sox11b SRY-box transcription factor 11b [Danio rerio (zebrafish)] - Gene

Summary

Official Symbol: sox11bprovided by ZNC
Official Full Name: SRY-box transcription factor 11bprovided by ZNC
Primary source: ZFIN:ZDB-GENE-980526-466
See related: Ensembl:ENSDARG00000095743 AllianceGenome:ZFIN:ZDB-GENE-980526-466
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: fc90d10; wu:fb53e02; wu:fc90d10
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. Acts upstream of or within several processes, including camera-type eye development; negative regulation of smoothened signaling pathway; and regulation of sprouting angiogenesis. Predicted to be located in nucleus. Is expressed in several structures, including axis; gonad; hindbrain neural keel; nervous system; and somite. Human ortholog(s) of this gene implicated in Coffin-Siris syndrome 9. Orthologous to human SOX11 (SRY-box transcription factor 11). [provided by Alliance of Genome Resources, Apr 2022]
Orthologs: all
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Genomic context

Location:: chromosome: 20

Exon count:: 1

Annotation release	Status	Assembly	Chr	Location
106	current	GRCz11 (GCF_000002035.6)	20	NC_007131.7 (30032636..30035292, complement)
105	previous assembly	GRCz10 (GCF_000002035.5)	20	NC_007131.6 (30129757..30132413, complement)

Chromosome 20 - NC_007131.7 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?

This study demonstrated that SOX11b strongly expressed in retinal ganglion cells (RGCs), and knockdown of Sox11b inhibited RGC axon regrowth in retinal explants.
Title: Expression of SoxC Transcription Factors during Zebrafish Retinal and Optic Nerve Regeneration.
Sox11a/b knockdown in zebrafish causes brain abnormalities, potentially explaining the brain phenotype of Coffin-Siris syndrome in humans.
Title: De novo SOX11 mutations cause Coffin-Siris syndrome.
Results find that Sox11b function is essential for developmental angiogenesis in zebrafish embryos, specifically regulating sprouting angiogenesis.
Title: Mutant-specific gene expression profiling identifies SRY-related HMG box 11b (SOX11b) as a novel regulator of vascular development in zebrafish.
Sox11b promotes neuronal determination of endogenous stem cells and regenerative neurogenesis following spinal cord injury in the adult zebrafish.
Title: Transcription factor Sox11b is involved in spinal cord regeneration in adult zebrafish.
the duplicated zebrafish sox11a and -b loci were used to test the duplication, degeneration, complementation model of genome evolution through whole genome duplication.
Title: Regulatory divergence of the duplicated chromosomal loci sox11a/b by subpartitioning and sequence evolution of enhancers in zebrafish.

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General gene information

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Markers

G47038 (e-PCR)
- UniSTS:107828

fb82b09.y1 (e-PCR)
- UniSTS:191671

fb53e02.x1 (e-PCR)
- UniSTS:190681

fc90d10.x1 (e-PCR)
- UniSTS:194785

Gene Ontology Provided by ZFIN

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 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	IBA Inferred from Biological aspect of Ancestor more info

Process	Evidence Code	Pubs
involved_in brain development	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within brain development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in camera-type eye morphogenesis	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within camera-type eye morphogenesis	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within closure of optic fissure	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within dorsal/ventral pattern formation	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within lens development in camera-type eye	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within negative regulation of smoothened signaling pathway	IGI Inferred from Genetic Interaction more info	PubMed
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
involved_in neuron differentiation	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within neuron differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within regulation of sprouting angiogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within response to wounding	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within retinal rod cell development	IGI Inferred from Genetic Interaction 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-11b

Names: SRY (sex determining region Y)-box 11b; SRY-box containing gene 11b; etID55462.20

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_131337.1 → NP_571412.1 transcription factor SOX-11b

See identical proteins and their annotated locations for NP_571412.1

Status: PROVISIONAL

Source sequence(s)

AJ237813

UniProtKB/TrEMBL

Q9I9C7

Related

ENSDARP00000122216.1, ENSDART00000141068.2

Conserved Domains (1) summary

cd01388
Location:45 → 112

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 ...