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    HP1BP3 heterochromatin protein 1 binding protein 3 [ Homo sapiens (human) ]

    Gene ID: 50809, updated on 7-Apr-2024

    Summary

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    Official Symbol
    HP1BP3provided by HGNC
    Official Full Name
    heterochromatin protein 1 binding protein 3provided by HGNC
    Primary source
    HGNC:HGNC:24973
    See related
    Ensembl:ENSG00000127483 MIM:616072; AllianceGenome:HGNC:24973
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    HP1BP74; HP1-BP74
    Summary
    Enables DNA binding activity and nucleosome binding activity. Involved in several processes, including cellular response to hypoxia; heterochromatin organization; and regulation of nucleus size. Located in chromosome and nuclear speck. [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Ubiquitous expression in thyroid (RPKM 36.6), endometrium (RPKM 35.9) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See HP1BP3 in Genome Data Viewer
    Location:
    1p36.12
    Exon count:
    15
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (20740266..20787307, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (20566829..20613865, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (21066759..21113800, complement)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:20987241-20988160 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:20988161-20989080 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:21011543-21012044 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:21015049-21015549 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:21015960-21016182 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 368 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:21036574-21037228 Neighboring gene kinesin family member 17 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 369 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 370 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:21054065-21054727 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:21054728-21055389 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:21056983-21057676 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:21057677-21058368 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:21058590-21059262 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:21059263-21059933 Neighboring gene SH2 domain containing 5 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:21112523-21112715 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 375 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 376 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:21146362-21146862 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:21146863-21147363 Neighboring gene eukaryotic translation initiation factor 4 gamma 3 Neighboring gene RNA, U7 small nuclear 200 pseudogene Neighboring gene uncharacterized LOC105376830 Neighboring gene uncharacterized LOC105376829

    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. HP1BP3, a Chromatin Retention Factor for Co-transcriptional MicroRNA Processing. Liu H, et al. Mol Cell, 2016 Aug 4. PMID 27425409, Free PMC Article
    2. Replication of Epigenetic Postpartum Depression Biomarkers and Variation with Hormone Levels. Osborne L, et al. Neuropsychopharmacology, 2016 May. PMID 26503311, Free PMC Article
    3. Proportionate Dwarfism in Mice Lacking Heterochromatin Protein 1 Binding Protein 3 (HP1BP3) Is Associated With Alterations in the Endocrine IGF-1 Pathway. Garfinkel BP, et al. Endocrinology, 2015 Dec. PMID 26402843, Free PMC Article
    4. HP1BP3 is a novel histone H1 related protein with essential roles in viability and growth. Garfinkel BP, et al. Nucleic Acids Res, 2015 Feb 27. PMID 25662603, Free PMC Article
    5. 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

    See all (136) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. EZH2 interacts with HP1BP3 to epigenetically activate WNT7B that promotes temozolomide resistance in glioblastoma.
      Title: EZH2 interacts with HP1BP3 to epigenetically activate WNT7B that promotes temozolomide resistance in glioblastoma.
    2. A fail-safe system to prevent oncogenesis by senescence is targeted by SV40 small T antigen.
      Title: A fail-safe system to prevent oncogenesis by senescence is targeted by SV40 small T antigen.
    3. HP1BP3 protein maintains heterochromatin integrity during G1-S progression and regulates the duration of G1 phase to critically influence cell proliferative capacity.
      Title: Profiling of the Chromatin-associated Proteome Identifies HP1BP3 as a Novel Regulator of Cell Cycle Progression.
    4. HP1BP3 promotes co-transcriptional miRNA processing via chromatin retention of nascent pri-miRNA transcripts.
      Title: HP1BP3, a Chromatin Retention Factor for Co-transcriptional MicroRNA Processing.
    5. DNA methylation at early antenatal time points associated with changes in estradiol and allopregnanolone and postpartum depression
      Title: Replication of Epigenetic Postpartum Depression Biomarkers and Variation with Hormone Levels.
    6. HP1BP3 is a component of heterochromatin, and its recruitment is dependent on a functional interaction with HP1 proteins.
      Title: HP1BP3 is a novel histone H1 related protein with essential roles in viability and growth.
    7. HP1BP3 regulates hepatic expression of IGF1 and its binding proteins in mice, thus modulating the endocrine IGF1 pathway.
      Title: Proportionate Dwarfism in Mice Lacking Heterochromatin Protein 1 Binding Protein 3 (HP1BP3) Is Associated With Alterations in the Endocrine IGF-1 Pathway.
    8. Quantitative profiling of chromatome dynamics reveals an important role for HP1BP3 in hypoxia-induced oncogenesis.
      Title: Quantitative profiling of chromatome dynamics reveals a novel role for HP1BP3 in hypoxia-induced oncogenesis.
    9. found two biomarker loci at HP1BP3 and TTC9B, which predicted postpartum depression
      Title: Seeing the future: epigenetic biomarkers of postpartum depression.
    10. Observational study of gene-disease association. (HuGE Navigator)
      Title: Investigation of genetic susceptibility factors for human longevity - a targeted nonsynonymous SNP study.
    Submit: New GeneRIF Correction See all GeneRIFs (13)

