sox9a SRY-box transcription factor 9a [Danio rerio (zebrafish)] - Gene

Summary

Official Symbol: sox9aprovided by ZNC
Official Full Name: SRY-box transcription factor 9aprovided by ZNC
Primary source: ZFIN:ZDB-GENE-001103-1
See related: Ensembl:ENSDARG00000003293 AllianceGenome:ZFIN:ZDB-GENE-001103-1
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: jef; wu:fj17b12; zgc:111921
Summary: Enables chromatin binding activity. Acts upstream of or within cartilage morphogenesis; embryonic morphogenesis; and glial cell differentiation. Located in cytoplasm. Is expressed in several structures, including brain; ectoderm; head; reproductive system; and skeletal system. Used to study campomelic dysplasia. Human ortholog(s) of this gene implicated in campomelic dysplasia; lung cancer; and lung carcinoma. Orthologous to human SOX9 (SRY-box transcription factor 9). [provided by Alliance of Genome Resources, Nov 2024]
Orthologs: human mouse all
NEW: Try the new Gene table
Try the new Transcript table

Genomic context

Location:: chromosome: 12

Exon count:: 3

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCz11 (GCF_000002035.6)	12	NC_007123.7 (1947593..1951233, complement)
105	previous assembly	GRCz10 (GCF_000002035.5)	12	NC_007123.6 (1927596..1931236, complement)

Chromosome 12 - NC_007123.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

Go to the top of the page Help

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

Go to the top of the page Help

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
Mutation of the EWS gene modulates Sox9 gene expression essential for chondrocyte differentiation.
Title: Ewing sarcoma ewsa protein regulates chondrogenesis of Meckel's cartilage through modulation of Sox9 in zebrafish.
Sox9a plays a critical role in statoacoustic ganglia development.
Title: Fgf-signaling-dependent Sox9a and Atoh1a regulate otic neural development in zebrafish.
Data demonstrated that the sox9 axis signaling that determines testis formation in mammals also induces zebrafish ovary-testis transition, and adds to its conserved role in sex reversal.
Title: Sox9-related signaling controls zebrafish juvenile ovary-testis transformation.
these results reveal that coordination of ZNF219L with Sox9a is involved in the regulation of notochord-specific expression of sncgb.
Title: Zinc finger protein 219-like (ZNF219L) and Sox9a regulate synuclein-γ2 (sncgb) expression in the developing notochord of zebrafish.
we found that miR-140 is regulated by the cartilage master transcription regulator Sox9 in zebrafish and mammalian cells.
Title: Sox9 is upstream of microRNA-140 in cartilage.
FGF-receptor signalling controls the development of both oligodendrocyte progenitors and astroglia through the regulation of sox9, a gliogenic transcription factor the function of which we show to be conserved in the zebrafish hindbrain.
Title: FGF-receptor signalling controls neural cell diversity in the zebrafish hindbrain by regulating olig2 and sox9.
The role of Sox9a in ff1a gene regulation and function was studied using sox9a morpholinos.
Title: Sox9a regulation of ff1a in zebrafish (Danio rerio) suggests an involvement of ff1a in cartilage development.
jef (sox9a) is essential for both morphogenesis of condensations and overt cartilage differentiation
Title: A zebrafish sox9 gene required for cartilage morphogenesis.
zebrafish Anti-Mullerian hormone (Amh) is regulated by sox9a, sox9b, and cyp19a1a during gonad development
Title: Characterization and expression pattern of zebrafish Anti-Müllerian hormone (Amh) relative to sox9a, sox9b, and cyp19a1a, during gonad development.

Submit: New GeneRIF Correction See all GeneRIFs (11)

General gene information

Go to the top of the page Help

Markers

GDB:580585 (e-PCR)
- UniSTS:157834

fj17b12.x1 (e-PCR)
- UniSTS:198655

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
enables chromatin binding	IDA Inferred from Direct Assay more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
acts_upstream_of_or_within astrocyte differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within cartilage development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within cartilage morphogenesis	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
involved_in heart development	IBA Inferred from Biological aspect of Ancestor more info
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
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 oligodendrocyte differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within otic placode formation	IGI Inferred from Genetic Interaction more info
acts_upstream_of_or_within otic vesicle formation	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within pectoral fin 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

Component	Evidence Code	Pubs
located_in cytoplasm	IMP Inferred from Mutant Phenotype more info	PubMed
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

Go to the top of the page Help

Preferred Names: transcription factor SOX-9a

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

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

NEW Try the new Transcript table

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_131643.1 → NP_571718.1 transcription factor SOX-9a

See identical proteins and their annotated locations for NP_571718.1

Status: PROVISIONAL

Source sequence(s)

AF277096

UniProtKB/TrEMBL

Q78AH9, Q9DFH2

Related

ENSDARP00000006945.4, ENSDART00000005676.6

Conserved Domains (2) summary

cd01388
Location:106 → 176

SOX-TCF_HMG-box; 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 ...

pfam12444
Location:22 → 96

Sox_N; Sox developmental protein N terminal