Cspg4b (chondroitin sulfate proteoglycan 4B) - Rat Genome Database

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Gene: Cspg4b (chondroitin sulfate proteoglycan 4B) Mus musculus
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Symbol: Cspg4b
Name: chondroitin sulfate proteoglycan 4B
RGD ID: 11083214
MGI Page MGI
Description: Orthologous to human CSPG4BP (chondroitin sulfate proteoglycan family member 4B, pseudogene).
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: BC067074; cDNA sequence BC067074; chondroitin sulfate proteoglycan 4; Chondroitin sulfate proteoglycan 4-like; uncharacterized protein LOC408066
RGD Orthologs
Human
Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCm39 - Mouse Genome Assembly GRCm39
Position:
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3913113,429,570 - 113,507,049 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl13113,429,693 - 113,516,245 (+)EnsemblGRCm39 Ensembl
GRCm3813113,293,052 - 113,370,513 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl13113,293,159 - 113,379,711 (+)EnsemblGRCm38mm10GRCm38
MGSCv3713114,106,733 - 114,160,723 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv3613114,437,403 - 114,491,393 (+)NCBIMGSCv36mm8
MGSCv3613110,916,844 - 110,970,784 (+)NCBIMGSCv36mm8
Celera13117,606,070 - 117,684,810 (+)NCBICelera
Cytogenetic Map13D2.2NCBI
cM Map1363.94NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Molecular Function

References
Additional References at PubMed
PMID:10349636   PMID:11042159   PMID:11076861   PMID:11217851   PMID:12466851   PMID:12477932   PMID:16141072   PMID:16141073   PMID:21267068   PMID:21677750  


Genomics

Comparative Map Data
Cspg4b
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3913113,429,570 - 113,507,049 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl13113,429,693 - 113,516,245 (+)EnsemblGRCm39 Ensembl
GRCm3813113,293,052 - 113,370,513 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl13113,293,159 - 113,379,711 (+)EnsemblGRCm38mm10GRCm38
MGSCv3713114,106,733 - 114,160,723 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv3613114,437,403 - 114,491,393 (+)NCBIMGSCv36mm8
MGSCv3613110,916,844 - 110,970,784 (+)NCBIMGSCv36mm8
Celera13117,606,070 - 117,684,810 (+)NCBICelera
Cytogenetic Map13D2.2NCBI
cM Map1363.94NCBI
CSPG4BP
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38554,810,139 - 54,872,034 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl554,808,210 - 54,872,551 (-)EnsemblGRCh38hg38GRCh38
GRCh37554,105,967 - 54,167,862 (-)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map5q11.2NCBI
HuRef551,079,943 - 51,141,576 (-)NCBIHuRef
CHM1_1554,108,898 - 54,170,798 (-)NCBICHM1_1
T2T-CHM13v2.0555,637,782 - 55,699,689 (-)NCBIT2T-CHM13v2.0
Cspg4b
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8246,673,142 - 46,743,288 (+)NCBIGRCr8
mRatBN7.2244,939,807 - 45,008,284 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl244,940,080 - 45,008,284 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx252,044,808 - 52,120,063 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0250,103,161 - 50,178,419 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0244,983,091 - 45,050,913 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0245,182,391 - 45,241,179 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl245,168,439 - 45,241,179 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0264,214,525 - 64,273,495 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4244,703,932 - 45,210,939 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera240,724,675 - 40,783,290 (+)NCBICelera
Cytogenetic Map2q14NCBI

Variants

.
Variants in Cspg4b
3281 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:847
Count of miRNA genes:366
Interacting mature miRNAs:421
Transcripts:ENSMUST00000078163, ENSMUST00000135096, ENSMUST00000136755
Prediction methods:Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


QTLs in Region (GRCm39)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
4142334Svtms_msurvival time modifier of Sod2 (mouse)Not determined13107613580119476372Mouse
1558741Ses10_msalmonella enteritidis susceptibility 10 (mouse)Not determined1382739968116740106Mouse
1301142Heal2_mwound healing/regeneration 2 (mouse)Not determined1393875267120883175Mouse
1357468Rplag_mreduced platelet aggregation (mouse)Not determined1395502130120883175Mouse
12879496Fexq2_mfear expression QTL 2 (mouse)13100741519120883175Mouse
14700691Cisaq1_mcoxsackieviral infection serum ALT QTL 1 (mouse)1386148119120461536Mouse
4141704Hipq1_mhyperinsulin production QTL 1 (mouse)Not determined110409487119476372Mouse
1300939Hrtfm6_mheart failure modifier 6 (mouse)Not determined1391383692120883175Mouse
1558763Gct9_mgranulosa cell tumorigenesis 9 (mouse)Not determined1395036824120883175Mouse
4140995Fbtq6_mfemoral bone trait QTL 6 (mouse)Not determined1386341617120341758Mouse
4142338Skmw18_mskeletal muscle weight 18 (mouse)Not determined1394528399120883175Mouse
4141826Tbqt5_mtibia bone quality traits 5 (mouse)Not determined13103341617117043216Mouse
4142465Pbwg17_mpostnatal body weight growth 17 (mouse)Not determined1383876060117876256Mouse
1300876Tanidd2_mtally ho associated non-insulin dependednt diabetes mellitus 2 (mouse)Not determined1391965303120883175Mouse
4142400Tgq24_mtriglyceride QTL 24 (mouse)Not determined102602630120883175Mouse
14746974Manh75_mmandible shape 75 (mouse)1399386647120883175Mouse


