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HMG20A high mobility group 20A [ Homo sapiens (human) ]

Gene ID: 10363, updated on 17-Apr-2020

Summary

Official Symbol
HMG20Aprovided by HGNC
Official Full Name
high mobility group 20Aprovided by HGNC
Primary source
HGNC:HGNC:5001
See related
Ensembl:ENSG00000140382 MIM:605534
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
HMGX1; HMGXB1
Expression
Ubiquitous expression in spleen (RPKM 13.0), testis (RPKM 10.4) and 25 other tissues See more
Orthologs

Genomic context

See HMG20A in Genome Data Viewer
Location:
15q24.3
Exon count:
13
Annotation release Status Assembly Chr Location
109.20200228 current GRCh38.p13 (GCF_000001405.39) 15 NC_000015.10 (77420651..77519899)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (77713018..77777945)

Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene pseudopodium enriched atypical kinase 1 Neighboring gene long intergenic non-protein coding RNA 597 Neighboring gene non-histone chromosomal protein HMG-17 pseudogene Neighboring gene uncharacterized LOC101929457 Neighboring gene uncharacterized LOC105370906 Neighboring gene Sharpr-MPRA regulatory region 8640

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

NHGRI GWAS Catalog

Description
Genome-wide association study in individuals of South Asian ancestry identifies six new type 2 diabetes susceptibility loci.
NHGRI GWA Catalog
Genome-wide trans-ancestry meta-analysis provides insight into the genetic architecture of type 2 diabetes susceptibility.
NHGRI GWA Catalog
Stratifying type 2 diabetes cases by BMI identifies genetic risk variants in LAMA1 and enrichment for risk variants in lean compared to obese cases.
NHGRI GWA Catalog
Transferability of type 2 diabetes implicated loci in multi-ethnic cohorts from Southeast Asia.
NHGRI GWA Catalog

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ10739

Gene Ontology Provided by GOA

Function Evidence Code Pubs
DNA binding IEA
Inferred from Electronic Annotation
more info
 
identical protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
chromatin organization NAS
Non-traceable Author Statement
more info
PubMed 
negative regulation of neuron differentiation IEA
Inferred from Electronic Annotation
more info
 
negative regulation of protein sumoylation IEA
Inferred from Electronic Annotation
more info
 
negative regulation of transcription by RNA polymerase II IEA
Inferred from Electronic Annotation
more info
 
regulation of gene expression IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
regulation of transcription, DNA-templated NAS
Non-traceable Author Statement
more info
PubMed 
Component Evidence Code Pubs
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nucleus NAS
Non-traceable Author Statement
more info
PubMed 

General protein information

Preferred Names
high mobility group protein 20A
Names
HMG box domain containing 1
HMG box-containing protein 20A
HMG domain-containing protein 1
HMG domain-containing protein HMGX1

NCBI Reference Sequences (RefSeq)

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.

mRNA and Protein(s)

  1. NM_001304504.2NP_001291433.1  high mobility group protein 20A isoform a

    See identical proteins and their annotated locations for NP_001291433.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks an exon in the 5' UTR compared to variant 1. Variants 1 and 2 encode the same isoform (a).
    Source sequence(s)
    AA233289, AK001601, AK096546
    Consensus CDS
    CCDS10295.1
    UniProtKB/Swiss-Prot
    Q9NP66
    Related
    ENSP00000336856.4, ENST00000336216.9
    Conserved Domains (2) summary
    cd01390
    Location:103168
    HMGB-UBF_HMG-box; class II and III members of the HMG-box superfamily of DNA-binding proteins. These proteins bind the minor groove of DNA in a non-sequence specific fashion and contain two or more tandem HMG boxes. Class II members include non-histone chromosomal ...
    pfam17380
    Location:143291
    DUF5401; Family of unknown function (DUF5401)
  2. NM_001304505.1NP_001291434.1  high mobility group protein 20A isoform b

    See identical proteins and their annotated locations for NP_001291434.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) lacks an exon and uses an alternate splice site in the 5' region, and initiates translation at a downstream start codon, compared to variant 1. The encoded isoform (b) has a shorter N-terminus than isoform a.
    Source sequence(s)
    AA233289, AK001601, AK096546, DA333471, DB068283, DB213761
    UniProtKB/Swiss-Prot
    Q9NP66
    UniProtKB/TrEMBL
    B4DMG1
    Conserved Domains (2) summary
    cd01390
    Location:155
    HMGB-UBF_HMG-box; HMGB-UBF_HMG-box, class II and III members of the HMG-box superfamily of DNA-binding proteins. These proteins bind the minor groove of DNA in a non-sequence specific fashion and contain two or more tandem HMG boxes. Class II members include non-histone ...
    cl25732
    Location:36181
    SMC_N; RecF/RecN/SMC N terminal domain
  3. NM_018200.3NP_060670.1  high mobility group protein 20A isoform a

    See identical proteins and their annotated locations for NP_060670.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longer isoform (a). Variants 1 and 2 encode the same isoform (a).
    Source sequence(s)
    AA233289, AK001601, AK096546, BC021959, DA333471, DB213761
    Consensus CDS
    CCDS10295.1
    UniProtKB/Swiss-Prot
    Q9NP66
    Related
    ENSP00000371133.3, ENST00000381714.7
    Conserved Domains (2) summary
    cd01390
    Location:103168
    HMGB-UBF_HMG-box; class II and III members of the HMG-box superfamily of DNA-binding proteins. These proteins bind the minor groove of DNA in a non-sequence specific fashion and contain two or more tandem HMG boxes. Class II members include non-histone chromosomal ...
    pfam17380
    Location:143291
    DUF5401; Family of unknown function (DUF5401)

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000015.10 Reference GRCh38.p13 Primary Assembly

    Range
    77420651..77519899
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011521158.3XP_011519460.1  high mobility group protein 20A isoform X1

    See identical proteins and their annotated locations for XP_011519460.1

    UniProtKB/Swiss-Prot
    Q9NP66
    Conserved Domains (2) summary
    cd01390
    Location:103168
    HMGB-UBF_HMG-box; class II and III members of the HMG-box superfamily of DNA-binding proteins. These proteins bind the minor groove of DNA in a non-sequence specific fashion and contain two or more tandem HMG boxes. Class II members include non-histone chromosomal ...
    pfam17380
    Location:143291
    DUF5401; Family of unknown function (DUF5401)

RNA

  1. XR_001751049.2 RNA Sequence

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