Human Gene CBX1 (uc002ind.4) Description and Page Index
  Description: Homo sapiens chromobox homolog 1 (CBX1), transcript variant 1, mRNA.
RefSeq Summary (NM_006807): This gene encodes a highly conserved nonhistone protein, which is a member of the heterochromatin protein family . The protein is enriched in the heterochromatin and associated with centromeres. The protein has a single N-terminal chromodomain which can bind to histone proteins via methylated lysine residues, and a C-terminal chromo shadow-domain (CSD) which is responsible for the homodimerization and interaction with a number of chromatin-associated nonhistone proteins. The protein may play an important role in the epigenetic control of chromatin structure and gene expression. Several related pseudogenes are located on chromosomes 1, 3, and X. Multiple alternatively spliced variants, encoding the same protein, have been identified. [provided by RefSeq, Jul 2008].
Transcript (Including UTRs)
   Position: hg19 chr17:46,147,414-46,178,560 Size: 31,147 Total Exon Count: 5 Strand: -
Coding Region
   Position: hg19 chr17:46,148,797-46,154,366 Size: 5,570 Coding Exon Count: 4 

Page IndexSequence and LinksUniProtKB CommentsMalaCardsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr17:46,147,414-46,178,560)mRNA (may differ from genome)Protein (185 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaBioGPS
CGAPEnsemblEntrez GeneExonPrimerGeneCardsGeneNetwork
H-INVHGNCHPRDLynxMGIneXtProt
OMIMPubMedStanford SOURCETreefamUniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: CBX1_HUMAN
DESCRIPTION: RecName: Full=Chromobox protein homolog 1; AltName: Full=HP1Hsbeta; AltName: Full=Heterochromatin protein 1 homolog beta; Short=HP1 beta; AltName: Full=Heterochromatin protein p25; AltName: Full=M31; AltName: Full=Modifier 1 protein; AltName: Full=p25beta;
FUNCTION: Component of heterochromatin. Recognizes and binds histone H3 tails methylated at 'Lys-9', leading to epigenetic repression. Interaction with lamin B receptor (LBR) can contribute to the association of the heterochromatin with the inner nuclear membrane.
SUBUNIT: Homodimer. Interacts directly with CHAF1A, EMSY, LBR, TIF1/TIF1A and TRIM28/TIF1B PXVXL motif via the chromoshadow domain. Interacts directly with histone H3 methylated at 'Lys-9' via the chromo domain. Interacts with SUV39H1 and SETDB1, SUV420H1 and SUV420H2. Interacts with PRDM6. Interacts with POGZ. Interacts with CHAMP1. Interacts with ASXL1.
INTERACTION: Q9H2P0:ADNP; NbExp=2; IntAct=EBI-78129, EBI-1764854; Q6IQ32:ADNP2; NbExp=2; IntAct=EBI-78129, EBI-2838654; P10588:NR2F6; NbExp=2; IntAct=EBI-78129, EBI-2681496;
SUBCELLULAR LOCATION: Nucleus. Note=Unassociated with chromosomes during mitosis.
TISSUE SPECIFICITY: Expressed in all adult and embryonic tissues.
PTM: Not phosphorylated.
PTM: Ubiquitinated.
SIMILARITY: Contains 2 chromo domains.
WEB RESOURCE: Name=Wikipedia; Note=Heterochromatin protein 1 entry; URL="http://en.wikipedia.org/wiki/Heterochromatin_Protein_1";

-  MalaCards Disease Associations
  MalaCards Gene Search: CBX1
Diseases sorted by gene-association score: mandibuloacral dysplasia (3), warsaw breakage syndrome (1)

-  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: 44.95 RPKM in Testis
Total median expression: 1141.05 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 -217.30481-0.452 Picture PostScript Text
3' UTR -401.381383-0.290 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

