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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

HMGA1 Gene

protein-coding   GIFtS: 67
GCID: GC06P036298

High Mobility Group AT-Hook 1

(Previous name: high-mobility group (nonhistone chromosomal) protein isoforms...)
(Previous symbol: HMGIY)
Microbiology & Infectious Diseases Congress
  See related diseases
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
About This Section

This gene clusters with an RNA gene
Subcategory (RNA class): lncRNA

Quality score for the ORGUL clustered with this gene is 3

Aliases
High Mobility Group AT-Hook 11 2     HMG-R2
HMGIY1 2 3 5     HMGA1A2
High-Mobility Group (Nonhistone Chromosomal) Protein Isoforms I And Y1 2     High Mobility Group Protein HMG-I/HMG-Y2
High Mobility Group Protein A12 3     Nonhistone Chromosomal High-Mobility Group Protein HMG-I/HMG-Y2
High Mobility Group Protein R2 3     High Mobility Group AT-Hook Protein 13
HMG-I(Y)2 3     

External Ids:    HGNC: 50101   Entrez Gene: 31592   Ensembl: ENSG000001373097   OMIM: 6007015   UniProtKB: P170963   
ORGUL members:         
NONCODE14:n342882      

Export aliases for HMGA1 gene to outside databases

Previous GC identifers: GC06P034206 GC06P034251 GC06P034312 GC06P034205 GC06P033927 GC06P034209 GC06P034445 GC06P035768


(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

Entrez Gene summary for HMGA1 Gene:
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)

GeneCards Summary for HMGA1 Gene: 
HMGA1 (high mobility group AT-hook 1) is a protein-coding gene, and is affiliated with the lncRNA class. Diseases associated with HMGA1 include ring chromosome 1, and pelvic lipomatosis, and among its related super-pathways are Integration of provirus and Integration of viral DNA into host genomic DNA. GO annotations related to this gene include enzyme binding and sequence-specific DNA binding transcription factor activity.

UniProtKB/Swiss-Prot: HMGA1_HUMAN, P17096
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 Wiki entry for HMGA1 Gene


(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 73), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000006.11  NT_007592.15  NC_018917.2  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the HMGA1 gene promoter:
         TBP   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search SABiosciences Chromatin IP Primers for HMGA1

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat HMGA1


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 6p21   Ensembl cytogenetic band:  6p21.31   HGNC cytogenetic band: 6p21

HMGA1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
HMGA1 gene location

GeneLoc information about chromosome 6         GeneLoc Exon Structure

GeneLoc location for GC06P036298:  view genomic region     (about GC identifiers)

Start:
34,204,577 bp from pter      End:
34,214,008 bp from pter
Size:
9,432 bases      Orientation:
plus strand

(According to UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MAXQB RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Ontologies according to Gene Ontology Consortium 01 Oct 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
About This Section

UniProtKB/Swiss-Prot: HMGA1_HUMAN, P17096 (See protein sequence)
Recommended Name: High mobility group protein HMG-I/HMG-Y  
Size: 107 amino acids; 11676 Da
Subunit: Interacts with HIPK2 (By similarity). Interacts with HIV-1 pre-integration complex
Subcellular location: Nucleus. Chromosome
Mass spectrometry: Mass=11750; Mass_error=12; Method=MALDI; Range=2-107 (P17096-1); Note=With 1 acetyl and 2
phosphate groups; Source=PubMed:15835918;
Mass spectrometry: Mass=11828; Mass_error=12; Method=MALDI; Range=2-107 (P17096-1); Note=With 1 acetyl and 3
phosphate groups; Source=PubMed:15835918;
Mass spectrometry: Mass=11765; Mass_error=12; Method=MALDI; Range=2-107 (P17096-1); Note=With 1 acetyl, 1 methyl
and 2 phosphate groups; Source=PubMed:15835918;
Mass spectrometry: Mass=11844; Mass_error=12; Method=MALDI; Range=2-107 (P17096-1); Note=With 1 acetyl, 1 methyl
and 3 phosphate groups; Source=PubMed:15835918;
Mass spectrometry: Mass=11780; Mass_error=12; Method=MALDI; Range=2-107 (P17096-1); Note=With 1 acetyl, 2 methyl
and 2 phosphate groups; Source=PubMed:15835918;
Mass spectrometry: Mass=11858; Mass_error=12; Method=MALDI; Range=2-107 (P17096-1); Note=With 1 acetyl, 2 methyl
and 3 phosphate groups; Source=PubMed:15835918;
4 PDB 3D structures from and Proteopedia for HMGA1:
2EZD (3D)        2EZE (3D)        2EZF (3D)        2EZG (3D)    
Secondary accessions: P10910 Q5T6U9 Q9UKB0
Alternative splicing: 3 isoforms:  P17096-1   P17096-2   P17096-3   (Contains a phosphothreonine at position 42)

Explore the universe of human proteins at neXtProt for HMGA1: NX_P17096

Explore proteomics data for HMGA1 at MOPED 

Post-translational modifications:

  • UniProtKB: 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
  • UniProtKB: HMG-Y is not methylated
  • UniProtKB: Methylation at Arg-58 is mutually exclusive with methylation at Arg-60
  • View modification sites using PhosphoSitePlus
  • View neXtProt modification sites for NX_P17096

  • HMGA1 Protein expression data from MOPED1, PaxDb2 and MAXQB3 :    About this image 

    HMGA1 Protein Expression
    REFSEQ proteins (6 alternative transcripts): 
    NP_002122.1  NP_665906.1  NP_665908.1  NP_665909.1  NP_665910.1  NP_665912.1  

    ENSEMBL proteins: 
     ENSP00000288245   ENSP00000385693   ENSP00000308227   ENSP00000378452   ENSP00000399888  
     ENSP00000363230  
    Reactome Protein details: P17096
    Human Recombinant Protein Products for HMGA1: 
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    Gene Ontology (GO): 5/6 cellular component terms (GO ID links to tree view) (see all 6):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000785chromatin ----
    GO:0005634nucleus IDA16901784
    GO:0005654nucleoplasm TAS--
    GO:0005667transcription factor complex TAS10428834
    GO:0005829cytosol TAS--

    HMGA1 for ontologies           About GeneDecksing



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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section
    HGNC Gene Families: 
    HMG: High-mobility group / Canonical

    4 InterPro protein domains:
     IPR020478 AT_hook-like
     IPR017956 AT_hook_DNA-bd_motif
     IPR000116 HMGI/HMGY
     IPR000637 HMGI/Y_DNA-bd_CS

    Graphical View of Domain Structure for InterPro Entry P17096

    ProtoNet protein and cluster: P17096

    1 Blocks protein domain: IPB000116 High mobility group protein (HMGY) signature

    UniProtKB/Swiss-Prot: HMGA1_HUMAN, P17096
    Similarity: Belongs to the HMGA family
    Similarity: Contains 3 A.T hook DNA-binding domains


    HMGA1 for domains           About GeneDecksing


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
    bound targets from SABiosciences, miRNA Gene Targets from miRTarBase, shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Sirion Biotech, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, Vector BioLabs, and Sirion Biotech, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene.)
    About This Section

    Molecular Function:

         UniProtKB/Swiss-Prot Summary: HMGA1_HUMAN, P17096
    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): 5/12 molecular function terms (GO ID links to tree view) (see all 12):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003677DNA binding TAS10871404
    GO:0003680AT DNA binding TAS10428834
    GO:0003700sequence-specific DNA binding transcription factor activity IMP10428834
    GO:0003906DNA-(apurinic or apyrimidinic site) lyase activity IDA19465398
    GO:0005515protein binding IPI10428834
         
    HMGA1 for ontologies           About GeneDecksing


    Phenotypes:
         1 GenomeRNAi human phenotype for HMGA1:
     Increased G1 DNA content 

         9 MGI mutant phenotypes (inferred from 5 alleles(MGI details for Hmga1):
     cardiovascular system  endocrine/exocrine gland  growth/size  hematopoietic system  homeostasis/metabolism 
     immune system  no phenotypic analysis  reproductive system  tumorigenesis 

    HMGA1 for phenotypes           About GeneDecksing

    Animal Models:
         MGI mouse knock-outs for HMGA1: Hmga1tm1Afus Hmga1tm1Brun Hmga1tm1Cha Hmga1tm2Afus

       inGenious Targeting Laboratory - Custom generated mouse model solutions for HMGA1 
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       genOway customized Knockin model: humanization, point mutation, expression monitoring, etc. for HMGA1 

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    QIAGEN Custom miScript Target Protector blocks miRNA-binding site of human, mouse, rat HMGA1
    8/54 QIAGEN miScript miRNA Assays for microRNAs that regulate HMGA1 (see all 54):
    hsa-miR-596 hsa-let-7d hsa-miR-4272 hsa-miR-1224-3p hsa-miR-15a hsa-miR-486-3p hsa-miR-3916 hsa-let-7g
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    (Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to SABiosciences, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene).
    About This Section

    SuperPaths for HMGA1 About   (see all 13)                                                                                              See pathways by source

    SuperPathContained pathways About
    1Integration of provirus
    Integration of provirus0.88
    Early Phase of HIV Life Cycle0.73
    2-LTR circle formation0.88
    2Integration of viral DNA into host genomic DNA
    Integration of viral DNA into host genomic DNA0.60
    APOBEC3G mediated resistance to HIV-1 infection0.60
    Autointegration results in viral DNA circles0.60
    3HIV Life Cycle
    HIV Life Cycle0.92
    Host Interactions of HIV factors0.60
    HIV Infection0.61
    4Regulation of Glucokinase by Glucokinase Regulatory Protein
    Vpr-mediated nuclear import of PICs0.91
    Interactions of Vpr with host cellular proteins0.91
    5Immune response IL-2 activation and signaling pathway
    Immune response IL-2 activation and signaling pathway0.41

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways

    1 EMD Millipore Pathway for HMGA1
        Immune response IL-2 activation and signaling pathway

    1 Downloadable PowerPoint Slide of QIAGEN Pathway Central Maps for HMGA1
        iNOS Signaling

    1 Cell Signaling Technology (CST) Pathway for HMGA1
        Chromatin Regulation / Acetylation

    1 GeneGo (Thomson Reuters) Pathway for HMGA1
        Immune response IL-2 activation and signaling pathway

    5 BioSystems Pathways for HMGA1
        Senescence and Autophagy
    Adipogenesis
    IL-4 signaling Pathway
    IL4-mediated signaling events
    Validated targets of C-MYC transcriptional activation


    5/12        Reactome Pathways for HMGA1 (see all 12)
        Interactions of Vpr with host cellular proteins
    Early Phase of HIV Life Cycle
    Disease
    Host Interactions of HIV factors
    HIV Life Cycle



    HMGA1 for pathways           About GeneDecksing

    Interactions:

        SABiosciences Gene Network CentralTM Interacting Genes and Proteins Network for HMGA1

    STRING Interaction Network Preview (showing 5 interactants - click image to see 25)

    5/81 Interacting proteins for HMGA1 (P170961, 2, 3 ENSP000003082274) via UniProtKB, MINT, STRING, and/or I2D (see all 81)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    SP1P080472, 3, ENSP000003293574MINT-49729 MINT-49730 MINT-49727 MINT-49728 I2D: score=4 STRING: ENSP00000329357
    CEBPBP176762, 3, ENSP000003054224MINT-49733 MINT-49732 MINT-49731 I2D: score=6 STRING: ENSP00000305422
    ORC2Q134162, 3, ENSP000002342964MINT-7295311 I2D: score=1 STRING: ENSP00000234296
    PRMT6Q96LA81, 3, ENSP000003551454EBI-746854,EBI-912440 I2D: score=1 STRING: ENSP00000355145
    ELF1P325193, ENSP000002398824I2D: score=4 STRING: ENSP00000239882
    About this table

    Gene Ontology (GO): 5/17 biological process terms (GO ID links to tree view) (see all 17):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006268DNA unwinding involved in DNA replication NAS10428834
    GO:0006284base-excision repair IDA19465398
    GO:0006337nucleosome disassembly TAS10428834
    GO:0006351transcription, DNA-dependent IEA--
    GO:0006355regulation of transcription, DNA-dependent TAS10871404

    HMGA1 for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
    About This Section

    HMGA1 for compounds           About GeneDecksing

    Browse Small Molecules at EMD Millipore
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    Browse Tocris compounds for HMGA1

