Cntnap5c (contactin associated protein-like 5C) - Rat Genome Database

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Gene: Cntnap5c (contactin associated protein-like 5C) Rattus norvegicus
Analyze
No known orthologs.
Symbol: Cntnap5c
Name: contactin associated protein-like 5C
RGD ID: 1566343
Description: Predicted to be involved in cell adhesion. Predicted to be integral component of membrane. Orthologous to human CNTNAP5 (contactin associated protein family member 5).
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: Caspr5-4; cell recognition molecule Caspr5-4; cell recognition molecule Caspr5d; Cntnap5; Cntnap5d; contactin associated protein-like 5; contactin associated protein-like 5-4; contactin-associated protein like 5-4; contactin-associated protein-like 5d; LOC297846; RGD1566343; similar to contactin associated protein-like 5 isoform 1
RGD Orthologs
Alliance Genes
More Info homologs ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2133,513,615 - 4,545,053 (+)NCBImRatBN7.2
Rnor_6.0136,312,302 - 7,538,647 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl136,679,368 - 7,537,275 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01312,597,108 - 12,804,561 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Rnor_5.01311,594,156 - 12,421,307 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41322,856,230 - 23,913,512 (+)NCBIRGSC3.4rn4RGSC3.4
Celera134,468,107 - 5,491,533 (+)NCBICelera
Cytogenetic Map13p13NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

References

References - curated
1. RGD automated data pipeline
2. RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:16845472  


