YBX1 Y-box binding protein 1 [Homo sapiens (human)] - Gene

Summary

Official Symbol: YBX1provided by HGNC
Official Full Name: Y-box binding protein 1provided by HGNC
Primary source: HGNC:HGNC:8014
See related: Ensembl:ENSG00000065978 MIM:154030; AllianceGenome:HGNC:8014
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: YB1; BP-8; CSDB; DBPB; YB-1; CBF-A; CSDA2; EFI-A; NSEP1; NSEP-1; MDR-NF1
Summary: 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]
Expression: Ubiquitous expression in testis (RPKM 220.6), fat (RPKM 121.2) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 1p34.2

Exon count:: 9

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	1	NC_000001.11 (42682418..42703805)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	1	NC_060925.1 (42552913..42574300)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	1	NC_000001.10 (43148089..43169476)

Chromosome 1 - NC_000001.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Tissue-specific circular RNA induction during human fetal development
Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
BioProject: PRJNA270632
Publication: PMID 26076956
Analysis date: Mon Apr 2 22:54:59 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

YBX1 promotes epithelial-mesenchymal transition in hepatocellular carcinoma via transcriptional regulation of PLRG1.
Title: YBX1 promotes epithelial-mesenchymal transition in hepatocellular carcinoma via transcriptional regulation of PLRG1.
TAGLN2 induces resistance signature ISGs by activating AKT-YBX1 signal with dual pathways and mediates the IFN-related DNA damage resistance in gastric cancer.
Title: TAGLN2 induces resistance signature ISGs by activating AKT-YBX1 signal with dual pathways and mediates the IFN-related DNA damage resistance in gastric cancer.
LNCHC directly binds and regulates YBX1 stability to ameliorate metabolic dysfunction-associated steatotic liver disease progression.
Title: LNCHC directly binds and regulates YBX1 stability to ameliorate metabolic dysfunction-associated steatotic liver disease progression.
Microglia-derived exosomes selective sorted by YB-1 alleviate nerve damage and cognitive outcome in Alzheimer's disease.
Title: Microglia-derived exosomes selective sorted by YB-1 alleviate nerve damage and cognitive outcome in Alzheimer's disease.
[Not Available].
Title: YBX1 Promotes Esophageal Squamous Cell Carcinoma Progression via m5C‐Dependent SMOX mRNA Stabilization.
Mechanism of Endogenous Peptide PDYBX1 and Precursor Protein YBX1 in Hirschsprung's Disease.
Title: Mechanism of Endogenous Peptide PDYBX1 and Precursor Protein YBX1 in Hirschsprung's Disease.
NSUN2/YBX1 promotes the progression of breast cancer by enhancing HGH1 mRNA stability through m[5]C methylation.
Title: NSUN2/YBX1 promotes the progression of breast cancer by enhancing HGH1 mRNA stability through m(5)C methylation.
The deubiquitinase USP5 promotes cholangiocarcinoma progression by stabilizing YBX1.
Title: The deubiquitinase USP5 promotes cholangiocarcinoma progression by stabilizing YBX1.
RNA m[5]C modification upregulates E2F1 expression in a manner dependent on YBX1 phase separation and promotes tumor progression in ovarian cancer.
Title: RNA m(5)C modification upregulates E2F1 expression in a manner dependent on YBX1 phase separation and promotes tumor progression in ovarian cancer.
In silico analysis of overall survival with YBX1 in male and female solid tumours.
Title: In silico analysis of overall survival with YBX1 in male and female solid tumours.

Submit: New GeneRIF Correction See all GeneRIFs (380)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Replication interactions

Interaction	Pubs
siRNA knockdown of YBX1 enhances HIV-1 replication; HIV-1 replication is restricted by EZR	PubMed
Knockdown of Y box binding protein 1 (YBX1) by siRNA inhibits the early stages of HIV-1 replication in 293T cells infected with VSV-G pseudotyped HIV-1	PubMed

Protein interactions

Protein	Gene	Interaction	Pubs
Envelope surface glycoprotein gp120	env	Tandem affinity purification and mass spectrometry analysis identify Y box binding protein 1 (YBX1), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells	PubMed
Gag-Pol	gag-pol	Tandem affinity purification and mass spectrometry analysis identify Y box binding protein 1 (YBX1), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells	PubMed
Nef	nef	Tandem affinity purification and mass spectrometry analysis identify Y box binding protein 1 (YBX1), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells	PubMed
Pr55(Gag)	gag	Tandem affinity purification and mass spectrometry analysis identify Y box binding protein 1 (YBX1), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells	PubMed
Tat	tat	YB-1 interacts with HIV-1 Tat and enhances Tat-induced activation of the HIV-1 LTR promoter	PubMed
	tat	Binding of YB-1 to HIV-1 Tat is mediated through the C-terminal region of Tat (amino acids 48-72) and through amino acids 75-203 of YB-1	PubMed
matrix	gag	HIV-1 MA interacts with YBX1	PubMed