Expression

RNA-SEQ Expression


Sequence


Ensembl Acc Id: ENSMUST00000078163   ⟹   ENSMUSP00000077297
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl13113,479,082 - 113,507,046 (+)Ensembl
GRCm38.p6 Ensembl13113,342,548 - 113,370,512 (+)Ensembl
Ensembl Acc Id: ENSMUST00000135096   ⟹   ENSMUSP00000131959
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl13113,488,137 - 113,516,245 (+)Ensembl
GRCm38.p6 Ensembl13113,351,603 - 113,379,711 (+)Ensembl
Ensembl Acc Id: ENSMUST00000136755   ⟹   ENSMUSP00000119993
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl13113,429,693 - 113,507,049 (+)Ensembl
GRCm38.p6 Ensembl13113,293,159 - 113,370,515 (+)Ensembl
RefSeq Acc Id: NM_001378698   ⟹   NP_001365627
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm3913113,429,704 - 113,507,047 (+)NCBI
GRCm3813113,293,170 - 113,370,513 (+)NCBI
Sequence:
RefSeq Acc Id: XM_030247485   ⟹   XP_030103345
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm3913113,429,570 - 113,483,027 (+)NCBI
GRCm3813113,293,052 - 113,346,492 (+)NCBI
Sequence:
RefSeq Acc Id: XM_036158083   ⟹   XP_036013976
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm3913113,429,570 - 113,487,229 (+)NCBI
Sequence:
RefSeq Acc Id: XR_004938045
Type: NON-CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm3913113,429,570 - 113,507,049 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001365627 (Get FASTA)   NCBI Sequence Viewer  
  XP_030103345 (Get FASTA)   NCBI Sequence Viewer  
  XP_036013976 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAH67074 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSMUSP00000119993
  ENSMUSP00000119993.4
  ENSMUSP00000131959.2
RefSeq Acc Id: XP_030103345   ⟸   XM_030247485
- Peptide Label: isoform X2
RefSeq Acc Id: NP_001365627   ⟸   NM_001378698
- Peptide Label: precursor
- UniProtKB: F6RXI4 (UniProtKB/TrEMBL)
Ensembl Acc Id: ENSMUSP00000131959   ⟸   ENSMUST00000135096
Ensembl Acc Id: ENSMUSP00000077297   ⟸   ENSMUST00000078163
Ensembl Acc Id: ENSMUSP00000119993   ⟸   ENSMUST00000136755
RefSeq Acc Id: XP_036013976   ⟸   XM_036158083
- Peptide Label: isoform X1
Protein Domains
Laminin G

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-F6RXI4-F1-model_v2 AlphaFold F6RXI4 1-2391 view protein structure


Additional Information

Database Acc Id Source(s)
AGR Gene MGI:3040697 AgrOrtholog
Ensembl Genes ENSMUSG00000021763 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSMUST00000135096.2 UniProtKB/TrEMBL
  ENSMUST00000136755 ENTREZGENE
  ENSMUST00000136755.10 UniProtKB/TrEMBL
Gene3D-CATH 2.60.120.200 UniProtKB/TrEMBL
InterPro ConA-like_dom UniProtKB/TrEMBL
  CSPG_rpt UniProtKB/TrEMBL
  FRAS1_ECM UniProtKB/TrEMBL
  Laminin_G UniProtKB/TrEMBL
MGD MGI:3040697 ENTREZGENE
NCBI Gene BC067074 ENTREZGENE
PANTHER CHONDROITIN SULFATE PROTEOGLYCAN 4-LIKE ISOFORM X2 UniProtKB/TrEMBL
  MATRIX PROTEIN, PUTATIVE-RELATED UniProtKB/TrEMBL
Pfam Cadherin_3 UniProtKB/TrEMBL
  Laminin_G_2 UniProtKB/TrEMBL
PhenoGen Cspg4b PhenoGen
PROSITE CSPG UniProtKB/TrEMBL
  LAM_G_DOMAIN UniProtKB/TrEMBL
SMART LamG UniProtKB/TrEMBL
Superfamily-SCOP SSF49899 UniProtKB/TrEMBL
UniProt F6RXI4 ENTREZGENE, UniProtKB/TrEMBL
  F6Z6Y0_MOUSE UniProtKB/TrEMBL
  Q6NXH4_MOUSE UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2020-04-21 Cspg4b  chondroitin sulfate proteoglycan 4B  BC067074  cDNA sequence BC067074  Symbol and/or name change 5135510 APPROVED