoidQ9JKB3.
KOK06099.
OMALSFNRND.
OrthoDBEOG7TBC44.
PhylomeDBQ9JKB3.
TreeFamTF317306.

Gene expression databases

BgeeQ9JKB3.
CleanExMM_CSDA.
GenevestigatorQ9JKB3.

Family and domain databases

Gene3D2.40.50.140. 1 hit.
InterProIPR019844. Cold-shock_CS.
IPR011129. Cold_shock_prot.
IPR002059. CSP_DNA-bd.
IPR012340. NA-bd_OB-fold.
[Graphical view]
PfamPF00313. CSD. 1 hit.
[Graphical view]
PRINTSPR00050. COLDSHOCK.
SMARTSM00357. CSP. 1 hit.
[Graphical view]
SUPFAMSSF50249. SSF50249. 1 hit.
PROSITEPS00352. COLD_SHOCK. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

ChiTaRSCSDA. mouse.
NextBio312662.
PROQ9JKB3.
SOURCESearch...

Entry information

Entry nameYBOX3_MOUSE
AccessionPrimary (citable) accession number: Q9JKB3
Secondary accession number(s): Q80WG4, Q9EQF7, Q9EQF8
Entry history
Integrated into UniProtKB/Swiss-Prot: March 15, 2005
Last sequence update: March 15, 2005
Last modified: July 9, 2014
This is version 100 of the entry and version 2 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

MGD cross-references

Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot