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

    Gene ID: 3159, updated on 11-May-2012

    Summary

    Official Symbol
    HMGA1provided by HGNC
    Official Full Name
    high mobility group AT-hook 1provided by HGNC
    Primary source
    HGNC:5010
    Locus tag
    RP11-513I15.2
    See related
    Ensembl:ENSG00000137309; HPRD:02829; 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; MGC4242; MGC4854; MGC12816
    Summary
    This gene encodes a non-histone protein involved in many cellular processes, including regulation of inducible gene transcription, integration of retroviruses into chromosomes, and the metastatic progression of cancer cells. The encoded protein preferentially binds to the minor groove of A+T-rich regions in double-stranded DNA. It has little secondary structure in solution but assumes distinct conformations when bound to substrates such as DNA or other proteins. The encoded protein is frequently acetylated and is found in the nucleus. At least seven transcript variants encoding two different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

    Genomic context

    Location :
    6p21
    Sequence :
    Chromosome: 6; NC_000006.11 (34204577..34214008)
    See HMGA1 in Epigenomics, MapViewer

    Chromosome 6 - NC_000006.11Genomic Context describing neighboring genes Neighboring gene keratin 18 pseudogene 9 Neighboring gene cytochrome c, somatic pseudogene 55 Neighboring gene chromosome 6 open reading frame 1 Neighboring gene ribosomal protein L35 pseudogene 2

    Genomic regions, transcripts, and products

    Bibliography

    GeneRIFs: Gene References Into Functions What's a GeneRIF?

    HIV-1 protein interactions

    Protein Gene Interaction Pubs
    integrase gag-pol HMG I(Y) 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 Protein Interaction Database

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description
    P17096 P15336 ATF2    HPRD  PubMed  
    P17096 P06493 CDK1    HPRD  PubMed  
    P17096 P17676 CEBPB    HPRD  PubMed  
    P17096 Q92793 CREBBP    HPRD  PubMed  
    P17096 P68400 CSNK2A1    HPRD  PubMed  
    P17096 P19784 CSNK2A2    HPRD  PubMed  
    P17096 P32519 ELF1    HPRD  PubMed  
    P17096 Q01844 EWSR1    HPRD  PubMed  
    P17096 Q9H2X6 HIPK2    HPRD  PubMed  
    P17096 P10914 IRF1    HPRD  PubMed  
    P17096 P05412 JUN    HPRD  PubMed  
    P17096 P23511 NFYA    HPRD  PubMed  
    P17096 Q03052 POU3F1    HPRD  PubMed  
    P17096 P37231 PPARG    HPRD  PubMed  
    P17096 Q96LA8 PRMT6    HPRD  PubMed  
    P17096 P13631 RARG    HPRD  PubMed  
    P17096 P78317 RNF4    HPRD  PubMed  
    P17096 P19793 RXRA    HPRD  PubMed  
    P17096 P08047 SP1    HPRD  PubMed  
    P17096 P11831 SRF    HPRD  PubMed  
    P17096 Q9UMX1 SUFU    HPRD  PubMed  
    BioGRID:109402 BioGRID:107776 ATF2    BioGRID  PubMed Reconstituted Complex 
    BioGRID:109402 BioGRID:114342 BANF1    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:109402 BioGRID:107480 CEBPB    BioGRID  PubMed Affinity Capture-Western; Reconstituted Complex 
    BioGRID:109402 BioGRID:107530 CHD1    BioGRID  PubMed Affinity Capture-Western 
    BioGRID:109402 BioGRID:107777 CREBBP    BioGRID  PubMed Biochemical Activity; Two-hybrid 
    BioGRID:109402 BioGRID:108312 ELF1    BioGRID  PubMed Reconstituted Complex 
    BioGRID:109402 BioGRID:108431 EWSR1    BioGRID  PubMed Two-hybrid 
    NC_000019.8 INSR    BIND  PubMed HMGA1 interacts with INSR locus. 
    BioGRID:109402 BioGRID:109867 IRF1    BioGRID  PubMed Reconstituted Complex 
    BioGRID:109402 BioGRID:109928 JUN    BioGRID  PubMed Reconstituted Complex; Two-hybrid 
    BioGRID:109402 BioGRID:114375 KAT2B    BioGRID  PubMed Biochemical Activity 
    BioGRID:109402 BioGRID:110857 NFKB1    BioGRID  PubMed Reconstituted Complex 
    BioGRID:109402 BioGRID:110866 NFYA    BioGRID  PubMed Far Western 
    BioGRID:109402 BioGRID:110929 NPM1    BioGRID  PubMed Far Western 
    BioGRID:109402 BioGRID:111041 ORC2    BioGRID  PubMed Affinity Capture-Western 
    BioGRID:109402 BioGRID:117129 ORC6    BioGRID  PubMed Reconstituted Complex 
    BioGRID:109402 BioGRID:106652 PARP1    BioGRID  PubMed Reconstituted Complex 
    BioGRID:109402 BioGRID:111447 POU2F1    BioGRID  PubMed Far Western; Reconstituted Complex 
    BioGRID:109402 BioGRID:111448 POU2F2    BioGRID  PubMed Far Western; Reconstituted Complex 
    BioGRID:109402 BioGRID:111449 POU3F1    BioGRID  PubMed Reconstituted Complex 
    BioGRID:109402 BioGRID:111464 PPARG    BioGRID  PubMed Reconstituted Complex; Two-hybrid 
    BioGRID:109402 BioGRID:111564 PRKCA    BioGRID  PubMed Biochemical Activity 
    BioGRID:109402 BioGRID:120469 PRMT6    BioGRID  PubMed Affinity Capture-Western; Biochemical Activity; Far Western 
    BioGRID:109402 BioGRID:111849 RARA    BioGRID  PubMed Reconstituted Complex; Two-hybrid 
    BioGRID:109402 BioGRID:125912 RN7SK    BioGRID  PubMed Protein-RNA 
    BioGRID:109402 BioGRID:112550 SP1    BioGRID  PubMed Affinity Capture-Western; Reconstituted Complex 
    BioGRID:109402 BioGRID:203518 Stag2    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:109402 BioGRID:113010 TP53    BioGRID  PubMed Affinity Capture-Western 
    BioGRID:109402 BioGRID:113164 UBC    BioGRID  PubMed Affinity Capture-MS 

