YBX1 Gene (Protein Coding)

Y-Box Binding Protein 1

GC01P042682
GIFtS:
40
This gene encodes a highly conserved cold shock domain protein that has broad nucleic acid binding properties. The encoded protein functions as both a DNA and RNA binding protein and has been implicated in numerous cellular processes including regulation of transcription and translation, pre-mRNA splicing, DNA reparation and mRNA packaging. This protein is also a component of m... See more...

Aliases for YBX1 Gene

Aliases for YBX1 Gene

  • Y-Box Binding Protein 1 2 3 5
  • DBPB 2 3 4
  • YB-1 2 3 4
  • YB1 2 3 4
  • CCAAT-Binding Transcription Factor I Subunit A 3 4
  • Nuclease-Sensitive Element-Binding Protein 1 3 4
  • Enhancer Factor I Subunit A 3 4
  • Y-Box Transcription Factor 3 4
  • Y-Box-Binding Protein 1 3 4
  • DNA-Binding Protein B 3 4
  • MDR-NF1 2 3
  • NSEP-1 2 3
  • CBF-A 3 4
  • CSDA2 2 3
  • EFI-A 3 4
  • NSEP1 3 4
  • BP-8 2 3
  • CSDB 2 3
  • Major Histocompatibility Complex, Class II, Y Box-Binding Protein I 3
  • Nuclease Sensitive Element Binding Protein 1 2
  • YBX1 5

External Ids for YBX1 Gene

Previous HGNC Symbols for YBX1 Gene

  • NSEP1

Previous GeneCards Identifiers for YBX1 Gene

  • GC01P042818
  • GC01P042920
  • GC01P043148
  • GC01P041268

Summaries for YBX1 Gene

Entrez Gene Summary for YBX1 Gene

  • This gene encodes a highly conserved cold shock domain protein that has broad nucleic acid binding properties. The encoded protein functions as both a DNA and RNA binding protein and has been implicated in numerous cellular processes including regulation of transcription and translation, pre-mRNA splicing, DNA reparation and mRNA packaging. This protein is also a component of messenger ribonucleoprotein (mRNP) complexes and may have a role in microRNA processing. This protein can be secreted through non-classical pathways and functions as an extracellular mitogen. Aberrant expression of the gene is associated with cancer proliferation in numerous tissues. This gene may be a prognostic marker for poor outcome and drug resistance in certain cancers. Alternate splicing results in multiple transcript variants. Pseudogenes of this gene are found on multiple chromosomes. [provided by RefSeq, Sep 2015]

GeneCards Summary for YBX1 Gene

YBX1 (Y-Box Binding Protein 1) is a Protein Coding gene. Diseases associated with YBX1 include Spinal Chordoma and Liposarcoma. Among its related pathways are MECP2 and Associated Rett Syndrome and PI3K / Akt Signaling. Gene Ontology (GO) annotations related to this gene include nucleic acid binding and DNA-binding transcription factor activity. An important paralog of this gene is YBX3.

UniProtKB/Swiss-Prot Summary for YBX1 Gene

  • DNA- and RNA-binding protein involved in various processes, such as translational repression, RNA stabilization, mRNA splicing, DNA repair and transcription regulation (PubMed:8188694, PubMed:10817758, PubMed:11698476, PubMed:14718551, PubMed:18809583, PubMed:31358969). 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) (PubMed:19561594, PubMed:31358969). Promotes mRNA stabilization: acts by binding to m5C-containing mRNAs and recruiting the mRNA stability maintainer ELAVL1, thereby preventing mRNA decay (PubMed:10817758, PubMed:11698476, PubMed:31358969). Component of the CRD-mediated complex that promotes MYC mRNA stability (PubMed:19029303). 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 (PubMed:27559612, PubMed:29073095). Probably sorts RNAs in exosomes by recognizing and binding C5-methylcytosine (m5C)-containing RNAs (PubMed:28341602, PubMed:29073095). 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 (PubMed:12604611). 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' (PubMed:18809583). Binds to promoters that contain a Y-box (5'-CTGATTGGCCAA-3'), such as MDR1 and HLA class II genes (PubMed:8188694, PubMed:18809583). Promotes separation of DNA strands that contain mismatches or are modified by cisplatin (PubMed:14718551). Has endonucleolytic activity and can introduce nicks or breaks into double-stranded DNA, suggesting a role in DNA repair (PubMed:14718551). The secreted form acts as an extracellular mitogen and stimulates cell migration and proliferation (PubMed:19483673).

