Human Gene BCOR (ENST00000342274.8)
  Description: Homo sapiens BCL6 corepressor (BCOR), transcript variant 3, mRNA. (from RefSeq NM_001123383)
RefSeq Summary (NM_001123383): 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].
Gencode Transcript: ENST00000342274.8
Gencode Gene: ENSG00000183337.17
Transcript (Including UTRs)
   Position: hg38 chrX:40,051,248-40,177,329 Size: 126,082 Total Exon Count: 15 Strand: -
Coding Region
   Position: hg38 chrX:40,052,109-40,077,929 Size: 25,821 Coding Exon Count: 14 

Page IndexSequence and LinksUniProtKB CommentsMalaCardsCTDRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
Other NamesMethods
Data last updated at UCSC: 2021-01-14 15:32:12

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chrX:40,051,248-40,177,329)mRNA (may differ from genome)Protein (1721 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaBioGPS
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HPRDLynxMGImyGene2neXtProtOMIM
PubMedUniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: BCOR_HUMAN
DESCRIPTION: RecName: Full=BCL-6 corepressor; Short=BCoR;
FUNCTION: Transcriptional corepressor. May specifically inhibit gene expression when recruited to promoter regions by sequence specific DNA-binding proteins such as BCL6 and MLLT3. This repression may be mediated at least in part by histone deacetylase activities which can associate with this corepressor. Involved in the repression of TFAP2A; impairs binding of BCL6 and KDM2B to TFAP2A promoter regions. Via repression of TFAP2A acts as a negative regulator of osteo-dentiogenic capacity in adult stem cells; the function implies inhibition of methylation on histone H3 'Lys-4' (H3K4me3) and 'Lys-36' (H3K36me2).
SUBUNIT: Isoform 1 may interact with MLLT3/AF9 (By similarity). Interacts with BCL6; the interaction is direct. Can interact with HDAC1, HDAC3 and HDAC5. Interacts with PCGF1; the interaction is direct. Interacts with KDM2B. Component of an approximative 800 kDa repressive BCOR complex at least composed of BCOR, RYBP, PCGF1, RING1, RNF2/RING2, KDM2B and SKP1.
INTERACTION: Q8NHM5:KDM2B; NbExp=2; IntAct=EBI-950027, EBI-3955564; Q9BSM1:PCGF1; NbExp=6; IntAct=EBI-950027, EBI-749901;
SUBCELLULAR LOCATION: Nucleus.
TISSUE SPECIFICITY: Ubiquitously expressed.
DISEASE: Defects in BCOR are the cause of microphthalmia syndromic type 2 (MCOPS2) [MIM:300166]. Microphthalmia is a clinically heterogeneous disorder of eye formation, ranging from small size of a single eye to complete bilateral absence of ocular tissues (anophthalmia). In many cases, microphthalmia/anophthalmia occurs in association with syndromes that include non-ocular abnormalities. MCOPS2 is a very rare multiple congenital anomaly syndrome characterized by eye anomalies (congenital cataract, microphthalmia, or secondary glaucoma), facial abnormalities (long narrow face, high nasal bridge, pointed nose with cartilages separated at the tip, cleft palate, or submucous cleft palate), cardiac anomalies (atrial septal defect, ventricular septal defect, or floppy mitral valve) and dental abnormalities (canine radiculomegaly, delayed dentition, oligodontia, persistent primary teeth, or variable root length).
SIMILARITY: Belongs to the BCOR family.
SIMILARITY: Contains 3 ANK repeats.
SEQUENCE CAUTION: Sequence=AAH63536.1; Type=Miscellaneous discrepancy; Note=Contaminating sequence. Presence of complementary strand sequence in the clone; Sequence=BAA91061.1; Type=Miscellaneous discrepancy; Note=Intron retention; Sequence=BAB13401.2; Type=Erroneous initiation; Sequence=BAB85037.1; Type=Frameshift; Positions=1353;
WEB RESOURCE: Name=GeneReviews; URL="http://www.ncbi.nlm.nih.gov/sites/GeneTests/lab/gene/BCOR";