    General gene information

    Markers

    Pathways from BioSystems

    • 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...
    • 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...
    • 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...
    • IL-4 signaling Pathway, organism-specific biosystem (from WikiPathways)
      IL-4 signaling Pathway, organism-specific biosystemInterleukin-4 belongs to the IL-2 family of cytokines, which includes IL-2, IL-7, IL-9, IL-15 and IL-21. It signals through 2 different receptor complexes; Receptor complex 1 comprises of IL-4 recept...
    • IL4-mediated signaling events, organism-specific biosystem (from Pathway Interaction Database)
      IL4-mediated signaling events, organism-specific biosystem
      IL4-mediated signaling events
    • 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...
    • Senescence and Autophagy, organism-specific biosystem (from WikiPathways)
      Senescence and Autophagy, 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.

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    5'-deoxyribose-5-phosphate lyase activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    AT DNA binding TAS
    Traceable Author Statement
    more info
    PubMed 
    DNA binding IEA
    Inferred from Electronic Annotation
    more info
     
    DNA-(apurinic or apyrimidinic site) lyase activity 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 
    sequence-specific DNA binding transcription factor activity IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    transcription factor binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Process Evidence Code Pubs
    DNA unwinding involved in replication NAS
    Non-traceable Author Statement
    more info
    PubMed 
    base-excision repair IDA
    Inferred from Direct Assay
    more info
    PubMed 
    initiation of viral infection TAS
    Traceable Author Statement
    more info
     
    interspecies interaction between organisms IEA
    Inferred from Electronic Annotation
    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-dependent IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    nucleosome disassembly TAS
    Traceable Author Statement
    more info
    PubMed 
    oncogene-induced 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, DNA-dependent IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    protein complex assembly TAS
    Traceable Author Statement
    more info
    PubMed 
    provirus integration TAS
    Traceable Author Statement
    more info
     
    regulation of transcription, DNA-dependent 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 
    viral reproduction TAS
    Traceable Author Statement
    more info
     
