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

    Gene ID: 50809, updated on 28-Oct-2024

    Summary

    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, Oct 2024]
    Expression
    Ubiquitous expression in thyroid (RPKM 36.6), endometrium (RPKM 35.9) and 25 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See HP1BP3 in Genome Data Viewer
    Location:
    1p36.12
    Exon count:
    15
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (20740266..20787307, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (20566829..20613865, complement)
    RS_2024_09 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

    Expression

    • Project title: HPA RNA-seq normal tissues 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    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

    Preferred Names
    heterochromatin protein 1-binding protein 3

    NCBI Reference Sequences (RefSeq)

    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_001372052.1NP_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:253319
      H15; Domain in histone families 1 and 5
      PRK14900
      Location:455531
      valS; valyl-tRNA synthetase; Provisional
      cd00073
      Location:155245
      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:346411
      Linker_histone; linker histone H1 and H5 family
    2. NM_001376787.1NP_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:253319
      H15; Domain in histone families 1 and 5
      PRK14900
      Location:455531
      valS; valyl-tRNA synthetase; Provisional
      cd00073
      Location:155245
      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:346411
      Linker_histone; linker histone H1 and H5 family
    3. NM_001376788.1NP_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:253319
      H15; Domain in histone families 1 and 5
      PRK14900
      Location:455531
      valS; valyl-tRNA synthetase; Provisional
      cd00073
      Location:155245
      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:346411
      Linker_histone; linker histone H1 and H5 family
    4. NM_001376789.1NP_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:253319
      H15; Domain in histone families 1 and 5
      PRK14900
      Location:455531
      valS; valyl-tRNA synthetase; Provisional
      cd00073
      Location:155245
      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:346411
      Linker_histone; linker histone H1 and H5 family
    5. NM_001376790.1NP_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:253319
      H15; Domain in histone families 1 and 5
      PRK14900
      Location:455531
      valS; valyl-tRNA synthetase; Provisional
      cd00073
      Location:155245
      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:346411
      Linker_histone; linker histone H1 and H5 family
    6. NM_001376791.1NP_001363720.1  heterochromatin protein 1-binding protein 3 isoform 2

      Status: VALIDATED

      Source sequence(s)
      AL606477, AL663074
      Conserved Domains (4) summary
      smart00526
      Location:215281
      H15; Domain in histone families 1 and 5
      PRK14900
      Location:417493
      valS; valyl-tRNA synthetase; Provisional
      cd00073
      Location:117207
      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:308373
      Linker_histone; linker histone H1 and H5 family
    7. NM_001376792.1NP_001363721.1  heterochromatin protein 1-binding protein 3 isoform 2

      Status: VALIDATED

      Source sequence(s)
      AL606477, AL663074
      Conserved Domains (4) summary
      smart00526
      Location:215281
      H15; Domain in histone families 1 and 5
      PRK14900
      Location:417493
      valS; valyl-tRNA synthetase; Provisional
      cd00073
      Location:117207
      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:308373
      Linker_histone; linker histone H1 and H5 family
    8. NM_001376793.1NP_001363722.1  heterochromatin protein 1-binding protein 3 isoform 2

      Status: VALIDATED

      Source sequence(s)
      AL606477, AL663074
      Conserved Domains (4) summary
      smart00526
      Location:215281
      H15; Domain in histone families 1 and 5
      PRK14900
      Location:417493
      valS; valyl-tRNA synthetase; Provisional
      cd00073
      Location:117207
      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:308373
      Linker_histone; linker histone H1 and H5 family
    9. NM_001376794.1NP_001363723.1  heterochromatin protein 1-binding protein 3 isoform 2

      Status: VALIDATED

      Source sequence(s)
      AL606477, AL663074
      Conserved Domains (4) summary
      smart00526
      Location:215281
      H15; Domain in histone families 1 and 5
      PRK14900
      Location:417493
      valS; valyl-tRNA synthetase; Provisional
      cd00073
      Location:117207
      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:308373
      Linker_histone; linker histone H1 and H5 family
    10. NM_001376795.1NP_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:253319
      H15; Domain in histone families 1 and 5
      cd00073
      Location:155245
      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_001376796.1NP_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:253319
      H15; Domain in histone families 1 and 5
      cd00073
      Location:155245
      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_001376797.1NP_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:215281
      H15; Domain in histone families 1 and 5
      cd00073
      Location:117207
      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_001399820.1NP_001386749.1  heterochromatin protein 1-binding protein 3 isoform 5

      Status: VALIDATED

      Source sequence(s)
      AL606477, AL663074
    14. NM_001399821.1NP_001386750.1  heterochromatin protein 1-binding protein 3 isoform 2

      Status: VALIDATED

      Source sequence(s)
      AL606477, AL663074
    15. NM_001399823.1NP_001386752.1  heterochromatin protein 1-binding protein 3 isoform 2

      Status: VALIDATED

      Source sequence(s)
      AL606477, AL663074
    16. NM_016287.5NP_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:253319
      H15; Domain in histone families 1 and 5
      PRK14900
      Location:455531
      valS; valyl-tRNA synthetase; Provisional
      cd00073
      Location:155245
      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:346411
      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_2024_08

    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)