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

    Gene ID: 3159, updated on 6-Aug-2017
    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; Vega:OTTHUMG00000014539
    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]
    Orthologs
    Location:
    6p21.31
    Exon count:
    7
    Annotation release Status Assembly Chr Location
    108 current GRCh38.p7 (GCF_000001405.33) 6 NC_000006.12 (34236800..34246231)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (34204577..34214008)

    Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene keratin 18 pseudogene 9 Neighboring gene cytochrome c, somatic pseudogene 55 Neighboring gene microRNA 6835 Neighboring gene small integral membrane protein 29 Neighboring gene ribosomal protein L35 pseudogene 2

    • 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 Jun 15 11:32:44 2016

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    Associated conditions

    Description Tests
    Diabetes mellitus type 2
    MedGen: C0011860 OMIM: 125853 GeneReviews: Not available
    Compare labs

    NHGRI GWAS Catalog

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

    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

    • 2-LTR circle formation, organism-specific biosystem (from REACTOME)
      2-LTR circle formation, organism-specific biosystemThe formation of 2-LTR circles requires the action of the cellular non-homologous DNA end-joining pathway. Specifically the cellular Ku, XRCC4 and ligase IV proteins are needed. Evidence for this i...
    • APOBEC3G mediated resistance to HIV-1 infection, organism-specific biosystem (from REACTOME)
      APOBEC3G mediated resistance to HIV-1 infection, organism-specific biosystemRepresentatives of the apolipoprotein B mRNA editing enzyme catalytic polypeptide 3 (APOBEC3) family provide innate resistance to exogeneous and endogenous retroviruses (see Cullen 2006 for a recent ...
    • Adipogenesis, organism-specific biosystem (from WikiPathways)
      Adipogenesis, organism-specific biosystemThe different classess of factors involved in adipogenesis are shown. Adipogenesis is the process by which fat cells differentiate from predadipocytes to adipocytes (fat cells). Adipose tissue, compo...
    • Autointegration results in viral DNA circles, organism-specific biosystem (from REACTOME)
      Autointegration results in viral DNA circles, organism-specific biosystemIn this pathway, the viral integration machinery uses a site within the viral DNA as an integration target. This results in a covalent rearrangment of the viral DNA. The resulting DNA forms are no...
    • Cellular Senescence, organism-specific biosystem (from REACTOME)
      Cellular Senescence, organism-specific biosystemCellular senescence involves irreversible growth arrest accompanied by phenotypic changes such as enlarged morphology, reorganization of chromatin through formation of senescence-associated heterochr...
    • Cellular responses to stress, organism-specific biosystem (from REACTOME)
      Cellular responses to stress, organism-specific biosystemCells are subject to external molecular and physical stresses such as foreign molecules that perturb metabolic or signaling processes, and changes in temperature or pH. The ability of cells and tissu...
    • DNA Damage/Telomere Stress Induced Senescence, organism-specific biosystem (from REACTOME)
      DNA Damage/Telomere Stress Induced Senescence, organism-specific biosystemReactive oxygen species (ROS), whose concentration increases in senescent cells due to oncogenic RAS-induced mitochondrial dysfunction (Moiseeva et al. 2009) or due to environmental stress, cause DNA...
    • Disease, organism-specific biosystem (from REACTOME)
      Disease, organism-specific biosystemBiological processes are captured in Reactome by identifying the molecules (DNA, RNA, protein, small molecules) involved in them and describing the details of their interactions. From this molecular ...
    • Early Phase of HIV Life Cycle, organism-specific biosystem (from REACTOME)
      Early Phase of HIV Life Cycle, organism-specific biosystemIn the early phase of HIV lifecycle, an active virion binds and enters a target cell mainly by specific interactions of the viral envelope proteins with host cell surface receptors. The virion core...
    • Formation of Senescence-Associated Heterochromatin Foci (SAHF), organism-specific biosystem (from REACTOME)
      Formation of Senescence-Associated Heterochromatin Foci (SAHF), organism-specific biosystemThe process of DNA damage/telomere stress induced senescence culminates in the formation of senescence associated heterochromatin foci (SAHF). These foci represent facultative heterochromatin that is...
    • HIV Infection, organism-specific biosystem (from REACTOME)
      HIV Infection, organism-specific biosystemThe global pandemic of Human Immunodeficiency Virus (HIV) infection has resulted in tens of millions of people infected by the virus and millions more affected. UNAIDS estimates around 40 million ...