    10/31 Novoseek inferred chemical compound relationships for HMGA1 gene (see all 31)    About this table
    Compound   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    hmga 95.2 8 12930952 (2), 14714251 (1), 19687300 (1), 18670638 (1) (see all 7)
    mevalonate 80.5 34 9237866 (4), 8970163 (2), 10506194 (2), 10698924 (2) (see all 22)
    3-hydroxy-3-methylglutaryl-coa 79.1 24 15686906 (2), 11349148 (1), 15949312 (1), 17516993 (1) (see all 20)
    sterol 69 23 1657912 (3), 12142284 (2), 7534808 (1), 20041128 (1) (see all 16)
    27-hydroxycholesterol 63.7 4 18024962 (2), 17516993 (1), 19401598 (1)
    25-hydroxycholesterol 62.9 10 10333389 (2), 15136164 (2), 8057282 (1), 10506194 (1)
    lovastatin 62.7 19 9869647 (2), 10506194 (2), 15755505 (2), 17213228 (2) (see all 10)
    ptms 62.2 7 17455969 (4), 16752910 (1), 17960875 (1), 15591590 (1)
    dbds 61.4 3 11087394 (1), 11034995 (1)
    lanosterol 58.6 10 10333389 (3), 7840615 (2), 1657912 (1), 18024962 (1)

    Search CenterWatch for drugs/clinical trials and news about HMGA1

    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    Conferences by KenesGroup, exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
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    About This Section

    REFSEQ mRNAs for HMGA1 gene (7 alternative transcripts): 
    NM_002131.3  NM_145899.2  NM_145901.2  NM_145902.2  NM_145903.2  NM_145905.2  NM_145904.1  

    Unigene Clusters for HMGA1:

    High mobility group AT-hook 1
    Hs.518805  [show with all ESTs], Hs.703764  [show with all ESTs]
    Unigene Representative Sequences: BC078664, BG027840
    7 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000347617(uc003oiy.3 uc003ojd.3) ENST00000401473(uc003oiv.3 uc003oiw.3 uc003oix.3)
    ENST00000311487(uc003oit.3 uc011dso.2 uc003oiu.3) ENST00000478214
    ENST00000395004 ENST00000447654(uc003oiz.3 uc003oja.3) ENST00000374116(uc003ojc.3)

    Congresses - knowledge worth sharing:  
    European Congress of Clinical Microbiology and Infectious Diseases (ECCMID) 10 - 13 May 2014

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    Additional mRNA sequence: BC071863.1 

    24/80 DOTS entries (see all 80):

    DT.100701974  DT.99926692  DT.453256  DT.100844933  DT.97823072  DT.100701923  DT.85104951  DT.100701978 
    DT.99926682  DT.95156524  DT.100701929  DT.91833221  DT.100040080  DT.121373399  DT.100701910  DT.100701937 
    DT.100860391  DT.92051550  DT.100701917  DT.100701950  DT.100701931  DT.100701955  DT.100701954  DT.91728915 

    24/2021 AceView cDNA sequences (see all 2021):

    BQ648276 BM828836 BM764148 BM558839 BM836500 BU557034 CB120811 BM766747 
    BQ690867 BM846657 BU931153 BU931779 BE255828 BQ230516 BU162902 BE797718 
    BM761227 AU124872 BF111433 CR596333 BM423604 BM842868 BU848667 N99526 

    GeneLoc Exon Structure

    5/24 Alternative Splicing Database (ASD) splice patterns (SP) for HMGA1 (see all 24)    About this scheme

    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:                                                  -     -                 -     -     -                                               -     -               

    ExUns: 13c · 13d
    SP1:            
    SP2:            
    SP3:            
    SP4:            
    SP5:            


    ECgene alternative splicing isoforms for HMGA1

    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
    About This Section

    HMGA1 expression in normal human tissues (normalized intensities)      HMGA1 embryonic expression: see
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: ATTTGTCCCA
    HMGA1 Expression
    About this image


    HMGA1 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database 
     5/12 selected tissues (see all 12) fully expand
     
     Gut Tube (Gastrointestinal Tract)    fully expand to see all 3 entries
             Hindgut
     
     Nose (Sensory Organs)    fully expand to see all 2 entries
             sensory organ/nose/nasal cavity   
     
     Lung (Respiratory System)    fully expand to see all 2 entries
             visceral organ/lung/right lung   
     
     Bone (Muscoskeletal System)
             Human Vertebral Mesenchymal Stem Cells (HVMSC)   
     
     Inner Cell Mass (Early Embryonic Tissues)
             Sox17-GFP genetically modified stem cells

    See HMGA1 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for HMGA1

    SOURCE GeneReport for Unigene clusters: Hs.518805 Hs.703764
        SABiosciences Expression via Pathway-Focused PCR Arrays including HMGA1: 
              HIV Host Response in human mouse rat
              Nuclear Receptors & Coregulators in human mouse rat
              JAK / STAT Signaling Pathway in human mouse rat

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    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
    About This Section

    This gene was present in the common ancestor of chordates.

