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    Hp1bp3 heterochromatin protein 1, binding protein 3 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 313647, updated on 11-Apr-2024

    Summary

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    Official Symbol
    Hp1bp3provided by RGD
    Official Full Name
    heterochromatin protein 1, binding protein 3provided by RGD
    Primary source
    RGD:735099
    See related
    Ensembl:ENSRNOG00000014445 AllianceGenome:RGD:735099
    Gene type
    protein coding
    RefSeq status
    PROVISIONAL
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Summary
    Predicted to enable DNA binding activity and nucleosome binding activity. Predicted to be involved in several processes, including cellular response to hypoxia; heterochromatin organization; and regulation of nucleus size. Predicted to be located in nuclear speck. Predicted to be part of nucleosome. Predicted to be active in chromosome and nucleus. Orthologous to human HP1BP3 (heterochromatin protein 1 binding protein 3). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Biased expression in Thymus (RPKM 371.3), Kidney (RPKM 359.7) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    Location:
    5q36
    Exon count:
    14
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 5 NC_086023.1 (155719109..155746329)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 5 NC_051340.1 (150435781..150463004)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 5 NC_005104.4 (156581732..156609059)

    Chromosome 5 - NC_086023.1Genomic Context describing neighboring genes Neighboring gene eukaryotic translation initiation factor 4 gamma, 3 Neighboring gene uncharacterized LOC134487020 Neighboring gene macrophage migration inhibitory factor, pseudogene 5 Neighboring gene uncharacterized LOC134487021 Neighboring gene SH2 domain containing 5 Neighboring gene kinesin family member 17

    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. Quantitative profiling of chromatome dynamics reveals a novel role for HP1BP3 in hypoxia-induced oncogenesis. Dutta B, et al. Mol Cell Proteomics, 2014 Dec. PMID 25100860, Free PMC Article
    2. Profiling of the Chromatin-associated Proteome Identifies HP1BP3 as a Novel Regulator of Cell Cycle Progression. Dutta B, et al. Mol Cell Proteomics, 2014 Sep. PMID 24830416, Free PMC Article
    3. The middle region of an HP1-binding protein, HP1-BP74, associates with linker DNA at the entry/exit site of nucleosomal DNA. Hayashihara K, et al. J Biol Chem, 2010 Feb 26. PMID 20042602, Free PMC Article
    4. A possible involvement of TIF1 alpha and TIF1 beta in the epigenetic control of transcription by nuclear receptors. Le Douarin B, et al. EMBO J, 1996 Dec 2. PMID 8978696, Free PMC Article
    5. JUNB-FBXO21-ERK axis promotes cartilage degeneration in osteoarthritis by inhibiting autophagy. Lin Z, et al. Aging Cell, 2021 Feb. PMID 33450132, 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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    Markers

    Homology

    Clone Names

    • MGC72624

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables DNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables DNA binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables DNA binding ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables nucleosome binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables nucleosome binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables nucleosome binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables nucleosome binding ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables structural constituent of chromatin IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in cellular response to hypoxia IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in cellular response to hypoxia ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in cellular response to hypoxia ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in heterochromatin organization IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in heterochromatin organization IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in heterochromatin organization ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in heterochromatin organization ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in nucleosome assembly IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in regulation of DNA-templated transcription IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in regulation of DNA-templated transcription ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in regulation of DNA-templated transcription ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in regulation of cell population proliferation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in regulation of cell population proliferation ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in regulation of cell population proliferation ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in regulation of nucleus size IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in regulation of nucleus size ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in regulation of nucleus size ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Component Evidence Code Pubs
    is_active_in chromosome IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in chromosome ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in chromosome ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in nuclear speck IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nuclear speck ISO
    Inferred from Sequence Orthology
    more info
    		  
    part_of nucleosome IEA
    Inferred from Electronic Annotation
    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
    		  
    located_in nucleus ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  

    General protein information

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    Preferred Names
    heterochromatin protein 1-binding protein 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_199108.1 → NP_954539.1  heterochromatin protein 1-binding protein 3

