Ccn4 (cellular communication network factor 4) - Rat Genome Database
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Gene: Ccn4 (cellular communication network factor 4) Rattus norvegicus
Analyze
Symbol: Ccn4
Name: cellular communication network factor 4
RGD ID: 69431
Description: Predicted to have heparin binding activity and integrin binding activity. Involved in positive regulation of cell growth involved in cardiac muscle cell development; positive regulation of smooth muscle cell migration; and positive regulation of smooth muscle cell proliferation. Predicted to localize to cytosol; extracellular matrix; and extracellular space. Orthologous to human CCN4 (cellular communication network factor 4); INTERACTS WITH 1-naphthyl isothiocyanate; 17alpha-ethynylestradiol; 2,2',4,4'-Tetrabromodiphenyl ether.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: CCN family member 4; ELM-1; MGC93340; WISP-1; Wisp1; WNT1 inducible signaling pathway protein 1; WNT1-inducible-signaling pathway protein 1
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2798,645,238 - 98,677,253 (+)NCBI
Rnor_6.0 Ensembl7107,695,215 - 107,723,772 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.07107,695,227 - 107,723,759 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.07107,644,976 - 107,673,508 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.47104,263,089 - 104,291,621 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.17104,297,318 - 104,325,846 (+)NCBI
Celera795,196,524 - 95,225,037 (+)NCBICelera
Cytogenetic Map7q34NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
1,1-bis(2-aminoethyl)-2-hydroxy-3-oxotriazane  (ISO)
1,2-dimethylhydrazine  (ISO)
1-naphthyl isothiocyanate  (EXP)
17alpha-ethynylestradiol  (EXP)
2,2',4,4'-Tetrabromodiphenyl ether  (EXP,ISO)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
2,4,6-trinitrobenzenesulfonic acid  (EXP,ISO)
3,4-methylenedioxymethamphetamine  (ISO)
3-methylcholanthrene  (ISO)
4,4'-diaminodiphenylmethane  (ISO)
4,4'-sulfonyldiphenol  (ISO)
5-aza-2'-deoxycytidine  (ISO)
6-propyl-2-thiouracil  (EXP)
actinomycin D  (ISO)
all-trans-retinoic acid  (ISO)
ammonium chloride  (EXP)
arsane  (ISO)
arsenic atom  (ISO)
arsenous acid  (ISO)
benzo[a]pyrene  (ISO)
benzo[b]fluoranthene  (ISO)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
cadmium dichloride  (ISO)
calcitriol  (ISO)
carbon nanotube  (ISO)
carmustine  (ISO)
chloroprene  (ISO)
cisplatin  (ISO)
copper atom  (ISO)
copper(0)  (ISO)
cycloheximide  (ISO)
decabromodiphenyl ether  (EXP)
dexamethasone  (ISO)
diarsenic trioxide  (ISO)
dibenz[a,h]anthracene  (ISO)
dibutyl phthalate  (ISO)
dioxygen  (ISO)
doxorubicin  (ISO)
fenvalerate  (EXP)
folic acid  (ISO)
graphite  (EXP)
homocysteine  (ISO)
indometacin  (ISO)
methotrexate  (ISO)
methylmercury chloride  (ISO)
N-nitrosodiethylamine  (ISO)
nitroprusside  (ISO)
ochratoxin A  (ISO)
oxaliplatin  (EXP)
pentane-2,3-dione  (EXP)
phenobarbital  (ISO)
pirinixic acid  (ISO)
propiconazole  (ISO)
silver atom  (ISO)
silver(0)  (ISO)
temozolomide  (ISO)
tetrachloromethane  (ISO)
titanium dioxide  (ISO)
topotecan  (EXP)
trimellitic anhydride  (ISO)
troglitazone  (ISO)
valproic acid  (ISO)
vancomycin  (ISO)

References

Additional References at PubMed
PMID:15331410   PMID:17616748   PMID:20684029   PMID:22272766   PMID:22475393   PMID:24006456   PMID:25281430   PMID:25864198   PMID:26242865   PMID:26627308   PMID:28496206   PMID:29319180  
PMID:29330021   PMID:30556898  