    Orthologs for HMGA1 gene from 4/9 species (see all 9)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Hmga15
    Hmga1-rs11
    high mobility group AT-hook 15
    high mobility group AT-hook I, related sequence 11
    92.01(n)1
    96.87(a)1
      17 (14.50 cM)5
    1112411  NM_001166476.11  NP_001159948.11 
     275566205 
    chicken
    (Gallus gallus)
    Aves HMGA11 high mobility group AT-hook 1 74.39(n)
    72.63(a)
      378795  NM_204369.1  NP_989700.1 
    lizard
    (Anolis carolinensis)
    Reptilia HMGA16
    --
    --
    63(a)
    10(a)
    1 ↔ 1
    possible ortholog
    4(121529454-121563662)
    GL343667.1(264294-281755)
    zebrafish
    (Danio rerio)
    Actinopterygii hmga1a1 high mobility group AT-hook 1a 58.61(n)
    58.24(a)
      406447  NM_213168.2  NP_998333.1 


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

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for HMGA1 gene

    HMGA1 for paralogs           About GeneDecksing


    5/7 Pseudogenes.org Pseudogenes for HMGA1 (see all 7)
    PGOHUM00000238542 PGOHUM00000239577 PGOHUM00000248528 PGOHUM00000245962 PGOHUM00000243380


    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
    About This Section

    10/281 SNPs in HMGA1 are shown (see all 281)    About this table     
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 6 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1843130011,2
    --33927236(+) TCCCAA/CACGCC 1 -- us2k10--------
    rs1890514191,2
    --33927239(+) CACACA/GCCCCT 1 -- us2k10--------
    rs1814380101,2
    --33927251(+) CCTGCC/TGTCAG 1 -- us2k10--------
    rs1484226851,2
    C--34118055(+) CGAGGC/TGGAAG 3 -- us2k10--------
    rs1860277971,2
    --34202589(+) CTCCCA/CTCCCC 3 -- us2k10--------
    rs1425834451,2
    C--34202629(+) GACGGG/TGAGAG 3 -- us2k10--------
    rs1900059721,2
    --34202639(+) GATGTA/GCCCGA 3 -- us2k10--------
    rs1169046461,2
    F--34202643(+) TACCCG/AAGAGA 3 -- us2k11Minor allele frequency- A:0.01EA 120
    rs578630131,2
    C,F--34202693(+) AGGCCG/ACCAGC 5 -- us2k12Minor allele frequency- A:0.10WA NA 238
    rs1826392301,2
    --34202839(+) TGGAGA/GCTGAG 5 -- us2k10--------

    HapMap Linkage Disequilibrium report for HMGA1 (34204577 - 34214008 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 5 variations for HMGA1:    About this table     
    Variant IDTypeSubtypePubMed ID
    nsv885784CNV Loss21882294
    dgv6830n71CNV Loss21882294
    nsv885781CNV Loss21882294
    esv24915CNV Loss19812545
    nsv823666CNV Gain20364138


    Human Gene Mutation Database (HGMD): HMGA1
    SABiosciences Cancer Mutation PCR Assays
    SeqTarget long-range PCR primers for resequencing HMGA1
    DNA2.0 Custom Variant and Variant Library Synthesis for HMGA1

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Novoseek, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section
    OMIM gene information: 600701    OMIM disorders: --

    UniProtKB/Swiss-Prot: HMGA1_HUMAN, P17096
  • Note=A chromosomal aberration involving HMGA1 is found in pulmonary chondroid hamartoma. Translocation
    t(6;14)(p21;q23-24) with RAD51B

  • 20/58 diseases for HMGA1 (see all 58):    About MalaCards
    ring chromosome 1    pelvic lipomatosis    atypical lipomatous tumor    ring chromosomes
    lipomatosis    xeroderma pigmentosum, group a    benign tumors    ganglioneuroma
    lipoma    dermatofibrosarcoma    dermatofibrosarcoma protuberans    malignant peripheral nerve sheath tumor
    leiomyoma    pleomorphic adenoma    xeroderma pigmentosum    pandas
    thyroid cancer    hypercholesterolemia    gestational diabetes    synovial sarcoma

    1 disease from the University of Copenhagen DISEASES database for HMGA1:
    Pelvic lipomatosis

    HMGA1 for disorders           About GeneDecksing


    Congresses - knowledge worth sharing:  
    Alzheimer's & Parkinson's Diseases Congress (ADPD) 18 - 22 March 2015

