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    HMGA1 high mobility group AT-hook 1 [ Homo sapiens (human) ]

    Gene ID: 3159, updated on 13-Jun-2024

    Summary

    Official Symbol
    HMGA1provided by HGNC
    Official Full Name
    high mobility group AT-hook 1provided by HGNC
    Primary source
    HGNC:HGNC:5010
    See related
    Ensembl:ENSG00000137309 MIM:600701; AllianceGenome:HGNC:5010
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    HMG-R; HMGIY; HMGA1A
    Summary
    This gene encodes a chromatin-associated protein involved in the regulation of gene transcription, integration of retroviruses into chromosomes, and the metastatic progression of cancer cells. The encoded protein preferentially binds to the minor groove of AT-rich regions in double-stranded DNA. Multiple transcript variants encoding different isoforms have been found for this gene. Pseudogenes of this gene have been identified on multiple chromosomes. [provided by RefSeq, Jan 2016]
    Expression
    Broad expression in lymph node (RPKM 58.3), bone marrow (RPKM 57.3) and 23 other tissues See more
    Orthologs
    NEW
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    Genomic context

    See HMGA1 in Genome Data Viewer
    Location:
    6p21.31
    Exon count:
    6
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (34236873..34246231)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (34060576..34069936)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (34204650..34214008)

    Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24378 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24379 Neighboring gene keratin 18 pseudogene 9 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17060 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17061 Neighboring gene CYCS pseudogene 55 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:34193929-34194744 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:34196972-34197516 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:34202091-34202714 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:34202715-34203338 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:34203339-34203962 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:34203963-34204584 Neighboring gene translation initiation factor IF-2-like Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17067 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17068 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17069 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr6:34211103-34212302 Neighboring gene NFE2L2 motif-containing MPRA enhancer 296 Neighboring gene microRNA 6835 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17070 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17071 Neighboring gene small integral membrane protein 29 Neighboring gene ribosomal protein L35 pseudogene 2

    Genomic regions, transcripts, and products

    Expression

    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    Associated conditions

    Description Tests
    Type 2 diabetes mellitus
    MedGen: C0011860 OMIM: 125853 GeneReviews: WFS1 Spectrum Disorder
    Compare labs

    EBI GWAS Catalog

    Description
    A genome-wide association study in 19 633 Japanese subjects identified LHX3-QSOX2 and IGF1 as adult height loci.
    EBI GWAS Catalog
    A large-scale genome-wide association study of Asian populations uncovers genetic factors influencing eight quantitative traits.
    EBI GWAS Catalog
    Association analyses of 249,796 individuals reveal 18 new loci associated with body mass index.
    EBI GWAS Catalog
    Genome-wide association study of height and body mass index in Australian twin families.
    EBI GWAS Catalog
    Genome-wide meta-analysis identifies 11 new loci for anthropometric traits and provides insights into genetic architecture.
    EBI GWAS Catalog
    Hundreds of variants clustered in genomic loci and biological pathways affect human height.
    EBI GWAS Catalog
    Identification of 15 loci influencing height in a Korean population.
    EBI GWAS Catalog
    Identification, replication, and fine-mapping of Loci associated with adult height in individuals of african ancestry.
    EBI GWAS Catalog
    Many sequence variants affecting diversity of adult human height.
    EBI GWAS Catalog
    Meta-analysis of genome-wide association studies of adult height in East Asians identifies 17 novel loci.
    EBI GWAS Catalog
    Meta-analysis of genome-wide scans for human adult stature identifies novel Loci and associations with measures of skeletal frame size.
    EBI GWAS Catalog

    HIV-1 interactions

    Protein interactions

    Protein Gene Interaction Pubs
    Tat tat HMGA1 competes with HIV-1 Tat for TAR-binding in vitro. The interaction of HMGA1 with TAR is mediated by the first N-terminal A/T-hook motif of the protein PubMed
    tat Interaction of HIV-1 Tat with HMGA1 in T-cells is identified by a proteomic strategy based on affinity chromatography coupled with mass spectrometry PubMed
    integrase gag-pol HMGIY is a component of the HIV-1 preintegration complex and stimulates integration by promoting formation of active HIV-1 Integrase-cDNA complexes PubMed
    matrix gag HIV-1 Matrix associates with HMG I(Y) which is present in the HIV-1 preintegration complex PubMed

    Go to the HIV-1, Human Interaction Database

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • MGC4242, MGC4854, MGC12816

