Human Gene CSPG4 (uc002baw.3) Description and Page Index
  Description: Homo sapiens chondroitin sulfate proteoglycan 4 (CSPG4), mRNA.
RefSeq Summary (NM_001897): A human melanoma-associated chondroitin sulfate proteoglycan plays a role in stabilizing cell-substratum interactions during early events of melanoma cell spreading on endothelial basement membranes. CSPG4 represents an integral membrane chondroitin sulfate proteoglycan expressed by human malignant melanoma cells. [provided by RefSeq, Jul 2008]. Publication Note: This RefSeq record includes a subset of the publications that are available for this gene. Please see the Gene record to access additional publications. ##Evidence-Data-START## Transcript exon combination :: X96753.1, AY359468.1 [ECO:0000332] RNAseq introns :: single sample supports all introns SAMEA2162568 [ECO:0000348] ##Evidence-Data-END## ##RefSeq-Attributes-START## MANE Ensembl match :: ENST00000308508.5/ ENSP00000312506.5 RefSeq Select criteria :: based on single protein-coding transcript ##RefSeq-Attributes-END##
Transcript (Including UTRs)
   Position: hg19 chr15:75,966,663-76,005,189 Size: 38,527 Total Exon Count: 10 Strand: -
Coding Region
   Position: hg19 chr15:75,967,891-76,005,096 Size: 37,206 Coding Exon Count: 10 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated: 2013-06-15

-  Sequence and Links to Tools and Databases
Genomic Sequence (chr15:75,966,663-76,005,189)mRNA (may differ from genome)Protein (2322 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
OMIMPubMedReactomeStanford SOURCETreefamUniProtKB

-  Comments and Description Text from UniProtKB
DESCRIPTION: RecName: Full=Chondroitin sulfate proteoglycan 4; AltName: Full=Chondroitin sulfate proteoglycan NG2; AltName: Full=Melanoma chondroitin sulfate proteoglycan; AltName: Full=Melanoma-associated chondroitin sulfate proteoglycan; Flags: Precursor;
FUNCTION: Proteoglycan playing a role in cell proliferation and migration which stimulates endothelial cells motility during microvascular morphogenesis. May also inhibit neurite outgrowth and growth cone collapse during axon regeneration. Cell surface receptor for collagen alpha 2(VI) which may confer cells ability to migrate on that substrate. Binds through its extracellular N- terminus growth factors, extracellular matrix proteases modulating their activity. May regulate MPP16-dependent degradation and invasion of type I collagen participating in melanoma cells invasion properties. May modulate the plasminogen system by enhancing plasminogen activation and inhibiting angiostatin. Functions also as a signal transducing protein by binding through its cytoplasmic C-terminus scaffolding and signaling proteins. May promote retraction fiber formation and cell polarization through Rho GTPase activation. May stimulate alpha-4, beta-1 integrin- mediated adhesion and spreading by recruiting and activating a signaling cascade through CDC42, ACK1 and BCAR1. May activate FAK and ERK1/ERK2 signaling cascades.
SUBUNIT: Interacts with the first PDZ domain of MPDZ. Interacts with PRKCA. Binds TNC, laminin-1, COL5A1 and COL6A2. Interacts with PLG and angiostatin. Binds FGF2 and PDGFA. Interacts with GRIP1, GRIP2 and GRIA2. Forms a ternary complex with GRIP1 and GRIA2 (By similarity). Interacts with LGALS3 and the integrin composed of ITGB1 and ITGA3. Interacts with ITGA4 through its chondroitin sulfate glycosaminoglycan. Interacts with BCAR1, CDC42 and ACK1. Interacts with MMP16.
SUBCELLULAR LOCATION: Apical cell membrane; Single-pass type I membrane protein; Extracellular side (By similarity). Cell projection, lamellipodium membrane; Single-pass type I membrane protein; Extracellular side (By similarity). Note=Localized at the apical plasma membrane it relocalizes to the lamellipodia of astrocytoma upon phosphorylation by PRKCA. Localizes to the retraction fibers. Localizes to the plasma membrane of oligodendrocytes (By similarity).
TISSUE SPECIFICITY: Detected only in malignant melanoma cells.
PTM: O-glycosylated; contains glycosaminoglycan chondroitin sulfate which are required for proper localization and function in stress fiber formation (By similarity). Involved in interaction with MMP16 and ITGA4.
PTM: Phosphorylation by PRKCA regulates its subcellular location and function in cell motility (By similarity).
MISCELLANEOUS: Valuable marker for several incompletely differentiated precursor cells.
SIMILARITY: Contains 15 CSPG (NG2) repeats.
SIMILARITY: Contains 2 laminin G-like domains.