    10/35 Novoseek inferred disease relationships for HMGA1 gene (see all 35)    About this table

    Disease   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    neoplastic transformation 75.8 21 11134344 (3), 10945639 (2), 15350136 (1), 19074878 (1) (see all 13)
    lipoma 62.2 20 9212729 (4), 10744071 (3), 12970064 (2), 9187132 (2) (see all 8)
    uterine leiomyoma 52.8 7 9989879 (2), 10472377 (1), 9824199 (1), 10744071 (1)
    hamartoma 49.6 9 9060828 (3), 10744071 (3), 9824199 (1)
    benign tumor 48.7 5 10347561 (1), 11672774 (1), 10744071 (1), 9495195 (1) (see all 5)
    tumors 43.6 99 19820691 (5), 11134344 (4), 10472377 (3), 14714251 (3) (see all 53)
    ganglioneuroma 38.8 1 15650238 (1)
    thyroid carcinoma 35.1 6 19060921 (1), 7731681 (1), 16510570 (1)
    cancer 34.7 54 17510387 (4), 17455969 (3), 19916743 (3), 20408779 (3) (see all 34)
    myxoma 32.5 1 11550285 (1)

    Genetic Association Database (GAD): HMGA1
    Human Genome Epidemiology (HuGE) Navigator: HMGA1 (9 documents)

    Export disorders for HMGA1 gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
    About This Section

    PubMed articles for HMGA1 gene, integrated from 9 sources (see all 401):
    (articles sorted by number of sources associating them with HMGA1)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Organization, inducible-expression and chromosome localization of the human HMG-I(Y) nonhistone protein gene. (PubMed id 8414980)1, 2, 3, 9 Friedmann M.... Reeves R. (1993)
    2. Homeodomain-interacting protein kinase-2 (HIPK2) phosphorylates HMGA1a at Ser-35, Thr-52, and Thr-77 and modulates its DNA binding affinity. (PubMed id 17960875)1, 2, 9 Zhang Q. and Wang Y. (2007)
    3. Tandem mass spectrometry for the examination of the posttranslational modifications of high-mobility group A1 proteins: symmetric and asymmetric dimethylation of Arg25 in HMGA1a protein. (PubMed id 15835918)1, 2, 9 Zou Y. and Wang Y. (2005)
    4. Identification, replication, and fine-mapping of Loci associated with adult height in individuals of african ancestry. (PubMed id 21998595)1, 4 N'Diaye A....Haiman C.A. (2011)
    5. Functional variants of the HMGA1 gene and type 2 diab etes mellitus. (PubMed id 21364139)1, 4 Chiefari E....Brunetti A. (2011)
    6. Human Variation in Alcohol Response Is Influenced by Variation in Neuronal Signaling Genes. (PubMed id 20201926)1, 4 Joslyn G....White R.L. (2010)
    7. The role of height-associated loci identified in geno me wide association studies in the determination of pediatric stature. (PubMed id 20546612)1, 4 Zhao J....Grant S.F. (2010)
    8. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PubMed id 20379614)1, 4 Rose J.E....Uhl G.R. (2010)
    9. Identification of 15 loci influencing height in a Kor ean population. (PubMed id 19893584)1, 4 Kim J.J....Lee J.K. (2010)
    10. Variation at the NFATC2 locus increases the risk of t hiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipr il and rosiglitazone Medication (DREAM) study. (PubMed id 20628086)1, 4 Bailey S.D....Anand S. (2010)

    (in PubMed, OMIM, and NCBI Bookshelf)
    About This Section
     ANDOR
    Aliases
    Disorders
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 3159 HGNC: 5010 AceView: HMGA1 Ensembl:ENSG00000137309 euGenes: HUgn3159
    ECgene: HMGA1 H-InvDB: HMGA1

    (According to HUGE)
    About This Section
      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
    About This Section
    NameDescription
    PharmGKB entry for HMGA1 Pharmacogenomics, SNPs, Pathways
    ATLAS Chromosomes in Cancer entry for HMGA1 Genetics and Cytogenetics in Oncology and Haematology

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section
    Patent Information for HMGA1 gene:
    Search GeneIP for patents involving HMGA1

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



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    About This Section

     
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    GeneCards Homepage - Last full update: 23 Oct 2013 - Incrementals: 3 Nov 2013 , 7 Nov 2013 , 23 Jan 2014

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