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Entry version 160 (16 Oct 2019)
Sequence version 3 (23 Jan 2007)
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Protein

Y-box-binding protein 1

Gene

Ybx1

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

Annotation score:5 out of 5

<p>The annotation score provides a heuristic measure of the annotation content of a UniProtKB entry or proteome. This score <strong>cannot</strong> be used as a measure of the accuracy of the annotation as we cannot define the ‘correct annotation’ for any given protein.<p><a href='/help/annotation_score' target='_top'>More...</a></p>
-Experimental evidence at protein leveli <p>This indicates the type of evidence that supports the existence of the protein. Note that the ‘protein existence’ evidence does not give information on the accuracy or correctness of the sequence(s) displayed.<p><a href='/help/protein_existence' target='_top'>More...</a></p>

<p>This section provides any useful information about the protein, mostly biological knowledge.<p><a href='/help/function_section' target='_top'>More...</a></p>Functioni

DNA- and RNA-binding protein involved in various processes, such as translational repression, RNA stabilization, mRNA splicing, DNA repair and transcription regulation (PubMed:8505341, PubMed:29712925). Predominantly acts as a RNA-binding protein: binds preferentially to the 5'-[CU]CUGCG-3' RNA motif and specifically recognizes mRNA transcripts modified by C5-methylcytosine (m5C) (By similarity). Promotes mRNA stabilization: acts by binding to m5C-containing mRNAs and recruiting the mRNA stability maintainer ELAVL1, thereby preventing mRNA decay (By similarity). Component of the CRD-mediated complex that promotes MYC mRNA stability (By similarity). Contributes to the regulation of translation by modulating the interaction between the mRNA and eukaryotic initiation factors (By similarity). Plays a key role in RNA composition of extracellular exosomes by defining the sorting of small non-coding RNAs, such as tRNAs, Y RNAs, Vault RNAs and miRNAs (By similarity). Probably sorts RNAs in exosomes by recognizing and binding C5-methylcytosine (m5C)-containing RNAs (By similarity). Acts as a key effector of epidermal progenitors by preventing epidermal progenitor senescence: acts by regulating the translation of a senescence-associated subset of cytokine mRNAs, possibly by binding to m5C-containing mRNAs (PubMed:29712925). Also involved in pre-mRNA alternative splicing regulation: binds to splice sites in pre-mRNA and regulates splice site selection (By similarity). Also able to bind DNA: regulates transcription of the multidrug resistance gene MDR1 is enhanced in presence of the APEX1 acetylated form at 'Lys-6' and 'Lys-7' (By similarity). Binds to promoters that contain a Y-box (5'-CTGATTGGCCAA-3'), such as MDR1 and HLA class II genes (By similarity). Promotes separation of DNA strands that contain mismatches or are modified by cisplatin (By similarity). Has endonucleolytic activity and can introduce nicks or breaks into double-stranded DNA, suggesting a role in DNA repair (By similarity). The secreted form acts as an extracellular mitogen and stimulates cell migration and proliferation (By similarity).By similarity2 Publications

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection describes interesting single amino acid sites on the sequence that are not defined in any other subsection. This subsection can be displayed in different sections (‘Function’, ‘PTM / Processing’, ‘Pathology and Biotech’) according to its content.<p><a href='/help/site' target='_top'>More...</a></p>Sitei63Important for C5-methylcytosine-recognitionBy similarity1

<p>The <a href="http://www.geneontology.org/">Gene Ontology (GO)</a> project provides a set of hierarchical controlled vocabulary split into 3 categories:<p><a href='/help/gene_ontology' target='_top'>More...</a></p>GO - Molecular functioni

GO - Biological processi

<p>UniProtKB Keywords constitute a <a href="http://www.uniprot.org/keywords">controlled vocabulary</a> with a hierarchical structure. Keywords summarise the content of a UniProtKB entry and facilitate the search for proteins of interest.<p><a href='/help/keywords' target='_top'>More...</a></p>Keywordsi

Molecular functionActivator, DNA-binding, Mitogen, Repressor, RNA-binding
Biological processmRNA processing, mRNA splicing, Transcription, Transcription regulation