Genomics

Comparative Map Data
Ccn4
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2798,645,238 - 98,677,253 (+)NCBI
Rnor_6.0 Ensembl7107,695,215 - 107,723,772 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.07107,695,227 - 107,723,759 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.07107,644,976 - 107,673,508 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.47104,263,089 - 104,291,621 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.17104,297,318 - 104,325,846 (+)NCBI
Celera795,196,524 - 95,225,037 (+)NCBICelera
Cytogenetic Map7q34NCBI
CCN4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl8133,191,039 - 133,231,690 (+)EnsemblGRCh38hg38GRCh38
GRCh388133,190,907 - 133,231,690 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh378134,203,282 - 134,243,933 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 368134,272,494 - 134,310,753 (+)NCBINCBI36hg18NCBI36
Build 348134,272,493 - 134,309,234NCBI
Celera8130,380,567 - 130,419,496 (+)NCBI
Cytogenetic Map8q24.22NCBI
HuRef8129,522,987 - 129,563,677 (+)NCBIHuRef
CHM1_18134,244,050 - 134,284,955 (+)NCBICHM1_1
Ccn4
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391566,763,218 - 66,795,054 (+)NCBIGRCm39mm39
GRCm39 Ensembl1566,763,169 - 66,795,050 (+)Ensembl
GRCm381566,891,369 - 66,923,201 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1566,891,320 - 66,923,201 (+)EnsemblGRCm38mm10GRCm38
MGSCv371566,722,955 - 66,754,761 (+)NCBIGRCm37mm9NCBIm37
MGSCv361566,721,062 - 66,752,868 (+)NCBImm8
Celera1568,424,047 - 68,455,874 (+)NCBICelera
Cytogenetic Map15D2NCBI
cM Map1529.3NCBI
Ccn4
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554617,748,005 - 7,780,427 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554617,748,399 - 7,780,359 (+)NCBIChiLan1.0ChiLan1.0
CCN4
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.18132,818,397 - 132,858,861 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl8132,818,397 - 132,858,861 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v08129,842,580 - 129,884,528 (+)NCBIMhudiblu_PPA_v0panPan3
CCN4
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11329,648,720 - 29,683,822 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1329,648,639 - 29,679,732 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1329,622,701 - 29,661,265 (+)NCBI
ROS_Cfam_1.01330,004,803 - 30,043,373 (+)NCBI
UMICH_Zoey_3.11329,731,434 - 29,769,975 (+)NCBI
UNSW_CanFamBas_1.01329,830,792 - 29,869,352 (+)NCBI
UU_Cfam_GSD_1.01330,180,453 - 30,219,020 (+)NCBI
Ccn4
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_ltri_2NW_0244053038,682,581 - 8,708,143 (-)NCBI
SpeTri2.0NW_00493647016,110,492 - 16,134,065 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CCN4
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl48,078,156 - 8,110,829 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.148,078,163 - 8,110,906 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.248,188,614 - 8,216,061 (+)NCBISscrofa10.2Sscrofa10.2susScr3
CCN4
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.18127,620,635 - 127,658,132 (+)NCBI
ChlSab1.1 Ensembl8127,642,598 - 127,661,462 (+)Ensembl
Ccn4
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462473522,789,784 - 22,819,527 (-)NCBI

