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    • Showing Current items.

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

    Gene ID: 140613, updated on 9-Dec-2024

    Summary

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    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, Dec 2024]
    Orthologs
    human all
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    Genomic context

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    See her9 in Genome Data Viewer
    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_007134.7Genomic Context describing neighboring genes Neighboring gene PPARGC1 and ESRR induced regulator, muscle 1a Neighboring gene uncharacterized LOC137489184 Neighboring gene uncharacterized LOC137489124 Neighboring gene agrin Neighboring gene protein tyrosine phosphatase non-receptor type 11b

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • 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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    Related articles in PubMed

    1. A role for hairy1 in regulating chick limb bud growth. Vasiliauskas D, et al. Dev Biol, 2003 Oct 1. PMID 14512021
    2. her9 promotes floor plate development in zebrafish. Latimer AJ, et al. Dev Dyn, 2005 Apr. PMID 15739223
    3. hnRNP I inhibits Notch signaling and regulates intestinal epithelial homeostasis in the zebrafish. Yang J, et al. PLoS Genet, 2009 Feb. PMID 19197356, Free PMC Article
    4. The amphioxus Hairy family: differential fate after duplication. Minguillón C, et al. Development, 2003 Dec. PMID 14561632
    5. Distinct and redundant roles for zebrafish her genes during mineralization and craniofacial patterning. Stenzel A, et al. Front Endocrinol (Lausanne), 2022. PMID 36578958, Free PMC Article

    See all (64) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Her9/Hes4 is required for retinal photoreceptor development, maintenance, and survival.
      Title: Her9/Hes4 is required for retinal photoreceptor development, maintenance, and survival.
    2. 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.
    3. 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

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    Markers

    Homology

    Clone Names

    • MGC100766

    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

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    Preferred Names
    hairy-related 9
    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)

    1. 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

    1. NC_007134.7 Reference GRCz11 Primary Assembly

      Range
      23399519..23401274 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. 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

    Reference GRCz11 ALT_DRER_TU_1

    Genomic

    1. NW_018395148.1 Reference GRCz11 ALT_DRER_TU_1

      Range
      332065..333809 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein Strain
    Heading Accession and Version

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