Human Gene CBX1 (ENST00000225603.9_8) from GENCODE V47lift37
  Description: chromobox 1, transcript variant 2 (from RefSeq NM_001127228.2)
Gencode Transcript: ENST00000225603.9_8
Gencode Gene: ENSG00000108468.15_12
Transcript (Including UTRs)
   Position: hg19 chr17:46,147,421-46,178,840 Size: 31,420 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 LinksPrimersMalaCardsCTDGene 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 (chr17:46,147,421-46,178,840)mRNA (may differ from genome)Protein (185 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsHGNC
MalacardsMGIOMIMPubMedUniProtKBWikipedia
BioGrid CRISPR DB

-  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


-  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

+  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 -117.70248-0.475 Picture PostScript Text
3' UTR -377.101376-0.274 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

ModBase Predicted Comparative 3D Structure on Q6IBN6
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 DetailsGene Details    
Gene SorterGene Sorter    
 RGDEnsembl   
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0042802 identical protein binding
GO:0042803 protein homodimerization activity

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

Cellular Component:
GO:0000785 chromatin
GO:0001939 female pronucleus
GO:0001940 male pronucleus
GO:0005634 nucleus
GO:0005721 pericentric heterochromatin
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.

-  Other Names for This Gene
  Alternate Gene Symbols: CBX1 , ENST00000225603.1, ENST00000225603.2, ENST00000225603.3, ENST00000225603.4, ENST00000225603.5, ENST00000225603.6, ENST00000225603.7, ENST00000225603.8, hCG_2000655 , NM_001127228, Q6IBN6, Q6IBN6_HUMAN, uc317djm.1, uc317djm.2
UCSC ID: ENST00000225603.9_8
RefSeq Accession: NM_001127228.2
Protein: Q6IBN6

-  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.