Genomics

Position Markers
D13Rat9  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2133,611,007 - 3,611,148 (+)MAPPERmRatBN7.2
Rnor_6.0136,411,215 - 6,411,355NCBIRnor6.0
Rnor_5.01311,693,801 - 11,693,941UniSTSRnor5.0
RGSC_v3.41322,952,154 - 22,952,295RGDRGSC3.4
RGSC_v3.41322,952,155 - 22,952,295UniSTSRGSC3.4
RGSC_v3.11322,954,895 - 22,955,036RGD
Celera134,564,861 - 4,565,001UniSTS
SHRSP x BN Map131.1799UniSTS
SHRSP x BN Map131.1799RGD
Cytogenetic Map13p12-p11UniSTS
D13Rat169  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2133,885,124 - 3,885,302 (+)MAPPERmRatBN7.2
Rnor_6.0136,836,597 - 6,836,774NCBIRnor6.0
Rnor_5.01312,114,539 - 12,114,716UniSTSRnor5.0
RGSC_v3.41323,227,922 - 23,228,100RGDRGSC3.4
RGSC_v3.41323,227,923 - 23,228,100UniSTSRGSC3.4
RGSC_v3.11323,230,663 - 23,230,841RGD
Celera134,834,975 - 4,835,152UniSTS
SHRSP x BN Map131.0999UniSTS
SHRSP x BN Map131.0999RGD
FHH x ACI Map131.4701RGD
Cytogenetic Map13p12-p11UniSTS
D13Rat168  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2133,885,090 - 3,885,298 (+)MAPPERmRatBN7.2
Rnor_6.0136,836,563 - 6,836,770NCBIRnor6.0
Rnor_5.01312,114,505 - 12,114,712UniSTSRnor5.0
RGSC_v3.41323,227,888 - 23,228,096RGDRGSC3.4
RGSC_v3.41323,227,889 - 23,228,096UniSTSRGSC3.4
RGSC_v3.11323,230,629 - 23,230,837RGD
Celera134,834,941 - 4,835,148UniSTS
SHRSP x BN Map131.1799UniSTS
SHRSP x BN Map131.1799RGD
Cytogenetic Map13p12-p11UniSTS
D6Got154  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2133,573,658 - 3,573,830 (+)MAPPERmRatBN7.2
Rnor_6.0136,373,876 - 6,374,047NCBIRnor6.0
Rnor_5.01311,656,462 - 11,656,633UniSTSRnor5.0
RGSC_v3.41322,914,852 - 22,915,024RGDRGSC3.4
RGSC_v3.41322,914,853 - 22,915,024UniSTSRGSC3.4
RGSC_v3.11322,917,594 - 22,917,765RGD
Celera134,527,108 - 4,527,279UniSTS
RH 3.4 Map6776.09UniSTS
RH 3.4 Map6776.09RGD
Cytogenetic Map13p12-p11UniSTS
D13Got264  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2134,269,328 - 4,269,614 (+)MAPPERmRatBN7.2
Rnor_6.0137,267,590 - 7,267,875NCBIRnor6.0
Rnor_5.01312,534,460 - 12,534,745UniSTSRnor5.0
RGSC_v3.41323,617,250 - 23,617,535UniSTSRGSC3.4
Celera135,218,546 - 5,218,831UniSTS
Cytogenetic Map13p12-p11UniSTS
D13Got234  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2133,956,109 - 3,956,248 (+)MAPPERmRatBN7.2
Rnor_6.0136,908,135 - 6,908,273NCBIRnor6.0
Rnor_5.01312,186,077 - 12,186,215UniSTSRnor5.0
RGSC_v3.41323,298,909 - 23,299,047UniSTSRGSC3.4
Celera134,905,852 - 4,905,989UniSTS
Cytogenetic Map13p12-p11UniSTS
D13Got203  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2134,363,875 - 4,364,022 (+)MAPPERmRatBN7.2
Rnor_6.0137,361,000 - 7,361,145NCBIRnor6.0
Rnor_5.01312,628,290 - 12,628,431NCBIRnor5.0
RGSC_v3.41323,714,026 - 23,714,171UniSTSRGSC3.4
Cytogenetic Map13p12-p11UniSTS
D13Got255  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2134,269,393 - 4,269,612 (+)MAPPERmRatBN7.2
Rnor_6.0137,267,655 - 7,267,873NCBIRnor6.0
Rnor_5.01312,534,525 - 12,534,743UniSTSRnor5.0
RGSC_v3.41323,617,315 - 23,617,533UniSTSRGSC3.4
Celera135,218,611 - 5,218,829UniSTS
Cytogenetic Map13p12-p11UniSTS
D13Got236  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0137,041,710 - 7,041,875NCBIRnor6.0
Rnor_5.01312,320,126 - 12,320,291UniSTSRnor5.0
RGSC_v3.41323,434,122 - 23,434,327UniSTSRGSC3.4
Celera135,040,381 - 5,040,586UniSTS
Cytogenetic Map13p12-p11UniSTS
AU048969  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2134,126,461 - 4,126,661 (+)MAPPERmRatBN7.2
Rnor_6.0137,092,403 - 7,092,602NCBIRnor6.0
Rnor_5.01312,362,625 - 12,362,824UniSTSRnor5.0
RGSC_v3.41323,470,008 - 23,470,207UniSTSRGSC3.4
Celera135,076,433 - 5,076,632UniSTS
Cytogenetic Map13p12-p11UniSTS
AU049039  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2134,346,072 - 4,346,220 (+)MAPPERmRatBN7.2
Rnor_6.0137,343,579 - 7,343,726NCBIRnor6.0
Rnor_5.01312,610,449 - 12,610,596UniSTSRnor5.0
RGSC_v3.41323,696,246 - 23,696,393UniSTSRGSC3.4
Celera135,294,973 - 5,295,120UniSTS
Cytogenetic Map13p12-p11UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2317027Aia22Adjuvant induced arthritis QTL 222.29joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)13134266636Rat