    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

    • MGC43701

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables DNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables nucleosome binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables nucleosome binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in cellular response to hypoxia IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in heterochromatin organization IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in heterochromatin organization IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in nucleosome assembly IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in regulation of DNA-templated transcription IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in regulation of cell population proliferation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in regulation of nucleus size IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    is_active_in chromosome IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in chromosome IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nuclear speck IDA
    Inferred from Direct Assay
    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 IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    heterochromatin protein 1-binding protein 3

    NCBI Reference Sequences (RefSeq)

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    NEW Try the new Transcript table

    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_001372052.1 → NP_001358981.1  heterochromatin protein 1-binding protein 3 isoform 1

      Status: VALIDATED

      Source sequence(s)
      AL606477, AL663074
      Consensus CDS
      CCDS30621.1
      UniProtKB/Swiss-Prot
      A6NI71, A8K5D7, B3KMZ8, B4E210, Q05BI0, Q5SSJ5, Q5SSJ6, Q5SWC6, Q6PIM9, Q8NDF0, Q9UHY0
      Related
      ENSP00000403039.2, ENST00000438032.6
      Conserved Domains (4) summary
      smart00526
      Location:253 → 319
      H15; Domain in histone families 1 and 5
      PRK14900
      Location:455 → 531
      valS; valyl-tRNA synthetase; Provisional
      cd00073
      Location:155 → 245
      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:346 → 411
      Linker_histone; linker histone H1 and H5 family

    2. NM_001376787.1 → NP_001363716.1  heterochromatin protein 1-binding protein 3 isoform 1

      Status: VALIDATED

      Source sequence(s)
      AL606477, AL663074
      Consensus CDS
      CCDS30621.1
      UniProtKB/Swiss-Prot
      A6NI71, A8K5D7, B3KMZ8, B4E210, Q05BI0, Q5SSJ5, Q5SSJ6, Q5SWC6, Q6PIM9, Q8NDF0, Q9UHY0
      Conserved Domains (4) summary
      smart00526
      Location:253 → 319
      H15; Domain in histone families 1 and 5
      PRK14900
      Location:455 → 531
      valS; valyl-tRNA synthetase; Provisional
      cd00073
      Location:155 → 245
      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:346 → 411
      Linker_histone; linker histone H1 and H5 family

    3. NM_001376788.1 → NP_001363717.1  heterochromatin protein 1-binding protein 3 isoform 1

      Status: VALIDATED

      Source sequence(s)
      AL606477, AL663074
      Consensus CDS
      CCDS30621.1
      UniProtKB/Swiss-Prot
      A6NI71, A8K5D7, B3KMZ8, B4E210, Q05BI0, Q5SSJ5, Q5SSJ6, Q5SWC6, Q6PIM9, Q8NDF0, Q9UHY0
      Conserved Domains (4) summary
      smart00526
      Location:253 → 319
      H15; Domain in histone families 1 and 5
      PRK14900
      Location:455 → 531
      valS; valyl-tRNA synthetase; Provisional
      cd00073
      Location:155 → 245
      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:346 → 411
      Linker_histone; linker histone H1 and H5 family

    4. NM_001376789.1 → NP_001363718.1  heterochromatin protein 1-binding protein 3 isoform 1

      Status: VALIDATED

      Source sequence(s)
      AL606477, AL663074
      Consensus CDS
      CCDS30621.1
      UniProtKB/Swiss-Prot
      A6NI71, A8K5D7, B3KMZ8, B4E210, Q05BI0, Q5SSJ5, Q5SSJ6, Q5SWC6, Q6PIM9, Q8NDF0, Q9UHY0
      Conserved Domains (4) summary
      smart00526
      Location:253 → 319
      H15; Domain in histone families 1 and 5
      PRK14900
      Location:455 → 531
      valS; valyl-tRNA synthetase; Provisional
      cd00073
      Location:155 → 245
      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:346 → 411
      Linker_histone; linker histone H1 and H5 family

    5. NM_001376790.1 → NP_001363719.1  heterochromatin protein 1-binding protein 3 isoform 1

      Status: VALIDATED

      Source sequence(s)
      AL606477, AL663074
      Consensus CDS
      CCDS30621.1
      UniProtKB/Swiss-Prot
      A6NI71, A8K5D7, B3KMZ8, B4E210, Q05BI0, Q5SSJ5, Q5SSJ6, Q5SWC6, Q6PIM9, Q8NDF0, Q9UHY0
      Conserved Domains (4) summary
      smart00526
      Location:253 → 319
      H15; Domain in histone families 1 and 5
      PRK14900
      Location:455 → 531
      valS; valyl-tRNA synthetase; Provisional
      cd00073
      Location:155 → 245
      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:346 → 411
      Linker_histone; linker histone H1 and H5 family

