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    hmga1a high mobility group AT-hook 1a [ Danio rerio (zebrafish) ]

    Gene ID: 406447, updated on 9-Dec-2024

    Summary

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    Official Symbol
    hmga1aprovided by ZNC
    Official Full Name
    high mobility group AT-hook 1aprovided by ZNC
    Primary source
    ZFIN:ZDB-GENE-010502-1
    See related
    Ensembl:ENSDARG00000028335 AllianceGenome:ZFIN:ZDB-GENE-010502-1
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Danio rerio
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
    Also known as
    hmga1; hmgiy; zgc:85677; wu:fb12b06; wu:fb18f11; wu:fc19f01; wu:fi38b05
    Summary
    Predicted to enable transcription coregulator activity. Acts upstream of or within regulation of RNA splicing. Predicted to be located in chromatin. Predicted to be active in nucleus. Is expressed in DEL; heart; margin; nervous system; and otic vesicle. Human ortholog(s) of this gene implicated in type 2 diabetes mellitus. Orthologous to human HMGA1 (high mobility group AT-hook 1). [provided by Alliance of Genome Resources, Dec 2024]
    Orthologs
    all
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    Genomic context

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    See hmga1a in Genome Data Viewer
    Location:
    chromosome: 23
    Exon count:
    7
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCz11 (GCF_000002035.6) 23 NC_007134.7 (3751451..3759511, complement)
    105 previous assembly GRCz10 (GCF_000002035.5) 23 NC_007134.6 (3808548..3816608, complement)

    Chromosome 23 - NC_007134.7Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC101885468 Neighboring gene uncharacterized LOC101885428 Neighboring gene small integral membrane protein 29 Neighboring gene opsin 7, group member b Neighboring gene uncharacterized LOC101885752

    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. Single-molecule imaging correlates decreasing nuclear volume with increasing TF-chromatin associations during zebrafish development. Reisser M, et al. Nat Commun, 2018 Dec 6. PMID 30523256, Free PMC Article
    2. The response of HMGA1 to changes in oxygen availability is evolutionarily conserved. Moussavi Nik SH, et al. Exp Cell Res, 2011 Jul 1. PMID 21530505
    3. Notch Inhibition Promotes Regeneration and Immunosuppression Supports Cone Survival in a Zebrafish Model of Inherited Retinal Dystrophy. Fogerty J, et al. J Neurosci, 2022 Jun 29. PMID 35672150, Free PMC Article
    4. The Ameliorative Effects of Isorhynchophylline on Morphine Dependence Are Mediated Through the Microbiota-Gut-Brain Axis. Chen Z, et al. Front Pharmacol, 2021. PMID 34168553, Free PMC Article
    5. Gene regulatory networks controlling vertebrate retinal regeneration. Hoang T, et al. Science, 2020 Nov 20. PMID 33004674, Free PMC Article

    See all (16) citations in PubMed

    GeneRIFs: Gene References Into Functions

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by ZFIN

    Function Evidence Code Pubs
    enables DNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables transcription coregulator activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Process Evidence Code Pubs
    involved_in positive regulation of macromolecule metabolic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in regulation of DNA-templated transcription IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within regulation of DNA-templated transcription IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within regulation of RNA splicing IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in chromatin IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in chromosome IEA
    Inferred from Electronic Annotation
    more info
    		  
    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
    high mobility group AT-hook 1a
    Names
    high mobility group AT-hook 1

    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_001289906.1 → NP_001276835.1  high mobility group AT-hook 1a isoform 2

      See identical proteins and their annotated locations for NP_001276835.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) uses an alternate splice site in the coding region compared to variant 1. The resulting protein (isoform 2) is shorter but has the same N- and C-termini compared to isoform 1.
      Source sequence(s)
      CU861894, EH590186
      UniProtKB/TrEMBL
      A0A8M2B8N7, E9QD31
      Related
      ENSDARP00000154454.1, ENSDART00000189382.1

    2. NM_001289907.1 → NP_001276836.1  high mobility group AT-hook 1a isoform 1

      See identical proteins and their annotated locations for NP_001276836.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR compared to variant 1. Variants 1 and 3 encode the same protein.
      Source sequence(s)
      CU861894, EH448024
      UniProtKB/TrEMBL
      F6NK50, F6NKA5, Q6NV11
      Related
      ENSDARP00000115025.1, ENSDART00000137826.3

    3. NM_213168.3 → NP_998333.1  high mobility group AT-hook 1a isoform 1

      See identical proteins and their annotated locations for NP_998333.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longer protein (isoform 1). Variants 1 and 3 encode the same protein.
      Source sequence(s)
      CU861894, EH589378
      UniProtKB/TrEMBL
      F6NK50, F6NKA5, Q6NV11
      Related
      ENSDARP00000036107.7, ENSDART00000028885.9

    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
      3751451..3759511 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_005161904.5 → XP_005161961.1  high mobility group AT-hook 1a isoform X2

      See identical proteins and their annotated locations for XP_005161961.1

      UniProtKB/TrEMBL
      A0A8M2B8N7, E9QD31

    2. XM_068216720.1 → XP_068072821.1  high mobility group AT-hook 1a isoform X1

      UniProtKB/TrEMBL
      F6NK50, F6NKA5, Q6NV11

    3. XM_068216721.1 → XP_068072822.1  high mobility group AT-hook 1a isoform X2

      UniProtKB/TrEMBL
      A0A8M2B8N7, E9QD31
      Related
      ENSDARP00000117564.1, ENSDART00000131536.2
    Nucleotide Protein Strain
    Heading Accession and Version

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