-  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

-  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
  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 -127.70363-0.352 Picture PostScript Text
3' UTR -186.60861-0.217 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
IPR002110 - Ankyrin_rpt
IPR020683 - Ankyrin_rpt-contain_dom

Pfam Domains:
PF12796 - Ankyrin repeats (3 copies)

Protein Data Bank (PDB) 3-D Structure
MuPIT help

3BIM
- X-ray MuPIT


ModBase Predicted Comparative 3D Structure on Q6W2J9
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-  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
Genome BrowserGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
MGIRGD    
Protein SequenceProtein Sequence    
AlignmentAlignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000977 RNA polymerase II regulatory region sequence-specific DNA binding
GO:0003714 transcription corepressor activity
GO:0005515 protein binding
GO:0008134 transcription factor binding
GO:0031072 heat shock protein binding
GO:0042826 histone deacetylase binding
GO:0044212 transcription regulatory region DNA binding
GO:0004842 ubiquitin-protein transferase activity

Biological Process:
GO:0000122 negative regulation of transcription from RNA polymerase II promoter
GO:0000415 negative regulation of histone H3-K36 methylation
GO:0006325 chromatin organization
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0007507 heart development
GO:0030502 negative regulation of bone mineralization
GO:0035518 histone H2A monoubiquitination
GO:0042476 odontogenesis
GO:0045892 negative regulation of transcription, DNA-templated
GO:0051572 negative regulation of histone H3-K4 methylation
GO:0060021 palate development
GO:0065001 specification of axis polarity
GO:0070171 negative regulation of tooth mineralization

