Human Gene BCAN (ENST00000329117.10_4) from GENCODE V47lift37
  Description: brevican, transcript variant 1 (from RefSeq NM_021948.5)
Gencode Transcript: ENST00000329117.10_4
Gencode Gene: ENSG00000132692.19_12
Transcript (Including UTRs)
   Position: hg19 chr1:156,611,909-156,629,320 Size: 17,412 Total Exon Count: 14 Strand: +
Coding Region
   Position: hg19 chr1:156,615,847-156,628,926 Size: 13,080 Coding Exon Count: 13 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr1:156,611,909-156,629,320)mRNA (may differ from genome)Protein (911 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCHuman Cortex Gene ExpressionMGIOMIMPubMedReactome
UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: PGCB_HUMAN
DESCRIPTION: RecName: Full=Brevican core protein; AltName: Full=Brain-enriched hyaluronan-binding protein; Short=BEHAB; AltName: Full=Chondroitin sulfate proteoglycan 7; Flags: Precursor;
FUNCTION: May play a role in the terminally differentiating and the adult nervous system during postnatal development. Could stabilize interactions between hyaluronan (HA) and brain proteoglycans.
SUBUNIT: Interacts with TNR (By similarity).
SUBCELLULAR LOCATION: Isoform 1: Secreted, extracellular space, extracellular matrix.
SUBCELLULAR LOCATION: Isoform 2: Membrane; Lipid-anchor, GPI- anchor.
DEVELOPMENTAL STAGE: Isoform 1 is highly expressed from birth through 8 years of age and is down-regulated by 20 years of age to low levels that are maintained in the normal adult cortex. Isoform 2 is expressed at uniformly low levels throughout development.
PTM: Contains mostly chondroitin sulfate (By similarity). O- glycosylated with a core 1 or possibly core 8 glycan.
SIMILARITY: Belongs to the aggrecan/versican proteoglycan family.
SIMILARITY: Contains 1 C-type lectin domain.
SIMILARITY: Contains 1 EGF-like domain.
SIMILARITY: Contains 1 Ig-like V-type (immunoglobulin-like) domain.
SIMILARITY: Contains 2 Link domains.
SIMILARITY: Contains 1 Sushi (CCP/SCR) domain.
WEB RESOURCE: Name=Functional Glycomics Gateway - Glycan Binding; Note=Brevican; URL="http://www.functionalglycomics.org/glycomics/GBPServlet?&operationType=view&cbpId=cbp_hum_Ctlect_212";

-  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


-  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: 100.60 RPKM in Brain - Amygdala
Total median expression: 735.18 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 -62.10167-0.372 Picture PostScript Text
3' UTR -138.40394-0.351 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
IPR001304 - C-type_lectin
IPR016186 - C-type_lectin-like
IPR018378 - C-type_lectin_CS
IPR016187 - C-type_lectin_fold
IPR016060 - Complement_control_module
IPR000742 - EG-like_dom
IPR013032 - EGF-like_CS
IPR007110 - Ig-like
IPR013783 - Ig-like_fold
IPR003006 - Ig/MHC_CS
IPR013106 - Ig_V-set
IPR003596 - Ig_V-set_subgr
IPR000538 - Link
IPR000436 - Sushi_SCR_CCP

Pfam Domains:
PF00008 - EGF-like domain
PF00059 - Lectin C-type domain
PF00084 - Sushi repeat (SCR repeat)
PF00193 - Extracellular link domain
PF07686 - Immunoglobulin V-set domain
PF12661 - Human growth factor-like EGF

SCOP Domains:
48726 - Immunoglobulin
56436 - C-type lectin-like
57535 - Complement control module/SCR domain
57196 - EGF/Laminin

ModBase Predicted Comparative 3D Structure on Q96GW7
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 Details  
Gene SorterGene Sorter Gene Sorter  
 RGD    
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005201 extracellular matrix structural constituent
GO:0005540 hyaluronic acid binding
GO:0030246 carbohydrate binding

Biological Process:
GO:0001501 skeletal system development
GO:0007155 cell adhesion
GO:0007417 central nervous system development
GO:0021766 hippocampus development
GO:0030198 extracellular matrix organization
GO:0030206 chondroitin sulfate biosynthetic process
GO:0030207 chondroitin sulfate catabolic process
GO:0030208 dermatan sulfate biosynthetic process

