U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

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

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

Summary

Go to the top of the page Help
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
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

Go to the top of the page Help
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

Go to the top of the page Help

Go to nucleotide: Graphics FASTA GenBank

Expression

Go to the top of the page Help
  • 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

Go to the top of the pageHelp

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

Go to the top of the page Help

Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

Go to the top of the page Help

See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Interactions

Go to the top of the page Help
Products Interactant Other Gene Complex Source Pubs Description

General gene information

Go to the top of the page Help

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

Go to the top of the page Help
Preferred Names
heterochromatin protein 1-binding protein 3

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

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.

Chemical Information
Molecular Biology Databases
Research Materials
Tools
Miscellaneous