sox2.L SRY-box 2 L homeolog [Xenopus laevis (African clawed frog)] - Gene

Summary

Official Symbol: sox2.L
Official Full Name: SRY-box 2 L homeolog
Primary source: Xenbase:XB-GENE-865099
Locus tag: XELAEV_18002672mg
See related: EnsemblRapid:ENSXLAG00005028868 AllianceGenome:Xenbase:XB-GENE-865099
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: sox2; anop3; sox-2; Xsox-2; mcops3; sox2.S; SRY-box2
Summary: Predicted to enable sequence-specific DNA binding activity. Acts upstream of or within nervous system development. Predicted to be located in cytoplasm and nucleus. Is expressed in anatomical system; pharyngeal arch; and primary germ layer. 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, Dec 2024]
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Genomic context

Location:: chromosome: 5L

Exon count:: 1

Annotation release	Status	Assembly	Chr	Location
101	current	Xenopus_laevis_v10.1 (GCF_017654675.1)	5L	NC_054379.1 (114959594..114960783, complement)
100	previous assembly	Xenopus_laevis_v2 (GCF_001663975.1)	5L	NC_030732.1 (104269182..104269505, complement)
100	previous assembly	Xenopus_laevis_v2 (GCF_001663975.1)	Unplaced Scaffold	NW_016724073.1 (1..596, complement)

Chromosome 5L - NC_054379.1 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?

beta-Catenin and SOX2 Interaction Regulate Visual Experience-Dependent Cell Homeostasis in the Developing Xenopus Thalamus.
Title: β-Catenin and SOX2 Interaction Regulate Visual Experience-Dependent Cell Homeostasis in the Developing Xenopus Thalamus.
Sox2 is necessary for spinal cord regeneration and suggest a model whereby spinal cord injury activates proliferation of Sox2/3 expressing cells and their differentiation into neurons, a mechanism that is lost in non-regenerative froglets.
Title: Regeneration of Xenopus laevis spinal cord requires Sox2/3 expressing cells.
Tail amputation results in a global increase of Sox2 levels and proliferation of Sox2-positive cells after spinal cord injury.
Title: Spinal cord regeneration in Xenopus tadpoles proceeds through activation of Sox2-positive cells.
Data indicate that pluripotency genes sox2, p63 and oct60 are upregulated early during the process of lens regeneration.
Title: Expression of pluripotency factors in larval epithelia of the frog Xenopus: evidence for the presence of cornea epithelial stem cells.
Suggest that SOX2 directly upregulates FGF8 gene expression in the early embryonic development of Xenopus.
Title: Regulation of XFGF8 gene expression through SRY (sex-determining region Y)-box 2 in developing Xenopus embryos.
Continuous expression of Sox1 and Sox2 in transgenic embryos represses neuron differentiation and inhibits anterior development while increasing cell proliferation.
Title: Interaction of Sox1, Sox2, Sox3 and Oct4 during primary neurogenesis.
A directional Wnt/beta-catenin-Sox2-proneural pathway regulates the transition from proliferation to differentiation in the retina.
Title: A directional Wnt/beta-catenin-Sox2-proneural pathway regulates the transition from proliferation to differentiation in the Xenopus retina.
Sox3 functions as an activator to induce expression of the early neural genes, sox2 and geminin in the absence of protein synthesis and to indirectly inhibit the Bmp target Xvent2
Title: Xenopus Sox3 activates sox2 and geminin and indirectly represses Xvent2 expression to induce neural progenitor formation at the expense of non-neural ectodermal derivatives.
direct interaction and interdependence between the Otx2 and Sox2 proteins coordinate Rax expression in eye development, providing molecular linkages among the genes responsible for ocular malformation.
Title: Molecular links among the causative genes for ocular malformation: Otx2 and Sox2 coregulate Rax expression.

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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 protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables sequence-specific DNA binding	ISS Inferred from Sequence or Structural Similarity more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within cell differentiation	IEA Inferred from Electronic Annotation 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	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within positive regulation of DNA-templated transcription	ISS Inferred from Sequence or Structural Similarity 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
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; SRY-box 2 S homeolog; XSox2; XlSOX-2; sex-determining region Y-box 2; transcription factor Sox2.L

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_001088222.1 → NP_001081691.1 transcription factor Sox-2

See identical proteins and their annotated locations for NP_001081691.1

Status: PROVISIONAL

Source sequence(s)

AF005476

UniProtKB/Swiss-Prot

O42569, O73690, Q6DFL8

UniProtKB/TrEMBL

A0A4P2X5R0

Related

ENSXLAP00005086060.1, ENSXLAT00005087722.1

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

RefSeqs of Annotated Genomes: Xenopus laevis Annotation Release 101 details...

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

Reference Xenopus_laevis_v10.1 Primary Assembly

Genomic

NC_054379.1 Reference Xenopus_laevis_v10.1 Primary Assembly

Range

114959594..114960783 complement

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GenBank, FASTA, Sequence Viewer (Graphics)