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 several processes, including bone mineralization; eye photoreceptor cell development; and photoreceptor cell maintenance. Predicted to be active in nucleus. Is expressed in several structures, including central nervous system; digestive system; neural plate; pronephros; and retina. Orthologous to human HES4 (hes family bHLH transcription factor 4). [provided by Alliance of Genome Resources, Jan 2025]
Orthologs: human all
NEW: Try the new Gene table
Try the new Transcript table

Genomic context

Location:: chromosome: 23

Exon count:: 4

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCz11 (GCF_000002035.6)	23	NC_007134.7 (23399519..23401274, 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

Go to the top of the page Help

Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

Go to the top of the page Help

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

Go to the top of the page Help

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.

Submit: New GeneRIF Correction

General gene information

Go to the top of the page Help

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 bone mineralization	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within cranial skeletal system development	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within dorsal/ventral pattern formation	IGI Inferred from Genetic Interaction more info	PubMed
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

Go to the top of the page Help

Preferred Names: hairy-related 9

Names: Hes1a

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

NEW Try the new Transcript table

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: GCF_000002035.6-RS_2024_08

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..23401274 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_005162143.5 → XP_005162200.1 hairy-related 9 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