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): CSPG4
CDC HuGE Published Literature: CSPG4

-  MalaCards Disease Associations
  MalaCards Gene Search: CSPG4
Diseases sorted by gene-association score: melanoma (11), demyelinating disease (3)

-  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: 88.99 RPKM in Artery - Tibial
Total median expression: 686.54 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 -32.5093-0.349 Picture PostScript Text
3' UTR -561.301228-0.457 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
IPR008985 - ConA-like_lec_gl_sf
IPR013320 - ConA-like_subgrp
IPR001791 - Laminin_G

Pfam Domains:
PF00054 - Laminin G domain
PF02210 - Laminin G domain
PF16184 - Cadherin-like

SCOP Domains:
49899 - Concanavalin A-like lectins/glucanases

ModBase Predicted Comparative 3D Structure on Q6UVK1
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 orthologGenome BrowserGenome BrowserGenome BrowserGenome BrowserNo ortholog
Gene DetailsGene Details Gene DetailsGene Details 
Gene SorterGene Sorter Gene SorterGene Sorter 
 Protein SequenceProtein SequenceProtein SequenceProtein Sequence 

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0004871 signal transducer activity
GO:0019901 protein kinase binding

Biological Process:
GO:0000187 activation of MAPK activity
GO:0001525 angiogenesis
GO:0007165 signal transduction
GO:0007169 transmembrane receptor protein tyrosine kinase signaling pathway
GO:0007275 multicellular organism development
GO:0008283 cell proliferation
GO:0008347 glial cell migration
GO:0030154 cell differentiation
GO:0030206 chondroitin sulfate biosynthetic process
GO:0030207 chondroitin sulfate catabolic process
GO:0030208 dermatan sulfate biosynthetic process
GO:0035556 intracellular signal transduction
GO:0048771 tissue remodeling
GO:0050731 positive regulation of peptidyl-tyrosine phosphorylation

Cellular Component:
GO:0005576 extracellular region
GO:0005796 Golgi lumen
GO:0005886 plasma membrane
GO:0005887 integral component of plasma membrane
GO:0005925 focal adhesion
GO:0009986 cell surface
GO:0016020 membrane
GO:0016021 integral component of membrane
GO:0016324 apical plasma membrane
GO:0031012 extracellular matrix
GO:0031258 lamellipodium membrane
GO:0042995 cell projection
GO:0043202 lysosomal lumen
GO:0070062 extracellular exosome