Enzyme and pathway databases

Reactome - a knowledgebase of biological pathways and processes

More...
Reactomei
R-MMU-72163 mRNA Splicing - Major Pathway
R-MMU-72165 mRNA Splicing - Minor Pathway
R-MMU-9017802 Noncanonical activation of NOTCH3

<p>This section provides information about the protein and gene name(s) and synonym(s) and about the organism that is the source of the protein sequence.<p><a href='/help/names_and_taxonomy_section' target='_top'>More...</a></p>Names & Taxonomyi

<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section provides an exhaustive list of all names of the protein, from commonly used to obsolete, to allow unambiguous identification of a protein.<p><a href='/help/protein_names' target='_top'>More...</a></p>Protein namesi
Recommended name:
Y-box-binding protein 11 Publication
Short name:
YB-11 Publication
Alternative name(s):
CCAAT-binding transcription factor I subunit A
Short name:
CBF-A
DNA-binding protein B1 Publication
Short name:
DBPB1 Publication
Enhancer factor I subunit ABy similarity
Short name:
EFI-ABy similarity
Nuclease-sensitive element-binding protein 1By similarity
Y-box transcription factor
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section indicates the name(s) of the gene(s) that code for the protein sequence(s) described in the entry. Four distinct tokens exist: ‘Name’, ‘Synonyms’, ‘Ordered locus names’ and ‘ORF names’.<p><a href='/help/gene_name' target='_top'>More...</a></p>Gene namesi
Name:Ybx1Imported
Synonyms:Msy-11 Publication, Msy11 Publication, Nsep1By similarity, Yb11 Publication
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section provides information on the name(s) of the organism that is the source of the protein sequence.<p><a href='/help/organism-name' target='_top'>More...</a></p>OrganismiMus musculus (Mouse)
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section shows the unique identifier assigned by the NCBI to the source organism of the protein. This is known as the ‘taxonomic identifier’ or ‘taxid’.<p><a href='/help/taxonomic_identifier' target='_top'>More...</a></p>Taxonomic identifieri10090 [NCBI]
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section contains the taxonomic hierarchical classification lineage of the source organism. It lists the nodes as they appear top-down in the taxonomic tree, with the more general grouping listed first.<p><a href='/help/taxonomic_lineage' target='_top'>More...</a></p>Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaMyomorphaMuroideaMuridaeMurinaeMusMus
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section is present for entries that are part of a <a href="http://www.uniprot.org/proteomes">proteome</a>, i.e. of a set of proteins thought to be expressed by organisms whose genomes have been completely sequenced.<p><a href='/help/proteomes_manual' target='_top'>More...</a></p>Proteomesi
  • UP000000589 <p>A UniProt <a href="http://www.uniprot.org/manual/proteomes_manual">proteome</a> can consist of several components. <br></br>The component name refers to the genomic component encoding a set of proteins.<p><a href='/help/proteome_component' target='_top'>More...</a></p> Componenti: Chromosome 4

Organism-specific databases

Mouse genome database (MGD) from Mouse Genome Informatics (MGI)

More...
MGIi
MGI:99146 Ybx1

<p>This section provides information on the location and the topology of the mature protein in the cell.<p><a href='/help/subcellular_location_section' target='_top'>More...</a></p>Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte & Seán O’Donoghue; Source: COMPARTMENTS

Keywords - Cellular componenti

Cytoplasm, Nucleus, Secreted

<p>This section provides information on the disease(s) and phenotype(s) associated with a protein.<p><a href='/help/pathology_and_biotech_section' target='_top'>More...</a></p>Pathology & Biotechi

<p>This subsection of the ‘Pathology and Biotech’ section describes the in vivo effects caused by ablation of the gene (or one or more transcripts) coding for the protein described in the entry. This includes gene knockout and knockdown, provided experiments have been performed in the context of a whole organism or a specific tissue, and not at the single-cell level.<p><a href='/help/disruption_phenotype' target='_top'>More...</a></p>Disruption phenotypei