      See identical proteins and their annotated locations for NP_954539.1

      Status: PROVISIONAL

      Source sequence(s)
      BC061837
      UniProtKB/Swiss-Prot
      Q6P747
      UniProtKB/TrEMBL
      A6ITG0, A6ITG3
      Related
      ENSRNOP00000067949.2, ENSRNOT00000075852.2
      Conserved Domains (4) summary
      smart00526
      Location:251 → 317
      H15; Domain in histone families 1 and 5
      PRK14900
      Location:454 → 530
      valS; valyl-tRNA synthetase; Provisional
      cd00073
      Location:155 → 239
      H15; linker histone 1 and histone 5 domains; the basic subunit of chromatin is the nucleosome, consisting of an octamer of core histones, two full turns of DNA, a linker histone (H1 or H5) and a variable length of linker DNA; H1/H5 are chromatin-associated ...
      pfam00538
      Location:344 → 409
      Linker_histone; linker histone H1 and H5 family

    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_086023.1 Reference GRCr8

      Range
      155719109..155746329
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_039110063.2 → XP_038965991.1  heterochromatin protein 1-binding protein 3 isoform X3

      UniProtKB/TrEMBL
      A6ITG6
      Conserved Domains (4) summary
      smart00526
      Location:213 → 279
      H15; Domain in histone families 1 and 5
      PRK14900
      Location:416 → 492
      valS; valyl-tRNA synthetase; Provisional
      cd00073
      Location:117 → 201
      H15; linker histone 1 and histone 5 domains; the basic subunit of chromatin is the nucleosome, consisting of an octamer of core histones, two full turns of DNA, a linker histone (H1 or H5) and a variable length of linker DNA; H1/H5 are chromatin-associated ...
      pfam00538
      Location:306 → 371
      Linker_histone; linker histone H1 and H5 family

    2. XM_039110060.2 → XP_038965988.1  heterochromatin protein 1-binding protein 3 isoform X1

      UniProtKB/TrEMBL
      A6ITF7, A6ITF8, F1M6V1
      Related
      ENSRNOP00000019696.6
      Conserved Domains (4) summary
      smart00526
      Location:276 → 342
      H15; Domain in histone families 1 and 5
      PRK14900
      Location:479 → 555
      valS; valyl-tRNA synthetase; Provisional
      cd00073
      Location:180 → 264
      H15; linker histone 1 and histone 5 domains; the basic subunit of chromatin is the nucleosome, consisting of an octamer of core histones, two full turns of DNA, a linker histone (H1 or H5) and a variable length of linker DNA; H1/H5 are chromatin-associated ...
      pfam00538
      Location:369 → 434
      Linker_histone; linker histone H1 and H5 family

    3. XM_039110062.2 → XP_038965990.1  heterochromatin protein 1-binding protein 3 isoform X2

      UniProtKB/Swiss-Prot
      Q6P747
      UniProtKB/TrEMBL
      A6ITG0, A6ITG3
      Conserved Domains (4) summary
      smart00526
      Location:251 → 317
      H15; Domain in histone families 1 and 5
      PRK14900
      Location:454 → 530
      valS; valyl-tRNA synthetase; Provisional
      cd00073
      Location:155 → 239
      H15; linker histone 1 and histone 5 domains; the basic subunit of chromatin is the nucleosome, consisting of an octamer of core histones, two full turns of DNA, a linker histone (H1 or H5) and a variable length of linker DNA; H1/H5 are chromatin-associated ...
      pfam00538
      Location:344 → 409
      Linker_histone; linker histone H1 and H5 family

    4. XM_063287789.1 → XP_063143859.1  heterochromatin protein 1-binding protein 3 isoform X3

    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q6P747.1 GenPept UniProtKB/Swiss-Prot:Q6P747

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