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

Gene ID: 3159, updated on 12-Jun-2018
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]
Expression
Broad expression in lymph node (RPKM 58.3), bone marrow (RPKM 57.3) and 23 other tissues See more
Orthologs
See HMGA1 in Genome Data Viewer
Location:
6p21.31
Exon count:
7
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 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 NFE2L2 motif-containing MPRA enhancer 296 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
not available

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) endonuclease activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
DNA-binding transcription factor activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
RNA polymerase II transcription factor activity, sequence-specific DNA binding ISA
Inferred from Sequence Alignment
more info
 
RNA polymerase II transcription factor activity, sequence-specific DNA binding ISM
Inferred from Sequence Model
more info
PubMed 
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 
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 binding IDA
Inferred from Direct Assay
more info
PubMed 
transcriptional activator activity, RNA polymerase II distal enhancer sequence-specific DNA 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
PubMed 
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 by RNA polymerase II ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of transcription, DNA-templated IMP
Inferred from Mutant Phenotype
more info
PubMed 
protein-containing complex assembly TAS
Traceable Author Statement
more info
PubMed 
regulation of transcription, DNA-templated IBA
Inferred from Biological aspect of Ancestor
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 by RNA polymerase II 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 HDA PubMed 
nucleoplasm TAS
Traceable Author Statement
more info
 
nucleus HDA PubMed 
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
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 109 details...Open this link in a new tab

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000006.12 Reference GRCh38.p12 Primary Assembly

    Range
    34236800..34246231
    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