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

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: mouse all
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Genomic context

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_000006.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

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Expression

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See details

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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
TFAP2A activates HMGA1 to promote glycolysis and lung adenocarcinoma progression.
Title: TFAP2A activates HMGA1 to promote glycolysis and lung adenocarcinoma progression.
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.
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.
HMGA1 induces FGF19 to drive pancreatic carcinogenesis and stroma formation.
Title: HMGA1 induces FGF19 to drive pancreatic carcinogenesis and stroma formation.
HMGA1 Aggravates Oxidative Stress Injury and Inflammatory Responses in IL-1beta-Induced Primary Chondrocytes through the JMJD3/ZEB1 Axis.
Title: HMGA1 Aggravates Oxidative Stress Injury and Inflammatory Responses in IL-1β-Induced Primary Chondrocytes through the JMJD3/ZEB1 Axis.
Long non-coding RNA MYU promotes ovarian cancer cell proliferation by sponging miR-6827-5p and upregulating HMGA1.
Title: Long non-coding RNA MYU promotes ovarian cancer cell proliferation by sponging miR-6827-5p and upregulating HMGA1.
Association between HMGA1 and immunosuppression in hepatocellular carcinoma: A comprehensive bioinformatics analysis.
Title: Association between HMGA1 and immunosuppression in hepatocellular carcinoma: A comprehensive bioinformatics analysis.
ST8SIA6-AS1 contributes to hepatocellular carcinoma progression by targeting miR-142-3p/HMGA1 axis.
Title: ST8SIA6-AS1 contributes to hepatocellular carcinoma progression by targeting miR-142-3p/HMGA1 axis.
Mast cells impair melanoma cell homing and metastasis by inhibiting HMGA1 secretion.
Title: Mast cells impair melanoma cell homing and metastasis by inhibiting HMGA1 secretion.

Submit: New GeneRIF Correction See all GeneRIFs (218)

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

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

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

G11813 (e-PCR)
- UniSTS:77671

MARC_1047-1048:991929773:1 (e-PCR)
- UniSTS:230835

RH46847 (e-PCR)
- UniSTS:90097

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

Process	Evidence Code	Pubs
involved_in DNA unwinding involved in DNA replication	NAS Non-traceable Author Statement 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 more info	PubMed
located_in nucleoplasm	TAS Traceable Author Statement more info
located_in nucleus	HDA more info	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

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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

NG_029020.1 RefSeqGene

Range

5074..14432

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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
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
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
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
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
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
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
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
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
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
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
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_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000006.12 Reference GRCh38.p14 Primary Assembly

Range

34236873..34246231

Download

GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

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

NM_145904.1: Suppressed sequence

Description

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