Gene Wiki entry for YBX1 Gene

Additional gene information for YBX1 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for YBX1 Gene

Genomics for YBX1 Gene

GeneHancer (GH) Regulatory Elements Pubs

Download GeneHancer 2017 data
Promoters and enhancers for YBX1 Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around YBX1 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for YBX1

Top Transcription factor binding sites by QIAGEN in the YBX1 gene promoter:
  • AP-1
  • ATF-2
  • c-Jun
  • CBF(2)
  • FAC1
  • LCR-F1
  • Max1
  • NF-1
  • NF-Y
  • YY1

Genomic Locations for YBX1 Gene

Latest Assembly
chr1:42,682,418-42,703,805
(GRCh38/hg38)
Size:
21,388 bases
Orientation:
Plus strand

Previous Assembly
chr1:43,148,089-43,169,476
(GRCh37/hg19 by Entrez Gene)
Size:
21,388 bases
Orientation:
Plus strand

chr1:43,148,098-43,168,020
(GRCh37/hg19 by Ensembl)
Size:
19,923 bases
Orientation:
Plus strand

Genomic View for YBX1 Gene

Genes around YBX1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
YBX1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for YBX1 Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for YBX1 Gene

Proteins for YBX1 Gene

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  • Protein details for YBX1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P67809-YBOX1_HUMAN
    Recommended name:
    Y-box-binding protein 1
    Protein Accession:
    P67809
    Secondary Accessions:
    • P16990
    • P16991
    • Q14972
    • Q15325
    • Q5FVF0

    Protein attributes for YBX1 Gene

    Size:
    324 amino acids
    Molecular mass:
    35924 Da
    Quaternary structure:
    • Homodimer in the presence of ATP (PubMed:10817758, PubMed:11851341). Component of the coding region determinant (CRD)-mediated complex, composed of DHX9, HNRNPU, IGF2BP1, SYNCRIP and YBX1 (PubMed:19029303). Identified in a IGF2BP1-dependent mRNP granule complex containing untranslated mRNAs (PubMed:17289661). Component of the U11/U12 snRNPs that are part of the U12-type spliceosome (PubMed:15146077). Identified in a histone pre-mRNA complex, at least composed of ERI1, LSM11, SLBP, SNRPB, SYNCRIP and YBX1 (By similarity). Interacts with IGF2BP1 and RBBP6 (PubMed:17289661, PubMed:18851979). Component of cytoplasmic messenger ribonucleoprotein particles (mRNPs) (PubMed:19029303). Interacts with AKT1, MBNL1, SFRS9, SFRS12, ALYREF/THOC4, MSH2, XRCC5, WRN and NCL (PubMed:12604611, PubMed:14559993, PubMed:14718551, PubMed:15806160, PubMed:18335541). Interacts (via C-terminus) with APEX1 (via N-terminus); the interaction is increased with APEX1 acetylated at 'Lys-6' and 'Lys-7' (PubMed:18809583). Interacts with AGO1 and AGO2 (PubMed:17932509). Interacts with ANKRD2 (PubMed:15136035). Interacts with DERA (PubMed:25229427). Interacts with FMR1; this interaction occurs in association with polyribosome (By similarity). Interacts with ZBTB7B (By similarity). Interacts with HDGF (isoform 1) (PubMed:26845719). Interacts with ELAVL1; leading to ELAVL1 recruitment on C5-methylcytosine (m5C)-containing mRNAs and subsequent mRNA stability (PubMed:31358969).
    SequenceCaution:
    • Sequence=AAA35750.1; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305}; Sequence=AAA59949.1; Type=Frameshift; Evidence={ECO:0000305}; Sequence=AAA61308.1; Type=Frameshift; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for YBX1 Gene

neXtProt entry for YBX1 Gene

Protein Expression for YBX1 Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Post-translational modifications for YBX1 Gene

  • Ubiquitinated by RBBP6; leading to a decrease of YBX1 transcactivational ability.
  • In the absence of phosphorylation the protein is retained in the cytoplasm.
  • 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).
  • Ubiquitination at Lys137, Lys170, and Lys264
  • Modification sites at PhosphoSitePlus

Other Protein References for YBX1 Gene

ENSEMBL proteins:
REFSEQ proteins:

Antibodies for research

  • Abcam antibodies for YBX1

No data available for DME Specific Peptides for YBX1 Gene

Domains & Families for YBX1 Gene

Gene Families for YBX1 Gene

HGNC:
Human Protein Atlas (HPA):
  • Cancer-related genes
  • Plasma proteins
  • Predicted intracellular proteins
  • Transcription factors

Protein Domains for YBX1 Gene

InterPro:
Blocks:
  • Cold-shock DNA-binding domain
  • Cold shock protein

Suggested Antigen Peptide Sequences for YBX1 Gene

GenScript: Design optimal peptide antigens:
  • YBX1 protein (A0JLU4_HUMAN)
  • YBX1 protein (Q05D43_HUMAN)
  • YB-1 protein (Q15905_HUMAN)
  • YBX1 protein (Q6PKI6_HUMAN)
  • Y-box-binding protein 1 (YBOX1_HUMAN)

Graphical View of Domain Structure for InterPro Entry

P67809

UniProtKB/Swiss-Prot:

YBOX1_HUMAN :
  • In the CSD domain, Trp-65 specifically recognizes C5-methylcytosine (m5C) modification through its indole ring.
  • Belongs to the YBX1 family.
Domain:
  • In the CSD domain, Trp-65 specifically recognizes C5-methylcytosine (m5C) modification through its indole ring.
Family:
  • Belongs to the YBX1 family.
genes like me logo Genes that share domains with YBX1: view

Function for YBX1 Gene

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  4. Inhibitory RNAs for research
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  6. Cell Lines for research

Molecular function for YBX1 Gene

UniProtKB/Swiss-Prot Function:
DNA- and RNA-binding protein involved in various processes, such as translational repression, RNA stabilization, mRNA splicing, DNA repair and transcription regulation (PubMed:8188694, PubMed:10817758, PubMed:11698476, PubMed:14718551, PubMed:18809583, PubMed:31358969). 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) (PubMed:19561594, PubMed:31358969). Promotes mRNA stabilization: acts by binding to m5C-containing mRNAs and recruiting the mRNA stability maintainer ELAVL1, thereby preventing mRNA decay (PubMed:10817758, PubMed:11698476, PubMed:31358969). Component of the CRD-mediated complex that promotes MYC mRNA stability (PubMed:19029303). 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 (PubMed:27559612, PubMed:29073095). Probably sorts RNAs in exosomes by recognizing and binding C5-methylcytosine (m5C)-containing RNAs (PubMed:28341602, PubMed:29073095). 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 (PubMed:12604611). 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' (PubMed:18809583). Binds to promoters that contain a Y-box (5'-CTGATTGGCCAA-3'), such as MDR1 and HLA class II genes (PubMed:8188694, PubMed:18809583). Promotes separation of DNA strands that contain mismatches or are modified by cisplatin (PubMed:14718551). Has endonucleolytic activity and can introduce nicks or breaks into double-stranded DNA, suggesting a role in DNA repair (PubMed:14718551). The secreted form acts as an extracellular mitogen and stimulates cell migration and proliferation (PubMed:19483673).

Phenotypes From GWAS Catalog for YBX1 Gene

Gene Ontology (GO) - Molecular Function for YBX1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003676 nucleic acid binding IEA,IBA 21873635
GO:0003677 DNA binding TAS 2977358
GO:0003690 double-stranded DNA binding TAS 1738588
GO:0003723 RNA binding IEA,IDA 19561594
GO:0005515 protein binding IPI 12674497
genes like me logo Genes that share ontologies with YBX1: view
genes like me logo Genes that share phenotypes with YBX1: view

Animal Models for YBX1 Gene

MGI Knock Outs for YBX1:

Animal Models for research

Transcription Factor Targets for YBX1 Gene

Selected GeneGlobe predicted Target genes for YBX1

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for YBX1

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology and HOMER Transcription for YBX1 Gene

Localization for YBX1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for YBX1 Gene

Cytoplasm. Nucleus. Cytoplasmic granule. Secreted. Secreted, extracellular exosome. Note=Predominantly cytoplasmic in proliferating cells (PubMed:12604611). Cytotoxic stress and DNA damage enhance translocation to the nucleus (PubMed:14718551). Localized in cytoplasmic mRNP granules containing untranslated mRNAs (PubMed:25229427). Shuttles between nucleus and cytoplasm (PubMed:25229427). Localized with DDX1, MBNL1 and TIAL1 in stress granules upon stress (PubMed:18335541). Secreted by mesangial and monocytic cells after inflammatory challenges (PubMed:19483673). {ECO:0000269 PubMed:12604611, ECO:0000269 PubMed:14718551, ECO:0000269 PubMed:18335541, ECO:0000269 PubMed:19483673, ECO:0000269 PubMed:25229427}.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for YBX1 gene
Compartment Confidence
extracellular 5
nucleus 5
cytosol 5
plasma membrane 2
cytoskeleton 2
mitochondrion 2
endoplasmic reticulum 2
endosome 2
peroxisome 1
lysosome 1
golgi apparatus 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (4)
  • Vesicles (3)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for YBX1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region TAS --
GO:0005634 nucleus TAS,IBA 21873635
GO:0005654 nucleoplasm TAS --
GO:0005689 U12-type spliceosomal complex IDA 15146077
GO:0005737 cytoplasm IDA 24965446
genes like me logo Genes that share ontologies with YBX1: view

Pathways & Interactions for YBX1 Gene

genes like me logo Genes that share pathways with YBX1: view

SIGNOR curated interactions for YBX1 Gene

Activates:
Inactivates:
Is activated by:

Gene Ontology (GO) - Biological Process for YBX1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000398 mRNA splicing, via spliceosome TAS --
GO:0006355 regulation of transcription, DNA-templated IDA 18809583
GO:0006397 mRNA processing IEA --
GO:0007219 Notch signaling pathway TAS --
GO:0008380 RNA splicing IEA --
genes like me logo Genes that share ontologies with YBX1: view

Drugs & Compounds for YBX1 Gene

Products:

  1. Drug products for research

(15) Drugs for YBX1 Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials

(6) Additional Compounds for YBX1 Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with YBX1: view

Transcripts for YBX1 Gene

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mRNA/cDNA for YBX1 Gene

1 REFSEQ mRNAs :
23 NCBI additional mRNA sequence :
4 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for YBX1

Alternative Splicing Database (ASD) splice patterns (SP) for YBX1 Gene

No ASD Table

Relevant External Links for YBX1 Gene

GeneLoc Exon Structure for
YBX1

Expression for YBX1 Gene

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  1. Primer products for research
  2. Gene Expression Assays for research

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for YBX1 Gene

mRNA expression in normal human tissues for YBX1 Gene
mRNA expression by GTEx for YBX1 GenemRNA expression by BioGPS for YBX1 Gene

Protein differential expression in normal tissues from HIPED for YBX1 Gene

This gene is overexpressed in Nasal epithelium (10.6) and Bone marrow stromal cell (8.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for YBX1 Gene



Protein tissue co-expression partners for YBX1 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for YBX1

SOURCE GeneReport for Unigene cluster for YBX1 Gene:

Hs.473583

Evidence on tissue expression from TISSUES for YBX1 Gene

  • Nervous system(4.8)
  • Liver(4.8)
  • Eye(4.6)
  • Lung(4.6)
  • Bone marrow(4.6)
  • Skin(4.5)
  • Pancreas(4.3)
  • Blood(4.2)
  • Stomach(4.1)
  • Intestine(3.8)
  • Bone(3.8)
  • Kidney(3.7)
  • Muscle(3.6)
  • Heart(3.6)
  • Spleen(3.4)
  • Lymph node(2.9)
  • Thyroid gland(2.6)
  • Adrenal gland(2.3)
genes like me logo Genes that share expression patterns with YBX1: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for YBX1 Gene

Orthologs for YBX1 Gene

This gene was present in the common ancestor of animals.

Orthologs for YBX1 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
 Mammalia YBX1 29 30
  • 99.9 (n)
 OneToOne
Oppossum
(Monodelphis domestica)
 Mammalia YBX1 30
  • 99 (a)
 OneToOne
Dog
(Canis familiaris)
 Mammalia LOC607025 29
  • 97.74 (n)
-- 30
  • 85 (a)
 OneToMany
Cow
(Bos Taurus)
 Mammalia YBX1 29 30
  • 97.63 (n)
 OneToOne
Rat
(Rattus norvegicus)
 Mammalia Ybx1 29
  • 96.58 (n)
Mouse
(Mus musculus)
 Mammalia Ybx1 29 16 30
  • 96.48 (n)
 OneToOne
Platypus
(Ornithorhynchus anatinus)
 Mammalia YBX1 30
  • 89 (a)
 OneToOne
Chicken
(Gallus gallus)
 Aves YBX1 30
  • 95 (a)
 OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
 Amphibia ybx1 29
  • 82.55 (n)
Str.8793 29
African clawed frog
(Xenopus laevis)
 Amphibia nsep1-prov 29
Zebrafish
(Danio rerio)
 Actinopterygii ybx1 29 30
  • 69.45 (n)
 OneToOne
nsep1 29
Rainbow Trout
(Oncorhynchus mykiss)
 Actinopterygii Omy.8781 29
Fruit Fly
(Drosophila melanogaster)
 Insecta yps 30
  • 39 (a)
 OneToMany
Worm
(Caenorhabditis elegans)
 Secernentea cey-1 30
  • 45 (a)
 ManyToMany
cey-4 30
  • 34 (a)
 ManyToMany
cey-2 30
  • 27 (a)
 ManyToMany
cey-3 30
  • 26 (a)
 ManyToMany
Sea Squirt
(Ciona savignyi)
 Ascidiacea CSA.10127 30
  • 44 (a)
 OneToMany
Species where no ortholog for YBX1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Baker's yeast (Saccharomyces cerevisiae)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Lizard (Anolis carolinensis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Wheat (Triticum aestivum)

Evolution for YBX1 Gene

ENSEMBL:
Gene Tree for YBX1 (if available)
TreeFam:
Gene Tree for YBX1 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for YBX1: view image
Alliance of Genome Resources:
Additional Orthologs for YBX1

Paralogs for YBX1 Gene

Paralogs for YBX1 Gene

(3) SIMAP similar genes for YBX1 Gene using alignment to 6 proteins:

  • YBOX1_HUMAN
  • A0JLU4_HUMAN
  • C9J5V9_HUMAN
  • H0Y449_HUMAN
  • Q05D43_HUMAN
  • Q6PKI6_HUMAN

Pseudogenes.org Pseudogenes for YBX1 Gene

genes like me logo Genes that share paralogs with YBX1: view

Variants for YBX1 Gene

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  1. SNP Genotyping and Copy Number Assays for research

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for YBX1 Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Structural Variations from Database of Genomic Variants (DGV) for YBX1 Gene

Variant ID Type Subtype PubMed ID
esv3577249 CNV gain 25503493
nsv1118116 CNV deletion 24896259
nsv829682 CNV loss 17160897
nsv945906 CNV duplication 23825009
nsv945907 CNV duplication 23825009
nsv945908 CNV duplication 23825009

Variation tolerance for YBX1 Gene

Residual Variation Intolerance Score: 36.1% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for YBX1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
YBX1
Leiden Open Variation Database (LOVD)
YBX1

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for YBX1 Gene

Disorders for YBX1 Gene

MalaCards: The human disease database

(9) MalaCards diseases for YBX1 Gene - From: COP and GCD

Disorder Aliases PubMed IDs
spinal chordoma
  • chordoma of spine
liposarcoma
  • lipomatous cancer
myxoid liposarcoma
  • myxoid/round cell liposarcoma
rett syndrome
  • rtt
breast cancer
  • breast cancer, familial
- elite association - COSMIC cancer census association via MalaCards
Search YBX1 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for YBX1

Atlas
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
Open Targets Platform
genes like me logo Genes that share disorders with YBX1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for YBX1 Gene

Publications for YBX1 Gene

  1. Y-box protein-1 is actively secreted through a non-classical pathway and acts as an extracellular mitogen. (PMID: 19483673) Frye BC … Mertens PR (EMBO reports 2009) 3 4 22
  2. Akt phosphorylates the Y-box binding protein 1 at Ser102 located in the cold shock domain and affects the anchorage-independent growth of breast cancer cells. (PMID: 15806160) Sutherland BW … Dunn SE (Oncogene 2005) 3 4 22
  3. The Ankrd2 protein, a link between the sarcomere and the nucleus in skeletal muscle. (PMID: 15136035) Kojic S … Faulkner G (Journal of molecular biology 2004) 3 4 22
  4. YB-1 promotes strand separation in vitro of duplex DNA containing either mispaired bases or cisplatin modifications, exhibits endonucleolytic activities and binds several DNA repair proteins. (PMID: 14718551) Gaudreault I … Lebel M (Nucleic acids research 2004) 3 4 22
  5. Splicing factor SRp30c interaction with Y-box protein-1 confers nuclear YB-1 shuttling and alternative splice site selection. (PMID: 12604611) Raffetseder U … Mertens PR (The Journal of biological chemistry 2003) 3 4 22

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