her1 hairy-related 1 [Danio rerio (zebrafish)] - Gene

Summary

Official Symbol: her1provided by ZNC
Official Full Name: hairy-related 1provided by ZNC
Primary source: ZFIN:ZDB-GENE-980526-125
See related: Ensembl:ENSDARG00000014722 AllianceGenome:ZFIN:ZDB-GENE-980526-125
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: HER-1; id:ibd5086
Summary: Enables identical protein binding activity and protein heterodimerization activity. Acts upstream of or within negative regulation of DNA-templated transcription and somite specification. Predicted to be part of transcription regulator complex. Predicted to be active in nucleus. Is expressed in several structures, including germ ring; margin; mesoderm; presumptive mesoderm; and tail bud. Human ortholog(s) of this gene implicated in spondylocostal dysostosis 4. Orthologous to human HES7 (hes family bHLH transcription factor 7). [provided by Alliance of Genome Resources, Nov 2024]
Orthologs: all
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Genomic context

Location:: chromosome: 5

Exon count:: 4

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCz11 (GCF_000002035.6)	5	NC_007116.7 (68788658..68795049, complement)
105	previous assembly	GRCz10 (GCF_000002035.5)	5	NC_007116.6 (68017991..68024382, complement)

Chromosome 5 - NC_007116.7 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 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?

Pairing of segmentation clock genes drives robust pattern formation.
Title: Pairing of segmentation clock genes drives robust pattern formation.
Pumilio response and AU-rich elements drive rapid decay of Pnrc2-regulated cyclic gene transcripts.
Title: Pumilio response and AU-rich elements drive rapid decay of Pnrc2-regulated cyclic gene transcripts.
Segmentation clock dynamics is strongly synchronized in the forming somite.
Title: Segmentation clock dynamics is strongly synchronized in the forming somite.
Studied source of noise in Zebrafish somite clock counteracted by Notch signalling; found clock desynch'n, in absence of Notch signalling, is due to stochastic dissociation of Her1/7 repressor proteins from oscillating her1/7 autorepressed target genes.
Title: Stochastic Regulation of her1/7 Gene Expression Is the Source of Noise in the Zebrafish Somite Clock Counteracted by Notch Signalling.
difference in anteroposterior elongagion is attributable to spatiotemporal inhibition of the clock gene her1 via retinoic acid regulation of the transcriptional repressor ripply1.
Title: Retinoic acid controls proper head-to-trunk linkage in zebrafish by regulating an anteroposterior somitogenetic rate difference.
loss of her1 or her7 can allow oscillations to continue with unchanged period but with reduced amplitude and impaired synchrony
Title: The elongation rate of RNA polymerase II in zebrafish and its significance in the somite segmentation clock.
the comparison between single her1hu2124 and her7hu2526 mutants and her1hu2124/bea tm98 double mutants suggests independent roles for both her genes in regulation of distinct phases of the segmentation clock.
Title: Analysis of her1 and her7 mutants reveals a spatio temporal separation of the somite clock module.
Fgf has an essential role in establishing the period gradient that is required for the her1 spatial oscillation pattern at the emergence of the traveling wave.
Title: Emergence of traveling waves in the zebrafish segmentation clock.
we present a detailed analysis of cis-regulatory elements that control oscillating expression of the zebrafish her1 gene in the anterior presomitic mesoderm
Title: Expression of the oscillating gene her1 is directly regulated by Hairy/Enhancer of Split, T-box, and Suppressor of Hairless proteins in the zebrafish segmentation clock.
Oscillations of the somite segmentation clock may be generated by a delayed negative feedback loop in which the products of two Notch target genes, her1 and her7, directly inhibit their own transcription.
Title: Setting the tempo in development: an investigation of the zebrafish somite clock mechanism.

Submit: New GeneRIF Correction See all GeneRIFs (13)

General gene information

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Markers

HER1 (e-PCR)
- UniSTS:205327

her1 (e-PCR), detects polymorphism
- UniSTS:205618

her1 (e-PCR), detects polymorphism
- UniSTS:238233

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 identical protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein dimerization activity	IEA Inferred from Electronic Annotation more info
enables protein heterodimerization activity	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in anterior/posterior pattern specification	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within negative regulation of DNA-templated transcription	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within negative regulation of DNA-templated transcription	IPI Inferred from Physical Interaction 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
acts_upstream_of_or_within somite specification	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within somite specification	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within somitogenesis	IEP Inferred from Expression Pattern more info	PubMed
acts_upstream_of_or_within somitogenesis	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within somitogenesis	IMP Inferred from Mutant Phenotype 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
part_of transcription regulator complex	IC Inferred by Curator more info	PubMed

General protein information

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Preferred Names: hairy-related 1

Names: Hes7; etID309753.5

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_131078.1 → NP_571153.1 hairy-related 1

See identical proteins and their annotated locations for NP_571153.1

Status: PROVISIONAL

Source sequence(s)

X97329

UniProtKB/TrEMBL

Q90463

Related

ENSDARP00000027076.4, ENSDART00000016307.6

Conserved Domains (2) summary

cd00083
Location:10 → 67

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:118 → 157

Hairy_orange; Hairy Orange