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Aliases for HMGA1 Gene

Aliases for HMGA1 Gene

  • High Mobility Group AT-Hook 1 2 3 5
  • High-Mobility Group (Nonhistone Chromosomal) Protein Isoforms I And Y 2 3
  • High Mobility Group Protein A1 3 4
  • High Mobility Group Protein R 3 4
  • HMGIY 3 4
  • Nonhistone Chromosomal High-Mobility Group Protein HMG-I/HMG-Y 3
  • High Mobility Group Protein HMG-I/HMG-Y 3
  • High Mobility Group AT-Hook Protein 1 4
  • HMG-I(Y) 4
  • HMGA1A 3
  • HMG-R 3

External Ids for HMGA1 Gene

Previous HGNC Symbols for HMGA1 Gene

  • HMGIY

Previous GeneCards Identifiers for HMGA1 Gene

  • GC06P034206
  • GC06P034251
  • GC06P034312
  • GC06P034205
  • GC06P033927
  • GC06P034209
  • GC06P034445
  • GC06P035768
  • GC06P036298
  • GC06P037284
  • GC06P034920
  • GC06P035503
  • GC06P037624
  • GC06P038313
  • GC06P038953

Summaries for HMGA1 Gene

Entrez Gene Summary for HMGA1 Gene

  • 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]

GeneCards Summary for HMGA1 Gene

HMGA1 (High Mobility Group AT-Hook 1) is a Protein Coding gene. Diseases associated with HMGA1 include Diabetes Mellitus, Noninsulin-Dependent and Ring Chromosome 1. Among its related pathways are Transport of the SLBP independent Mature mRNA and Validated targets of C-MYC transcriptional activation. GO annotations related to this gene include enzyme binding and ligand-dependent nuclear receptor transcription coactivator activity.

UniProtKB/Swiss-Prot for HMGA1 Gene

  • HMG-I/Y bind preferentially to the minor groove of A+T rich regions in double-stranded DNA. It is suggested that these proteins could function in nucleosome phasing and in the 3-end processing of mRNA transcripts. They are also involved in the transcription regulation of genes containing, or in close proximity to A+T-rich regions.

Gene Wiki entry for HMGA1 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for HMGA1 Gene

Genomics for HMGA1 Gene

Regulatory Elements for HMGA1 Gene

Enhancers for HMGA1 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH06G034223 2 FANTOM5 Ensembl ENCODE dbSUPER 5.2 -12.4 -12363 2.7 HDGF ARNT ARID4B SIN3A YBX1 DMAP1 ZNF2 ZBTB7B ZNF766 ZNF207 RPS10 ITPR3 LEMD2 DAXX RGL2 WDR46 B3GALT4 VPS52 HCG25 NUDT3
GH06G033837 1.7 Ensembl ENCODE dbSUPER 5.5 -396.9 -396900 4.2 HDGF PKNOX1 FOXA2 CREB3L1 ARNT ARID4B SIN3A DMAP1 ZNF2 ZBTB7B LEMD2 RING1 RXRB VPS52 WDR46 SYNGAP1 BRD2 IP6K3 DAXX ITPR3
GH06G034181 1.3 FANTOM5 Ensembl ENCODE 4.5 -54.0 -54022 1.7 CTCF PKNOX1 MXI1 CBX3 USF1 MAX POLR2A NFYB EED SMC3 GRM4 IP6K3 LEMD2 RPS10 HMGA1 KRT18P9
GH06G034663 1.9 FANTOM5 Ensembl ENCODE dbSUPER 2.8 +427.7 427658 3.4 HDGF PKNOX1 ATF1 FOXA2 ARNT YY1 ZNF766 ELK1 CAVIN1 JUNB UHRF1BP1 ENSG00000220643 C6orf106 FANCE HMGA1 GC06M037428 RN7SL200P GC06P041046
GH06G033842 1 dbSUPER 5.3 -392.0 -391993 5.1 PKNOX1 ZFP64 ARID4B SIN3A ZNF48 SLC30A9 ZNF766 ZNF143 NCOA1 MXD4 SYNGAP1 MLN LEMD2 GRM4 MIR1275 IP6K3 HMGA1 PIRC26 LOC105375025
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around HMGA1 on UCSC Golden Path with GeneCards custom track

Promoters for HMGA1 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000320387 700 2201 PKNOX1 MLX CREB3L1 ARNT AGO1 ZFP64 WRNIP1 ARID4B SIN3A DMAP1
ENSR00000195912 -900 601 ARNT AGO1 YY1 ETS1 ZNF766 ZNF143 FOS TAF15 REST SMARCB1

Transcription factor binding sites by QIAGEN in the HMGA1 gene promoter:

Genomic Location for HMGA1 Gene

Chromosome:
6
Start:
34,236,800 bp from pter
End:
34,246,231 bp from pter
Size:
9,432 bases
Orientation:
Plus strand

Genomic View for HMGA1 Gene

Genes around HMGA1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
HMGA1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for HMGA1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for HMGA1 Gene

Proteins for HMGA1 Gene

  • Protein details for HMGA1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P17096-HMGA1_HUMAN
    Recommended name:
    High mobility group protein HMG-I/HMG-Y
    Protein Accession:
    P17096
    Secondary Accessions:
    • P10910
    • Q5T6U9
    • Q9UKB0

    Protein attributes for HMGA1 Gene

    Size:
    107 amino acids
    Molecular mass:
    11676 Da
    Quaternary structure:
    • Interacts with HIPK2 (By similarity). Interacts with HIV-1 pre-integration complex.

    Three dimensional structures from OCA and Proteopedia for HMGA1 Gene

    Alternative splice isoforms for HMGA1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for HMGA1 Gene

Post-translational modifications for HMGA1 Gene

  • Constitutively phosphorylated on two or three sites. Hyperphosphorylated at early stages of apoptosis, followed by dephosphorylation and methylation, which coincides with chromatin condensation. Isoforms HMG-I and HMG-Y can be phosphorylated by HIPK2. Phosphorylation of HMG-I at Ser-36, Thr-53 and Thr-78 and of HMG-Y at Thr-42 and Thr-67 by HIPK2 modulates DNA-binding affinity.
  • HMG-Y is not methylated.
  • Methylation at Arg-58 is mutually exclusive with methylation at Arg-60.
  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Antibody Products

  • Cell Signaling Technology (CST) Antibodies for HMGA1 (HMGA1)
  • Cloud-Clone Corp. Antibodies for HMGA1

No data available for DME Specific Peptides for HMGA1 Gene

Domains & Families for HMGA1 Gene

Gene Families for HMGA1 Gene

Suggested Antigen Peptide Sequences for HMGA1 Gene

Graphical View of Domain Structure for InterPro Entry

P17096

UniProtKB/Swiss-Prot:

HMGA1_HUMAN :
  • Belongs to the HMGA family.
Family:
  • Belongs to the HMGA family.
genes like me logo Genes that share domains with HMGA1: view

Function for HMGA1 Gene

Molecular function for HMGA1 Gene

UniProtKB/Swiss-Prot Function:
HMG-I/Y bind preferentially to the minor groove of A+T rich regions in double-stranded DNA. It is suggested that these proteins could function in nucleosome phasing and in the 3-end processing of mRNA transcripts. They are also involved in the transcription regulation of genes containing, or in close proximity to A+T-rich regions.

Gene Ontology (GO) - Molecular Function for HMGA1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001158 enhancer sequence-specific DNA binding IDA 9253416
GO:0001205 transcriptional activator activity, RNA polymerase II distal enhancer sequence-specific binding ISS --
GO:0003677 DNA binding TAS 10871404
GO:0003680 AT DNA binding TAS 10428834
GO:0003682 chromatin binding ISS --
genes like me logo Genes that share ontologies with HMGA1: view
genes like me logo Genes that share phenotypes with HMGA1: view

Animal Model Products

miRNA for HMGA1 Gene

miRTarBase miRNAs that target HMGA1

Inhibitory RNA Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for HMGA1 Gene

Localization for HMGA1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for HMGA1 Gene

Nucleus. Chromosome.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for HMGA1 gene
Compartment Confidence
nucleus 5
cytosol 5
endoplasmic reticulum 2
plasma membrane 1
extracellular 1
mitochondrion 1
peroxisome 1

Gene Ontology (GO) - Cellular Components for HMGA1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IDA 16791210
GO:0005654 nucleoplasm TAS --
GO:0005667 transcription factor complex TAS 10428834
GO:0005694 chromosome IEA --
GO:0005829 cytosol TAS --
genes like me logo Genes that share ontologies with HMGA1: view

Pathways & Interactions for HMGA1 Gene

genes like me logo Genes that share pathways with HMGA1: view

SIGNOR curated interactions for HMGA1 Gene

Is inactivated by:

Gene Ontology (GO) - Biological Process for HMGA1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006268 DNA unwinding involved in DNA replication NAS 10428834
GO:0006284 base-excision repair IBA --
GO:0006337 nucleosome disassembly TAS 10428834
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated TAS 10871404
genes like me logo Genes that share ontologies with HMGA1: view

Drugs & Compounds for HMGA1 Gene

(18) Drugs for HMGA1 Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials

(13) Additional Compounds for HMGA1 Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with HMGA1: view

Transcripts for HMGA1 Gene

Unigene Clusters for HMGA1 Gene

High mobility group AT-hook 1:
Representative Sequences:

Inhibitory RNA Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for HMGA1 Gene

ExUns: 1 ^ 2 ^ 3 ^ 4a · 4b · 4c · 4d · 4e · 4f ^ 5a · 5b · 5c ^ 6 ^ 7 ^ 8 ^ 9a · 9b · 9c · 9d ^ 10a · 10b ^ 11 ^ 12a · 12b ^ 13a · 13b ·
SP1: - - - - - - -
SP2: - - - - - - -
SP3: - - - - - - - -
SP4: - - - - - - - -
SP5: - - - - - - -
SP6: - - - - - - - -
SP7: - - - - - - -
SP8: - - - - - -
SP9: - - - - - - - - - - - -
SP10: - - - - - - - - - -
SP11: - - - - - - - - -
SP12: - - - - - - - - -
SP13: - - - - - - - - -
SP14: - - - - - - - - - -
SP15: - - - - - - - -
SP16: - - - - -
SP17: - - - - - -
SP18: - - - - -
SP19: -
SP20: - - - - - -
SP21: - - - - - - - -
SP22:
SP23: - -
SP24: - - - - - - - -

ExUns: 13c · 13d
SP1:
SP2:
SP3:
SP4:
SP5:
SP6:
SP7:
SP8:
SP9:
SP10:
SP11:
SP12:
SP13:
SP14:
SP15:
SP16:
SP17:
SP18:
SP19:
SP20:
SP21:
SP22:
SP23:
SP24:

Relevant External Links for HMGA1 Gene

GeneLoc Exon Structure for
HMGA1
ECgene alternative splicing isoforms for
HMGA1

Expression for HMGA1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for HMGA1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for HMGA1 Gene

This gene is overexpressed in Esophagus - Mucosa (x4.6).

Protein differential expression in normal tissues from HIPED for HMGA1 Gene

This gene is overexpressed in Peripheral blood mononuclear cells (9.6), Amniocyte (8.2), Tlymphocyte (7.7), Blymphocyte (6.7), and CD8 Tcells (6.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for HMGA1 Gene



Protein tissue co-expression partners for HMGA1 Gene

NURSA nuclear receptor signaling pathways regulating expression of HMGA1 Gene:

HMGA1

SOURCE GeneReport for Unigene cluster for HMGA1 Gene:

Hs.518805

Evidence on tissue expression from TISSUES for HMGA1 Gene

  • Liver(4.9)
  • Pancreas(4.9)
  • Nervous system(4.9)
  • Blood(4.8)
  • Lung(4.8)
  • Skin(4.8)
  • Eye(4.7)
  • Intestine(4.7)
  • Muscle(4.7)
  • Stomach(3.9)
  • Kidney(3.2)
  • Heart(2.9)
  • Bone(2.8)

Phenotype-based relationships between genes and organs from Gene ORGANizer for HMGA1 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • cardiovascular
  • digestive
  • endocrine
  • immune
  • integumentary
  • nervous
  • reproductive
  • skeletal muscle
  • skeleton
  • urinary
Organs:
Head and neck:
  • brain
  • ear
  • eye
  • head
  • jaw
  • mandible
  • maxilla
  • mouth
  • neck
  • skull
Thorax:
  • chest wall
  • clavicle
  • heart
  • rib
  • rib cage
  • scapula
  • sternum
Abdomen:
  • kidney
  • liver
  • pancreas
Pelvis:
  • ovary
  • pelvis
  • uterus
Limb:
  • ankle
  • arm
  • digit
  • elbow
  • femur
  • fibula
  • finger
  • foot
  • forearm
  • hand
  • hip
  • humerus
  • knee
  • lower limb
  • radius
  • shin
  • shoulder
  • thigh
  • tibia
  • toe
  • ulna
  • upper limb
  • wrist
General:
  • blood
  • blood vessel
  • peripheral nerve
  • peripheral nervous system
  • skin
  • spinal column
  • vertebrae
  • white blood cell
genes like me logo Genes that share expression patterns with HMGA1: view

No data available for mRNA Expression by UniProt/SwissProt for HMGA1 Gene

Orthologs for HMGA1 Gene

This gene was present in the common ancestor of chordates.

