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HMGN3 high mobility group nucleosomal binding domain 3 [ Homo sapiens (human) ]

Gene ID: 9324, updated on 5-Mar-2024

Summary

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Official Symbol
HMGN3provided by HGNC
Official Full Name
high mobility group nucleosomal binding domain 3provided by HGNC
Primary source
HGNC:HGNC:12312
See related
Ensembl:ENSG00000118418 MIM:604502; AllianceGenome:HGNC:12312
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
TRIP7; PNAS-24; PNAS-25
Summary
The protein encoded by this gene binds thyroid hormone receptor beta in the presence of thyroid hormone. The encoded protein, a member of the HMGN protein family, is thought to reduce the compactness of the chromatin fiber in nucleosomes, thereby enhancing transcription from chromatin templates. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. There is a related pseudogene on chromosome 1. [provided by RefSeq, Jan 2016]
Expression
Ubiquitous expression in heart (RPKM 45.8), adrenal (RPKM 40.5) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
6q14.1
Exon count:
7
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (79201245..79234682, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (80378935..80412370, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (79910962..79944399, complement)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene pleckstrin homology domain interacting protein Neighboring gene uncharacterized LOC124901346 Neighboring gene nucleoporin 155kDa pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17345 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17346 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17347 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24767 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:79844665-79845165 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr6:79861851-79862574 Neighboring gene uncharacterized LOC124901347 Neighboring gene MPRA-validated peak5913 silencer Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:79915779-79916280 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:79916281-79916780 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:79939419-79939919 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:79942937-79943727 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:79943728-79944517 Neighboring gene HMGN3 antisense RNA 1 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr6:79966597-79967796 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr6:80022437-80023636 Neighboring gene dnaJ homolog subfamily B member 6-like Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24768 Neighboring gene lung cancer associated lncRNA 1

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
  • 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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Related articles in PubMed

  1. Genome-wide association study identifies HMGN3 locus for spine bone size variation in Chinese. Lei SF, et al. Hum Genet, 2012 Mar. PMID 21947420, Free PMC Article
  2. Differential display RT-PCR analysis of enterovirus-71-infected rhabdomyosarcoma cells reveals mRNA expression responses of multiple human genes with known and novel functions. Leong PW, et al. Virology, 2002 Mar 30. PMID 12033773
  3. WTAP dysregulation-mediated HMGN3-m6A modification inhibited trophoblast invasion in early-onset preeclampsia. Bian Y, et al. FASEB J, 2022 Dec. PMID 36412513
  4. HMGN3 represses transcription of epithelial regulators to promote migration of cholangiocarcinoma in a SNAI2-dependent manner. Sorin S, et al. FASEB J, 2022 Jul. PMID 35635715
  5. A short ORF-encoded transcriptional regulator. Koh M, et al. Proc Natl Acad Sci U S A, 2021 Jan 26. PMID 33468658, Free PMC Article

See all (34) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. WTAP dysregulation-mediated HMGN3-m6A modification inhibited trophoblast invasion in early-onset preeclampsia.
    Title: WTAP dysregulation-mediated HMGN3-m6A modification inhibited trophoblast invasion in early-onset preeclampsia.
  2. HMGN3 represses transcription of epithelial regulators to promote migration of cholangiocarcinoma in a SNAI2-dependent manner.
    Title: HMGN3 represses transcription of epithelial regulators to promote migration of cholangiocarcinoma in a SNAI2-dependent manner.
  3. The SNPs in the region of HMGN3 gene formed a tightly combined haplotype block in both Chinese and Caucasians. The results suggest that the genomic region containing HMGN3 gene may be associated with spine BS in Chinese.
    Title: Genome-wide association study identifies HMGN3 locus for spine bone size variation in Chinese.
  4. loss of HMGN3 impairs glucose-stimulated insulin secretion and leads to a diabetic phenotype.
    Title: The nucleosome binding protein HMGN3 modulates the transcription profile of pancreatic beta cells and affects insulin secretion.
Submit: New GeneRIF Correction

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

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ42187, DKFZp686E20226

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables chromatin binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables nuclear thyroid hormone receptor binding NAS
Non-traceable Author Statement
more info
 PubMed 
enables nucleosomal DNA binding IEA
Inferred from Electronic Annotation
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in biological_process ND
No biological Data available
more info
  
involved_in chromatin organization IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
part_of chromatin IEA
Inferred from Electronic Annotation
more info
  
located_in cytosol IDA
Inferred from Direct Assay
more info
  
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
high mobility group nucleosome-binding domain-containing protein 3
Names
TR-interacting protein 7
thyroid hormone receptor interacting protein 7

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_029598.1 RefSeqGene

    Range
    5057..38494
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001201362.2 → NP_001188291.1  high mobility group nucleosome-binding domain-containing protein 3 isoform c

    See identical proteins and their annotated locations for NP_001188291.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) retains an alternate segment in the 3' region compared to variant 1, which results in a different 3' coding region and 3' UTR. The resulting isoform (c) is shorter and has a distinct C-terminus compared to isoform a.
    Source sequence(s)
    AI028183, AL355796, BU619570, BX641808
    UniProtKB/TrEMBL
    A0A9L9PXD4
    Related
    ENSP00000516488.1, ENST00000706660.1
    Conserved Domains (1) summary
    smart00527
    Location:2 → 87
    HMG17; domain in high mobilty group proteins HMG14 and HMG 17

