Ccn6 (cellular communication network factor 6) - Rat Genome Database

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Gene: Ccn6 (cellular communication network factor 6) Rattus norvegicus
Analyze
Symbol: Ccn6
Name: cellular communication network factor 6
RGD ID: 1564120
Description: Predicted to enable heparin binding activity and integrin binding activity. Predicted to be involved in several processes, including positive regulation of cell differentiation; regulation of mitochondrial membrane potential; and regulation of reactive oxygen species biosynthetic process. Predicted to act upstream of or within negative regulation of angiogenesis and negative regulation of cell population proliferation. Predicted to be located in mitochondrion. Predicted to be active in extracellular matrix and extracellular space. Human ortholog(s) of this gene implicated in arthropathy and progressive pseudorheumatoid arthropathy of childhood. Orthologous to human CCN6 (cellular communication network factor 6); INTERACTS WITH 6-propyl-2-thiouracil; alpha-Zearalanol; amphetamine.
Type: protein-coding
RefSeq Status: INFERRED
Previously known as: LOC499461; RGD1564120; similar to WNT1 inducible signaling pathway protein 3 precursor (WISP-3) ; similar to WNT1 inducible signaling pathway protein 3 precursor (WISP-3) (UNQ462/PRO790); Wisp3; WNT1 inducible signaling pathway protein 3; WNT1-inducible-signaling pathway protein 3
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr82044,123,932 - 44,139,745 (-)NCBIGRCr8
mRatBN7.22042,569,309 - 42,585,126 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl2042,569,309 - 42,585,126 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx2044,318,205 - 44,334,184 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.02043,977,415 - 43,993,392 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.02044,710,380 - 44,726,274 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.02044,237,491 - 44,255,064 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2044,237,491 - 44,255,064 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02045,964,515 - 45,980,204 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42043,297,076 - 43,312,790 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera2043,285,682 - 43,301,319 (-)NCBICelera
Cytogenetic Map20q12NCBI
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

Cellular Component

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2. Mutations in the CCN gene family member WISP3 cause progressive pseudorheumatoid dysplasia. Hurvitz JR, etal., Nat Genet. 1999 Sep;23(1):94-8.
3. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
4. GOA pipeline RGD automated data pipeline
5. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
6. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
7. Comprehensive gene review and curation RGD comprehensive gene curation
Additional References at PubMed
PMID:12082632   PMID:27252383   PMID:29353205  