    • HIV Life Cycle, organism-specific biosystem (from REACTOME)
      HIV Life Cycle, organism-specific biosystemThe life cycle of HIV-1 is divided into early and late phases, shown schematically in the figure. In the early phase, an HIV-1 virion binds to receptors and co-receptors on the human host cell surfac...
    • Host Interactions of HIV factors, organism-specific biosystem (from REACTOME)
      Host Interactions of HIV factors, organism-specific biosystemLike all viruses, HIV-1 must co-opt the host cell macromolecular transport and processing machinery. HIV-1 Vpr and Rev proteins play key roles in this co-optation. Efficient HIV-1 replication likewis...
    • IL4-mediated signaling events, organism-specific biosystem (from Pathway Interaction Database)
      IL4-mediated signaling events, organism-specific biosystem
      IL4-mediated signaling events
    • Infectious disease, organism-specific biosystem (from REACTOME)
      Infectious disease, organism-specific biosystem
      Infectious disease
    • Integration of provirus, organism-specific biosystem (from REACTOME)
      Integration of provirus, organism-specific biosystemFor retroviral DNA to direct production of progeny virions it must become covalently integrated into the host cell chromosome (reviewed in Coffin et al. 1997; Hansen et al. 1998). Analyses of mutants...
    • Integration of viral DNA into host genomic DNA, organism-specific biosystem (from REACTOME)
      Integration of viral DNA into host genomic DNA, organism-specific biosystemFollowing nuclear entry, the viral preintegration complex (PIC) must select a site for integration in a host cell chromosome, and then carry out the chemical steps of the reaction. At the chromosomal...
    • Interactions of Vpr with host cellular proteins, organism-specific biosystem (from REACTOME)
      Interactions of Vpr with host cellular proteins, organism-specific biosystemVpr has been implicated in multiple processes during HIV-1 replication, including nuclear import of the pre-integration complex (PIC)(Heinzinger et al., 1994), apoptosis (Stewart et al., 1997) and in...
    • Preimplantation Embryo, organism-specific biosystem (from WikiPathways)
      Preimplantation Embryo, organism-specific biosystemThe source of this pathway is RNA-Seq data from single-cell pre-implantation embryos (Supplemental Table 1): http://www.nature.com/nsmb/journal/v20/n9/full/nsmb.2660.html Analysis options for runnin...
    • Senescence and Autophagy in Cancer, organism-specific biosystem (from WikiPathways)
      Senescence and Autophagy in Cancer, organism-specific biosystemSenescense and Autophagy Pathways in Cancer
    • Validated targets of C-MYC transcriptional activation, organism-specific biosystem (from Pathway Interaction Database)
      Validated targets of C-MYC transcriptional activation, organism-specific biosystem
      Validated targets of C-MYC transcriptional activation
    • Vpr-mediated nuclear import of PICs, organism-specific biosystem (from REACTOME)
      Vpr-mediated nuclear import of PICs, organism-specific biosystemVpr appears to function in anchoring the PIC to the nuclear envelope. This anchoring likely involves interactions between Vpr and host nucleoporins.
    Products Interactant Other Gene Complex Source Pubs Description

    Markers

    Homology

    Clone Names

    • MGC4242, MGC4854, MGC12816

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    AT DNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    AT DNA binding ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    AT DNA binding TAS
    Traceable Author Statement
    more info
    PubMed 
    DNA binding TAS
    Traceable Author Statement
    more info
    PubMed 
    DNA-(apurinic or apyrimidinic site) lyase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    chromatin binding ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    enhancer sequence-specific DNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enzyme binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    ligand-dependent nuclear receptor transcription coactivator activity IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    peroxisome proliferator activated receptor binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    retinoic acid receptor binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    retinoid X receptor binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    transcription factor activity, sequence-specific DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    transcription factor binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    transcriptional activator activity, RNA polymerase II distal enhancer sequence-specific binding ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    Process Evidence Code Pubs
    DNA unwinding involved in DNA replication NAS
    Non-traceable Author Statement
    more info
    PubMed 
    base-excision repair IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    establishment of integrated proviral latency TAS
    Traceable Author Statement
    more info
     