Perinatal lethality (PubMed:15899865). Embryos develop normally up to embryonic day 13.5 (E13.5) and then show progressive mortality (PubMed:15899865). Embryos display severe growth retardation caused by hypoplasia in multiple organs (PubMed:15899865). Fibroblasts show a normal rate of protein synthesis and minimal alterations in the transcriptome and proteome (PubMed:15899865). Mice show defects in the architecture of the skin characterized by markedly reduced thickness of the epidermis and delayed onset of the placodes to hair follicle transition (PubMed:29712925).2 Publications

<p>This section describes post-translational modifications (PTMs) and/or processing events.<p><a href='/help/ptm_processing_section' target='_top'>More...</a></p>PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/ptm_processing_section">PTM / Processing</a> section indicates that the initiator methionine is cleaved from the mature protein.<p><a href='/help/init_met' target='_top'>More...</a></p>Initiator methionineiRemovedBy similarity
<p>This subsection of the ‘PTM / Processing’ section describes the extent of a polypeptide chain in the mature protein following processing.<p><a href='/help/chain' target='_top'>More...</a></p>ChainiPRO_00001002202 – 322Y-box-binding protein 1Add BLAST321

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘PTM / Processing’ section specifies the position and type of each modified residue excluding <a href="http://www.uniprot.org/manual/lipid">lipids</a>, <a href="http://www.uniprot.org/manual/carbohyd">glycans</a> and <a href="http://www.uniprot.org/manual/crosslnk">protein cross-links</a>.<p><a href='/help/mod_res' target='_top'>More...</a></p>Modified residuei2N-acetylserineBy similarity1
<p>This subsection of the <a href="http://www.uniprot.org/help/ptm_processing_section">PTM / Processing</a> section describes <strong>covalent linkages</strong> of various types formed <strong>between two proteins (interchain cross-links)</strong> or <strong>between two parts of the same protein (intrachain cross-links)</strong>, except the disulfide bonds that are annotated in the <a href="http://www.uniprot.org/manual/disulfid">'Disulfide bond'</a> subsection.<p><a href='/help/crosslnk' target='_top'>More...</a></p>Cross-linki24Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)By similarity
Modified residuei100Phosphoserine; by PKB/AKT1By similarity1
Cross-linki135Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)By similarity
Modified residuei160PhosphotyrosineBy similarity1
Modified residuei163PhosphoserineCombined sources1
Modified residuei165PhosphoserineBy similarity1
Modified residuei172PhosphoserineCombined sources1
Modified residuei174PhosphoserineCombined sources1
Modified residuei299N6-acetyllysineBy similarity1
Modified residuei302N6-acetyllysineBy similarity1
Modified residuei312PhosphoserineCombined sources1

<p>This subsection of the <a href="http://www.uniprot.org/help/ptm_processing_section">PTM/processing</a> section describes post-translational modifications (PTMs). This subsection <strong>complements</strong> the information provided at the sequence level or describes modifications for which <strong>position-specific data is not yet available</strong>.<p><a href='/help/post-translational_modification' target='_top'>More...</a></p>Post-translational modificationi

Ubiquitinated by RBBP6; leading to a decrease of YBX1 transcactivational ability.By similarity
In the absence of phosphorylation the protein is retained in the cytoplasm.By similarity
Cleaved by a 20S proteasomal protease in response to agents that damage DNA. Cleavage takes place in the absence of ubiquitination and ATP. The resulting N-terminal fragment accumulates in the nucleus (By similarity).By similarity

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sitei217 – 218Cleavage; by 20S proteasomal proteaseBy similarity2

Keywords - PTMi

Acetylation, Isopeptide bond, Phosphoprotein, Ubl conjugation

Proteomic databases

Encyclopedia of Proteome Dynamics

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EPDi
P62960

jPOST - Japan Proteome Standard Repository/Database

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jPOSTi
P62960

PaxDb, a database of protein abundance averages across all three domains of life

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PaxDbi
P62960

PeptideAtlas

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PeptideAtlasi
P62960

PRoteomics IDEntifications database

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PRIDEi
P62960

PTM databases

iPTMnet integrated resource for PTMs in systems biology context

More...
iPTMneti
P62960

Comprehensive resource for the study of protein post-translational modifications (PTMs) in human, mouse and rat.

