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

    Gene ID: 9324, updated on 14-Nov-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
    mouse all
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    Genomic context

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    See HMGN3 in Genome Data Viewer
    Location:
    6q14.1
    Exon count:
    7
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (79201245..79234682, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (80378935..80412370, complement)
    RS_2024_09 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 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?
    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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    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)

    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 chromatin organization IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    located_in 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_2024_08

    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

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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