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sox9.S SRY-box 9 S homeolog [ Xenopus laevis (African clawed frog) ]

Gene ID: 399405, updated on 4-Nov-2024

Summary

Official Symbol
sox9.S
Official Full Name
SRY-box 9 S homeolog
Primary source
Xenbase:XB-GENE-6253910
Locus tag
XELAEV_18046405mg
See related
EnsemblRapid:ENSXLAG00005026552 AllianceGenome:Xenbase:XB-GENE-6253910
Gene type
protein coding
RefSeq status
PROVISIONAL
Organism
Xenopus laevis
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Amphibia; Batrachia; Anura; Pipoidea; Pipidae; Xenopodinae; Xenopus; Xenopus
Also known as
cmd1; sox9; sra1; cmpd1; sox-9; sox9-a; sox9-b
Summary
Enables ubiquitin-like protein ligase binding activity. Acts upstream of or within neural crest formation; otic placode formation; and positive regulation of transcription by RNA polymerase II. Located in nucleus. Is expressed in anatomical system; appendage; mesenchyme; pharyngeal arch; and primary germ layer. 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]
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Genomic context

See sox9.S in Genome Data Viewer
Location:
chromosome: 9_10S
Exon count:
3
Annotation release Status Assembly Chr Location
101 current Xenopus_laevis_v10.1 (GCF_017654675.1) 9_10S NC_054388.1 (19840590..19846183)
100 previous assembly Xenopus_laevis_v2 (GCF_001663975.1) 9_10S NC_030741.1 (19079357..19084950)

Chromosome 9_10S - NC_054388.1Genomic Context describing neighboring genes Neighboring gene potassium inwardly rectifying channel subfamily J member 2 S homeolog Neighboring gene uncharacterized XB5729910 S homeolog Neighboring gene uncharacterized LOC121398868 Neighboring gene uncharacterized LOC121398761

Genomic regions, transcripts, and products

Bibliography

General gene information

Gene Ontology Provided by Xenbase

Function Evidence Code Pubs
enables DNA binding IEA
Inferred from Electronic Annotation
more info
 
enables DNA binding ISS
Inferred from Sequence or Structural Similarity
more info
 
enables DNA-binding transcription factor activity, RNA polymerase II-specific IEA
Inferred from Electronic Annotation
more info
 
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IEA
Inferred from Electronic Annotation
more info
 
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables sequence-specific DNA binding ISS
Inferred from Sequence or Structural Similarity
more info
 
enables ubiquitin-like protein ligase binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
acts_upstream_of_or_within cartilage development IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within cartilage development ISS
Inferred from Sequence or Structural Similarity
more info
 
acts_upstream_of_or_within cell differentiation IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within chondrocyte differentiation IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within chondrocyte differentiation ISS
Inferred from Sequence or Structural Similarity
more info
 
acts_upstream_of_or_within gonadal mesoderm development IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within growth plate cartilage chondrocyte growth ISS
Inferred from Sequence or Structural Similarity
more info
 
acts_upstream_of_or_within heart development IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within morphogenesis of an epithelium IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within negative regulation of canonical Wnt signaling pathway ISS
Inferred from Sequence or Structural Similarity
more info
 
acts_upstream_of_or_within negative regulation of fatty acid oxidation ISS
Inferred from Sequence or Structural Similarity
more info
 
acts_upstream_of_or_within negative regulation of osteoblast differentiation ISS
Inferred from Sequence or Structural Similarity
more info
 
acts_upstream_of_or_within negative regulation of transcription by RNA polymerase II IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within neural crest formation IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within oligodendrocyte differentiation IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within otic placode formation IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within positive regulation of DNA-templated transcription IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within positive regulation of chondrocyte differentiation IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within response to fatty acid ISS
Inferred from Sequence or Structural Similarity
more info
 
Component Evidence Code Pubs
located_in cytoplasm IEA
Inferred from Electronic Annotation
more info
 
located_in cytoplasm ISS
Inferred from Sequence or Structural Similarity
more info
 
located_in nucleus IDA
Inferred from Direct Assay
more info
PubMed 
located_in nucleus IEA
Inferred from Electronic Annotation
more info
 
located_in nucleus ISS
Inferred from Sequence or Structural Similarity
more info
 

General protein information

Preferred Names
transcription factor Sox-9-A
Names
SRY (sex determining region Y)-box 9
sex determining region Y-box 9
transcription factor SOX9

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)

  1. NM_001090807.1NP_001084276.1  transcription factor Sox-9-A

    See identical proteins and their annotated locations for NP_001084276.1

    Status: PROVISIONAL

    Source sequence(s)
    AY035397
    UniProtKB/Swiss-Prot
    B7ZR65, B7ZR67, Q90YL1
    UniProtKB/TrEMBL
    A0A974BT90, I3QHH4
    Related
    ENSXLAP00005078903.1, ENSXLAT00005080494.1
    Conserved Domains (2) summary
    cd01388
    Location:104174
    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:2294
    Sox_N; Sox developmental protein N terminal

RefSeqs of Annotated Genomes: Xenopus laevis Annotation Release 101 details...Open this link in a new tab

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference Xenopus_laevis_v10.1 Primary Assembly

Genomic

  1. NC_054388.1 Reference Xenopus_laevis_v10.1 Primary Assembly

    Range
    19840590..19846183
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)