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PhosphoSitePlusi
P62960

SwissPalm database of S-palmitoylation events

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SwissPalmi
P62960

<p>This section provides information on the expression of a gene at the mRNA or protein level in cells or in tissues of multicellular organisms.<p><a href='/help/expression_section' target='_top'>More...</a></p>Expressioni

<p>This subsection of the ‘Expression’ section provides information on the expression of a gene at the mRNA or protein level in cells or in tissues of multicellular organisms. By default, the information is derived from experiments at the mRNA level, unless specified ‘at protein level’. <br></br>Examples: <a href="http://www.uniprot.org/uniprot/P92958#expression">P92958</a>, <a href="http://www.uniprot.org/uniprot/Q8TDN4#expression">Q8TDN4</a>, <a href="http://www.uniprot.org/uniprot/O14734#expression">O14734</a><p><a href='/help/tissue_specificity' target='_top'>More...</a></p>Tissue specificityi

Expressed at high levels in the testis (PubMed:8505341). Present in the mRNP particles that mediate the storage and masking of mRNAs during spermiogenesis (PubMed:8505341). In epidermis, expression is restricted to the cycling keratinocyte progenitors (PubMed:29712925).2 Publications

<p>This subsection of the ‘Expression’ section provides information on the expression of the gene product at various stages of a cell, tissue or organism development. By default, the information is derived from experiments at the mRNA level, unless specified ‘at the protein level’.<p><a href='/help/developmental_stage' target='_top'>More...</a></p>Developmental stagei

Found at very low levels at day 10 and levels increase at day 15 and persist throughout adulthood.1 Publication

Gene expression databases

Bgee dataBase for Gene Expression Evolution

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Bgeei
ENSMUSG00000028639 Expressed in 304 organ(s), highest expression level in pharyngeal arch 1

ExpressionAtlas, Differential and Baseline Expression

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ExpressionAtlasi
P62960 baseline and differential

Genevisible search portal to normalized and curated expression data from Genevestigator

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Genevisiblei
P62960 MM

<p>This section provides information on the quaternary structure of a protein and on interaction(s) with other proteins or protein complexes.<p><a href='/help/interaction_section' target='_top'>More...</a></p>Interactioni

<p>This subsection of the <a href="http://www.uniprot.org/help/interaction_section">'Interaction'</a> section provides information about the protein quaternary structure and interaction(s) with other proteins or protein complexes (with the exception of physiological receptor-ligand interactions which are annotated in the <a href="http://www.uniprot.org/help/function_section">'Function'</a> section).<p><a href='/help/subunit_structure' target='_top'>More...</a></p>Subunit structurei

Homodimer in the presence of ATP (PubMed:10318844, PubMed:8505341).

Component of the coding region determinant (CRD)-mediated complex, composed of DHX9, HNRNPU, IGF2BP1, SYNCRIP and YBX1 (By similarity).

Identified in a IGF2BP1-dependent mRNP granule complex containing untranslated mRNAs (By similarity).

Component of the U11/U12 snRNPs that are part of the U12-type spliceosome (By similarity).

Identified in a histone pre-mRNA complex, at least composed of ERI1, LSM11, SLBP, SNRPB, SYNCRIP and YBX1 (PubMed:11162447).

Interacts with IGF2BP1 and RBBP6 (By similarity).

Component of cytoplasmic messenger ribonucleoprotein particles (mRNPs) (By similarity).

Interacts with AKT1, MBNL1, SFRS9, SFRS12, ALYREF/THOC4, MSH2, XRCC5, WRN and NCL (By similarity).

Interacts (via C-terminus) with APEX1 (via N-terminus); the interaction is increased with APEX1 acetylated at 'Lys-6' and 'Lys-7' (By similarity).

Interacts with AGO1 and AGO2 (By similarity).

Interacts with ANKRD2 (By similarity).

Interacts with DERA (By similarity).

