Human Gene CBX3 (ENST00000396386.7_4) from GENCODE V47lift37
  Description: chromobox 3, transcript variant 2 (from RefSeq NM_016587.4)
Gencode Transcript: ENST00000396386.7_4
Gencode Gene: ENSG00000122565.19_10
Transcript (Including UTRs)
   Position: hg19 chr7:26,241,365-26,253,227 Size: 11,863 Total Exon Count: 6 Strand: +
Coding Region
   Position: hg19 chr7:26,242,619-26,251,828 Size: 9,210 Coding Exon Count: 5 

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

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr7:26,241,365-26,253,227)mRNA (may differ from genome)Protein (183 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
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BioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: CBX3_HUMAN
DESCRIPTION: RecName: Full=Chromobox protein homolog 3; AltName: Full=HECH; AltName: Full=Heterochromatin protein 1 homolog gamma; Short=HP1 gamma; AltName: Full=Modifier 2 protein;
FUNCTION: Seems to be involved in transcriptional silencing in heterochromatin-like complexes. Recognizes and binds histone H3 tails methylated at 'Lys-9', leading to epigenetic repression. May contribute to the association of the heterochromatin with the inner nuclear membrane through its interaction with lamin B receptor (LBR). Involved in the formation of functional kinetochore through interaction with MIS12 complex proteins.
SUBUNIT: Binds directly to CHAF1A. Interacts with histone H3 methylated at 'Lys-9'. Part of the E2F6.com-1 complex in G0 phase composed of E2F6, MGA, MAX, TFDP1, CBX3, BAT8, EUHMTASE1, RING1, RNF2, MBLR, L3MBTL2 and YAF2. Interacts with LBR, INCENP, TRIM28/TIF1B, SUV420H1, SUV420H2 and SP100. Interacts with TIF1A (By similarity). Interacts with MIS12 and DSN1. Can interact directly with CBX5 via the chromoshadow domain. Interacts with POGZ. Interacts with CHAMP1. Interacts with ASXL1.
INTERACTION: Self; NbExp=2; IntAct=EBI-78176, EBI-78176; Q9H2P0:ADNP; NbExp=2; IntAct=EBI-78176, EBI-1764854; Q14739:LBR; NbExp=4; IntAct=EBI-78176, EBI-1055147; Q13263:TRIM28; NbExp=3; IntAct=EBI-78176, EBI-78139;
SUBCELLULAR LOCATION: Nucleus (Potential). Note=Associates with euchromatin and is largely excluded from constitutive heterochromatin. May be associated with microtubules and mitotic poles during mitosis (Potential).
PTM: Phosphorylated by PIM1. Phosphorylated during interphase and possibly hyper-phosphorylated during mitosis.
SIMILARITY: Contains 2 chromo domains.

-  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

+  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: 69.50 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 1162.80 RPKM



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

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -34.10110-0.310 Picture PostScript Text
3' UTR -317.501399-0.227 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
IPR017984 - Chromo_dom_subgr
IPR023780 - Chromo_domain
IPR000953 - Chromo_domain/shadow
IPR008251 - Chromo_shadow_dom
IPR016197 - Chromodomain-like
IPR023779 - Chromodomain_CS

Pfam Domains:
PF00385 - Chromo (CHRromatin Organisation MOdifier) domain
PF01393 - Chromo shadow domain

SCOP Domains:
54160 - Chromo domain-like

Protein Data Bank (PDB) 3-D Structure
MuPIT help
2L11 - NMR MuPIT 3DM1 - X-ray MuPIT 3KUP - X-ray MuPIT 3TZD - X-ray


ModBase Predicted Comparative 3D Structure on Q13185
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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 orthologGenome BrowserNo ortholog
Gene DetailsGene Details  Gene Details 
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 RGDEnsembl WormBase 
    Protein Sequence 
    Alignment 

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding
GO:0019899 enzyme binding
GO:0019904 protein domain specific binding
GO:0042802 identical protein binding
GO:1990226 histone methyltransferase binding

Biological Process:
GO:0006325 chromatin organization
GO:0006338 chromatin remodeling
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0045892 negative regulation of transcription, DNA-templated
GO:0048511 rhythmic process
GO:0070317 negative regulation of G0 to G1 transition

