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

Gene ID: 313647, updated on 2-Nov-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
EnsemblRapid: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, Nov 2024]
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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See Hp1bp3 in Genome Data Viewer
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, ENSRNOT00000075852.3
    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
    ENSRNOP00000068507.3, ENSRNOT00000076772.4
    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
    Related
    ENSRNOP00000019696.7, ENSRNOT00000019696.9
    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

Gene LinkOut

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

Chemical Information
Molecular Biology Databases
Research Materials