Position Markers
BE117857  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.07107,723,549 - 107,723,698NCBIRnor6.0
Rnor_5.07107,673,298 - 107,673,447UniSTSRnor5.0
RGSC_v3.47104,291,411 - 104,291,560UniSTSRGSC3.4
Celera795,224,827 - 95,224,976UniSTS
RH 3.4 Map7681.1UniSTS
Cytogenetic Map7q33UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
634336Anxrr17Anxiety related response QTL 173.66locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)72920071124838025Rat
61357Bp38Blood pressure QTL 381.60.052arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)748118835128611831Rat
631504Cm27Cardiac mass QTL 273.45heart left ventricle mass (VT:0007031)heart left ventricle wet weight (CMO:0000071)750704769128085642Rat
1358361Sradr5Stress Responsive Adrenal Weight QTL 55.55adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)751251919118477612Rat
1300179Kidm5Kidney mass QTL 53.51kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)751251919145729302Rat
1300149Cm6Cardiac mass QTL 64.09heart mass (VT:0007028)heart left ventricle weight to body weight ratio (CMO:0000530)751252005111589099Rat
2316947Rf58Renal function QTL 587.8kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)755072862123602998Rat
2316952Pur22Proteinuria QTL 225.2urine protein amount (VT:0005160)urine protein level (CMO:0000591)755072862123602998Rat
2316955Stl24Serum triglyceride level QTL 247.1blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)755072862123602998Rat
1300151Bp181Blood pressure QTL 1813.36arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)761047589113228378Rat
2317035Aia16Adjuvant induced arthritis QTL 162.71joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)768518460113518460Rat
1576303Ept7Estrogen-induced pituitary tumorigenesis QTL 73.7pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)769399586111043530Rat
1559283Emca4Estrogen-induced mammary cancer QTL 43.7mammary gland integrity trait (VT:0010552)percentage of study population developing mammary tumors during a period of time (CMO:0000948)769399586111043530Rat
1298528Bp169Blood pressure QTL 1690.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)770421228115421228Rat
70173Niddm19Non-insulin dependent diabetes mellitus QTL 194.330.00005blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)771448715145729302Rat
631540Bw9Body weight QTL 94.5body mass (VT:0001259)body weight (CMO:0000012)777428105127748511Rat
1357338Stl17Serum triglyceride level QTL 173.23blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)777428234122421148Rat
634331Pia17Pristane induced arthritis QTL 174.7joint integrity trait (VT:0010548)arthritic paw count (CMO:0001460)781645773140745067Rat
7411607Foco15Food consumption QTL 150.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)785595369130595369Rat
7411654Foco25Food consumption QTL 259.30.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)785595369130595369Rat
631529Tls2T-lymphoma susceptibility QTL 200.001thymus integrity trait (VT:0010555)percentage of study population developing T-cell lymphomas during a period of time (CMO:0001911)788365265119318087Rat
1331746Kidm9Kidney mass QTL 93.934kidney mass (VT:0002707)right kidney wet weight (CMO:0000082)788365265121986709Rat
1331768Kidm10Kidney mass QTL 104.62096kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)788365265133365265Rat
1331728Bp214Blood pressure QTL 2142.825arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)788365265134673427Rat
2317052Aia17Adjuvant induced arthritis QTL 172.13joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)791018361136018361Rat
1358914Bp266Blood pressure QTL 266arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)791832949145158140Rat
1358891Bp265Blood pressure QTL 2652.21arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)791832949145158140Rat
71114Niddm14Non-insulin dependent diabetes mellitus QTL 144.5blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)793726906138726906Rat
2298475Eau6Experimental allergic uveoretinitis QTL 60.0029uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)793726906138726906Rat
1558655Swd4Spike wave discharge measurement QTL 43.680.0002brain electrophysiology trait (VT:0010557)brain spike-and-wave discharge severity grade (CMO:0001988)796630946141630946Rat
10450828Scl79Serum cholesterol level QTL 793.50.001blood HDL cholesterol amount (VT:0000184)blood low density lipoprotein cholesterol level (CMO:0000053)798200188111043530Rat
2299163Iddm34Insulin dependent diabetes mellitus QTL 342.71blood glucose amount (VT:0000188)age at onset/diagnosis of type 1 diabetes mellitus (CMO:0001140)7100028953145729302Rat
631687Hcas1Hepatocarcinoma susceptibility QTL 13.90.001liver integrity trait (VT:0010547)liver tumorous lesion volume to total liver volume ratio (CMO:0001082)7100160423140335001Rat
1549899Stresp8Stress response QTL 84.370.0008stress-related behavior trait (VT:0010451)defensive burying duration (CMO:0001961)7100192194145192194Rat
61397Bw17Body weight QTL 176.3body mass (VT:0001259)body weight (CMO:0000012)7102588256116249643Rat
2313102Bmd79Bone mineral density QTL 792.30.0001tibia mineral mass (VT:1000283)total volumetric bone mineral density (CMO:0001728)7103815550126525386Rat
1357336Gluco6Glucose level QTL 63.4blood glucose amount (VT:0000188)serum glucose level (CMO:0000543)7103867802126080176Rat
731176Glom5Glomerulus QTL 52.50.0035kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)7106564316145729302Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:71
Count of miRNA genes:55
Interacting mature miRNAs:67
Transcripts:ENSRNOT00000009673
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.