  2. NM_001201363.2 → NP_001188292.1  high mobility group nucleosome-binding domain-containing protein 3 isoform d

    See identical proteins and their annotated locations for NP_001188292.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) contains an alternate in-frame exon in the 3' coding region compared to variant 1. The resulting isoform (d) is longer than isoform a.
    Source sequence(s)
    AL355796
    Consensus CDS
    CCDS75485.1
    UniProtKB/TrEMBL
    A0A087WZE9, A0A9L9PY81
    Related
    ENSP00000482613.1, ENST00000620514.2
    Conserved Domains (1) summary
    pfam01101
    Location:1 → 96
    HMG14_17; HMG14 and HMG17

  3. NM_001318884.2 → NP_001305813.1  high mobility group nucleosome-binding domain-containing protein 3 isoform e

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) contains an alternate exon in the 3' coding region, which results in a frameshift, compared to variant 1. The resulting isoform (e) is longer and has a distinct C-terminus compared to isoform a.
    Source sequence(s)
    AL355796
    UniProtKB/TrEMBL
    A0A9L9PXC9, A0A9L9PY81
    Related
    ENSP00000516483.1, ENST00000706657.1
    Conserved Domains (1) summary
    pfam01101
    Location:1 → 96
    HMG14_17; HMG14 and HMG17

  4. NM_001318885.2 → NP_001305814.1  high mobility group nucleosome-binding domain-containing protein 3 isoform f

    Status: REVIEWED

    Description
    Transcript Variant: This variant (6) lacks an alternate in-frame exon in the 5' coding region compared to variant 1. The resulting isoform (f) is shorter than isoform a.
    Source sequence(s)
    AL355796
    UniProtKB/Swiss-Prot
    Q15651
    Conserved Domains (1) summary
    pfam01101
    Location:3 → 76
    HMG14_17; HMG14 and HMG17

  5. NM_001318886.2 → NP_001305815.1  high mobility group nucleosome-binding domain-containing protein 3 isoform g

    Status: REVIEWED

    Description
    Transcript Variant: This variant (7) contains an alternate in-frame exon in the 3' coding region compared to variant 1. The resulting isoform (g) is longer than isoform a.
    Source sequence(s)
    AL355796
    Consensus CDS
    CCDS93952.1
    UniProtKB/TrEMBL
    A0A994J3W4, A0A9L9PY81
    Related
    ENSP00000515488.1, ENST00000703810.2
    Conserved Domains (1) summary
    pfam01101
    Location:1 → 95
    HMG14_17; HMG14 and HMG17

  6. NM_001318887.2 → NP_001305816.1  high mobility group nucleosome-binding domain-containing protein 3 isoform h

    Status: REVIEWED

    Description
    Transcript Variant: This variant (8) uses an alternate splice site in the 3' region compared to variant 1, which results in a different 3' coding region and 3' UTR. The resulting isoform (h) is longer and has a distinct C-terminus compared to isoform a.
    Source sequence(s)
    AL355796
    UniProtKB/TrEMBL
    A0A9L9PY81
    Conserved Domains (1) summary
    pfam01101
    Location:1 → 96
    HMG14_17; HMG14 and HMG17

  7. NM_001318888.2 → NP_001305817.1  high mobility group nucleosome-binding domain-containing protein 3 isoform i

    Status: REVIEWED

    Description
    Transcript Variant: This variant (9) lacks an in-frame exon compared to variant 1. The encoded isoform (i) is shorter than isoform a.
    Source sequence(s)
    AL355796
    UniProtKB/Swiss-Prot
    Q15651

  8. NM_004242.4 → NP_004233.1  high mobility group nucleosome-binding domain-containing protein 3 isoform a

    See identical proteins and their annotated locations for NP_004233.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes isoform a.
    Source sequence(s)
    AL355796
    Consensus CDS
    CCDS4988.1
    UniProtKB/Swiss-Prot
    B2RD37, Q15651, Q5HYD3, Q7RTT0, Q969M5, Q9BZT7
    UniProtKB/TrEMBL
    A0A9L9PXD4
    Related
    ENSP00000341267.5, ENST00000344726.10
    Conserved Domains (1) summary
    pfam01101
    Location:1 → 93
    HMG14_17; HMG14 and HMG17

  9. NM_138730.3 → NP_620058.1  high mobility group nucleosome-binding domain-containing protein 3 isoform b

    See identical proteins and their annotated locations for NP_620058.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses an alternate splice site in the 3' coding region, which results in a frameshift, compared to variant 1. The resulting isoform (b) is shorter and has a distinct C-terminus compared to isoform a.
    Source sequence(s)
    AL355796
    Consensus CDS
    CCDS4989.1
    UniProtKB/Swiss-Prot
    Q15651
    Related
    ENSP00000275036.7, ENST00000275036.11
    Conserved Domains (1) summary
    pfam01101
    Location:1 → 77
    HMG14_17; HMG14 and HMG17

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

  1. NC_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    79201245..79234682 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    80378935..80412370 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q15651.2 GenPept UniProtKB/Swiss-Prot:Q15651

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