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables DNA binding EXP
    Inferred from Experiment
    more info
    PubMed 
    enables DNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables DNA binding, bending EXP
    Inferred from Experiment
    more info
    PubMed 
    enables RNA binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables RNA polymerase II cis-regulatory region sequence-specific DNA binding ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    enables chromatin binding ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    enables cis-regulatory region sequence-specific DNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables enzyme binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables minor groove of adenine-thymine-rich DNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables minor groove of adenine-thymine-rich DNA binding ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    enables minor groove of adenine-thymine-rich DNA binding TAS
    Traceable Author Statement
    more info
    PubMed 
    enables molecular adaptor activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables molecular function activator activity IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    enables nuclear receptor coactivator activity IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    enables nuclear retinoic acid receptor binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables nuclear retinoid X receptor binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables peroxisome proliferator activated receptor binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables structural constituent of chromatin TAS
    Traceable Author Statement
    more info
    PubMed 
    enables transcription coactivator activity EXP
    Inferred from Experiment
    more info
    PubMed 
    enables transcription coactivator activity IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    enables transcription coactivator activity ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    enables transcription coregulator activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables transcription coregulator binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Component Evidence Code Pubs
    part_of RNA polymerase II transcription regulator complex ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in cytosol TAS
    Traceable Author Statement
    more info
     
    located_in focal adhesion HDA PubMed 
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
     
    located_in nucleus HDA PubMed 
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    part_of senescence-associated heterochromatin focus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    part_of transcription regulator complex TAS
    Traceable Author Statement
    more info
    PubMed 

    General protein information

    Preferred Names
    high mobility group protein HMG-I/HMG-Y
    Names
    high mobility group protein A1
    high mobility group protein R
    nonhistone chromosomal high-mobility group protein HMG-I/HMG-Y

    NCBI Reference Sequences (RefSeq)

    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.

    Genomic

    1. NG_029020.1 RefSeqGene

      Range
      5074..14432
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001319077.2NP_001306006.1  high mobility group protein HMG-I/HMG-Y isoform b

      Status: REVIEWED

      Description
      Transcript Variant: This variant (8) uses an alternate splice site in the 5' UTR and uses an alternate in-frame splice site compared to variant 1. It encodes isoform b (also called HMG-Y), which is shorter than isoform a. Variants 2, 4, 5, 7, and 8 encode the same isoform (b).
      Source sequence(s)
      AL354740, BC008832, DA049639, M23616
      Consensus CDS
      CCDS4788.1
      UniProtKB/TrEMBL
      Q5T6U8
    2. NM_001319078.2NP_001306007.1  high mobility group protein HMG-I/HMG-Y isoform a

      Status: REVIEWED

      Description
      Transcript Variant: This variant (9) lacks an exon in the 5' UTR compared to variant 1. Variants 1, 3, 9, 10, 12, and 13 encode isoform (a, also called HMG-I).
      Source sequence(s)
      AL354740, BC008832, BC063434, DA049639
      Consensus CDS
      CCDS4789.1
      UniProtKB/Swiss-Prot
      P10910, P17096, Q5T6U9, Q9UKB0
    3. NM_001319079.2NP_001306008.1  high mobility group protein HMG-I/HMG-Y isoform a

      Status: REVIEWED

      Description
      Transcript Variant: This variant (10) uses an alternate splice site in the 5' UTR compared to variant 1. Variants 1, 3, 9, 10, 12, and 13 encode isoform (a, also called HMG-I).
      Source sequence(s)
      AL354740, BC008832, DA467015
      Consensus CDS
      CCDS4789.1
      UniProtKB/Swiss-Prot
      P10910, P17096, Q5T6U9, Q9UKB0
    4. NM_001319080.2NP_001306009.1  high mobility group protein HMG-I/HMG-Y isoform c

      Status: REVIEWED

      Description
      Transcript Variant: This variant (11) uses an alternate in-frame splice site compard to variant 1. The encoded isoform (c) is shorter than isoform a.
      Source sequence(s)
      AL354740, BC008832, DA049639, DA936387
      Consensus CDS
      CCDS93895.1
      UniProtKB/TrEMBL
      A0A994J434
      Related
      ENSP00000515486.1, ENST00000703808.1
    5. NM_001319081.2NP_001306010.1  high mobility group protein HMG-I/HMG-Y isoform a

      Status: REVIEWED

      Description
      Transcript Variant: This variant (13) uses an alternate splice site and lacks an exon in the 5' UTR compared to variant 1. Variants 1, 3, 9, 10, 12, and 13 encode isoform (a, also called HMG-I).
      Source sequence(s)
      AL354740, BC008832, CX785762, DA049639
      Consensus CDS
      CCDS4789.1
      UniProtKB/Swiss-Prot
      P10910, P17096, Q5T6U9, Q9UKB0
    6. NM_001319082.2NP_001306011.1  high mobility group protein HMG-I/HMG-Y isoform a