2FMM
- X-ray MuPIT

3F2U
- X-ray MuPIT

3Q6S
- X-ray MuPIT


ModBase Predicted Comparative 3D Structure on P83916
FrontTopSide
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 Details     
Gene Sorter     
      
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003682 chromatin binding
GO:0005515 protein binding
GO:0019899 enzyme binding
GO:0042802 identical protein binding
GO:0042803 protein homodimerization activity
GO:1990226 histone methyltransferase binding

Biological Process:
GO:0045892 negative regulation of transcription, DNA-templated

Cellular Component:
GO:0000775 chromosome, centromeric region
GO:0000784 nuclear chromosome, telomeric region
GO:0000785 chromatin
GO:0001939 female pronucleus
GO:0001940 male pronucleus
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005720 nuclear heterochromatin
GO:0005721 pericentric heterochromatin
GO:0005819 spindle
GO:0010369 chromocenter


-  Descriptions from all associated GenBank mRNAs
  BC002609 - Homo sapiens chromobox homolog 1 (HP1 beta homolog Drosophila), mRNA (cDNA clone MGC:1267 IMAGE:3140815), complete cds.
BC021302 - Homo sapiens chromobox homolog 1 (HP1 beta homolog Drosophila), mRNA (cDNA clone MGC:29537 IMAGE:5013102), complete cds.
U35451 - Homo sapiens heterochromatin protein p25 mRNA, complete cds.
JD296070 - Sequence 277094 from Patent EP1572962.
JD166248 - Sequence 147272 from Patent EP1572962.
JD327411 - Sequence 308435 from Patent EP1572962.
JD251026 - Sequence 232050 from Patent EP1572962.
JD019648 - Sequence 672 from Patent EP1572962.
JD034852 - Sequence 15876 from Patent EP1572962.
JD488705 - Sequence 469729 from Patent EP1572962.
JD509115 - Sequence 490139 from Patent EP1572962.
JD039108 - Sequence 20132 from Patent EP1572962.
JD243752 - Sequence 224776 from Patent EP1572962.
JD553934 - Sequence 534958 from Patent EP1572962.
JD042077 - Sequence 23101 from Patent EP1572962.
JD111475 - Sequence 92499 from Patent EP1572962.
JD252678 - Sequence 233702 from Patent EP1572962.
JD282129 - Sequence 263153 from Patent EP1572962.
CR456766 - Homo sapiens full open reading frame cDNA clone RZPDo834D084D for gene CBX1, chromobox homolog 1 (HP1 beta homolog Drosophila); complete cds, incl. stopcodon.
AK312615 - Homo sapiens cDNA, FLJ92997, Homo sapiens chromobox homolog 1 (HP1 beta homolog Drosophila) (CBX1), mRNA.
EU446771 - Synthetic construct Homo sapiens clone IMAGE:100070284; IMAGE:100011980; FLH258763.01L chromobox homolog 1 (HP1 beta homolog Drosophila) (CBX1) gene, encodes complete protein.
AB587426 - Synthetic construct DNA, clone: pF1KB6810, Homo sapiens CBX1 gene for chromobox homolog 1, without stop codon, in Flexi system.
DQ598442 - Homo sapiens piRNA piR-36508, complete sequence.
JD531083 - Sequence 512107 from Patent EP1572962.
JD395240 - Sequence 376264 from Patent EP1572962.
JD409152 - Sequence 390176 from Patent EP1572962.
JD182166 - Sequence 163190 from Patent EP1572962.
JD198705 - Sequence 179729 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: CBX, CBX1_HUMAN, NM_006807, NP_006798, P23197, P83916
UCSC ID: uc002ind.4
RefSeq Accession: NM_006807
Protein: P83916 (aka CBX1_HUMAN)
CCDS: CCDS11525.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_006807.4
exon count: 5CDS single in 3' UTR: no RNA size: 2443
ORF size: 558CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 1064.00frame shift in genome: no % Coverage: 99.14
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
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.