sox4b SRY-box transcription factor 4b [Danio rerio (zebrafish)] - Gene

Summary

Official Symbol: sox4bprovided by ZNC
Official Full Name: SRY-box transcription factor 4bprovided by ZNC
Primary source: ZFIN:ZDB-GENE-040426-1274
See related: Ensembl:ENSDARG00000098834 AllianceGenome:ZFIN:ZDB-GENE-040426-1274
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: zgc:63851
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 closure of optic fissure; endocrine pancreas development; and negative regulation of smoothened signaling pathway. Predicted to be active in nucleus. Is expressed in several structures, including basal plate midbrain region; central nervous system; integument; pancreatic system; and retina. Human ortholog(s) of this gene implicated in Coffin-Siris syndrome 10 and urinary bladder cancer. Orthologous to human SOX4 (SRY-box transcription factor 4). [provided by Alliance of Genome Resources, Dec 2024]
Orthologs: all
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Genomic context

Location:: chromosome: 16

Exon count:: 2

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCz11 (GCF_000002035.6)	16	NC_007127.7 (68069..71110)
105	previous assembly	GRCz10 (GCF_000002035.5)	16	NC_007127.6 (68069..71110)

Chromosome 16 - NC_007127.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Sox4b is expressed in zebrafish during pituitary development and plays a crucial role in the differentiation of thyrotrope and gonadotrope cells through induction of gata2a expression
Title: The HMG-box transcription factor Sox4b is required for pituitary expression of gata2a and specification of thyrotrope and gonadotrope cells in zebrafish.
sox4b is expressed transiently during endocrine cell differentiation and plays a crucial role in the generation of alpha endocrine cells.
Title: sox4b is a key player of pancreatic alpha cell differentiation in zebrafish.

Submit: New GeneRIF Correction

General gene information

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Markers

G40344 (e-PCR)
- UniSTS:28215

z3741 (e-PCR), detects polymorphism
- UniSTS:205204

z41022 (e-PCR), detects polymorphism
- UniSTS:238531

G40804 (e-PCR)
- UniSTS:8673

z9520 (e-PCR), detects polymorphism
- UniSTS:205034

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
involved_in camera-type eye morphogenesis	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within closure of optic fissure	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within endocrine pancreas development	IMP Inferred from Mutant Phenotype 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
involved_in neuron differentiation	IBA Inferred from Biological aspect of Ancestor more info
involved_in positive regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info

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-4b

Names: SRY (sex determining region Y)-box 4b; SRY-box containing gene 4b

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_200901.1 → NP_957195.1 transcription factor SOX-4b

See identical proteins and their annotated locations for NP_957195.1

Status: PROVISIONAL

Source sequence(s)

BC064664

UniProtKB/TrEMBL

Q6P2A2

Related

ENSDARP00000150987.1, ENSDART00000185385.1

Conserved Domains (1) summary

cd01388
Location:54 → 125

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 ...