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    Hmgn3 high mobility group nucleosomal binding domain 3 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 113990, updated on 5-Mar-2024

    Summary

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    Official Symbol
    Hmgn3provided by RGD
    Official Full Name
    high mobility group nucleosomal binding domain 3provided by RGD
    Primary source
    RGD:1359106
    See related
    Ensembl:ENSRNOG00000031032 AllianceGenome:RGD:1359106
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Summary
    Predicted to enable chromatin binding activity. Predicted to be involved in chromatin organization. Predicted to act upstream of or within positive regulation of DNA-binding transcription factor activity; positive regulation of transcription by RNA polymerase II; and regulation of insulin secretion involved in cellular response to glucose stimulus. Predicted to be located in cytosol and nucleoplasm. Predicted to be active in nucleus. Orthologous to human HMGN3 (high mobility group nucleosomal binding domain 3). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Biased expression in Muscle (RPKM 138.0), Spleen (RPKM 128.0) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    Location:
    8q31
    Exon count:
    9
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 8 NC_086026.1 (92902555..92939980, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 8 NC_051343.1 (84022493..84059329, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 8 NC_005107.4 (90628203..90665055, complement)

    Chromosome 8 - NC_086026.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC108351752 Neighboring gene uncharacterized LOC120094214 Neighboring gene platelet-activating factor acetylhydrolase IB subunit alpha2-like Neighboring gene heat shock protein HSP 90-beta-like

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Bibliography

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    Related articles in PubMed

    1. The nucleosome binding protein HMGN3 is expressed in pancreatic alpha-cells and affects plasma glucagon levels in mice. Kurahashi T, et al. J Cell Biochem, 2010 Jan 1. PMID 19885867, Free PMC Article
    2. Chromosomal proteins HMGN3a and HMGN3b regulate the expression of glycine transporter 1. West KL, et al. Mol Cell Biol, 2004 May. PMID 15082770, Free PMC Article
    3. The nucleosome binding protein HMGN3 modulates the transcription profile of pancreatic beta cells and affects insulin secretion. Ueda T, et al. Mol Cell Biol, 2009 Oct. PMID 19651901, Free PMC Article
    4. HMGN3a and HMGN3b, two protein isoforms with a tissue-specific expression pattern, expand the cellular repertoire of nucleosome-binding proteins. West KL, et al. J Biol Chem, 2001 Jul 13. PMID 11356838
    5. Effects of HMGN variants on the cellular transcription profile. Rochman M, et al. Nucleic Acids Res, 2011 May. PMID 21278158, Free PMC Article

    See all (10) citations in PubMed

    GeneRIFs: Gene References Into Functions

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables chromatin binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables chromatin binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables nucleosomal DNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in chromatin organization IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within regulation of insulin secretion involved in cellular response to glucose stimulus ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within regulation of transcription by RNA polymerase II ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of transcription by RNA polymerase II ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    part_of chromatin IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in cytosol ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nucleoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nucleus ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    high mobility group nucleosome-binding domain-containing protein 3
    Names
    high mobility group nucleosome binding domain 3

    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.

    mRNA and Protein(s)

    1. NM_001007020.2 → NP_001007021.1  high mobility group nucleosome-binding domain-containing protein 3 isoform 2

      See identical proteins and their annotated locations for NP_001007021.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) is not spliced at the 3' end, resulting in an upstream stop codon, as compared to variant 1. The resulting isoform (2) has a shorter and distinct C-terminus, as compared to isoform 1.
      Source sequence(s)
      BC082036, FM058030
      UniProtKB/Swiss-Prot
      Q66H40
      UniProtKB/TrEMBL
      A6I1R0
      Conserved Domains (1) summary
      smart00527
      Location:20 → 87
      HMG17; domain in high mobilty group proteins HMG14 and HMG 17

    2. NM_001201353.1 → NP_001188282.1  high mobility group nucleosome-binding domain-containing protein 3 isoform 1

      See identical proteins and their annotated locations for NP_001188282.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) is a predominant transcript and encodes a longer isoform (1).
      Source sequence(s)
      BC082036, CB774488, FM058030
      UniProtKB/TrEMBL
      A6I1Q8
      Conserved Domains (1) summary
      smart00527
      Location:20 → 94
      HMG17; domain in high mobilty group proteins HMG14 and HMG 17

    3. NM_001201354.1 → NP_001188283.1  high mobility group nucleosome-binding domain-containing protein 3 isoform 3

      See identical proteins and their annotated locations for NP_001188283.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) has an alternate splice site in the 3' region, as compared to variant 1. The resulting isoform (3) has a shorter and distinct C-terminus, as compared to isoform 1.
      Source sequence(s)
      BC082036, CB751211, FM058030
      UniProtKB/TrEMBL
      A6I1Q9
      Conserved Domains (1) summary
      pfam01101
      Location:2 → 73
      HMG14_17; HMG14 and HMG17

    4. NM_001201355.1 → NP_001188284.1  high mobility group nucleosome-binding domain-containing protein 3 isoform 4

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) has an additional exon in the 3' region, as compared to variant 1. The resulting isoform (4) has a longer and distinct C-terminus, as compared to isoform 1.
      Source sequence(s)
      BC082036, FM058030
      UniProtKB/Swiss-Prot
      Q66H40
      UniProtKB/TrEMBL
      M0R953
      Conserved Domains (1) summary
      pfam01101
      Location:2 → 94
      HMG14_17; HMG14 and HMG17

    RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

    Reference GRCr8

    Genomic

    1. NC_086026.1 Reference GRCr8

      Range
      92902555..92939980 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_063264731.1 → XP_063120801.1  high mobility group nucleosome-binding domain-containing protein 3 isoform X3

    2. XM_017595405.3 → XP_017450894.1  high mobility group nucleosome-binding domain-containing protein 3 isoform X5

    3. XM_039080658.2 → XP_038936586.1  high mobility group nucleosome-binding domain-containing protein 3 isoform X4

      UniProtKB/TrEMBL
      M0R953
      Related
      ENSRNOP00000066015.2
      Conserved Domains (1) summary
      pfam01101
      Location:56 → 151
      HMG14_17; HMG14 and HMG17

    4. XM_006243445.5 → XP_006243507.1  high mobility group nucleosome-binding domain-containing protein 3 isoform X2

      See identical proteins and their annotated locations for XP_006243507.1

      UniProtKB/TrEMBL
      M0R953
      Conserved Domains (1) summary
      pfam01101
      Location:57 → 149
      HMG14_17; HMG14 and HMG17

    5. XM_017595402.3 → XP_017450891.1  high mobility group nucleosome-binding domain-containing protein 3 isoform X1

    6. XM_039080659.2 → XP_038936587.1  high mobility group nucleosome-binding domain-containing protein 3 isoform X6

    7. XM_039080656.2 → XP_038936584.1  high mobility group nucleosome-binding domain-containing protein 3 isoform X3

      Conserved Domains (1) summary
      pfam01101
      Location:56 → 91
      HMG14_17; HMG14 and HMG17

    8. XM_017595404.3 → XP_017450893.1  high mobility group nucleosome-binding domain-containing protein 3 isoform X3

      Conserved Domains (1) summary
      pfam01101
      Location:56 → 91
      HMG14_17; HMG14 and HMG17
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q66H40.1 GenPept UniProtKB/Swiss-Prot:Q66H40

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