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

Gene ID: 3159, updated on 3-Nov-2024

Summary

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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
mouse all
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Genomic context

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See HMGA1 in Genome Data Viewer
Location:
6p21.31
Exon count:
6
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (34236873..34246231)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (34060576..34069936)
RS_2024_09 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

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues 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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. NAT10 Promotes Prostate Cancer Growth and Metastasis by Acetylating mRNAs of HMGA1 and KRT8.
    Title: NAT10 Promotes Prostate Cancer Growth and Metastasis by Acetylating mRNAs of HMGA1 and KRT8.
  2. HMGA1 orchestrates chromatin compartmentalization and sequesters genes into 3D networks coordinating senescence heterogeneity.
    Title: HMGA1 orchestrates chromatin compartmentalization and sequesters genes into 3D networks coordinating senescence heterogeneity.
  3. HMGA1 regulates trabectedin sensitivity in advanced soft-tissue sarcoma (STS): A Spanish Group for Research on Sarcomas (GEIS) study.
    Title: HMGA1 regulates trabectedin sensitivity in advanced soft-tissue sarcoma (STS): A Spanish Group for Research on Sarcomas (GEIS) study.
  4. Hsa_circ_0054220 Upregulates HMGA1 by the Competitive RNA Pattern to Promote Neural Impairment in MPTP Model of Parkinson's Disease.
    Title: Hsa_circ_0054220 Upregulates HMGA1 by the Competitive RNA Pattern to Promote Neural Impairment in MPTP Model of Parkinson's Disease.
  5. HMGA1 sensitizes esophageal squamous cell carcinoma to mTOR inhibitors through the ETS1-FKBP12 axis.
    Title: HMGA1 sensitizes esophageal squamous cell carcinoma to mTOR inhibitors through the ETS1-FKBP12 axis.
  6. m6A-mediated lncRNA NEAT1 plays an oncogenic role in non-small cell lung cancer by upregulating the HMGA1 expression through binding miR-361-3p.
    Title: m6A-mediated lncRNA NEAT1 plays an oncogenic role in non-small cell lung cancer by upregulating the HMGA1 expression through binding miR-361-3p.
  7. TFAP2A activates HMGA1 to promote glycolysis and lung adenocarcinoma progression.
    Title: TFAP2A activates HMGA1 to promote glycolysis and lung adenocarcinoma progression.
  8. Proteomics screening uncovers HMGA1 as a promising negative regulator for gamma-globin expression in response to decreased beta-globin levels.
    Title: Proteomics screening uncovers HMGA1 as a promising negative regulator for γ-globin expression in response to decreased β-globin levels.
  9. Targeting HMGA1 contributes to immunotherapy in aggressive breast cancer while suppressing EMT.
    Title: Targeting HMGA1 contributes to immunotherapy in aggressive breast cancer while suppressing EMT.
  10. HMGA1 induces FGF19 to drive pancreatic carcinogenesis and stroma formation.
    Title: HMGA1 induces FGF19 to drive pancreatic carcinogenesis and stroma formation.
Submit: New GeneRIF Correction See all GeneRIFs (223)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description Tests
Type 2 diabetes mellitus
MedGen: C0011860 OMIM: 125853 GeneReviews: WFS1 Spectrum Disorder
not available

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

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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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

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • MGC4242, MGC4854, MGC12816

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables 5'-deoxyribose-5-phosphate lyase activity IDA
Inferred from Direct Assay
more info
 PubMed 
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 DNA-(apurinic or apyrimidinic site) endonuclease activity IDA
Inferred from Direct Assay
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 
Process Evidence Code Pubs
involved_in DNA unwinding involved in DNA replication NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in base-excision repair IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in negative regulation of DNA-templated transcription IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in negative regulation of cell population proliferation IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in nucleosome disassembly TAS
Traceable Author Statement
more info
 PubMed 
involved_in oncogene-induced cell senescence IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in positive regulation of DNA-templated transcription IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in positive regulation of transcription by RNA polymerase II ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in regulation of DNA-templated transcription IBA
Inferred from Biological aspect of Ancestor
more info
  
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 
located_in 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

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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)

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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.

Genomic

  1. NG_029020.1 RefSeqGene

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

mRNA and Protein(s)

  1. NM_001319077.2 → NP_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_001319078.2 → NP_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_001319079.2 → NP_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_001319080.2 → NP_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_001319081.2 → NP_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_001319082.2 → NP_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_002131.4 → NP_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_145899.3 → NP_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_145901.3 → NP_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_145902.3 → NP_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_145903.3 → NP_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_145905.3 → NP_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_2024_08

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.
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P17096.3 GenPept UniProtKB/Swiss-Prot:P17096

Gene LinkOut

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