Human Gene CBX5 (ENST00000209875.9_7) from GENCODE V47lift37
  Description: chromobox 5, transcript variant 3 (from RefSeq NM_012117.3)
Gencode Transcript: ENST00000209875.9_7
Gencode Gene: ENSG00000094916.16_12
Transcript (Including UTRs)
   Position: hg19 chr12:54,624,726-54,673,906 Size: 49,181 Total Exon Count: 5 Strand: -
Coding Region
   Position: hg19 chr12:54,635,539-54,651,434 Size: 15,896 Coding Exon Count: 4 

Page IndexSequence and LinksPrimersMalaCardsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureOther SpeciesmRNA DescriptionsOther Names
Model InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr12:54,624,726-54,673,906)mRNA (may differ from genome)Protein (191 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedUniProtKB
WikipediaBioGrid 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: CBX5
Diseases sorted by gene-association score: reynolds syndrome (9), immunodeficiency-centromeric instability-facial anomalies syndrome (6)

-  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: 26.51 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 443.18 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 -50.80157-0.324 Picture PostScript Text
3' UTR -3190.3010813-0.295 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.

-  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    
 RGD    
      
      

-  Descriptions from all associated GenBank mRNAs
  S62077 - HP1Hs alpha=25 kda chromosomal autoantigen [human, mRNA, 876 nt].
EU794599 - Homo sapiens epididymis luminal protein 25 (HEL25) mRNA, complete cds.
L07515 - Human heterochromatin protein homologue (HP1) mRNA, complete cds.
BC030149 - Homo sapiens cDNA clone IMAGE:4842353, partial cds.
BC047432 - Homo sapiens cDNA clone IMAGE:5288883.
AK055641 - Homo sapiens cDNA FLJ31079 fis, clone HSYRA2001595.
JD225155 - Sequence 206179 from Patent EP1572962.
HZ409081 - JP 2015528002-A/1678: CHIRAL CONTROL.
LG052415 - KR 1020150036642-A/1681: CHIRAL CONTROL.
FR772780 - Homo sapiens microRNA hsa-miR-3198-3p.
FR772968 - Homo sapiens microRNA hsa-miR-4702-3p.
HZ074909 - JP 2013535982-A/1000: Single-Stranded RNAi Agents Containing an Internal, Non-Nucleic Acid Spacer.
HZ083290 - JP 2015513906-A/647: Stem Cell Microparticles.
HZ437071 - JP 2015529450-A/647: Stem Cell Microparticles.
HZ480188 - JP 2015535430-A/694: TERMINALLY MODIFIED RNA.
HZ790119 - JP 2016504050-A/1864: SIGNAL-SENSOR POLYNUCLEOTIDES FOR THE ALTERATION OF CELLULAR PHENOTYPES.
JB074972 - Sequence 232 from Patent WO2012168448.
JB621094 - Sequence 1074 from Patent WO2013063544.
JC172275 - Sequence 647 from Patent WO2013150303.
JC512851 - Sequence 3104 from Patent WO2014113089.
JC573086 - Sequence 647 from Patent WO2014125276.
JC582774 - Sequence 647 from Patent WO2014125277.
JE954470 - Sequence 647 from Patent WO2015052526.
JE956223 - Sequence 647 from Patent WO2015052527.
LF137975 - JP 2016507550-A/647: Method of Producing Microparticles.
LF161509 - JP 2016513950-A/1575: Oligomers with improved off-target profile.
LF162940 - JP 2016513095-A/647: Stem Cell Microparticles and miRNA.
LF644437 - JP 2016144439-A/28: Method for assessing cell aging.
LF953692 - JP 2016534103-A/647: Stem Cell Microparticles and miRNA.
LG006037 - KR 1020150004822-A/647: STEM CELL MICROPARTICLES.
LG053733 - KR 1020150059168-A/647: STEM CELL MICROPARTICLES.
LG240972 - KR 1020160035087-A/647: STEM CELL MICROPARTICLES AND MIRNA.
LP951747 - Sequence 253 from Patent WO2017157650.
LQ070439 - Sequence 763 from Patent EP2964234.
LQ422104 - Sequence 42 from Patent EP3026121.
LQ441225 - Sequence 232 from Patent EP3029157.
LV471057 - JP 2016534036-A/647: Stem Cell Microparticles and miRNA.
JD429840 - Sequence 410864 from Patent EP1572962.
JD038301 - Sequence 19325 from Patent EP1572962.
DQ572727 - Homo sapiens piRNA piR-40839, complete sequence.
JD469029 - Sequence 450053 from Patent EP1572962.