Interacts with FMR1; this interaction occurs in association with polyribosome (PubMed:11162447).

Interacts with ZBTB7B (PubMed:28784777).

Interacts with HDGF.

Interacts with ELAVL1; leading to ELAVL1 recruitment on C5-methylcytosine (m5C)-containing mRNAs and subsequent mRNA stability (By similarity).

By similarity4 Publications

GO - Molecular functioni

Protein-protein interaction databases

The Biological General Repository for Interaction Datasets (BioGrid)

More...
BioGridi
204613, 69 interactors

ComplexPortal: manually curated resource of macromolecular complexes

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ComplexPortali
CPX-1089 CRD-mediated mRNA stability complex

Database of interacting proteins

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DIPi
DIP-34256N

Protein interaction database and analysis system

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IntActi
P62960, 75 interactors

Molecular INTeraction database

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MINTi
P62960

STRING: functional protein association networks

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STRINGi
10090.ENSMUSP00000078589

<p>This section provides information on the tertiary and secondary structure of a protein.<p><a href='/help/structure_section' target='_top'>More...</a></p>Structurei

3D structure databases

SWISS-MODEL Repository - a database of annotated 3D protein structure models

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SMRi
P62960

Database of comparative protein structure models

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ModBasei
Search...

<p>This section provides information on sequence similarities with other proteins and the domain(s) present in a protein.<p><a href='/help/family_and_domains_section' target='_top'>More...</a></p>Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/family_and_domains_section">Family and Domains</a> section describes the position and type of a domain, which is defined as a specific combination of secondary structures organized into a characteristic three-dimensional structure or fold.<p><a href='/help/domain' target='_top'>More...</a></p>Domaini59 – 123CSDAdd BLAST65

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘Family and Domains’ section describes a region of interest that cannot be described in other subsections.<p><a href='/help/region' target='_top'>More...</a></p>Regioni16 – 69Interaction with ss-DNABy similarityAdd BLAST54
Regioni63 – 68C5-methylcytosine bindingBy similarity6

<p>This subsection of the ‘Family and domains’ section provides general information on the biological role of a domain. The term ‘domain’ is intended here in its wide acceptation, it may be a structural domain, a transmembrane region or a functional domain. Several domains are described in this subsection.<p><a href='/help/domain_cc' target='_top'>More...</a></p>Domaini

In the CSD domain, Trp-63 specifically recognizes C5-methylcytosine (m5C) modification through its indole ring.By similarity

<p>This subsection of the ‘Family and domains’ section provides information about the sequence similarity with other proteins.<p><a href='/help/sequence_similarities' target='_top'>More...</a></p>Sequence similaritiesi

Belongs to the YBX1 family.Curated

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

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eggNOGi
KOG3070 Eukaryota
COG1278 LUCA

Ensembl GeneTree

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GeneTreei
ENSGT00940000153341

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

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HOGENOMi
HOG000116439

InParanoid: Eukaryotic Ortholog Groups

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InParanoidi
P62960

KEGG Orthology (KO)

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KOi
K09276

Identification of Orthologs from Complete Genome Data

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OMAi
GQQRRPY

Database of Orthologous Groups

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OrthoDBi
1431946at2759

Database for complete collections of gene phylogenies

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PhylomeDBi
P62960

TreeFam database of animal gene trees

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TreeFami
TF317306

Family and domain databases

Conserved Domains Database

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CDDi
cd04458 CSP_CDS, 1 hit

Integrated resource of protein families, domains and functional sites

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InterProi
View protein in InterPro
IPR011129 CSD
IPR019844 CSD_1
IPR002059 CSP_DNA-bd
IPR012340 NA-bd_OB-fold

Pfam protein domain database

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Pfami
View protein in Pfam
PF00313 CSD, 1 hit

Protein Motif fingerprint database; a protein domain database

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PRINTSi
PR00050 COLDSHOCK

Simple Modular Architecture Research Tool; a protein domain database

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SMARTi
View protein in SMART
SM00357 CSP, 1 hit