    Component Evidence Code Pubs
    chromatin IEA
    Inferred from Electronic Annotation
    more info
     
    chromosome IEA
    Inferred from Electronic Annotation
    more info
     
    cytosol TAS
    Traceable Author Statement
    more info
     
    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 

    General protein information

    Preferred Names
    high mobility group protein HMG-I/HMG-Y
    Names
    high mobility group protein HMG-I/HMG-Y
    HMG-I(Y)
    high mobility group protein R
    high mobility group protein A1
    nonhistone chromosomal high-mobility group protein HMG-I/HMG-Y
    high-mobility group (nonhistone chromosomal) protein isoforms I and Y

    NCBI Reference Sequences (RefSeq)

    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_002131.3NP_002122.1  high mobility group protein HMG-I/HMG-Y isoform b

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) utilizes an alternate in-frame splice site in one of the coding exons compared to variant 1, resulting in a shorter isoform (b, also called HMG-Y) than isoform a (also called HMG-I).
      Source sequence(s)
      AL354740, BC004924, BC008832, DA049639
      Consensus CDS
      CCDS4788.1
      UniProtKB/Swiss-Prot
      P17096
      UniProtKB/TrEMBL
      Q5T6U8
      Related
      ENSP00000385693, ENST00000401473
    2. NM_145899.2NP_665906.1  high mobility group protein HMG-I/HMG-Y isoform a

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (a, also called HMG-I).
      Source sequence(s)
      AL354740, BC008832, DA049639
      Consensus CDS
      CCDS4789.1
      UniProtKB/Swiss-Prot
      P17096
      Related
      ENSP00000308227, ENST00000311487
    3. NM_145901.2NP_665908.1  high mobility group protein HMG-I/HMG-Y isoform a

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR compared to variant 1. Both variants 1 and 3 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, ENST00000447654
    4. NM_145902.2NP_665909.1  high mobility group protein HMG-I/HMG-Y isoform b

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) utilizes an alternate in-frame splice site in one of the coding exons and differs in the 5' UTR compared to variant 1. Variant 4 encodes isoform b (also called HMG-Y), which is shorter than isoform a (also called HMG-I) encoded by variant 1.
      Source sequence(s)
      AL354740, BC008832, DA574958, DC374225, M23615
      Consensus CDS
      CCDS4788.1
      UniProtKB/Swiss-Prot
      P17096
      UniProtKB/TrEMBL
      Q5T6U8
    5. NM_145903.2NP_665910.1  high mobility group protein HMG-I/HMG-Y isoform b

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) utilizes an alternate in-frame splice site in one of the coding exons and differs in the 5' UTR compared to variant 1. Variant 5 encodes isoform b (also called HMG-Y), which is shorter than isoform a (also called HMG-I) encoded by variant 1.
      Source sequence(s)
      AL354740, BC008832, DC338100, M23617
      Consensus CDS
      CCDS4788.1
      UniProtKB/Swiss-Prot
      P17096
      UniProtKB/TrEMBL
      Q5T6U8
      Related
      ENSP00000288245, OTTHUMP00000016222, ENST00000347617, OTTHUMT00000040214
    6. NM_145905.2NP_665912.1  high mobility group protein HMG-I/HMG-Y isoform b

      Status: REVIEWED

      Description
      Transcript Variant: This variant (7) utilizes an alternate in-frame splice site in one of the coding exons and differs in the 5' UTR compared to variant 1. Variant 7 encodes isoform b (also called HMG-Y), which is shorter than isoform a (also called HMG-I) encoded by variant 1.
      Source sequence(s)
      AL354740, BC008832, BC015789
      Consensus CDS
      CCDS4788.1
      UniProtKB/Swiss-Prot
      P17096
      UniProtKB/TrEMBL
      Q5T6U8
      Related
      ENSP00000363230, ENST00000374116

    RefSeqs of Annotated Genomes: Build 37.3

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

    Reference GRCh37.p5 Primary Assembly

    Genomic

    1. NC_000006.11 Reference GRCh37.p5 Primary Assembly

      Range
      34204577..34214008
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate HuRef

    Genomic

    1. AC_000138.1 Alternate HuRef

      Range
      33927318..33936673
      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.

      Supplemental Content

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