ybx1 Y box binding protein 1 [Danio rerio (zebrafish)] - Gene

Summary

Official Symbol: ybx1provided by ZNC
Official Full Name: Y box binding protein 1provided by ZNC
Primary source: ZFIN:ZDB-GENE-000629-3
See related: Ensembl:ENSDARG00000004757 AllianceGenome:ZFIN:ZDB-GENE-000629-3
Gene type: protein coding
RefSeq status: PROVISIONAL
Organism: Danio rerio
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
Also known as: yb1; YB-1; zfY1; nsep1; zgc:85599; hm:zeh0308; wu:fb01g10; wu:fb08c05; wu:fb16e10; wu:fj26c09
Summary: Enables C5-methylcytidine-containing RNA reader activity; eukaryotic initiation factor 4E binding activity; and nucleic acid binding activity. Involved in embryonic morphogenesis; mRNA stabilization; and negative regulation of translation. Acts upstream of or within establishment of RNA localization; negative regulation of mRNA splicing, via spliceosome; and negative regulation of translational initiation. Located in P-body and nucleus. Is expressed in blastoderm; blastodisc; blastomere; eye; and telencephalon. Orthologous to human YBX1 (Y-box binding protein 1). [provided by Alliance of Genome Resources, Nov 2024]
Orthologs: human mouse all
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Genomic context

Location:: chromosome: 8

Exon count:: 8

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCz11 (GCF_000002035.6)	8	NC_007119.7 (47143829..47152086, complement)
105	previous assembly	GRCz10 (GCF_000002035.5)	8	NC_007119.6 (47153363..47161620, complement)

Chromosome 8 - NC_007119.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

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Expression

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See details

Project title: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
Description: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
BioProject: PRJEB1986
Analysis date: Fri Dec 8 19:48:10 2017

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Proteomic analysis of zebrafish folliculogenesis identifies YB-1 (Ybx1/ybx1) as a potential gatekeeping molecule controlling early ovarian folliculogenesis.
Title: Proteomic analysis of zebrafish folliculogenesis identifies YB-1 (Ybx1/ybx1) as a potential gatekeeping molecule controlling early ovarian folliculogenesis.
YB-1 recruitment to stress granules in zebrafish cells reveals a differential adaptive response to stress.
Title: YB-1 recruitment to stress granules in zebrafish cells reveals a differential adaptive response to stress.
These results identify maternal Ybx1 as a global translational repressor required for oocyte maturation and early embryogenesis.
Title: Maternal Ybx1 safeguards zebrafish oocyte maturation and maternal-to-zygotic transition by repressing global translation.
By acting as a direct target of cyclic posttranslational regulatory mechanisms, YB-1 serves as a bridge between the circadian clock and its cell cycle control.
Title: The tumor-associated YB-1 protein: new player in the circadian control of cell proliferation.

Submit: New GeneRIF Correction

General gene information

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Markers

fb08c05.x1 (e-PCR)
- UniSTS:189959

fb08c05.x1 (e-PCR)
- UniSTS:189960

fb01g10.x1 (e-PCR)
- UniSTS:189795

fb01g10.x1 (e-PCR)
- UniSTS:189796

fb13e01.y1 (e-PCR)
- UniSTS:190106

Clone Names

MGC85599, MGC158477, MGC174067, MGC174962

Gene Ontology Provided by ZFIN

Function	Evidence Code	Pubs
enables C5-methylcytidine-containing RNA reader activity	IDA Inferred from Direct Assay more info	PubMed
enables DNA binding	IEA Inferred from Electronic Annotation more info
enables RNA binding	IEA Inferred from Electronic Annotation more info
enables RNA binding	IPI Inferred from Physical Interaction more info	PubMed
enables eukaryotic initiation factor 4E binding	IDA Inferred from Direct Assay more info	PubMed
enables methyl-CpG binding	IDA Inferred from Direct Assay more info	PubMed
enables miRNA binding	ISS Inferred from Sequence or Structural Similarity more info
enables nucleic acid binding	IBA Inferred from Biological aspect of Ancestor more info
enables nucleic acid binding	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
acts_upstream_of_or_within RNA splicing	IEA Inferred from Electronic Annotation more info
involved_in RNA transport	ISS Inferred from Sequence or Structural Similarity more info
acts_upstream_of chordate embryonic development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of egg activation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in embryonic morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in epidermis development	ISS Inferred from Sequence or Structural Similarity more info
acts_upstream_of_or_within establishment of RNA localization	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within mRNA processing	IEA Inferred from Electronic Annotation more info
involved_in mRNA stabilization	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in miRNA transport	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of cellular senescence	ISS Inferred from Sequence or Structural Similarity more info
acts_upstream_of_or_within negative regulation of mRNA processing	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within negative regulation of mRNA splicing, via spliceosome	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within negative regulation of translation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of translation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within negative regulation of translational initiation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of oocyte maturation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of gene expression	IBA Inferred from Biological aspect of Ancestor more info
involved_in tRNA transport	ISS Inferred from Sequence or Structural Similarity more info

Component	Evidence Code	Pubs
located_in P-body	IDA Inferred from Direct Assay more info	PubMed
located_in cytoplasm	IEA Inferred from Electronic Annotation more info
located_in extracellular exosome	ISS Inferred from Sequence or Structural Similarity more info
located_in extracellular region	IEA Inferred from Electronic Annotation more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
located_in nucleus	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: Y-box-binding protein 1

Names: Y-box transcription factor; 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.