Superfamily database of structural and functional annotation

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SUPFAMi
SSF50249 SSF50249, 1 hit

PROSITE; a protein domain and family database

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PROSITEi
View protein in PROSITE
PS00352 CSD_1, 1 hit
PS51857 CSD_2, 1 hit

<p>This section displays by default the canonical protein sequence and upon request all isoforms described in the entry. It also includes information pertinent to the sequence(s), including <a href="http://www.uniprot.org/help/sequence_length">length</a> and <a href="http://www.uniprot.org/help/sequences">molecular weight</a>. The information is filed in different subsections. The current subsections and their content are listed below:<p><a href='/help/sequences_section' target='_top'>More...</a></p>Sequence (1+)i

<p>This subsection of the <a href="http://www.uniprot.org/help/sequences_section">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical_and_isoforms">canonical sequence</a> displayed by default in the entry is complete or not.<p><a href='/help/sequence_status' target='_top'>More...</a></p>Sequence statusi: Complete.

<p>This subsection of the <a href="http://www.uniprot.org/help/sequences_section">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical_and_isoforms">canonical sequence</a> displayed by default in the entry is in its mature form or if it represents the precursor.<p><a href='/help/sequence_processing' target='_top'>More...</a></p>Sequence processingi: The displayed sequence is further processed into a mature form.

This entry has 1 described isoform and 1 potential isoform that is computationally mapped.Show allAlign All

P62960-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MSSEAETQQP PAAPAAALSA ADTKPGSTGS GAGSGGPGGL TSAAPAGGDK
60 70 80 90 100
KVIATKVLGT VKWFNVRNGY GFINRNDTKE DVFVHQTAIK KNNPRKYLRS
110 120 130 140 150
VGDGETVEFD VVEGEKGAEA ANVTGPGGVP VQGSKYAADR NHYRRYPRRR
160 170 180 190 200
GPPRNYQQNY QNSESGEKNE GSESAPEGQA QQRRPYRRRR FPPYYMRRPY
210 220 230 240 250
ARRPQYSNPP VQGEVMEGAD NQGAGEQGRP VRQNMYRGYR PRFRRGPPRQ
260 270 280 290 300
RQPREDGNEE DKENQGDETQ GQQPPQRRYR RNFNYRRRRP ENPKPQDGKE
310 320
TKAADPPAEN SSAPEAEQGG AE
Length:322
Mass (Da):35,730
Last modified:January 23, 2007 - v3
<p>The checksum is a form of redundancy check that is calculated from the sequence. It is useful for tracking sequence updates.</p> <p>It should be noted that while, in theory, two different sequences could have the same checksum value, the likelihood that this would happen is extremely low.</p> <p>However UniProtKB may contain entries with identical sequences in case of multiple genes (paralogs).</p> <p>The checksum is computed as the sequence 64-bit Cyclic Redundancy Check value (CRC64) using the generator polynomial: x<sup>64</sup> + x<sup>4</sup> + x<sup>3</sup> + x + 1. The algorithm is described in the ISO 3309 standard. </p> <p class="publication">Press W.H., Flannery B.P., Teukolsky S.A. and Vetterling W.T.<br /> <strong>Cyclic redundancy and other checksums</strong><br /> <a href="http://www.nrbook.com/b/bookcpdf.php">Numerical recipes in C 2nd ed., pp896-902, Cambridge University Press (1993)</a>)</p> Checksum:iC6667CF7CA10D45D
GO

<p>In eukaryotic reference proteomes, unreviewed entries that are likely to belong to the same gene are computationally mapped, based on gene identifiers from Ensembl, EnsemblGenomes and model organism databases.<p><a href='/help/gene_centric_isoform_mapping' target='_top'>More...</a></p>Computationally mapped potential isoform sequencesi

There is 1 potential isoform mapped to this entry.BLASTAlignShow allAdd to basket
EntryEntry nameProtein names
Gene namesLengthAnnotation
A2BGG7A2BGG7_MOUSE
Nuclease-sensitive element-binding ...
Ybx1
214Annotation score:

Annotation score:1 out of 5

<p>The annotation score provides a heuristic measure of the annotation content of a UniProtKB entry or proteome. This score <strong>cannot</strong> be used as a measure of the accuracy of the annotation as we cannot define the ‘correct annotation’ for any given protein.<p><a href='/help/annotation_score' target='_top'>More...</a></p>

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘Sequence’ section reports difference(s) between the canonical sequence (displayed by default in the entry) and the different sequence submissions merged in the entry. These various submissions may originate from different sequencing projects, different types of experiments, or different biological samples. Sequence conflicts are usually of unknown origin.<p><a href='/help/conflict' target='_top'>More...</a></p>Sequence conflicti29G → A in AAA63390 (PubMed:1622927).Curated1
Sequence conflicti43 – 45AAP → RR in CAA40847 (PubMed:1741293).Curated3
Sequence conflicti238G → P in CAA40847 (PubMed:1741293).Curated1

Sequence databases

Select the link destinations:

EMBL nucleotide sequence database

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EMBLi

GenBank nucleotide sequence database

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GenBanki

DNA Data Bank of Japan; a nucleotide sequence database

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DDBJi
Links Updated
M60419 mRNA Translation: AAA40577.1
M62867 mRNA Translation: AAA63390.1
X57621 mRNA Translation: CAA40847.1
BC013450 mRNA Translation: AAH13450.1
BC013620 mRNA Translation: AAH13620.1
BC029747 mRNA Translation: AAH29747.1
BC031472 mRNA Translation: AAH31472.1
BC061634 mRNA Translation: AAH61634.1

The Consensus CDS (CCDS) project

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CCDSi
CCDS18579.1

Protein sequence database of the Protein Information Resource

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PIRi
I58195

NCBI Reference Sequences

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RefSeqi
NP_035862.2, NM_011732.2

Genome annotation databases

Ensembl eukaryotic genome annotation project

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Ensembli
ENSMUST00000079644; ENSMUSP00000078589; ENSMUSG00000028639

Database of genes from NCBI RefSeq genomes

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GeneIDi
22608

KEGG: Kyoto Encyclopedia of Genes and Genomes

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KEGGi
mmu:22608

UCSC genome browser

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UCSCi
uc008ulu.1 mouse

<p>This section provides links to proteins that are similar to the protein sequence(s) described in this entry at different levels of sequence identity thresholds (100%, 90% and 50%) based on their membership in UniProt Reference Clusters (<a href="http://www.uniprot.org/help/uniref">UniRef</a>).<p><a href='/help/similar_proteins_section' target='_top'>More...</a></p>Similar proteinsi

<p>This section is used to point to information related to entries and found in data collections other than UniProtKB.<p><a href='/help/cross_references_section' target='_top'>More...</a></p>Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M60419 mRNA Translation: AAA40577.1
M62867 mRNA Translation: AAA63390.1
X57621 mRNA Translation: CAA40847.1
BC013450 mRNA Translation: AAH13450.1
BC013620 mRNA Translation: AAH13620.1
BC029747 mRNA Translation: AAH29747.1
BC031472 mRNA Translation: AAH31472.1
BC061634 mRNA Translation: AAH61634.1
CCDSiCCDS18579.1
PIRiI58195
RefSeqiNP_035862.2, NM_011732.2

3D structure databases

SMRiP62960
ModBaseiSearch...

Protein-protein interaction databases

BioGridi204613, 69 interactors
ComplexPortaliCPX-1089 CRD-mediated mRNA stability complex
DIPiDIP-34256N
IntActiP62960, 75 interactors
MINTiP62960
STRINGi10090.ENSMUSP00000078589

PTM databases

iPTMnetiP62960
PhosphoSitePlusiP62960
SwissPalmiP62960

Proteomic databases

EPDiP62960
jPOSTiP62960
PaxDbiP62960
PeptideAtlasiP62960
PRIDEiP62960

Genome annotation databases

EnsembliENSMUST00000079644; ENSMUSP00000078589; ENSMUSG00000028639
GeneIDi22608
KEGGimmu:22608
UCSCiuc008ulu.1 mouse