Orthologs for HMGA1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia HMGA1 34 35
  • 100 (n)
cow
(Bos Taurus)
Mammalia HMGA1 35
  • 98 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Hmga1 35
  • 97 (a)
OneToMany
Hmga1-rs1 34 16 35
  • 91.9 (n)
dog
(Canis familiaris)
Mammalia HMGA1 34 35
  • 95.33 (n)
oppossum
(Monodelphis domestica)
Mammalia HMGA1 35
  • 94 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Hmga1 34
  • 90.97 (n)
chicken
(Gallus gallus)
Aves HMGA1 34
  • 74.51 (n)
lizard
(Anolis carolinensis)
Reptilia HMGA1 35
  • 67 (a)
OneToOne
zebrafish
(Danio rerio)
Actinopterygii hmga1b 35
  • 52 (a)
OneToMany
hmga1a 35
  • 51 (a)
OneToMany
Species where no ortholog for HMGA1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for HMGA1 Gene

ENSEMBL:
Gene Tree for HMGA1 (if available)
TreeFam:
Gene Tree for HMGA1 (if available)

Paralogs for HMGA1 Gene

Pseudogenes.org Pseudogenes for HMGA1 Gene

genes like me logo Genes that share paralogs with HMGA1: view

No data available for Paralogs for HMGA1 Gene

Variants for HMGA1 Gene

Sequence variations from dbSNP and Humsavar for HMGA1 Gene

SNP ID Clin Chr 06 pos Sequence Context AA Info Type
rs1000055979 -- 34,236,150(+) CTCCA(A/G)AACAC upstream-variant-2KB
rs1000097676 -- 34,239,965(+) TCTGA(A/C)AAAGT intron-variant, upstream-variant-2KB
rs1000159077 -- 34,236,368(+) CTGAC(-/A)ACCTG upstream-variant-2KB
rs1000396258 -- 34,246,423(+) AAAAT(A/G)TATAC downstream-variant-500B, utr-variant-3-prime
rs1000947920 -- 34,236,759(+) CGGCG(A/G)CGGCG upstream-variant-2KB

Structural Variations from Database of Genomic Variants (DGV) for HMGA1 Gene

Variant ID Type Subtype PubMed ID
dgv10616n54 CNV gain 21841781
dgv10617n54 CNV gain 21841781
esv24915 CNV loss 19812545
nsv1137544 CNV deletion 24896259
nsv602863 CNV loss 21841781
nsv602865 CNV loss 21841781
nsv602866 CNV loss 21841781
nsv823666 CNV gain 20364138
nsv969388 CNV duplication 23825009

Variation tolerance for HMGA1 Gene

Residual Variation Intolerance Score: 55.9% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.81; 34.03% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for HMGA1 Gene

Human Gene Mutation Database (HGMD)
HMGA1
SNPedia medical, phenotypic, and genealogical associations of SNPs for
HMGA1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for HMGA1 Gene

Disorders for HMGA1 Gene

MalaCards: The human disease database

(10) MalaCards diseases for HMGA1 Gene - From: OMIM, ClinVar, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
diabetes mellitus, noninsulin-dependent
  • diabetes, type 2
ring chromosome 1
  • chromosome 1 ring
ectomesenchymoma
  • rhabdomyosarcoma with ganglionic differentiation
pelvic lipomatosis
  • excess of mature unencapsulated fatty tissue in the pelvis
malignant ectomesenchymoma
  • ectomesenchymoma
- elite association - COSMIC cancer census association via MalaCards
Search HMGA1 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

HMGA1_HUMAN
  • Note=A chromosomal aberration involving HMGA1 is found in pulmonary chondroid hamartoma. Translocation t(6;14)(p21;q23-24) with RAD51B. {ECO:0000269 PubMed:11978964}.

Relevant External Links for HMGA1

Genetic Association Database (GAD)
HMGA1
Human Genome Epidemiology (HuGE) Navigator
HMGA1
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
HMGA1
genes like me logo Genes that share disorders with HMGA1: view

No data available for Genatlas for HMGA1 Gene

Publications for HMGA1 Gene

  1. Organization, inducible-expression and chromosome localization of the human HMG-I(Y) nonhistone protein gene. (PMID: 8414980) Friedmann M. … Reeves R. (Nucleic Acids Res. 1993) 2 3 4 22 64
  2. Homeodomain-interacting protein kinase-2 (HIPK2) phosphorylates HMGA1a at Ser-35, Thr-52, and Thr-77 and modulates its DNA binding affinity. (PMID: 17960875) Zhang Q. … Wang Y. (J. Proteome Res. 2007) 3 4 22 64
  3. Serine ADP-ribosylation depends on HPF1. (PMID: 28190768) Bonfiglio J.J. … Matic I. (Mol. Cell 2017) 3 4 64
  4. Functional variants of the HMGA1 gene and type 2 diabetes mellitus. (PMID: 21364139) Chiefari E. … Brunetti A. (JAMA 2011) 3 46 64
  5. Identification, replication, and fine-mapping of Loci associated with adult height in individuals of african ancestry. (PMID: 21998595) N'Diaye A. … Haiman C.A. (PLoS Genet. 2011) 3 46 64

Products for HMGA1 Gene

Sources for HMGA1 Gene

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