Human Gene BCOR (uc004deq.4) Description and Page Index
  Description: Homo sapiens BCL6 corepressor (BCOR), transcript variant 1, mRNA.
RefSeq Summary (NM_001123384): The protein encoded by this gene was identified as an interacting corepressor of BCL6, a POZ/zinc finger transcription repressor that is required for germinal center formation and may influence apoptosis. This protein selectively interacts with the POZ domain of BCL6, but not with eight other POZ proteins. Specific class I and II histone deacetylases (HDACs) have been shown to interact with this protein, which suggests a possible link between the two classes of HDACs. Several transcript variants encoding different isoforms have been found for this gene. A pseudogene of this gene is found on chromosome Y.[provided by RefSeq, Jun 2010].
Transcript (Including UTRs)
   Position: hg19 chrX:39,931,176-39,956,719 Size: 25,544 Total Exon Count: 4 Strand: -
Coding Region
   Position: hg19 chrX:39,931,584-39,937,182 Size: 5,599 Coding Exon Count: 3 

Page IndexSequence and LinksMalaCardsCTDGene AllelesRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesmRNA DescriptionsOther Names
Model InformationMethods
Data last updated: 2013-06-15

-  Sequence and Links to Tools and Databases
Genomic Sequence (chrX:39,931,176-39,956,719)mRNA (may differ from genome)Protein (1004 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
PubMedStanford SOURCEUniProtKBWikipedia

-  MalaCards Disease Associations
  MalaCards Gene Search: BCOR
Diseases sorted by gene-association score: microphthalmia, syndromic 2* (1340), microphthalmia, syndromic 1* (247), kidney clear cell sarcoma* (143), cataract 9, multiple types* (121), bcor-related lenz microphthalmia syndrome* (100), lenz microphthalmia syndromic* (71), myxoid leiomyosarcoma (24), microphthalmia (16), clear cell sarcoma (8), ogden syndrome (8), pulmonary neuroendocrine tumor (8), retroperitoneal sarcoma (7), ventricular septal defect (6), nance-horan syndrome (6), endometrial stromal sarcoma (6), hallermann-streiff syndrome (5), ewing sarcoma (2), leukemia, acute myeloid (0)
* = Manually curated disease association

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

+  Common Gene Haplotype Alleles
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-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 11.46 RPKM in Artery - Tibial
Total median expression: 262.26 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 -102.30292-0.350 Picture PostScript Text
3' UTR -104.50408-0.256 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
  ModBase Predicted Comparative 3D Structure on Q6W2J9-3
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     

-  Descriptions from all associated GenBank mRNAs
  BC114220 - Homo sapiens BCL6 co-repressor, mRNA (cDNA clone MGC:131961 IMAGE:4384724), complete cds.
LF211417 - JP 2014500723-A/18920: Polycomb-Associated Non-Coding RNAs.
AK056538 - Homo sapiens cDNA FLJ31976 fis, clone NT2RP7008315, weakly similar to ENVELOPE GLYCOPROTEIN GP340.
MA446994 - JP 2018138019-A/18920: Polycomb-Associated Non-Coding RNAs.
AK074286 - Homo sapiens cDNA FLJ23706 fis, clone HEP11450, highly similar to Homo sapiens BCL-6 corepressor (BCOR) mRNA.
AF317391 - Homo sapiens BCL-6 corepressor (BCOR) mRNA, complete cds; alternatively spliced.
AY316592 - Homo sapiens BCL-6 corepressor long isoform (BCOR) mRNA, complete cds, alternatively spliced.
JN813375 - Homo sapiens BCL6 corepressor-cyclin B3 fusion protein mRNA, complete cds.
HM597846 - Homo sapiens BCL6 corepressor/retinoic acid receptor alpha fusion protein (BCOR-RARA) mRNA, complete cds.
AB046795 - Homo sapiens mRNA for KIAA1575 protein, partial cds.
AF317392 - Homo sapiens BCL-6 corepressor short isoform (BCOR) mRNA, complete cds; alternatively spliced.
BC128387 - Homo sapiens BCL6 co-repressor, mRNA (cDNA clone IMAGE:40123825), complete cds.
BC128456 - Homo sapiens BCL6 co-repressor, mRNA (cDNA clone IMAGE:40123827).
JD512311 - Sequence 493335 from Patent EP1572962.
AB385483 - Synthetic construct DNA, clone: pF1KA1575, Homo sapiens BCOR gene for BCL-6 corepressor, complete cds, without stop codon, in Flexi system.
LF379269 - JP 2014500723-A/186772: Polycomb-Associated Non-Coding RNAs.
LF379270 - JP 2014500723-A/186773: Polycomb-Associated Non-Coding RNAs.
LF379271 - JP 2014500723-A/186774: Polycomb-Associated Non-Coding RNAs.
LF379272 - JP 2014500723-A/186775: Polycomb-Associated Non-Coding RNAs.
LF379273 - JP 2014500723-A/186776: Polycomb-Associated Non-Coding RNAs.
LF379274 - JP 2014500723-A/186777: Polycomb-Associated Non-Coding RNAs.
LF379275 - JP 2014500723-A/186778: Polycomb-Associated Non-Coding RNAs.
LF379277 - JP 2014500723-A/186780: Polycomb-Associated Non-Coding RNAs.
JD329711 - Sequence 310735 from Patent EP1572962.
LF212803 - JP 2014500723-A/20306: Polycomb-Associated Non-Coding RNAs.
JD141126 - Sequence 122150 from Patent EP1572962.
JD218756 - Sequence 199780 from Patent EP1572962.
LF379280 - JP 2014500723-A/186783: Polycomb-Associated Non-Coding RNAs.
MA614846 - JP 2018138019-A/186772: Polycomb-Associated Non-Coding RNAs.
MA614847 - JP 2018138019-A/186773: Polycomb-Associated Non-Coding RNAs.
MA614848 - JP 2018138019-A/186774: Polycomb-Associated Non-Coding RNAs.
MA614849 - JP 2018138019-A/186775: Polycomb-Associated Non-Coding RNAs.
MA614850 - JP 2018138019-A/186776: Polycomb-Associated Non-Coding RNAs.
MA614851 - JP 2018138019-A/186777: Polycomb-Associated Non-Coding RNAs.
MA614852 - JP 2018138019-A/186778: Polycomb-Associated Non-Coding RNAs.
MA614854 - JP 2018138019-A/186780: Polycomb-Associated Non-Coding RNAs.
MA448380 - JP 2018138019-A/20306: Polycomb-Associated Non-Coding RNAs.
MA614857 - JP 2018138019-A/186783: Polycomb-Associated Non-Coding RNAs.

-  Other Names for This Gene
  Alternate Gene Symbols: AF317392, KIAA1575, NM_001123384, NP_001116856, Q6W2J9-3
UCSC ID: uc004deq.4
RefSeq Accession: NM_001123384
Protein: Q6W2J9-3, splice isoform of Q6W2J9

-  Gene Model Information
category: coding nonsense-mediated-decay: no RNA accession: AF317392.1
exon count: 4CDS single in 3' UTR: no RNA size: 3676
ORF size: 3015CDS single in intron: no Alignment % ID: 99.86
txCdsPredict score: 6017.00frame shift in genome: no % Coverage: 99.35
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: 426# 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.