Genomics

Comparative Map Data
Ccn6
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr82044,123,932 - 44,139,745 (-)NCBIGRCr8
mRatBN7.22042,569,309 - 42,585,126 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl2042,569,309 - 42,585,126 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx2044,318,205 - 44,334,184 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.02043,977,415 - 43,993,392 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.02044,710,380 - 44,726,274 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.02044,237,491 - 44,255,064 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2044,237,491 - 44,255,064 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02045,964,515 - 45,980,204 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42043,297,076 - 43,312,790 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera2043,285,682 - 43,301,319 (-)NCBICelera
Cytogenetic Map20q12NCBI
CCN6
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh386112,052,813 - 112,069,686 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl6112,054,075 - 112,069,686 (+)EnsemblGRCh38hg38GRCh38
GRCh376112,375,307 - 112,390,889 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 366112,481,971 - 112,497,582 (+)NCBINCBI36Build 36hg18NCBI36
Build 346112,482,063 - 112,497,578NCBI
Celera6113,116,562 - 113,132,191 (+)NCBICelera
Cytogenetic Map6q21NCBI
HuRef6109,950,089 - 109,965,718 (+)NCBIHuRef
CHM1_16112,637,620 - 112,653,229 (+)NCBICHM1_1
T2T-CHM13v2.06113,236,232 - 113,253,104 (+)NCBIT2T-CHM13v2.0
Ccn6
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391039,026,966 - 39,049,484 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1039,026,966 - 39,039,790 (-)EnsemblGRCm39 Ensembl
GRCm381039,150,970 - 39,174,376 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1039,150,970 - 39,163,794 (-)EnsemblGRCm38mm10GRCm38
MGSCv371038,870,777 - 38,883,600 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361038,930,930 - 38,943,587 (-)NCBIMGSCv36mm8
Celera1040,035,173 - 40,048,005 (-)NCBICelera
Cytogenetic Map10B1NCBI
cM Map1020.19NCBI
Ccn6
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555264,502,654 - 4,522,259 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049555264,501,331 - 4,525,866 (-)NCBIChiLan1.0ChiLan1.0
CCN6
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v25132,059,715 - 132,086,634 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan16129,947,929 - 129,973,902 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v06109,863,877 - 109,880,480 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.16113,939,882 - 113,955,433 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl6113,939,975 - 113,955,427 (+)Ensemblpanpan1.1panPan2
CCN6
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11268,488,846 - 68,499,104 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1268,478,905 - 68,498,049 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1268,299,647 - 68,317,878 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01269,362,873 - 69,381,112 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1269,361,014 - 69,380,055 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11268,722,395 - 68,740,609 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01268,560,032 - 68,578,123 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01268,886,687 - 68,905,127 (+)NCBIUU_Cfam_GSD_1.0
Ccn6
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404946103,519,416 - 103,534,951 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936679750,934 - 769,242 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_004936679751,664 - 767,126 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CCN6
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl178,005,847 - 78,019,709 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1178,005,442 - 78,020,595 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2187,626,572 - 87,687,187 (+)NCBISscrofa10.2Sscrofa10.2susScr3
CCN6
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11361,786,246 - 61,806,010 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1361,786,312 - 61,803,610 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604034,121,867 - 34,138,513 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Ccn6
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462500748,593 - 50,771 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Ccn6
301 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:161
Count of miRNA genes:119
Interacting mature miRNAs:140
Transcripts:ENSRNOT00000000735
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 (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2305926Iddm37Insulin dependent diabetes mellitus QTL 376blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)20152784246527842Rat
1641915Colcr9Colorectal carcinoma resistance QTL 92.970.0024intestine integrity trait (VT:0010554)benign colorectal tumor number (CMO:0001795)20153065546530655Rat
1598816Memor12Memory QTL 122.4exploratory behavior trait (VT:0010471)average horizontal distance between subject and target during voluntary locomotion in an experimental apparatus (CMO:0002674)20260683647606836Rat
7411652Foco24Food consumption QTL 240.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)201175751554435887Rat
9590092Insglur9Insulin/glucose ratio QTL 918.380.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)201175751554435887Rat
4889610Pancm3Pancreatic morphology QTL 33.750.001pancreas mass (VT:0010144)pancreas wet weight (CMO:0000626)201761783247606836Rat
2317880Alcrsp25Alcohol response QTL 252.3response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)201769755054435887Rat
2303626Vencon10Ventilatory control QTL 100.001respiration trait (VT:0001943)respiration rate (CMO:0000289)201919072154435887Rat
2303578Gluco50Glucose level QTL 502blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)202510672254435887Rat
2303587Bw93Body weight QTL 9313body mass (VT:0001259)body weight (CMO:0000012)202510672254435887Rat
2300188Bmd68Bone mineral density QTL 686.40.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)202510672254435887Rat
1331747Hrtrt16Heart rate QTL 163.163heart pumping trait (VT:2000009)heart rate (CMO:0000002)202520973454435887Rat
1598869Memor6Memory QTL 63.1exploratory behavior trait (VT:0010471)total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)202924438854435887Rat
70158Bp60Blood pressure QTL 603arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)203161428444396023Rat

Markers in Region
RH129238  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22042,569,551 - 42,569,759 (+)MAPPERmRatBN7.2
Rnor_6.02044,237,734 - 44,237,941NCBIRnor6.0
Rnor_5.02045,964,758 - 45,964,965UniSTSRnor5.0
RGSC_v3.42043,297,319 - 43,297,526UniSTSRGSC3.4
Celera2043,285,925 - 43,286,132UniSTS
RH 3.4 Map20460.5UniSTS
Cytogenetic Map20q12UniSTS
AI013034  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22042,570,720 - 42,570,846 (+)MAPPERmRatBN7.2
Rnor_6.02044,238,903 - 44,239,028NCBIRnor6.0
Rnor_5.02045,965,927 - 45,966,052UniSTSRnor5.0
RGSC_v3.42043,298,488 - 43,298,613UniSTSRGSC3.4
Celera2043,287,094 - 43,287,219UniSTS
RH 3.4 Map20463.3UniSTS
Cytogenetic Map20q12UniSTS
AI577391  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22042,570,174 - 42,570,296 (+)MAPPERmRatBN7.2
Rnor_6.02044,238,357 - 44,238,478NCBIRnor6.0
Rnor_5.02045,965,381 - 45,965,502UniSTSRnor5.0
RGSC_v3.42043,297,942 - 43,298,063UniSTSRGSC3.4
Celera2043,286,548 - 43,286,669UniSTS
RH 3.4 Map20463.4UniSTS
Cytogenetic Map20q12UniSTS


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium
Low 1 7 8 3 17
Below cutoff 1 5 13 4 11 4 2 2 62 30 23 10 2