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 4 10 9
Low 3 23 13 10 2 10 6 9 50 25 24 9 6
Below cutoff 15 31 18 17 18 2 2 20 5 2 2

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000009673   ⟹   ENSRNOP00000009673
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl7107,695,227 - 107,723,764 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000093628   ⟹   ENSRNOP00000076326
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl7107,695,215 - 107,723,772 (+)Ensembl
RefSeq Acc Id: NM_031716   ⟹   NP_113904
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2798,645,542 - 98,674,073 (+)NCBI
Rnor_6.07107,695,227 - 107,723,759 (+)NCBI
Rnor_5.07107,644,976 - 107,673,508 (+)NCBI
RGSC_v3.47104,263,089 - 104,291,621 (+)RGD
Celera795,196,524 - 95,225,037 (+)RGD
Sequence:
RefSeq Acc Id: XM_039079864   ⟹   XP_038935792
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2798,645,238 - 98,677,253 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_113904   ⟸   NM_031716
- Peptide Label: precursor
- Sequence:
RefSeq Acc Id: ENSRNOP00000076326   ⟸   ENSRNOT00000093628
RefSeq Acc Id: ENSRNOP00000009673   ⟸   ENSRNOT00000009673
RefSeq Acc Id: XP_038935792   ⟸   XM_039079864
- Peptide Label: isoform X1
Protein Domains
CTCK   IGFBP N-terminal   TSP type-1   VWFC

Transcriptome

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

Promoters
RGD ID:13695365
Promoter ID:EPDNEW_R5890
Type:initiation region
Name:Wisp1_1
Description:WNT1 inducible signaling pathway protein 1
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.07107,695,305 - 107,695,365EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:69431 AgrOrtholog
Ensembl Genes ENSRNOG00000007078 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000009673 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000076326 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000009673 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000093628 UniProtKB/TrEMBL
Gene3D-CATH 2.20.100.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7131232 IMAGE-MGC_LOAD
InterPro Cys_knot_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Glyco_hormone_CN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Growth_fac_rcpt_cys_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  IGFBP-like UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  IGFBP_CNN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Insulin_GF-bd_Cys-rich_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TSP1_CCN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TSP1_rpt UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TSP1_rpt_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  VWF_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:65154 UniProtKB/Swiss-Prot
MGC_CLONE MGC:93340 IMAGE-MGC_LOAD
NCBI Gene 65154 ENTREZGENE
Pfam Cys_knot UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  IGFBP UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TSP1_CCN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  VWC UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Ccn4 PhenoGen
PIRSF IGFBP_rP_CNN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE CTCK_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  CTCK_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  IGFBP_N_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  IGFBP_N_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TSP1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  VWFC_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  VWFC_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART SM00041 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SM00121 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TSP1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  VWC UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF57184 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF82895 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
TIGR TC206062
UniProt A0A1W2Q6N9_RAT UniProtKB/TrEMBL
  G3V6X0_RAT UniProtKB/TrEMBL
  Q99PP0 ENTREZGENE, UniProtKB/Swiss-Prot
UniProt Secondary Q9WUW4 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2018-10-23 Ccn4  cellular communication network factor 4  Wisp1  WNT1 inducible signaling pathway protein 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2002-06-10 Wisp1  WNT1 inducible signaling pathway protein 1       Name updated 70584 APPROVED

RGD Curation Notes
Note Type Note Reference