738036Lnnr4Liver neoplastic nodule remodeling QTL 43.64liver integrity trait (VT:0010547)liver remodeling tumorous lesion number (CMO:0001461)13142356786Rat
1354666Bp244Blood pressure QTL 2444.9arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)131101056920Rat
1354666Bp244Blood pressure QTL 2444.9arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)131101056920Rat
1354666Bp244Blood pressure QTL 2444.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)131101056920Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:175
Count of miRNA genes:132
Interacting mature miRNAs:141
Transcripts:ENSRNOT00000067198
Prediction methods:Miranda
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

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 8
Low 4 58 12 2
Below cutoff 13 11 6 1 6 2 2 8 2 24 6 2

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000067198   ⟹   ENSRNOP00000062287
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl136,679,368 - 7,537,275 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000092965   ⟹   ENSRNOP00000076029
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl136,679,369 - 7,382,961 (+)Ensembl
RefSeq Acc Id: NM_001047866   ⟹   NP_001041331
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2133,514,267 - 4,542,565 (+)NCBI
Rnor_6.0136,312,877 - 7,537,275 (+)NCBI
Rnor_5.01311,594,156 - 12,421,307 (+)NCBI
Rnor_5.01312,597,108 - 12,804,561 (+)NCBI
RGSC_v3.41322,856,230 - 23,913,512 (+)RGD
Celera134,468,107 - 5,491,533 (+)RGD
Sequence:
RefSeq Acc Id: XM_017598776   ⟹   XP_017454265
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2133,513,618 - 4,545,053 (+)NCBI
Rnor_6.0136,312,302 - 7,538,647 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039090653   ⟹   XP_038946581
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2133,513,617 - 4,545,053 (+)NCBI
RefSeq Acc Id: XM_039090654   ⟹   XP_038946582
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2133,513,615 - 4,372,179 (+)NCBI
Protein Sequences
Protein RefSeqs NP_001041331 (Get FASTA)   NCBI Sequence Viewer  
  XP_017454265 (Get FASTA)   NCBI Sequence Viewer  
  XP_038946581 (Get FASTA)   NCBI Sequence Viewer  
  XP_038946582 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein CAJ55733 (Get FASTA)   NCBI Sequence Viewer  
  Q0V8T3 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001041331   ⟸   NM_001047866
- Peptide Label: precursor
- UniProtKB: Q0V8T3 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_017454265   ⟸   XM_017598776
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000062287   ⟸   ENSRNOT00000067198
RefSeq Acc Id: ENSRNOP00000076029   ⟸   ENSRNOT00000092965
RefSeq Acc Id: XP_038946582   ⟸   XM_039090654
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038946581   ⟸   XM_039090653
- Peptide Label: isoform X2
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 (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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-Lx/CubMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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)
DA/OlaHsd (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
F344/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
FXLE16/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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/FarMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
HXB10/IpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
LEXF10A/StmMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
LH/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
LL/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
LN/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
M520/NRrrcMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
MWF/Hsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
SHR/OlalpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
WAG/RijCrl (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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: mRatBN7.2

