Human Gene HP1BP3 (ENST00000438032.6_8) from GENCODE V47lift37
  Description: heterochromatin protein 1 binding protein 3, transcript variant 15 (from RefSeq NR_164851.1)
Gencode Transcript: ENST00000438032.6_8
Gencode Gene: ENSG00000127483.19_14
Transcript (Including UTRs)
   Position: hg19 chr1:21,066,759-21,113,800 Size: 47,042 Total Exon Count: 13 Strand: -
Coding Region
   Position: hg19 chr1:21,071,290-21,106,933 Size: 35,644 Coding Exon Count: 12 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr1:21,066,759-21,113,800)mRNA (may differ from genome)Protein (553 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
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HGNCMGIOMIMPubMedUniProtKBWikipedia
BioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: HP1B3_HUMAN
DESCRIPTION: RecName: Full=Heterochromatin protein 1-binding protein 3; AltName: Full=Protein HP1-BP74;
FUNCTION: Component of heterochromatin, may be involved in chromatin structure and function (By similarity).
SUBUNIT: Interacts with CBX5 (By similarity).
SUBCELLULAR LOCATION: Nucleus (By similarity). Chromosome (By similarity).
PTM: Phosphorylated upon DNA damage, probably by ATM or ATR.
SIMILARITY: Contains 3 H15 (linker histone H1/H5 globular) domains.
SEQUENCE CAUTION: Sequence=AAF14871.1; Type=Frameshift; Positions=226, 237, 243;

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 58.09 RPKM in Ovary
Total median expression: 1609.37 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -83.80213-0.393 Picture PostScript Text
3' UTR -1183.704531-0.261 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR005818 - Histone_H1/H5
IPR011991 - WHTH_trsnscrt_rep_DNA-bd

Pfam Domains:
PF00538 - linker histone H1 and H5 family

SCOP Domains:
46785 - "Winged helix" DNA-binding domain
53955 - Lysozyme-like

Protein Data Bank (PDB) 3-D Structure
MuPIT help
2RQP - NMR MuPIT


ModBase Predicted Comparative 3D Structure on Q5SSJ5
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The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003677 DNA binding
GO:0003682 chromatin binding
GO:0005515 protein binding
GO:0031491 nucleosome binding

Biological Process:
GO:0006334 nucleosome assembly
GO:0006355 regulation of transcription, DNA-templated
GO:0042127 regulation of cell proliferation
GO:0070828 heterochromatin organization
GO:0071456 cellular response to hypoxia
GO:0097298 regulation of nucleus size

Cellular Component:
GO:0000786 nucleosome
GO:0005634 nucleus
GO:0005694 chromosome
GO:0016607 nuclear speck


-  Descriptions from all associated GenBank mRNAs
  BC053327 - Homo sapiens heterochromatin protein 1, binding protein 3, mRNA (cDNA clone IMAGE:6573235), with apparent retained intron.
AK023129 - Homo sapiens cDNA FLJ13067 fis, clone NT2RP3001712, highly similar to Homo sapiens heterochromatin protein 1, binding protein 3 (HP1BP3), mRNA.
AF113534 - Homo sapiens HP1-BP74 protein mRNA, complete cds.
AK291252 - Homo sapiens cDNA FLJ78256 complete cds, highly similar to Homo sapiens heterochromatin protein 1, binding protein 3 (HP1BP3), mRNA.
AK304065 - Homo sapiens cDNA FLJ50949 complete cds, highly similar to Homo sapiens heterochromatin protein 1, binding protein 3 (HP1BP3), mRNA.
EU832526 - Synthetic construct Homo sapiens clone HAIB:100067555; DKFZo008H1229 heterochromatin protein 1, binding protein 3 protein (HP1BP3) gene, encodes complete protein.
BC046170 - Homo sapiens heterochromatin protein 1, binding protein 3, mRNA (cDNA clone IMAGE:6153774).
KJ902537 - Synthetic construct Homo sapiens clone ccsbBroadEn_11931 HP1BP3 gene, encodes complete protein.
BC032139 - Homo sapiens heterochromatin protein 1, binding protein 3, mRNA (cDNA clone IMAGE:5013089), complete cds.
KJ902536 - Synthetic construct Homo sapiens clone ccsbBroadEn_11930 HP1BP3 gene, encodes complete protein.
JD094075 - Sequence 75099 from Patent EP1572962.
JD379589 - Sequence 360613 from Patent EP1572962.
BC045660 - Homo sapiens heterochromatin protein 1, binding protein 3, mRNA (cDNA clone MGC:43701 IMAGE:5271429), complete cds.
AK025754 - Homo sapiens cDNA: FLJ22101 fis, clone HEP17280.
AL833978 - Homo sapiens mRNA; cDNA DKFZp434I0612 (from clone DKFZp434I0612).
JD212896 - Sequence 193920 from Patent EP1572962.
JD219451 - Sequence 200475 from Patent EP1572962.
JD407506 - Sequence 388530 from Patent EP1572962.
JD256728 - Sequence 237752 from Patent EP1572962.
JD059546 - Sequence 40570 from Patent EP1572962.
JD152187 - Sequence 133211 from Patent EP1572962.
JD212895 - Sequence 193919 from Patent EP1572962.
JD342001 - Sequence 323025 from Patent EP1572962.
AK303456 - Homo sapiens cDNA FLJ61197 complete cds, highly similar to Homo sapiens heterochromatin protein 1, binding protein 3 (HP1BP3), mRNA.

-  Other Names for This Gene
  Alternate Gene Symbols: A6NI71, A8K5D7, B3KMZ8, B4E210, ENST00000438032.1, ENST00000438032.2, ENST00000438032.3, ENST00000438032.4, ENST00000438032.5, HP1B3_HUMAN, NR_164851, Q05BI0, Q5SSJ5, Q5SSJ6, Q5SWC6, Q6PIM9, Q8NDF0, Q9UHY0, uc320gho.1, uc320gho.2
UCSC ID: ENST00000438032.6_8
RefSeq Accession: NM_001372052.1
Protein: Q5SSJ5 (aka HP1B3_HUMAN)

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.