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

Gene ID: 406447, updated on 2-Nov-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, Nov 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

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

    Related
    ENSDARP00000117564.1, ENSDART00000131536.2
Nucleotide Protein Strain
Heading Accession and Version

Gene LinkOut

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