      Status: REVIEWED

      Description
      Transcript Variant: This variant (12) uses an alternate splice site in the 5' UTR compared to variant 1. Variants 1, 3, 9, 10, 12, and 13 encode isoform (a, also called HMG-I).
      Source sequence(s)
      AL354740, BC008832, BE269847, DB029421
      Consensus CDS
      CCDS4789.1
      UniProtKB/Swiss-Prot
      P10910, P17096, Q5T6U9, Q9UKB0
    7. NM_002131.4NP_002122.1  high mobility group protein HMG-I/HMG-Y isoform b

      See identical proteins and their annotated locations for NP_002122.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) uses an alternate in-frame splice site compared to variant 1, resulting in a shorter isoform (b, also called HMG-Y) than isoform a. Variants 2, 4, 5, 7, and 8 encode the same isoform (b).
      Source sequence(s)
      AL354740, BC004924, BC008832, DA049639
      Consensus CDS
      CCDS4788.1
      UniProtKB/TrEMBL
      Q5T6U8
      Related
      ENSP00000385693.2, ENST00000401473.7
    8. NM_145899.3NP_665906.1  high mobility group protein HMG-I/HMG-Y isoform a

      See identical proteins and their annotated locations for NP_665906.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longer isoform (a, also called HMG-I). Variants 1, 3, 9, 10, 12, and 13 encode isoform (a).
      Source sequence(s)
      AL354740, BC008832, DA049639
      Consensus CDS
      CCDS4789.1
      UniProtKB/Swiss-Prot
      P10910, P17096, Q5T6U9, Q9UKB0
      Related
      ENSP00000308227.4, ENST00000311487.9
    9. NM_145901.3NP_665908.1  high mobility group protein HMG-I/HMG-Y isoform a

      See identical proteins and their annotated locations for NP_665908.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR compared to variant 1. Variants 1, 3, 9, 10, 12, and 13 encode isoform (a, also called HMG-I).
      Source sequence(s)
      AL354740, BC008832, DA574958, DC374225, M23614
      Consensus CDS
      CCDS4789.1
      UniProtKB/Swiss-Prot
      P10910, P17096, Q5T6U9, Q9UKB0
      Related
      ENSP00000399888.1, ENST00000447654.5
    10. NM_145902.3NP_665909.1  high mobility group protein HMG-I/HMG-Y isoform b

      See identical proteins and their annotated locations for NP_665909.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) differs in the 5' UTR and uses an alternate in-frame splice site compared to variant 1. It encodes isoform b (also called HMG-Y), which is shorter than isoform a. Variants 2, 4, 5, 7, and 8 encode the same isoform (b).
      Source sequence(s)
      AL354740, BC008832, DA574958, DC374225, M23615
      Consensus CDS
      CCDS4788.1
      UniProtKB/TrEMBL
      Q5T6U8
    11. NM_145903.3NP_665910.1  high mobility group protein HMG-I/HMG-Y isoform b

      See identical proteins and their annotated locations for NP_665910.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) lacks an exon in the 5' UTR and uses an alternate in-frame splice site compared to variant 1. It encodes isoform b (also called HMG-Y), which is shorter than isoform a. Variants 2, 4, 5, 7, and 8 encode the same isoform (b).
      Source sequence(s)
      AL354740, BC008832, DC338100, M23617
      Consensus CDS
      CCDS4788.1
      UniProtKB/TrEMBL
      Q5T6U8
      Related
      ENSP00000288245.9, ENST00000347617.10
    12. NM_145905.3NP_665912.1  high mobility group protein HMG-I/HMG-Y isoform b

      See identical proteins and their annotated locations for NP_665912.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (7) differs in the 5' UTR and uses an alternate in-frame splice site compared to variant 1. It encodes isoform b (also called HMG-Y), which is shorter than isoform a. Variants 2, 4, 5, 7, and 8 encode the same isoform (b).
      Source sequence(s)
      AL354740, BC008832, BC015789
      Consensus CDS
      CCDS4788.1
      UniProtKB/TrEMBL
      Q5T6U8
      Related
      ENSP00000363230.3, ENST00000374116.3

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000006.12 Reference GRCh38.p14 Primary Assembly

      Range
      34236873..34246231
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060930.1 Alternate T2T-CHM13v2.0

      Range
      34060576..34069936
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_145904.1: Suppressed sequence

      Description
      NM_145904.1: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript.