Cntn1 (contactin 1) - Rat Genome Database
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Gene: Cntn1 (contactin 1) Rattus norvegicus
Analyze
Symbol: Cntn1
Name: contactin 1
RGD ID: 621300
Description: Predicted to have carbohydrate binding activity. Involved in positive regulation of peptidyl-tyrosine phosphorylation. Localizes to membrane raft. Human ortholog(s) of this gene implicated in Compton-North congenital myopathy. Orthologous to human CNTN1 (contactin 1); PARTICIPATES IN Notch signaling pathway; INTERACTS WITH ammonium chloride; bisphenol A; Brodifacoum.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: contactin-1; F3; neural cell surface protein F3
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
mRatBN7.27123,263,146 - 123,560,896 (+)NCBI
Rnor_6.0 Ensembl7133,400,485 - 133,586,677 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.07133,290,606 - 133,588,314 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.07132,976,416 - 133,272,747 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.47130,658,836 - 130,845,071 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.17130,735,272 - 130,921,508 (+)NCBI
Celera7119,777,077 - 119,962,153 (+)NCBICelera
Cytogenetic Map7q35NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:1729438   PMID:7628014   PMID:9081628   PMID:9118959   PMID:15967539   PMID:16029194   PMID:17634366   PMID:18354028   PMID:19026398   PMID:19458237   PMID:20451518   PMID:23376485  
PMID:23533145   PMID:29476059  


Genomics

Comparative Map Data
Cntn1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.27123,263,146 - 123,560,896 (+)NCBI
Rnor_6.0 Ensembl7133,400,485 - 133,586,677 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.07133,290,606 - 133,588,314 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.07132,976,416 - 133,272,747 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.47130,658,836 - 130,845,071 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.17130,735,272 - 130,921,508 (+)NCBI
Celera7119,777,077 - 119,962,153 (+)NCBICelera
Cytogenetic Map7q35NCBI
CNTN1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1240,692,439 - 41,072,415 (+)EnsemblGRCh38hg38GRCh38
GRCh381240,692,429 - 41,072,415 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371241,086,241 - 41,466,217 (+)NCBIGRCh37GRCh37hg19GRCh37
GRCh371241,086,244 - 41,466,214 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361239,372,625 - 39,750,361 (+)NCBINCBI36hg18NCBI36
Build 341239,372,624 - 39,750,361NCBI
Celera1239,889,695 - 40,267,406 (+)NCBI
Cytogenetic Map12q12NCBI
HuRef1238,112,937 - 38,492,512 (+)NCBIHuRef
CHM1_11241,051,536 - 41,431,091 (+)NCBICHM1_1
Cntn1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391591,949,034 - 92,239,848 (+)NCBIGRCm39mm39
GRCm381592,051,152 - 92,341,967 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1592,051,165 - 92,341,967 (+)EnsemblGRCm38mm10GRCm38
MGSCv371591,881,596 - 92,172,398 (+)NCBIGRCm37mm9NCBIm37
MGSCv361591,956,372 - 92,168,291 (+)NCBImm8
Celera1594,177,246 - 94,486,845 (+)NCBICelera
Cytogenetic Map15E3NCBI
cM Map1546.39NCBI
Cntn1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955500245,896 - 540,600 (+)EnsemblChiLan1.0
ChiLan1.0NW_004955500154,704 - 540,546 (+)NCBIChiLan1.0ChiLan1.0
CNTN1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11248,492,558 - 48,877,396 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1248,492,564 - 48,670,126 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01247,630,295 - 48,014,766 (-)NCBIMhudiblu_PPA_v0panPan3
CNTN1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl2712,657,287 - 12,920,315 (-)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.12712,655,021 - 13,005,536 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Cntn1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_0049366078,430 - 291,964 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CNTN1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl572,168,511 - 72,495,633 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1572,168,496 - 72,495,454 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2575,140,748 - 75,389,289 (+)NCBISscrofa10.2Sscrofa10.2susScr3
CNTN1
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11136,950,020 - 37,332,058 (+)NCBI
ChlSab1.1 Ensembl1137,167,079 - 37,333,314 (+)Ensembl
Cntn1
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_004624917292,404 - 752,017 (+)NCBI

Position Markers
D7Got118  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.07133,435,313 - 133,435,589NCBIRnor6.0
Rnor_5.07133,119,880 - 133,120,156UniSTSRnor5.0
RGSC_v3.47130,694,295 - 130,694,572RGDRGSC3.4
RGSC_v3.47130,694,296 - 130,694,572UniSTSRGSC3.4
RGSC_v3.17130,770,733 - 130,771,009RGD
Celera7119,812,135 - 119,812,405UniSTS
RH 3.4 Map71020.3RGD
RH 3.4 Map71020.3UniSTS
RH 2.0 Map7745.3RGD
Cytogenetic Map7q35UniSTS
Cntn1  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.07133,586,252 - 133,586,408NCBIRnor6.0
Rnor_5.07133,270,685 - 133,270,841UniSTSRnor5.0
RGSC_v3.47130,845,364 - 130,845,520UniSTSRGSC3.4
Celera7119,962,446 - 119,962,602UniSTS
Cytogenetic Map7q35UniSTS
BF415915  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.07133,526,038 - 133,526,174NCBIRnor6.0
Rnor_5.07133,210,471 - 133,210,607UniSTSRnor5.0
RGSC_v3.47130,783,937 - 130,784,073UniSTSRGSC3.4
Celera7119,902,121 - 119,902,257UniSTS
RH 3.4 Map71009.8UniSTS
Cytogenetic Map7q35UniSTS
AU048466  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.07133,435,294 - 133,435,565NCBIRnor6.0
Rnor_5.07133,119,861 - 133,120,132UniSTSRnor5.0
RGSC_v3.47130,694,277 - 130,694,548UniSTSRGSC3.4
Celera7119,812,116 - 119,812,381UniSTS
Cytogenetic Map7q35UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1300179Kidm5Kidney mass QTL 53.51kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)751251919145729302Rat
70173Niddm19Non-insulin dependent diabetes mellitus QTL 194.330.00005blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)771448715145729302Rat
634331Pia17Pristane induced arthritis QTL 174.7joint integrity trait (VT:0010548)arthritic paw count (CMO:0001460)781645773140745067Rat
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
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
731176Glom5Glomerulus QTL 52.50.0035kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)7106564316145729302Rat
1331731Bp216Blood pressure QTL 2162.851arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)7111519266143965591Rat
731174Uae23Urinary albumin excretion QTL 232.40.0042urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)7114825174145729302Rat
2306821Bp335Blood pressure QTL 3350.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)7115922628145729302Rat
631663Bw6Body weight QTL 63.4body mass (VT:0001259)body weight (CMO:0000012)7120746024145692398Rat
1300112Bp183Blood pressure QTL 1833.51arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)7121654760145729302Rat
1331748Bp215Blood pressure QTL 2154.043arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)7121986439143965591Rat
1357339Stl14Serum triglyceride level QTL 143.450.0001blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)7122421276143965415Rat
1582240Sffal1Serum free fatty acids level QTL 13.40.0021blood free fatty acid amount (VT:0001553)serum free fatty acids level (CMO:0000547)7126463649134098026Rat
631201Panci1Pancreas inflammation QTL 100.001pancreas integrity trait (VT:0010560)percentage of study population displaying chronic pancreatitis at a point in time (CMO:0001214)7126463827137325116Rat
1354582Stl11Serum triglyceride level QTL 113.42blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)7129412003145729302Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:115
Count of miRNA genes:93
Interacting mature miRNAs:100
Transcripts:ENSRNOT00000006219
Prediction methods:Microtar, 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 64 16 2 11
Low 3 24 18 3 18 3 8 9 10 17 39 8
Below cutoff 18 37 36 1 36 2 2

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000006219   ⟹   ENSRNOP00000006219
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl7133,400,485 - 133,585,959 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000080621   ⟹   ENSRNOP00000071355
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl7133,457,255 - 133,586,677 (+)Ensembl
RefSeq Acc Id: NM_057118   ⟹   NP_476459
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27123,372,792 - 123,558,541 (+)NCBI
Rnor_6.07133,400,485 - 133,585,959 (+)NCBI
Rnor_5.07132,976,416 - 133,272,747 (+)NCBI
RGSC_v3.47130,658,836 - 130,845,071 (+)RGD
Celera7119,777,077 - 119,962,153 (+)RGD
Sequence:
RefSeq Acc Id: XM_006242177   ⟹   XP_006242239
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27123,404,063 - 123,560,896 (+)NCBI
Rnor_6.07133,399,891 - 133,588,314 (+)NCBI
Rnor_5.07132,976,416 - 133,272,747 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008765659   ⟹   XP_008763881
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27123,263,146 - 123,499,462 (+)NCBI
Rnor_6.07133,290,606 - 133,526,962 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017594616   ⟹   XP_017450105
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27123,263,146 - 123,560,896 (+)NCBI
Rnor_6.07133,290,606 - 133,588,314 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039078298   ⟹   XP_038934226
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27123,263,146 - 123,560,896 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_476459   ⟸   NM_057118
- Peptide Label: precursor
- UniProtKB: Q63198 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006242239   ⟸   XM_006242177
- Peptide Label: isoform X1
- UniProtKB: Q63198 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_008763881   ⟸   XM_008765659
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_017450105   ⟸   XM_017594616
- Peptide Label: isoform X1
- UniProtKB: Q63198 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000006219   ⟸   ENSRNOT00000006219
RefSeq Acc Id: ENSRNOP00000071355   ⟸   ENSRNOT00000080621
RefSeq Acc Id: XP_038934226   ⟸   XM_039078298
- Peptide Label: isoform X1
Transcriptome

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


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)
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)
GK/Ox (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
LE/Stm (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
LEW/Crl (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
LEW/NCrlBR (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
LH/MavRrrc (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
LL/MavRrrc (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
LN/MavRrrc (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
M520/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
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
Damaging Variants


Assembly: Rnor_5.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
7 133216084 133216085 A G snv HWY/Slc (KyushuU)
7 133216168 133216169 A G snv Crl:SD (UDEL)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:621300 AgrOrtholog
Ensembl Genes ENSRNOG00000004438 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000006219 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOP00000071355 UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000006219 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOT00000080621 UniProtKB/Swiss-Prot
Gene3D-CATH 2.60.40.10 UniProtKB/Swiss-Prot
InterPro Contactin-1 UniProtKB/Swiss-Prot
  FN3_dom UniProtKB/Swiss-Prot
  FN3_sf UniProtKB/Swiss-Prot
  Ig-like_dom UniProtKB/Swiss-Prot
  Ig-like_dom_sf UniProtKB/Swiss-Prot
  Ig-like_fold UniProtKB/Swiss-Prot
  Ig_I-set UniProtKB/Swiss-Prot
  Ig_sub UniProtKB/Swiss-Prot
  Ig_sub2 UniProtKB/Swiss-Prot
  Immunoglobulin UniProtKB/Swiss-Prot
KEGG Report rno:117258 UniProtKB/Swiss-Prot
NCBI Gene 117258 ENTREZGENE
PANTHER PTHR44170:SF10 UniProtKB/Swiss-Prot
Pfam fn3 UniProtKB/Swiss-Prot
  I-set UniProtKB/Swiss-Prot
  PF00047 UniProtKB/Swiss-Prot
PhenoGen Cntn1 PhenoGen
PROSITE FN3 UniProtKB/Swiss-Prot
  IG_LIKE UniProtKB/Swiss-Prot
SMART FN3 UniProtKB/Swiss-Prot
  IGc2 UniProtKB/Swiss-Prot
  SM00409 UniProtKB/Swiss-Prot
Superfamily-SCOP SSF48726 UniProtKB/Swiss-Prot
  SSF49265 UniProtKB/Swiss-Prot
UniProt CNTN1_RAT UniProtKB/Swiss-Prot
  Q53I74_RAT UniProtKB/TrEMBL
  Q63198 ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2004-09-10 Cntn1  contactin 1      Symbol and Name status set to approved 1299863 APPROVED
2002-08-07 Cntn1  contactin 1      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_homology 99% amino acid identity with mouse homolog 728268
gene_protein 1021 amino acids 728268