DQ601556 - Homo sapiens piRNA piR-39622, complete sequence.
JD207503 - Sequence 188527 from Patent EP1572962.
DQ582998 - Homo sapiens piRNA piR-50110, complete sequence.
JD392244 - Sequence 373268 from Patent EP1572962.
JD499150 - Sequence 480174 from Patent EP1572962.
DQ599282 - Homo sapiens piRNA piR-37348, complete sequence.
JD020249 - Sequence 1273 from Patent EP1572962.
JD029923 - Sequence 10947 from Patent EP1572962.
JD029896 - Sequence 10920 from Patent EP1572962.
DQ599843 - Homo sapiens piRNA piR-37909, complete sequence.
DQ599842 - Homo sapiens piRNA piR-37908, complete sequence.
JD425224 - Sequence 406248 from Patent EP1572962.
DQ599945 - Homo sapiens piRNA piR-38011, complete sequence.
JD512217 - Sequence 493241 from Patent EP1572962.
JD367614 - Sequence 348638 from Patent EP1572962.
JD396175 - Sequence 377199 from Patent EP1572962.
JD489080 - Sequence 470104 from Patent EP1572962.
AK056315 - Homo sapiens cDNA FLJ31753 fis, clone NT2RI2007468.
JD331078 - Sequence 312102 from Patent EP1572962.
JD242753 - Sequence 223777 from Patent EP1572962.
DQ589808 - Homo sapiens piRNA piR-56920, complete sequence.
DQ596656 - Homo sapiens piRNA piR-34722, complete sequence.
AK023520 - Homo sapiens cDNA FLJ13458 fis, clone PLACE1003361.
AK095108 - Homo sapiens cDNA FLJ37789 fis, clone BRHIP3000081.
DQ579891 - Homo sapiens piRNA piR-48003, complete sequence.
JD074150 - Sequence 55174 from Patent EP1572962.
JD228565 - Sequence 209589 from Patent EP1572962.
JD488193 - Sequence 469217 from Patent EP1572962.
DQ582501 - Homo sapiens piRNA piR-32613, complete sequence.
DQ601816 - Homo sapiens piRNA piR-39882, complete sequence.
AF147443 - Homo sapiens full length insert cDNA clone ZC65B08.
BC006821 - Homo sapiens chromobox homolog 5 (HP1 alpha homolog, Drosophila), mRNA (cDNA clone MGC:4985 IMAGE:3448801), complete cds.
U26311 - Human heterochromatin protein HP1Hs-alpha mRNA, partial cds.
JD151553 - Sequence 132577 from Patent EP1572962.
JD113250 - Sequence 94274 from Patent EP1572962.
JD053128 - Sequence 34152 from Patent EP1572962.
JD082876 - Sequence 63900 from Patent EP1572962.
DQ570316 - Homo sapiens piRNA piR-30428, complete sequence.
CR457418 - Homo sapiens full open reading frame cDNA clone RZPDo834G1110D for gene CBX5, chromobox homolog 5 (HP1 alpha homolog, Drosophila); complete cds, incl. stopcodon.
AK313506 - Homo sapiens cDNA, FLJ94062, Homo sapiens chromobox homolog 5 (HP1 alpha homolog, Drosophila)(CBX5), mRNA.
EU446624 - Synthetic construct Homo sapiens clone IMAGE:100070025; IMAGE:100011833; FLH258252.01L chromobox homolog 5 (HP1 alpha homolog, Drosophila) (CBX5) gene, encodes complete protein.
EU446784 - Synthetic construct Homo sapiens clone IMAGE:100070352; IMAGE:100011993; FLH262809.01L chromobox homolog 5 (HP1 alpha homolog, Drosophila) (CBX5) gene, encodes complete protein.
AB528597 - Synthetic construct DNA, clone: pF1KB3469, Homo sapiens CBX5 gene for chromobox homolog 5, without stop codon, in Flexi system.
MA643940 - JP 2017113010-A/1864: SIGNAL-SENSOR POLYNUCLEOTIDES FOR THE ALTERATION OF CELLULAR PHENOTYPES.
MA731824 - JP 2017140048-A/694: TERMINALLY MODIFIED RNA.
MA406001 - WO 2018155427-A/775: A probe with reduced false positive binding, a method to desing the probe, and the use thereof.
MA800993 - JP 2018183181-A/1864: SIGNAL-SENSOR POLYNUCLEOTIDES FOR THE ALTERATION OF CELLULAR PHENOTYPES.
MP129747 - Sequence 647 from Patent EP3470073.
MP162670 - Sequence 647 from Patent WO2019069093.
MB420660 - JP 2019154320-A/28: Method for evaluating cell quality.

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000209875.1, ENST00000209875.2, ENST00000209875.3, ENST00000209875.4, ENST00000209875.5, ENST00000209875.6, ENST00000209875.7, ENST00000209875.8, HEL25 , NM_012117, uc317ckt.1, uc317ckt.2, V9HWG0, V9HWG0_HUMAN
UCSC ID: ENST00000209875.9_7
RefSeq Accession: NM_012117.3

-  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.