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000000735   ⟹   ENSRNOP00000000735
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl2042,569,309 - 42,585,126 (-)Ensembl
Rnor_6.0 Ensembl2044,237,491 - 44,255,064 (-)Ensembl
RefSeq Acc Id: NM_001170483   ⟹   NP_001163954
RefSeq Status: INFERRED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr82044,123,932 - 44,139,745 (-)NCBI
mRatBN7.22042,569,309 - 42,585,126 (-)NCBI
Rnor_6.02044,237,491 - 44,255,064 (-)NCBI
Rnor_5.02045,964,515 - 45,980,204 (-)NCBI
RGSC_v3.42043,297,076 - 43,312,790 (-)RGD
Celera2043,285,682 - 43,301,319 (-)RGD
Sequence:
RefSeq Acc Id: XM_039099026   ⟹   XP_038954954
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr82044,125,192 - 44,133,824 (-)NCBI
mRatBN7.22042,570,562 - 42,579,203 (-)NCBI
Protein Sequences
Protein RefSeqs NP_001163954 (Get FASTA)   NCBI Sequence Viewer  
  XP_038954954 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL87813 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000000735
  ENSRNOP00000000735.5
Reference Protein Sequences
RefSeq Acc Id: NP_001163954   ⟸   NM_001170483
- Peptide Label: precursor
- UniProtKB: D3ZDL5 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000000735   ⟸   ENSRNOT00000000735
RefSeq Acc Id: XP_038954954   ⟸   XM_039099026
- Peptide Label: isoform X1
Protein Domains
CTCK   IGFBP N-terminal

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZDL5-F1-model_v2 AlphaFold D3ZDL5 1-354 view protein structure

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1564120 AgrOrtholog
BioCyc Gene G2FUF-3477 BioCyc
Ensembl Genes ENSRNOG00000000597 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000000735 ENTREZGENE
  ENSRNOT00000000735.6 UniProtKB/TrEMBL
Gene3D-CATH 2.20.100.10 UniProtKB/TrEMBL
  Complement Module, domain 1 UniProtKB/TrEMBL
InterPro Cys_knot UniProtKB/TrEMBL
  Cys_knot_C UniProtKB/TrEMBL
  Growth_fac_rcpt_N_dom UniProtKB/TrEMBL
  IGFBP-like UniProtKB/TrEMBL
  IGFBP_CNN UniProtKB/TrEMBL
  Insulin_GF-bd_Cys-rich_CS UniProtKB/TrEMBL
  Thrombospondin_1_rpt UniProtKB/TrEMBL
  TSP1_CCN UniProtKB/TrEMBL
  TSP1_rpt_sf UniProtKB/TrEMBL
KEGG Report rno:499461 UniProtKB/TrEMBL
NCBI Gene 499461 ENTREZGENE
PANTHER CELLULAR COMMUNICATION NETWORK FACTOR 6 UniProtKB/TrEMBL
  CONNECTIVE TISSUE GROWTH FACTOR-RELATED UniProtKB/TrEMBL
Pfam Cys_knot UniProtKB/TrEMBL
  IGFBP UniProtKB/TrEMBL
  TSP1_CCN UniProtKB/TrEMBL
PhenoGen Ccn6 PhenoGen
PIRSF IGFBP_rP_CNN UniProtKB/TrEMBL
PROSITE CTCK_2 UniProtKB/TrEMBL
  IGFBP_N_1 UniProtKB/TrEMBL
  IGFBP_N_2 UniProtKB/TrEMBL
  TSP1 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000000597 RatGTEx
SMART SM00041 UniProtKB/TrEMBL
  SM00121 UniProtKB/TrEMBL
  TSP1 UniProtKB/TrEMBL
Superfamily-SCOP FnI-like domain UniProtKB/TrEMBL
  SSF57184 UniProtKB/TrEMBL
  TSP1 UniProtKB/TrEMBL
UniProt D3ZDL5 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2018-10-23 Ccn6  cellular communication network factor 6  Wisp3  WNT1 inducible signaling pathway protein 3  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2009-01-20 Wisp3  WNT1 inducible signaling pathway protein 3  RGD1564120  similar to WNT1 inducible signaling pathway protein 3 precursor (WISP-3)   Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 RGD1564120  similar to WNT1 inducible signaling pathway protein 3 precursor (WISP-3)   RGD1564120_predicted  similar to WNT1 inducible signaling pathway protein 3 precursor (WISP-3) (predicted)  'predicted' is removed 2292626 APPROVED
2006-03-10 RGD1564120_predicted  similar to WNT1 inducible signaling pathway protein 3 precursor (WISP-3) (predicted)    similar to WNT1 inducible signaling pathway protein 3 precursor (WISP-3) (UNQ462/PRO790) (predicted)  Name updated 1299863 APPROVED
2006-03-07 RGD1564120_predicted  similar to WNT1 inducible signaling pathway protein 3 precursor (WISP-3) (UNQ462/PRO790) (predicted)  LOC499461  similar to WNT1 inducible signaling pathway protein 3 precursor (WISP-3) (UNQ462/PRO790)  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC499461  similar to WNT1 inducible signaling pathway protein 3 precursor (WISP-3) (UNQ462/PRO790)      Symbol and Name status set to provisional 70820 PROVISIONAL