Cellular Component:
GO:0005634 nucleus
GO:0031519 PcG protein complex


-  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.
MA446994 - JP 2018138019-A/18920: Polycomb-Associated Non-Coding RNAs.
AK056538 - Homo sapiens cDNA FLJ31976 fis, clone NT2RP7008315, weakly similar to ENVELOPE GLYCOPROTEIN GP340.
BC063536 - Homo sapiens BCL6 co-repressor, mRNA (cDNA clone IMAGE:4441370), complete cds.
AK000292 - Homo sapiens cDNA FLJ20285 fis, clone HEP04260.
AK225581 - Homo sapiens mRNA for BCL-6 interacting corepressor isoform 1 variant, clone: LNG04976.
AK095360 - Homo sapiens cDNA FLJ38041 fis, clone CTONG2013986, highly similar to BCoR protein.
BC009675 - Homo sapiens BCL6 co-repressor, mRNA (cDNA clone IMAGE:3905618), partial cds.
AK074286 - Homo sapiens cDNA FLJ23706 fis, clone HEP11450, highly similar to Homo sapiens BCL-6 corepressor (BCOR) mRNA.
JD503216 - Sequence 484240 from Patent EP1572962.
JD563081 - Sequence 544105 from Patent EP1572962.
JD228932 - Sequence 209956 from Patent EP1572962.
JD174763 - Sequence 155787 from Patent EP1572962.
JD263915 - Sequence 244939 from Patent EP1572962.
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.
JD433093 - Sequence 414117 from Patent EP1572962.
JD353652 - Sequence 334676 from Patent EP1572962.
KJ902708 - Synthetic construct Homo sapiens clone ccsbBroadEn_12102 BCOR gene, encodes complete protein.
JN813375 - Homo sapiens BCL6 corepressor-cyclin B3 fusion protein mRNA, complete cds.
LF379253 - JP 2014500723-A/186756: Polycomb-Associated Non-Coding RNAs.
MA614830 - JP 2018138019-A/186756: Polycomb-Associated Non-Coding RNAs.
HM597846 - Homo sapiens BCL6 corepressor/retinoic acid receptor alpha fusion protein (BCOR-RARA) mRNA, complete cds.
LF379259 - JP 2014500723-A/186762: Polycomb-Associated Non-Coding RNAs.
MA614836 - JP 2018138019-A/186762: Polycomb-Associated Non-Coding RNAs.
LF379260 - JP 2014500723-A/186763: Polycomb-Associated Non-Coding RNAs.
MA614837 - JP 2018138019-A/186763: Polycomb-Associated Non-Coding RNAs.
LF379261 - JP 2014500723-A/186764: Polycomb-Associated Non-Coding RNAs.
MA614838 - JP 2018138019-A/186764: Polycomb-Associated Non-Coding RNAs.
LF379262 - JP 2014500723-A/186765: Polycomb-Associated Non-Coding RNAs.
MA614839 - JP 2018138019-A/186765: Polycomb-Associated Non-Coding RNAs.
LF379263 - JP 2014500723-A/186766: Polycomb-Associated Non-Coding RNAs.
MA614840 - JP 2018138019-A/186766: Polycomb-Associated Non-Coding RNAs.
LF379264 - JP 2014500723-A/186767: Polycomb-Associated Non-Coding RNAs.
MA614841 - JP 2018138019-A/186767: Polycomb-Associated Non-Coding RNAs.
LF379265 - JP 2014500723-A/186768: Polycomb-Associated Non-Coding RNAs.
MA614842 - JP 2018138019-A/186768: Polycomb-Associated Non-Coding RNAs.
LF379267 - JP 2014500723-A/186770: Polycomb-Associated Non-Coding RNAs.
MA614844 - JP 2018138019-A/186770: Polycomb-Associated Non-Coding RNAs.
LF379268 - JP 2014500723-A/186771: Polycomb-Associated Non-Coding RNAs.
MA614845 - JP 2018138019-A/186771: Polycomb-Associated Non-Coding RNAs.
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).
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.
MA614846 - JP 2018138019-A/186772: Polycomb-Associated Non-Coding RNAs.
LF379270 - JP 2014500723-A/186773: Polycomb-Associated Non-Coding RNAs.
MA614847 - JP 2018138019-A/186773: Polycomb-Associated Non-Coding RNAs.
LF379271 - JP 2014500723-A/186774: Polycomb-Associated Non-Coding RNAs.
MA614848 - JP 2018138019-A/186774: Polycomb-Associated Non-Coding RNAs.
LF379272 - JP 2014500723-A/186775: Polycomb-Associated Non-Coding RNAs.
MA614849 - JP 2018138019-A/186775: Polycomb-Associated Non-Coding RNAs.
LF379273 - JP 2014500723-A/186776: Polycomb-Associated Non-Coding RNAs.
MA614850 - JP 2018138019-A/186776: Polycomb-Associated Non-Coding RNAs.
LF379274 - JP 2014500723-A/186777: Polycomb-Associated Non-Coding RNAs.
MA614851 - JP 2018138019-A/186777: Polycomb-Associated Non-Coding RNAs.
LF379275 - JP 2014500723-A/186778: Polycomb-Associated Non-Coding RNAs.
MA614852 - JP 2018138019-A/186778: Polycomb-Associated Non-Coding RNAs.
LF379277 - JP 2014500723-A/186780: Polycomb-Associated Non-Coding RNAs.
MA614854 - JP 2018138019-A/186780: Polycomb-Associated Non-Coding RNAs.
JD329711 - Sequence 310735 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: BCOR_HUMAN, D3DWB3, D3DWB4, ENST00000342274.1, ENST00000342274.2, ENST00000342274.3, ENST00000342274.4, ENST00000342274.5, ENST00000342274.6, ENST00000342274.7, KIAA1575, NM_001123383, Q29RF6, Q6P4B6, Q6W2J9, Q7Z2K7, Q8TEB4, Q96DB3, Q9H232, Q9H233, Q9HCJ7, Q9NXF2, uc004dep.1, uc004dep.2, uc004dep.3, uc004dep.4, uc004dep.5
UCSC ID: ENST00000342274.8
RefSeq Accession: NM_001123383
Protein: Q6W2J9 (aka BCOR_HUMAN)
CCDS: CCDS14250.1, CCDS48092.1, CCDS48093.1

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