her9 hairy-related 9 [Danio rerio (zebrafish)] - Gene

Summary

Official Symbol: her9provided by ZNC
Official Full Name: hairy-related 9provided by ZNC
Primary source: ZFIN:ZDB-GENE-011213-1
See related: Ensembl:ENSDARG00000056438 AllianceGenome:ZFIN:ZDB-GENE-011213-1
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: wu:fc30a03; zgc:100766
Summary: Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Acts upstream of or within negative regulation of neurogenesis. Predicted to be active in nucleus. Is expressed in several structures, including axis; central nervous system; neural plate; presumptive hypochord; and pronephros. Orthologous to human HES4 (hes family bHLH transcription factor 4). [provided by Alliance of Genome Resources, Apr 2022]
Orthologs: human all
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Genomic context

Location:: chromosome: 23

Exon count:: 4

Annotation release	Status	Assembly	Chr	Location
106	current	GRCz11 (GCF_000002035.6)	23	NC_007134.7 (23399519..23401315, complement)
105	previous assembly	GRCz10 (GCF_000002035.5)	23	NC_007134.6 (23472968..23474738, complement)

Chromosome 23 - NC_007134.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

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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?

Her9/Hes4 is required for retinal photoreceptor development, maintenance, and survival.
Title: Her9/Hes4 is required for retinal photoreceptor development, maintenance, and survival.
Her9 represses neurogenic fate downstream of Tbx1 and retinoic acid signaling in the inner ear.
Title: Her9 represses neurogenic fate downstream of Tbx1 and retinoic acid signaling in the inner ear.
Links the positional dorsoventral polarity information in the neuroectoderm to the regulation of neurogenesis.
Title: Patterning of proneuronal and inter-proneuronal domains by hairy- and enhancer of split-related genes in zebrafish neuroectoderm.

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General gene information

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Markers

hry (e-PCR)
- UniSTS:205602

fc30a03.x1 (e-PCR)
- UniSTS:203912

Gene Ontology Provided by ZFIN

Function	Evidence Code	Pubs
enables DNA binding	IEA Inferred from Electronic Annotation more info
enables DNA-binding transcription factor 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 protein dimerization activity	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in anterior/posterior pattern specification	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within eye photoreceptor cell development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within negative regulation of neurogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within photoreceptor cell maintenance	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within regulation of DNA-templated transcription	IEA Inferred from Electronic Annotation more info
involved_in regulation of neurogenesis	IBA Inferred from Biological aspect of Ancestor more info
involved_in 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

General protein information

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Preferred Names: hairy-related 9; transcription factor HES-4

Names: Hes1a

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_131873.1 → NP_571948.1 hairy-related 9

See identical proteins and their annotated locations for NP_571948.1

Status: PROVISIONAL

Source sequence(s)

AF301264

UniProtKB/TrEMBL

Q6AXJ0, Q9DF41

Related

ENSDARP00000073394.3, ENSDART00000078936.4

Conserved Domains (2) summary

cd00083
Location:32 → 93

HLH; Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, ...

pfam07527
Location:110 → 147

Hairy_orange; Hairy Orange

RefSeqs of Annotated Genomes: Danio rerio Annotation Release 106 details...

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

Reference GRCz11 Primary Assembly

Genomic

NC_007134.7 Reference GRCz11 Primary Assembly

Range

23399519..23401315 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_005162143.4 → XP_005162200.1 transcription factor HES-4 isoform X1

UniProtKB/TrEMBL

A0A8M2B8Z8

Conserved Domains (2) summary

cd00083
Location:32 → 93

HLH; Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, ...

pfam07527
Location:109 → 146

Hairy_orange; Hairy Orange