-  Descriptions from all associated GenBank mRNAs
  BC033194 - Homo sapiens chondroitin sulfate proteoglycan 4, mRNA (cDNA clone IMAGE:4841488), with apparent retained intron.
JD303591 - Sequence 284615 from Patent EP1572962.
X96753 - H.sapiens mRNA for melanoma-associated chondroitin sulfate proteoglycan (MCSP).
JD203858 - Sequence 184882 from Patent EP1572962.
JD466577 - Sequence 447601 from Patent EP1572962.
JD077931 - Sequence 58955 from Patent EP1572962.
JD178518 - Sequence 159542 from Patent EP1572962.
JD485906 - Sequence 466930 from Patent EP1572962.
JD231174 - Sequence 212198 from Patent EP1572962.
JD450247 - Sequence 431271 from Patent EP1572962.
JD145525 - Sequence 126549 from Patent EP1572962.
JD345457 - Sequence 326481 from Patent EP1572962.
JD397703 - Sequence 378727 from Patent EP1572962.
JD116077 - Sequence 97101 from Patent EP1572962.
JD055865 - Sequence 36889 from Patent EP1572962.
JD440562 - Sequence 421586 from Patent EP1572962.
JD193598 - Sequence 174622 from Patent EP1572962.
JD218549 - Sequence 199573 from Patent EP1572962.
JD480846 - Sequence 461870 from Patent EP1572962.
JD070986 - Sequence 52010 from Patent EP1572962.
JD416550 - Sequence 397574 from Patent EP1572962.
JD210245 - Sequence 191269 from Patent EP1572962.
JD547246 - Sequence 528270 from Patent EP1572962.
JD449521 - Sequence 430545 from Patent EP1572962.
AY359468 - Homo sapiens melanoma chondroitin sulfate proteoglycan (CSPG4) mRNA, complete cds.
JD449520 - Sequence 430544 from Patent EP1572962.
JD281527 - Sequence 262551 from Patent EP1572962.
JD220739 - Sequence 201763 from Patent EP1572962.
JD224767 - Sequence 205791 from Patent EP1572962.
JD313955 - Sequence 294979 from Patent EP1572962.
BC172270 - Synthetic construct Homo sapiens clone IMAGE:100068964, MGC:198975 chondroitin sulfate proteoglycan 4 (CSPG4) mRNA, encodes complete protein.
BC172576 - Synthetic construct Homo sapiens clone IMAGE:100069270, MGC:199281 chondroitin sulfate proteoglycan 4 (CSPG4) mRNA, encodes complete protein.
AB462981 - Synthetic construct DNA, clone: pF1KB9563, Homo sapiens CSPG4 gene for chondroitin sulfate proteoglycan 4, without stop codon, in Flexi system.
BC128110 - Homo sapiens chondroitin sulfate proteoglycan 4, mRNA (cDNA clone IMAGE:40112128), partial cds.
JD338552 - Sequence 319576 from Patent EP1572962.
JD371947 - Sequence 352971 from Patent EP1572962.
JD554223 - Sequence 535247 from Patent EP1572962.
JD179033 - Sequence 160057 from Patent EP1572962.
JD554222 - Sequence 535246 from Patent EP1572962.
JD266575 - Sequence 247599 from Patent EP1572962.
JD471460 - Sequence 452484 from Patent EP1572962.
JD400587 - Sequence 381611 from Patent EP1572962.
JD400607 - Sequence 381631 from Patent EP1572962.
JD115004 - Sequence 96028 from Patent EP1572962.
JD187682 - Sequence 168706 from Patent EP1572962.
JD048560 - Sequence 29584 from Patent EP1572962.
JD303056 - Sequence 284080 from Patent EP1572962.
JD477339 - Sequence 458363 from Patent EP1572962.
JD402057 - Sequence 383081 from Patent EP1572962.
JD425651 - Sequence 406675 from Patent EP1572962.
JD075631 - Sequence 56655 from Patent EP1572962.
JD107111 - Sequence 88135 from Patent EP1572962.
JD192453 - Sequence 173477 from Patent EP1572962.
JD151438 - Sequence 132462 from Patent EP1572962.

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

Protein Q6UVK1 (Reactome details) participates in the following event(s):

R-HSA-1889981 B4GALT7 transfers Gal group to xylosyl-unit of the tetrasaccharide linker
R-HSA-1878002 XYLTs transfer Xyl to core protein
R-HSA-2018682 CHST3,7 transfer SO4(2-) to position 6 of GalNAc on chondroitin chains
R-HSA-1889955 B3GATs transfer GlcA to tetrasaccharide linker
R-HSA-1889978 B3GALT6 transfers Gal to 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-1971482 The addition of GalNAc to the terminal glucuronate residue forms chondroitin
R-HSA-1971483 Chondroitin can be sulfated on position 4 of GalNAc by CHST9, 11, 12 and 13
R-HSA-2018659 Chondroitin 4-sulfate (C4S) can be further sulfated on position 6 by CHST15
R-HSA-2022061 Dermatan sulfate can be further sulfated on position 2 of iduronate
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-1971475 A tetrasaccharide linker sequence is required for GAG synthesis
R-HSA-3560783 Defective B4GALT7 causes EDS, progeroid type
R-HSA-2022870 Chondroitin sulfate biosynthesis
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-3595172 Defective CHST3 causes SEDCJD
R-HSA-2024101 CS/DS degradation
R-HSA-2022923 Dermatan sulfate biosynthesis
R-HSA-1638091 Heparan sulfate/heparin (HS-GAG) metabolism
R-HSA-1793185 Chondroitin sulfate/dermatan sulfate metabolism
R-HSA-3560782 Diseases associated with glycosaminoglycan metabolism
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: CSPG4_HUMAN, D3DW77, MCSP, NM_001897, NP_001888, Q6UVK1, Q92675
UCSC ID: uc002baw.3
RefSeq Accession: NM_001897
Protein: Q6UVK1 (aka CSPG4_HUMAN)
CCDS: CCDS10284.1

-  Gene Model Information
category: coding nonsense-mediated-decay: no RNA accession: NM_001897.4
exon count: 10CDS single in 3' UTR: no RNA size: 8305
ORF size: 6969CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 13702.00frame shift in genome: no % Coverage: 99.82
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: 0# strange splices: 0
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-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.