    negative regulation of cell proliferation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    negative regulation of chromatin silencing TAS
    Traceable Author Statement
    more info
    PubMed 
    negative regulation of transcription, DNA-templated IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    nuclear transport TAS
    Traceable Author Statement
    more info
     
    nucleosome disassembly TAS
    Traceable Author Statement
    more info
    PubMed 
    oncogene-induced cell senescence IDA
    Inferred from Direct Assay
    more info
    PubMed 
    positive regulation of cellular senescence IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    positive regulation of transcription from RNA polymerase II promoter ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    positive regulation of transcription, DNA-templated IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    protein complex assembly TAS
    Traceable Author Statement
    more info
    PubMed 
    regulation of transcription, DNA-templated TAS
    Traceable Author Statement
    more info
    PubMed 
    response to virus IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    senescence-associated heterochromatin focus assembly IDA
    Inferred from Direct Assay
    more info
    PubMed 
    transcription from RNA polymerase II promoter IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    RNA polymerase II transcription factor complex ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    cytosol TAS
    Traceable Author Statement
    more info
     
    focal adhesion IDA
    Inferred from Direct Assay
    more info
    PubMed 
    nucleoplasm TAS
    Traceable Author Statement
    more info
     
    nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    senescence-associated heterochromatin focus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    transcription factor complex TAS
    Traceable Author Statement
    more info
    PubMed 
    Preferred Names
    high mobility group protein HMG-I/HMG-Y
    Names
    high mobility group protein A1
    high mobility group protein R
    high-mobility group (nonhistone chromosomal) protein isoforms I and Y
    nonhistone chromosomal high-mobility group protein HMG-I/HMG-Y

    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
      5001..14432
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001319077.1NP_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/Swiss-Prot
      P17096
      UniProtKB/TrEMBL
      Q5T6U8
    2. NM_001319078.1NP_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
      P17096
    3. NM_001319079.1NP_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, DA049639, DA467015
      Consensus CDS
      CCDS4789.1
      UniProtKB/Swiss-Prot
      P17096
    4. NM_001319080.1NP_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
      UniProtKB/Swiss-Prot
      P17096
    5. NM_001319081.1NP_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
      P17096
    6. NM_001319082.1NP_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, DA049639, DB029421
      Consensus CDS
      CCDS4789.1
      UniProtKB/Swiss-Prot
      P17096
    7. NM_002131.3NP_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/Swiss-Prot
      P17096
      UniProtKB/TrEMBL
      Q5T6U8
      Related
      ENSP00000385693.2, OTTHUMP00000016223, ENST00000401473.7, OTTHUMT00000040215
    8. NM_145899.2NP_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
      P17096
      Related
      ENSP00000308227.4, OTTHUMP00000016224, ENST00000311487.9, OTTHUMT00000040217
    9. NM_145901.2NP_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
      P17096
      Related
      ENSP00000399888.1, ENST00000447654.5
    10. NM_145902.2NP_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/Swiss-Prot
      P17096
      UniProtKB/TrEMBL
      Q5T6U8
    11. NM_145903.2NP_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/Swiss-Prot
      P17096
      UniProtKB/TrEMBL
      Q5T6U8
      Related
      ENSP00000288245.9, OTTHUMP00000016222, ENST00000347617.10, OTTHUMT00000040214
    12. NM_145905.2NP_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/Swiss-Prot
      P17096
      UniProtKB/TrEMBL
      Q5T6U8
      Related
      ENSP00000363230.3, ENST00000374116.3

    RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 108 details...Open this link in a new tab

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

    Reference GRCh38.p7 Primary Assembly

    Genomic

    1. NC_000006.12 Reference GRCh38.p7 Primary Assembly

      Range
      34236800..34246231
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate CHM1_1.1

    Genomic

    1. NC_018917.2 Alternate CHM1_1.1

      Range
      34207231..34216597
      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.
    Support Center