Go to the HIV-1, Human Interaction Database

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

Ybx1 (e-PCR), detects polymorphism
- UniSTS:265528

Nsep1 (e-PCR), detects polymorphism
- UniSTS:265530

PMC140751P1 (e-PCR)
- UniSTS:270973

RH79815 (e-PCR)
- UniSTS:85383

SHGC-149519 (e-PCR)
- UniSTS:177053

AL033735 (e-PCR)
- UniSTS:93604

PMC127671P1 (e-PCR)
- UniSTS:270556

Ybx1 (e-PCR), detects polymorphism
- UniSTS:527608

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables C5-methylcytidine-containing RNA reader activity	IDA Inferred from Direct Assay more info	PubMed
enables DNA binding	TAS Traceable Author Statement more info	PubMed
enables GTPase binding	IPI Inferred from Physical Interaction more info	PubMed
enables RNA binding	HDA more info	PubMed
enables RNA binding	IDA Inferred from Direct Assay more info	PubMed
enables chromatin binding	IEA Inferred from Electronic Annotation more info
enables double-stranded DNA binding	TAS Traceable Author Statement more info	PubMed
enables mRNA binding	IEA Inferred from Electronic Annotation more info
enables miRNA binding	IDA Inferred from Direct Assay more info	PubMed
enables nucleic acid binding	IBA Inferred from Biological aspect of Ancestor more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables sequence-specific double-stranded DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables single-stranded DNA binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in CRD-mediated mRNA stabilization	IDA Inferred from Direct Assay more info	PubMed
involved_in CRD-mediated mRNA stabilization	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in RNA splicing	IEA Inferred from Electronic Annotation more info
involved_in RNA transport	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in cellular response to interleukin-7	IEA Inferred from Electronic Annotation more info
involved_in embryonic morphogenesis	ISS Inferred from Sequence or Structural Similarity more info
involved_in epidermis development	ISS Inferred from Sequence or Structural Similarity more info
involved_in in utero embryonic development	IEA Inferred from Electronic Annotation more info
involved_in mRNA processing	IEA Inferred from Electronic Annotation more info
involved_in mRNA stabilization	IDA Inferred from Direct Assay more info	PubMed
involved_in miRNA transport	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of cellular senescence	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of striated muscle cell differentiation	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of transcription by RNA polymerase II	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of translation	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of cell division	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of cytoplasmic translation	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of transcription by RNA polymerase II	IDA Inferred from Direct Assay more info	PubMed
involved_in protein localization to cytoplasmic stress granule	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of DNA-templated transcription	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of gene expression	IBA Inferred from Biological aspect of Ancestor more info
involved_in tRNA transport	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
part_of CRD-mediated mRNA stability complex	IDA Inferred from Direct Assay more info	PubMed
part_of CRD-mediated mRNA stability complex	IPI Inferred from Physical Interaction more info	PubMed
located_in P-body	IEA Inferred from Electronic Annotation more info
part_of U12-type spliceosomal complex	IDA Inferred from Direct Assay more info	PubMed
located_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in cytoplasmic stress granule	IDA Inferred from Direct Assay more info	PubMed
located_in cytosol	IDA Inferred from Direct Assay more info	PubMed
located_in cytosol	TAS Traceable Author Statement more info
located_in endoplasmic reticulum	IDA Inferred from Direct Assay more info
located_in extracellular exosome	HDA more info	PubMed
located_in extracellular exosome	IDA Inferred from Direct Assay more info	PubMed
located_in extracellular region	TAS Traceable Author Statement more info
part_of histone pre-mRNA 3'end processing complex	ISS Inferred from Sequence or Structural Similarity more info
located_in intracellular membrane-bounded organelle	IDA Inferred from Direct Assay more info
located_in nucleoplasm	TAS Traceable Author Statement more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in plasma membrane	IDA Inferred from Direct Assay more info
part_of ribonucleoprotein complex	IDA Inferred from Direct Assay more info	PubMed
located_in synapse	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: Y-box-binding protein 1

Names: CCAAT-binding transcription factor I subunit A; DNA-binding protein B; Y-box transcription factor; enhancer factor I subunit A; major histocompatibility complex, class II, Y box-binding protein I; nuclease-sensitive element-binding protein 1

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

NM_004559.5 → NP_004550.2 Y-box-binding protein 1

See identical proteins and their annotated locations for NP_004550.2

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longer transcript and encodes the functional protein.

Source sequence(s)

AC098484, BC090038, CN353145

Consensus CDS

CCDS470.1

UniProtKB/Swiss-Prot

P16990, P16991, P67809, Q14972, Q15325, Q5FVF0

Related

ENSP00000361626.3, ENST00000321358.12

Conserved Domains (1) summary

pfam00313
Location:59 → 128

CSD; 'Cold-shock' DNA-binding domain

RNA

NR_132737.2 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (2) contains an alternate 5' exon and lacks an internal exon, compared to variant 1. This variant is represented as non-coding because the predicted protein does not meet RefSeq quality criteria.

Source sequence(s)

AC098484, BC013838