sox2 SRY-box 2 [Xenopus tropicalis (tropical clawed frog)] - Gene

Summary

Official Symbol: sox2provided by Xenbase
Official Full Name: SRY-box 2provided by Xenbase
Primary source: Xenbase:XB-GENE-484553
See related: Ensembl:ENSXETG00000036807 AllianceGenome:Xenbase:XB-GENE-484553
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Xenopus tropicalis
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Amphibia; Batrachia; Anura; Pipoidea; Pipidae; Xenopodinae; Xenopus; Silurana
Also known as: Sox-2; XSox2; anop3; Xsox-2; mcops3; XLSOX-2
Summary: Predicted to enable DNA-binding transcription activator activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in nervous system development and regulation of transcription by RNA polymerase II. Predicted to act upstream of or within nervous system development and positive regulation of DNA-templated transcription. Predicted to be located in cytoplasm. Predicted to be active in nucleus. Is expressed in ectoderm; nervous system; vestibuloauditory system; and visual system. Human ortholog(s) of this gene implicated in breast cancer; nasal cavity cancer; and syndromic microphthalmia 3. Orthologous to human SOX2 (SRY-box transcription factor 2). [provided by Alliance of Genome Resources, Nov 2024]
Orthologs: human mouse all
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Genomic context

Location:: chromosome: 5

Exon count:: 1

Annotation release	Status	Assembly	Chr	Location
104	current	UCB_Xtro_10.0 (GCF_000004195.4)	5	NC_030681.2 (108035485..108037707, complement)
103	previous assembly	Xenopus_tropicalis_v9.1 (GCF_000004195.3)	5	NC_030681.1 (95888751..95890973)

Chromosome 5 - NC_030681.2 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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General gene information

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Gene Ontology Provided by Xenbase

Function	Evidence Code	Pubs
enables DNA binding	IEA Inferred from Electronic Annotation more info
enables DNA-binding transcription activator 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 sequence-specific DNA binding	ISS Inferred from Sequence or Structural Similarity more info

Process	Evidence Code	Pubs
involved_in brain development	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within cell differentiation	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within nervous system development	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within nervous system development	ISS Inferred from Sequence or Structural Similarity more info
involved_in neuron differentiation	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within positive regulation of DNA-templated transcription	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II	ISS Inferred from Sequence or Structural Similarity more info
acts_upstream_of_or_within regulation of DNA-templated transcription	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
located_in cytoplasm	ISS Inferred from Sequence or Structural Similarity more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
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

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Preferred Names: transcription factor Sox-2

Names: SRY (sex determining region Y)-box 2

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_213704.3 → NP_998869.1 transcription factor Sox-2

See identical proteins and their annotated locations for NP_998869.1

Status: VALIDATED

Source sequence(s)

AL782141, BC067975, CR566396

UniProtKB/Swiss-Prot

Q6NVN0

Related

ENSXETP00000072675.1, ENSXETT00000077539.2

Conserved Domains (2) summary

cd01388
Location:36 → 107

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 ...

pfam12336
Location:106 → 194

SOXp; SOX transcription factor