Cellular Component:
GO:0000775 chromosome, centromeric region
GO:0000779 condensed chromosome, centromeric region
GO:0000784 nuclear chromosome, telomeric region
GO:0000785 chromatin
GO:0005634 nucleus
GO:0005635 nuclear envelope
GO:0005637 nuclear inner membrane
GO:0005654 nucleoplasm
GO:0005719 nuclear euchromatin
GO:0005720 nuclear heterochromatin
GO:0005819 spindle
GO:0031618 nuclear pericentric heterochromatin


-  Descriptions from all associated GenBank mRNAs
  BC000954 - Homo sapiens chromobox homolog 3 (HP1 gamma homolog, Drosophila), mRNA (cDNA clone MGC:4912 IMAGE:3450099), complete cds.
JD464426 - Sequence 445450 from Patent EP1572962.
BX648807 - Homo sapiens mRNA; cDNA DKFZp686G19188 (from clone DKFZp686G19188).
BX647444 - Homo sapiens mRNA; cDNA DKFZp686L0599 (from clone DKFZp686L0599).
FW339977 - Screening.
AF136630 - Homo sapiens heterochromatin-like protein 1 (HECH) mRNA, complete cds.
AF086270 - Homo sapiens full length insert cDNA clone ZD44C02.
EU831928 - Synthetic construct Homo sapiens clone HAIB:100066957; DKFZo008C0523 chromobox homolog 3 (HP1 gamma homolog, Drosophila) protein (CBX3) gene, encodes complete protein.
EU832023 - Synthetic construct Homo sapiens clone HAIB:100067052; DKFZo004C0524 chromobox homolog 3 (HP1 gamma homolog, Drosophila) protein (CBX3) gene, encodes complete protein.
AB463500 - Synthetic construct DNA, clone: pF1KB5359, Homo sapiens CBX3 gene for chromobox homolog 3, without stop codon, in Flexi system.
U26312 - Human heterochromatin protein HP1Hs-gamma mRNA, complete cds.
AB030905 - Homo sapiens hp1-gamma mRNA for Heterochromatin protein 1 gamma, complete cds.
JD025989 - Sequence 7013 from Patent EP1572962.
BC014380 - Homo sapiens, clone IMAGE:4045143, mRNA, partial cds.
JD030471 - Sequence 11495 from Patent EP1572962.
JD020101 - Sequence 1125 from Patent EP1572962.
JD509833 - Sequence 490857 from Patent EP1572962.
JD493490 - Sequence 474514 from Patent EP1572962.
JD249428 - Sequence 230452 from Patent EP1572962.
JD059989 - Sequence 41013 from Patent EP1572962.
DL492123 - Novel nucleic acids.
DL490659 - Novel nucleic acids.
JD314906 - Sequence 295930 from Patent EP1572962.
JD563297 - Sequence 544321 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q13185 (Reactome details) participates in the following event(s):

R-HSA-427383 CBX3 (HP1gamma) binds histone H3 dimethylated at lysine-9
R-HSA-9007283 CBX3 and PRC1.6 associate with E2F6.com-1
R-HSA-9007447 E2F6 forms the PRC1L4 complex
R-HSA-8953452 E2F6.com-1 complex binds the E2F1 gene promoter
R-HSA-9007464 The PRC1L4 complex binds the UXT gene promoter
R-HSA-9007467 The PRC1L4 complex binds the CDC7 gene promoter
R-HSA-427389 ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression
R-HSA-8953750 Transcriptional Regulation by E2F6
R-HSA-5250913 Positive epigenetic regulation of rRNA expression
R-HSA-212436 Generic Transcription Pathway
R-HSA-212165 Epigenetic regulation of gene expression
R-HSA-73857 RNA Polymerase II Transcription
R-HSA-74160 Gene expression (Transcription)

-  Other Names for This Gene
  Alternate Gene Symbols: CBX3_HUMAN, ENST00000396386.1, ENST00000396386.2, ENST00000396386.3, ENST00000396386.4, ENST00000396386.5, ENST00000396386.6, NM_016587, Q13185, Q96CD7, Q99409, Q9BVS3, Q9P0Z6, uc318yfd.1, uc318yfd.2
UCSC ID: ENST00000396386.7_4
RefSeq Accession: NM_016587.4
Protein: Q13185 (aka CBX3_HUMAN)

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