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Protein

Nuclease-sensitive element-binding protein 1

Gene

YBX1

Organism
Gallus gallus (Chicken)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Experimental evidence at transcript leveli

Functioni

Mediates pre-mRNA alternative splicing regulation. Binds to splice sites in pre-mRNA and regulates splice site selection. Binds and stabilizes cytoplasmic mRNA. Binds to promoters that contain a Y-box (5'-CTGATTGGCCAA-3'). Regulates the transcription of numerous genes (By similarity). Component of the coding region determinant (CRD)-mediated complex that promotes mRNA stability (By similarity).By similarity

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Repressor

Keywords - Biological processi

mRNA processing, mRNA splicing, Transcription, Transcription regulation

Keywords - Ligandi

DNA-binding, RNA-binding

Enzyme and pathway databases

ReactomeiREACT_307022. mRNA Splicing - Major Pathway.

Names & Taxonomyi

Protein namesi
Recommended name:
Nuclease-sensitive element-binding protein 1
Alternative name(s):
Y-box transcription factor
Y-box-binding protein 1
Short name:
YB-1
Gene namesi
Name:YBX1
Synonyms:NSEP1, YB-1, YB1
OrganismiGallus gallus (Chicken)
Taxonomic identifieri9031 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiArchelosauriaArchosauriaDinosauriaSaurischiaTheropodaCoelurosauriaAvesNeognathaeGalloanseraeGalliformesPhasianidaePhasianinaeGallus
ProteomesiUP000000539 Componenti: Unplaced

Subcellular locationi

  • Cytoplasm
  • Nucleus
  • Cytoplasmic granule By similarity

  • Note: Shuttles between nucleus and cytoplasm. Predominantly cytoplasmic in proliferating cells. Cytotoxic stress and DNA damage enhance translocation to the nucleus. Probably localized in cytoplasmic mRNP granules containing untranslated mRNAs (By similarity).By similarity

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 321321Nuclease-sensitive element-binding protein 1PRO_0000100222Add
BLAST

Proteomic databases

PaxDbiQ06066.
PRIDEiQ06066.

Expressioni

Gene expression databases

ExpressionAtlasiQ06066. baseline.

Interactioni

Subunit structurei

Component of the CRD-mediated complex. Component of cytoplasmic messenger ribonucleoprotein particles (mRNPs). Component of the U11/U12 snRNPs that are part of the U12-type spliceosome. Can bind to DNA as a homomultimer (By similarity).By similarity

Protein-protein interaction databases

STRINGi9031.ENSGALP00000038395.

Structurei

3D structure databases

ProteinModelPortaliQ06066.
SMRiQ06066. Positions 49-126.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini58 – 12265CSDAdd
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni15 – 6854Interaction with ss-DNABy similarityAdd
BLAST

Sequence similaritiesi

Contains 1 CSD (cold-shock) domain.Curated

Phylogenomic databases

eggNOGiNOG326255.
HOGENOMiHOG000116439.
HOVERGENiHBG008757.
InParanoidiQ06066.

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.

Q06066-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSSEAETQPP AAPVPAAPAA APADSKPNGG SGNGSSGLAS AAPPAGGDKK
60 70 80 90 100
VIATKVLGTV KWFNVRNGYG FINRNDTKED VFVHQTAIKK NNPRKYLRSV
110 120 130 140 150
GDGETVEFDV VEGEKGAEAA NVTGPGGVPV QGSKYAADRN HYRRYPRRRG
160 170 180 190 200
PPRNYQQNYQ NSESGEKNEG AENIPEGQAQ QRRPYRRRRY PPYYMRRPYG
210 220 230 240 250
RRPQYSNPPV QGEIVEGADN QGAGEQGRPV RQNMYRGYRP RFRRGPPRQR
260 270 280 290 300
QPREDGNEED KENQGDETQG QQPPQRRYRR NFNYRRRRPE NPKPQDGKET
310 320
KTAEPPAENT SAPEAEQGGA E
Length:321
Mass (Da):35,799
Last modified:February 1, 1994 - v1
Checksum:i6496F306C1432274
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L13032 mRNA. Translation: AAA02573.1.
PIRiA48136.
UniGeneiGga.4145.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L13032 mRNA. Translation: AAA02573.1.
PIRiA48136.
UniGeneiGga.4145.

3D structure databases

ProteinModelPortaliQ06066.
SMRiQ06066. Positions 49-126.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi9031.ENSGALP00000038395.

Proteomic databases

PaxDbiQ06066.
PRIDEiQ06066.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Phylogenomic databases

eggNOGiNOG326255.
HOGENOMiHOG000116439.
HOVERGENiHBG008757.
InParanoidiQ06066.

Enzyme and pathway databases

ReactomeiREACT_307022. mRNA Splicing - Major Pathway.

Miscellaneous databases

PROiQ06066.

Gene expression databases

ExpressionAtlasiQ06066. baseline.

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

  1. "Cloning and characterization of chicken YB-1: regulation of expression in the liver."
    Grant C.E., Deeley R.G.
    Mol. Cell. Biol. 13:4186-4196(1993) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA], FUNCTION.
    Tissue: Embryonic liver.

Entry informationi

Entry nameiYBOX1_CHICK
AccessioniPrimary (citable) accession number: Q06066
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 1, 1994
Last sequence update: February 1, 1994
Last modified: May 27, 2015
This is version 95 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. 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.