    6. NM_001376791.1 → NP_001363720.1  heterochromatin protein 1-binding protein 3 isoform 2

      Status: VALIDATED

      Source sequence(s)
      AL606477, AL663074
      Conserved Domains (4) summary
      smart00526
      Location:215 → 281
      H15; Domain in histone families 1 and 5
      PRK14900
      Location:417 → 493
      valS; valyl-tRNA synthetase; Provisional
      cd00073
      Location:117 → 207
      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:308 → 373
      Linker_histone; linker histone H1 and H5 family

    7. NM_001376792.1 → NP_001363721.1  heterochromatin protein 1-binding protein 3 isoform 2

      Status: VALIDATED

      Source sequence(s)
      AL606477, AL663074
      Conserved Domains (4) summary
      smart00526
      Location:215 → 281
      H15; Domain in histone families 1 and 5
      PRK14900
      Location:417 → 493
      valS; valyl-tRNA synthetase; Provisional
      cd00073
      Location:117 → 207
      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:308 → 373
      Linker_histone; linker histone H1 and H5 family

    8. NM_001376793.1 → NP_001363722.1  heterochromatin protein 1-binding protein 3 isoform 2

      Status: VALIDATED

      Source sequence(s)
      AL606477, AL663074
      Conserved Domains (4) summary
      smart00526
      Location:215 → 281
      H15; Domain in histone families 1 and 5
      PRK14900
      Location:417 → 493
      valS; valyl-tRNA synthetase; Provisional
      cd00073
      Location:117 → 207
      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:308 → 373
      Linker_histone; linker histone H1 and H5 family

    9. NM_001376794.1 → NP_001363723.1  heterochromatin protein 1-binding protein 3 isoform 2

      Status: VALIDATED

      Source sequence(s)
      AL606477, AL663074
      Conserved Domains (4) summary
      smart00526
      Location:215 → 281
      H15; Domain in histone families 1 and 5
      PRK14900
      Location:417 → 493
      valS; valyl-tRNA synthetase; Provisional
      cd00073
      Location:117 → 207
      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:308 → 373
      Linker_histone; linker histone H1 and H5 family

    10. NM_001376795.1 → NP_001363724.1  heterochromatin protein 1-binding protein 3 isoform 3

      Status: VALIDATED

      Source sequence(s)
      AL606477, AL663074
      UniProtKB/TrEMBL
      Q5SWC8
      Conserved Domains (2) summary
      smart00526
      Location:253 → 319
      H15; Domain in histone families 1 and 5
      cd00073
      Location:155 → 245
      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 ...

    11. NM_001376796.1 → NP_001363725.1  heterochromatin protein 1-binding protein 3 isoform 3

      Status: VALIDATED

      Source sequence(s)
      AL606477, AL663074
      UniProtKB/TrEMBL
      Q5SWC8
      Conserved Domains (2) summary
      smart00526
      Location:253 → 319
      H15; Domain in histone families 1 and 5
      cd00073
      Location:155 → 245
      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 ...

    12. NM_001376797.1 → NP_001363726.1  heterochromatin protein 1-binding protein 3 isoform 4

      Status: VALIDATED

      Source sequence(s)
      AL606477, AL663074
      UniProtKB/TrEMBL
      Q5SWC8
      Related
      ENSP00000402754.1, ENST00000424732.5
      Conserved Domains (2) summary
      smart00526
      Location:215 → 281
      H15; Domain in histone families 1 and 5
      cd00073
      Location:117 → 207
      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 ...

    13. NM_001399820.1 → NP_001386749.1  heterochromatin protein 1-binding protein 3 isoform 5

      Status: VALIDATED

      Source sequence(s)
      AL606477, AL663074

    14. NM_001399821.1 → NP_001386750.1  heterochromatin protein 1-binding protein 3 isoform 2

      Status: VALIDATED

      Source sequence(s)
      AL606477, AL663074

    15. NM_001399823.1 → NP_001386752.1  heterochromatin protein 1-binding protein 3 isoform 2

      Status: VALIDATED

      Source sequence(s)
      AL606477, AL663074

    16. NM_016287.5 → NP_057371.2  heterochromatin protein 1-binding protein 3 isoform 1

      See identical proteins and their annotated locations for NP_057371.2

      Status: VALIDATED

      Source sequence(s)
      AK023129, AL663074
      Consensus CDS
      CCDS30621.1
      UniProtKB/Swiss-Prot
      A6NI71, A8K5D7, B3KMZ8, B4E210, Q05BI0, Q5SSJ5, Q5SSJ6, Q5SWC6, Q6PIM9, Q8NDF0, Q9UHY0
      Related
      ENSP00000312625.5, ENST00000312239.10
      Conserved Domains (4) summary
      smart00526
      Location:253 → 319
      H15; Domain in histone families 1 and 5
      PRK14900
      Location:455 → 531
      valS; valyl-tRNA synthetase; Provisional
      cd00073
      Location:155 → 245
      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:346 → 411
      Linker_histone; linker histone H1 and H5 family

    RNA

    1. NR_164850.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AL606477, AL663074

    2. NR_164851.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AL606477, AL663074

    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_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      20740266..20787307 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      20566829..20613865 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q5SSJ5.1 GenPept UniProtKB/Swiss-Prot:Q5SSJ5

    Gene LinkOut

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

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