Cellular Component:
GO:0005576 extracellular region
GO:0005796 Golgi lumen
GO:0016020 membrane
GO:0031225 anchored component of membrane
GO:0043202 lysosomal lumen


-  Descriptions from all associated GenBank mRNAs
  LF211903 - JP 2014500723-A/19406: Polycomb-Associated Non-Coding RNAs.
LF206160 - JP 2014500723-A/13663: Polycomb-Associated Non-Coding RNAs.
JA482196 - Sequence 179 from Patent WO2011072091.
JE980488 - Sequence 179 from Patent EP2862929.
AY358372 - Homo sapiens clone DNA98565 Brevican Core Pro (UNQ2525) mRNA, complete cds.
JA482195 - Sequence 178 from Patent WO2011072091.
JE980487 - Sequence 178 from Patent EP2862929.
LF385406 - JP 2014500723-A/192909: Polycomb-Associated Non-Coding RNAs.
AK289759 - Homo sapiens cDNA FLJ76746 complete cds, highly similar to Homo sapiens brevican (BCAN), transcript variant 1, mRNA.
BC029348 - Homo sapiens cDNA clone IMAGE:4180213, containing frame-shift errors.
AY007241 - Homo sapiens hyaluronan binding protein (HABP2) mRNA, partial cds.
BC022938 - Homo sapiens brevican, mRNA (cDNA clone MGC:24965 IMAGE:4932894), complete cds.
BC035457 - Homo sapiens brevican, mRNA (cDNA clone IMAGE:4156034).
BC027971 - Homo sapiens brevican, mRNA (cDNA clone MGC:34716 IMAGE:5309663), complete cds.
BC009117 - Homo sapiens brevican, mRNA (cDNA clone MGC:18150 IMAGE:4154474), complete cds.
JD520361 - Sequence 501385 from Patent EP1572962.
JD458421 - Sequence 439445 from Patent EP1572962.
BC010571 - Homo sapiens brevican, mRNA (cDNA clone IMAGE:4215184).
JD204053 - Sequence 185077 from Patent EP1572962.
AF229053 - Homo sapiens chondroitin sulfate proteoglycan BEHAB/brevican mRNA, GPI isoform, complete cds.
AF228710 - Homo sapiens chondroitin sulfate proteoglycan BEHAB/brevican mRNA, soluble isoform, complete cds.
JD070890 - Sequence 51914 from Patent EP1572962.
CU692756 - Synthetic construct Homo sapiens gateway clone IMAGE:100020528 5' read BCAN mRNA.
KJ899412 - Synthetic construct Homo sapiens clone ccsbBroadEn_08806 BCAN gene, encodes complete protein.
KJ899413 - Synthetic construct Homo sapiens clone ccsbBroadEn_08807 BCAN gene, encodes complete protein.
AB527863 - Synthetic construct DNA, clone: pF1KB8564, Homo sapiens BCAN gene for brevican, without stop codon, in Flexi system.
AB209570 - Homo sapiens mRNA for brevican isoform 1 variant protein.
BC029313 - Homo sapiens brevican, mRNA (cDNA clone IMAGE:4157828).
BC023209 - Homo sapiens brevican, mRNA (cDNA clone IMAGE:4940883).
LF352062 - JP 2014500723-A/159565: Polycomb-Associated Non-Coding RNAs.
LF352061 - JP 2014500723-A/159564: Polycomb-Associated Non-Coding RNAs.
BC013234 - Homo sapiens brevican, mRNA (cDNA clone IMAGE:4154690).
AL137504 - Homo sapiens mRNA; cDNA DKFZp761L191 (from clone DKFZp761L191); partial cds.
AK126588 - Homo sapiens cDNA FLJ44625 fis, clone BRACE2017438, highly similar to Homo sapiens chondroitin sulfate proteoglycan BEHAB/brevican (BCAN).
JD218981 - Sequence 200005 from Patent EP1572962.
JD221396 - Sequence 202420 from Patent EP1572962.
JD383410 - Sequence 364434 from Patent EP1572962.
JD332592 - Sequence 313616 from Patent EP1572962.
JD417913 - Sequence 398937 from Patent EP1572962.
JD061176 - Sequence 42200 from Patent EP1572962.
JD456733 - Sequence 437757 from Patent EP1572962.
JD288791 - Sequence 269815 from Patent EP1572962.
JD356065 - Sequence 337089 from Patent EP1572962.
MA620983 - JP 2018138019-A/192909: Polycomb-Associated Non-Coding RNAs.
MA587639 - JP 2018138019-A/159565: Polycomb-Associated Non-Coding RNAs.
MA587638 - JP 2018138019-A/159564: Polycomb-Associated Non-Coding RNAs.
MA447480 - JP 2018138019-A/19406: Polycomb-Associated Non-Coding RNAs.
MA441737 - JP 2018138019-A/13663: Polycomb-Associated Non-Coding RNAs.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q96GW7 (Reactome details) participates in the following event(s):