Organism-specific databases

Comparative Toxicogenomics Database

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CTDi
4904
MGIiMGI:99146 Ybx1

Phylogenomic databases

eggNOGiKOG3070 Eukaryota
COG1278 LUCA
GeneTreeiENSGT00940000153341
HOGENOMiHOG000116439
InParanoidiP62960
KOiK09276
OMAiGQQRRPY
OrthoDBi1431946at2759
PhylomeDBiP62960
TreeFamiTF317306

Enzyme and pathway databases

ReactomeiR-MMU-72163 mRNA Splicing - Major Pathway
R-MMU-72165 mRNA Splicing - Minor Pathway
R-MMU-9017802 Noncanonical activation of NOTCH3

Miscellaneous databases

ChiTaRS: a database of human, mouse and fruit fly chimeric transcripts and RNA-sequencing data

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ChiTaRSi
Ybx1 mouse

Protein Ontology

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PROi
PR:P62960

The Stanford Online Universal Resource for Clones and ESTs

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SOURCEi
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Gene expression databases

BgeeiENSMUSG00000028639 Expressed in 304 organ(s), highest expression level in pharyngeal arch 1
ExpressionAtlasiP62960 baseline and differential
GenevisibleiP62960 MM

Family and domain databases

CDDicd04458 CSP_CDS, 1 hit
InterProiView protein in InterPro
IPR011129 CSD
IPR019844 CSD_1
IPR002059 CSP_DNA-bd
IPR012340 NA-bd_OB-fold
PfamiView protein in Pfam
PF00313 CSD, 1 hit
PRINTSiPR00050 COLDSHOCK
SMARTiView protein in SMART
SM00357 CSP, 1 hit
SUPFAMiSSF50249 SSF50249, 1 hit
PROSITEiView protein in PROSITE
PS00352 CSD_1, 1 hit
PS51857 CSD_2, 1 hit

ProtoNet; Automatic hierarchical classification of proteins

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ProtoNeti
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MobiDB: a database of protein disorder and mobility annotations

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MobiDBi
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<p>This section provides general information on the entry.<p><a href='/help/entry_information_section' target='_top'>More...</a></p>Entry informationi

<p>This subsection of the ‘Entry information’ section provides a mnemonic identifier for a UniProtKB entry, but it is not a stable identifier. Each reviewed entry is assigned a unique entry name upon integration into UniProtKB/Swiss-Prot.<p><a href='/help/entry_name' target='_top'>More...</a></p>Entry nameiYBOX1_MOUSE
<p>This subsection of the ‘Entry information’ section provides one or more accession number(s). These are stable identifiers and should be used to cite UniProtKB entries. Upon integration into UniProtKB, each entry is assigned a unique accession number, which is called ‘Primary (citable) accession number’.<p><a href='/help/accession_numbers' target='_top'>More...</a></p>AccessioniPrimary (citable) accession number: P62960
Secondary accession number(s): P22568, P27817, P43482
<p>This subsection of the ‘Entry information’ section shows the date of integration of the entry into UniProtKB, the date of the last sequence update and the date of the last annotation modification (‘Last modified’). The version number for both the entry and the <a href="http://www.uniprot.org/help/canonical_and_isoforms">canonical sequence</a> are also displayed.<p><a href='/help/entry_history' target='_top'>More...</a></p>Entry historyiIntegrated into UniProtKB/Swiss-Prot: August 31, 2004
Last sequence update: January 23, 2007
Last modified: October 16, 2019
This is version 160 of the entry and version 3 of the sequence. See complete history.
<p>This subsection of the ‘Entry information’ section indicates whether the entry has been manually annotated and reviewed by UniProtKB curators or not, in other words, if the entry belongs to the Swiss-Prot section of UniProtKB (<strong>reviewed</strong>) or to the computer-annotated TrEMBL section (<strong>unreviewed</strong>).<p><a href='/help/entry_status' target='_top'>More...</a></p>Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

<p>This section contains any relevant information that doesn’t fit in any other defined sections<p><a href='/help/miscellaneous_section' target='_top'>More...</a></p>Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

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