sox9b SRY-box transcription factor 9b [Danio rerio (zebrafish)] - Gene

Summary

Official Symbol: sox9bprovided by ZNC
Official Full Name: SRY-box transcription factor 9bprovided by ZNC
Primary source: ZFIN:ZDB-GENE-001103-2
See related: Ensembl:ENSDARG00000043923 AllianceGenome:ZFIN:ZDB-GENE-001103-2
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: fb18d01; wu:fb18d01
Summary: Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Acts upstream of or within several processes, including animal organ development; embryonic pectoral fin morphogenesis; and iridophore differentiation. Predicted to be active in nucleus. Is expressed in several structures, including digestive system; head; nervous system; neural crest; and pleuroperitoneal region. Human ortholog(s) of this gene implicated in 46,XX sex reversal 2; 46,XY sex reversal 10; and campomelic dysplasia. Orthologous to human SOX9 (SRY-box transcription factor 9). [provided by Alliance of Genome Resources, Apr 2022]
Orthologs: all
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Genomic context

Location:: chromosome: 3

Exon count:: 3

Annotation release	Status	Assembly	Chr	Location
106	current	GRCz11 (GCF_000002035.6)	3	NC_007114.7 (62522542..62527667, complement)
105	previous assembly	GRCz10 (GCF_000002035.5)	3	NC_007114.6 (62343297..62348422, complement)

Chromosome 3 - NC_007114.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

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?

A CRISPR-Cas9 mutation in sox9b long intergenic noncoding RNA (slincR) affects zebrafish development, behavior, and regeneration.
Title: A CRISPR-Cas9 mutation in sox9b long intergenic noncoding RNA (slincR) affects zebrafish development, behavior, and regeneration.
High temperature induced masculinization of zebrafish by down-regulation of sox9b and esr1 via DNA methylation.
Title: High temperature induced masculinization of zebrafish by down-regulation of sox9b and esr1 via DNA methylation.
Molecular characterization and expression profiles of transcription factor Sox gene family in Culter alburnus.
Title: Molecular characterization and expression profiles of transcription factor Sox gene family in Culter alburnus.
By genome-wide transcriptome mining and gonadal microinjections, results identify two G protein-coupled receptor (GPCR)-regulatory circuits: miR430a-Sox9a (SRY-box transcription factor 9a) in the testis and miR218a-Sox9b (SRY-box transcription factor 9b) in the ovary.
Title: Specific miRNA-G Protein-Coupled Receptor Networks Regulate Sox9a/Sox9b Activities to Promote Gonadal Rejuvenation in Zebrafish.
Hdac1 regulates differentiation of liver progenitor cells into hepatocytes via Sox9b and differentiation of LPCs into biliary epithelial cells via Cdk8, Fbxw7, and Notch3 in zebrafish with severe hepatocyte loss.
Title: Hdac1 Regulates Differentiation of Bipotent Liver Progenitor Cells During Regeneration via Sox9b and Cdk8.
this report used two different methods and showed that Sox9b function is required for retinoic acid-dependent restriction of Centroacinar cell differentiation.
Title: Sox9b is a mediator of retinoic acid signaling restricting endocrine progenitor differentiation.
Antisense knockdown of long noncoding RNA results in an increase in sox9b expression during normal development.
Title: In Vivo Characterization of an AHR-Dependent Long Noncoding RNA Required for Proper Sox9b Expression.
These results can account for the tissue-specific expression of sox9b in the developing zebrafish.
Title: Analysis of the zebrafish sox9b promoter: Identification of elements that recapitulate organ-specific expression of sox9b.
sox9b is involved in signals between the cardiomyocytes and the nascent epicardial cells.
Title: Sox9b is required for epicardium formation and plays a role in TCDD-induced heart malformation in zebrafish.
sox9b is a key player in the generation of secondary endocrine cells deriving from pancreatic ducts in zebrafish
Title: Zebrafish sox9b is crucial for hepatopancreatic duct development and pancreatic endocrine cell regeneration.

Submit: New GeneRIF Correction See all GeneRIFs (15)

General gene information

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Markers

fb18d01.x1 (e-PCR)
- UniSTS:190241

fb18d01.x1 (e-PCR)
- UniSTS:190242

sox9b (e-PCR), detects polymorphism
- UniSTS:205501

fc70c07.y1 (e-PCR)
- UniSTS:194302

Gene Ontology Provided by ZFIN

Function	Evidence Code	Pubs
enables DNA binding	IEA Inferred from Electronic Annotation more info
enables DNA-binding transcription factor activity, RNA polymerase II-specific	IBA Inferred from Biological aspect of Ancestor more info
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	IBA Inferred from Biological aspect of Ancestor more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within cartilage development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in chondrocyte differentiation	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within embryonic pectoral fin morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within endocrine pancreas development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in heart development	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within heart valve development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within hepaticobiliary system development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within inner ear development	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within inner ear development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within iridophore differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within melanocyte differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in morphogenesis of an epithelium	IBA Inferred from Biological aspect of Ancestor more info
involved_in negative regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
involved_in oligodendrocyte differentiation	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within otic placode formation	IGI Inferred from Genetic Interaction more info
acts_upstream_of_or_within otic placode formation	IMP Inferred from Mutant Phenotype more info
acts_upstream_of_or_within otic vesicle formation	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within pancreas development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of chondrocyte differentiation	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within proepicardium development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within regeneration	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within retina development in camera-type eye	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within roof of mouth development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within type B pancreatic cell differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within visceral serous pericardium development	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: transcription factor SOX-9b

Names: SRY (sex determining region Y)-box 9b; SRY-box containing gene 9b

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_131644.1 → NP_571719.1 transcription factor SOX-9b

See identical proteins and their annotated locations for NP_571719.1

Status: PROVISIONAL

Source sequence(s)

AF277097

UniProtKB/TrEMBL

A0A8M1PBU3, Q9DFH1

Related

ENSDARP00000064499.3, ENSDART00000064500.5

Conserved Domains (2) summary

cd01388
Location:90 → 160

SOX-TCF_HMG-box; class I member of the HMG-box superfamily of DNA-binding proteins. These proteins contain a single HMG box, and bind the minor groove of DNA in a highly sequence-specific manner. Members include SRY and its homologs in insects and vertebrates, and ...

pfam12444
Location:16 → 80

Sox_N; Sox developmental protein N terminal