R-HSA-2018659 Chondroitin 4-sulfate (C4S) can be further sulfated on position 6 by CHST15
R-HSA-1889955 B3GATs transfer GlcA to tetrasaccharide linker
R-HSA-1889978 B3GALT6 transfers Gal to the tetrasaccharide linker
R-HSA-1889981 B4GALT7 transfers Gal group to xylosyl-unit of the tetrasaccharide linker
R-HSA-1971487 CHPF,CHSY1,CHSY3 transfer GalNAc to chondroitin
R-HSA-1971491 CHPF,CHPF2,CHSY1,CHSY3 transfer GlcA to chondroitin
R-HSA-1878002 XYLTs transfer Xyl to core protein
R-HSA-3788075 Brevican degradation by ADAMTS4, ADAMTS5
R-HSA-3791149 Brevican degradation by MMP1, 2, 3, 7,8,10,13,19
R-HSA-1971483 Chondroitin can be sulfated on position 4 of GalNAc by CHST9, 11, 12 and 13
R-HSA-2018682 CHST3,7 transfer SO4(2-) to position 6 of GalNAc on chondroitin chains
R-HSA-1971482 The addition of GalNAc to the terminal glucuronate residue forms chondroitin
R-HSA-2022061 Dermatan sulfate can be further sulfated on position 2 of iduronate
R-HSA-2424246 Tenascins C, R, (X, N) bind lecticans
R-HSA-2022052 Dermatan-sulfate epimerase (DSE) converts chondroitin sulfate (CS) to dermatan sulfate (DS)
R-HSA-2022063 CHST14 transfers SO4(2-) to GalNAc in dermatan or DS
R-HSA-2022870 Chondroitin sulfate biosynthesis
R-HSA-1971475 A tetrasaccharide linker sequence is required for GAG synthesis
R-HSA-3560801 Defective B3GAT3 causes JDSSDHD
R-HSA-4420332 Defective B3GALT6 causes EDSP2 and SEMDJL1
R-HSA-3595177 Defective CHSY1 causes TPBS
R-HSA-1474228 Degradation of the extracellular matrix
R-HSA-3595172 Defective CHST3 causes SEDCJD
R-HSA-3560783 Defective B4GALT7 causes EDS, progeroid type
R-HSA-2024101 CS/DS degradation
R-HSA-2022923 Dermatan sulfate biosynthesis
R-HSA-1793185 Chondroitin sulfate/dermatan sulfate metabolism
R-HSA-1638091 Heparan sulfate/heparin (HS-GAG) metabolism
R-HSA-3560782 Diseases associated with glycosaminoglycan metabolism
R-HSA-3000178 ECM proteoglycans
R-HSA-1474244 Extracellular matrix organization
R-HSA-3595174 Defective CHST14 causes EDS, musculocontractural type
R-HSA-1630316 Glycosaminoglycan metabolism
R-HSA-3781865 Diseases of glycosylation
R-HSA-71387 Metabolism of carbohydrates
R-HSA-1643685 Disease
R-HSA-1430728 Metabolism

-  Other Names for This Gene
  Alternate Gene Symbols: BEHAB, CSPG7, D3DVC2, ENST00000329117.1, ENST00000329117.2, ENST00000329117.3, ENST00000329117.4, ENST00000329117.5, ENST00000329117.6, ENST00000329117.7, ENST00000329117.8, ENST00000329117.9, NM_021948, PGCB_HUMAN, Q5SZ10, Q5T3I5, Q8TBB9, Q96GW7, Q9HBK1, Q9HBK4, uc317squ.1, uc317squ.2, UNQ2525/PRO6018
UCSC ID: ENST00000329117.10_4
RefSeq Accession: NM_021948.5
Protein: Q96GW7 (aka PGCB_HUMAN)

-  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.