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
13 3753738 3753739 G T snv ACI/EurMcwi (2019), ACI/N (2020), LEXF3/Stm (2020), HXB4/IpcvMcwi (2020), HXB2/IpcvMcwi (2019), HXB10/IpcvMcwi (2019), F344/N (2020), BUF/N (2020), DA/OlaHsd (2019), F344/DuCrl (2019), F344/NCrl (2019), F344/Stm (2019), FXLE16/Stm (2020), GK/FarMcwi (2019), HXB20/IpcvMcwi (2020), LEXF1A/Stm (2019), LEXF1C/Stm (2019), LEXF2B/Stm (2019), MWF/Hsd (2019), PVG/Seac (2019), SHRSP/A3NCrl (2019), SHR/OlalpcvMcwi (2019), WKY/NCrl (2019), WKY/N (2020), BXH2/CubMcwi (2020)
13 3960714 3960715 G A snv LE/Stm (2019), LEXF4/Stm (2020), LEXF11/Stm (2020), FXLE18/Stm (2020), WN/N (2020), LEXF10A/StmMcwi (2020)


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
13 6705113 6705114 G T snv SHRSP/Gcrc (RGD), WKY/NCrl (2019), SHR/OlalpcvMcwi (2019), SHRSP/A3NCrl (2019), PVG/Seac (2019), MWF/Hsd (2019), LEXF3/Stm (2020), LEXF2B/Stm (2019), LEXF1C/Stm (2019), LEXF1A/Stm (2019), HXB4/IpcvMcwi (2020), HXB2/IpcvMcwi (2019), CDR, ACI/EurMcwi (MCW), COP/CrCrl (MCW & UW), GH/OmrMcwi (MCW), SBN/Ygl (MCW), ACI/N (MCW), Buf/N (MCW), F344/NRrrc (MCW), MR/N (MCW), WKY/N (MCW), ACI/EurMcwi (RGD), F344/NCrl (RGD), GK/Ox (RGD), SBN/Ygl (RGD), SHR/NHsd (RGD), WKY/N (2020), WKY/NCrl (RGD), WKY/Gcrc (RGD), WKY/NHsd (RGD), ACI/EurMcwi (2019), ACI/N (2020), BUF/N (2020), BXH2/CubMcwi (2020), DA/OlaHsd (2019), F344/DuCrl (2019), F344/NCrl (2019), F344/N (2020), F344/Stm (2019), FXLE16/Stm (2020), GK/FarMcwi (2019), HXB10/IpcvMcwi (2019), HXB20/IpcvMcwi (2020)
13 6912739 6912740 G A snv WN/N (2020), LEXF10A/StmMcwi (2020), LE/Stm (2019), LEXF4/Stm (2020), LEXF11/Stm (2020), SBH/Ygl (MCW), SBH/Ygl (RGD), MHS/Gib (RGD), LE/Stm (RGD), BBDP/Wor (RGD), WN/N (MCW), FXLE18/Stm (2020)
13 6995598 6995599 G A snv CDR, ACI/EurMcwi (MCW), COP/CrCrl (MCW & UW), GH/OmrMcwi (MCW), SBN/Ygl (MCW), ACI/N (MCW), Buf/N (MCW), F344/NRrrc (MCW), MR/N (MCW), WKY/N (MCW), ACI/EurMcwi (RGD), SHR/NHsd (RGD), WKY/NCrl (RGD), WKY/Gcrc (RGD), WKY/NHsd (RGD), ACI/EurMcwi (2019), ACI/N (2020), BUF/N (2020), BXH2/CubMcwi (2020), DA/OlaHsd (2019), F344/DuCrl (2019), F344/NCrl (2019), F344/N (2020), F344/Stm (2019), FXLE16/Stm (2020), GK/FarMcwi (2019), HXB10/IpcvMcwi (2019), HXB20/IpcvMcwi (2020), HXB2/IpcvMcwi (2019), HXB4/IpcvMcwi (2020), LEXF1A/Stm (2019), LEXF1C/Stm (2019), LEXF2B/Stm (2019), LEXF3/Stm (2020), MWF/Hsd (2019), PVG/Seac (2019), SHRSP/A3NCrl (2019), SHR/OlalpcvMcwi (2019), WKY/NCrl (2019), WKY/N (2020)
13 7000049 7000050 G C snv GK/FarMcwi (2019), HXB10/IpcvMcwi (2019), HXB20/IpcvMcwi (2020), HXB2/IpcvMcwi (2019), HXB4/IpcvMcwi (2020), LEXF1A/Stm (2019), LEXF1C/Stm (2019), LEXF2B/Stm (2019), LEXF3/Stm (2020), MWF/Hsd (2019), PVG/Seac (2019), SHRSP/A3NCrl (2019), SHR/OlalpcvMcwi (2019), WKY/NCrl (2019), WKY/N (2020), CDR, ACI/EurMcwi (MCW), COP/CrCrl (MCW & UW), GH/OmrMcwi (MCW), SBN/Ygl (MCW), ACI/N (MCW), Buf/N (MCW), F344/NRrrc (MCW), MR/N (MCW), WKY/N (MCW), GK/Ox (RGD), ACI/EurMcwi (2019), ACI/N (2020), BUF/N (2020), BXH2/CubMcwi (2020), DA/OlaHsd (2019), F344/DuCrl (2019), F344/NCrl (2019), F344/N (2020), F344/Stm (2019), FXLE16/Stm (2020)
13 7039540 7039541 G T snv CDR, WKY/N (2020), COP/CrCrl (MCW & UW), GH/OmrMcwi (MCW), SBN/Ygl (MCW), ACI/N (MCW), Buf/N (MCW), F344/NRrrc (MCW), MR/N (MCW), WKY/N (MCW), ACI/EurMcwi (RGD), F344/NCrl (RGD), SBN/Ygl (RGD), SHR/NHsd (RGD), SHRSP/Gcrc (RGD), WKY/NCrl (RGD), WKY/Gcrc (RGD), WKY/NHsd (RGD), ACI/EurMcwi (2019), ACI/N (2020), BUF/N (2020), BXH2/CubMcwi (2020), DA/OlaHsd (2019), F344/DuCrl (2019), F344/NCrl (2019), F344/N (2020), F344/Stm (2019), FXLE16/Stm (2020), GK/FarMcwi (2019), HXB10/IpcvMcwi (2019), HXB20/IpcvMcwi (2020), HXB2/IpcvMcwi (2019), HXB4/IpcvMcwi (2020), LEXF1A/Stm (2019), LEXF1C/Stm (2019), LEXF2B/Stm (2019), LEXF3/Stm (2020), MWF/Hsd (2019), PVG/Seac (2019), SHRSP/A3NCrl (2019), SHR/OlalpcvMcwi (2019), WKY/NCrl (2019), ACI/EurMcwi (MCW)


Assembly: RGSC_v3.4

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
13 23096547 23096548 G T snv ACI/EurMcwi (MCW), F344/NHsd (ICAHN), SHRSP/Gcrc (MDC), ACI/N (KNAW), BUF/N (KNAW), F344/NRrrc (KNAW), MR/N (KNAW), WKY/N (KNAW), SHR/OlaIpcv (KNAW), COP/CrCrl (MCW & UW), GH/OmrMcwi (MCW), ACI/EurMcwi (ICL), F344/NCrl (ICL), GK/Ox (ICL), SBN/Ygl (ICL), SHR/OlaIpcv (ICL), SHR/NHsd (ICL), SHRSP/Gcrc (ICL), WKY/NCrl (ICL), WKY/Gcrc (ICL), WKY/NHsd (ICL), DA/BklArbNsi (ICAHN), SHR/OlaIpcv (ICL)
13 23303513 23303514 G A snv LE/Stm (KNAW), WN/N (KNAW), BBDP/WorN (ICL), LE/Stm (ICL), LCR/2Mco (UMich), SBH/Ygl (ICL), HCR/1Mco (UMich), LCR/1Mco (UMich), HCR/2Mco (UMich), MHS/Gib (ICL)
13 23388010 23388011 G A snv ACI/EurMcwi (MCW), F344/NHsd (ICAHN), SHRSP/Gcrc (MDC), ACI/N (KNAW), BUF/N (KNAW), F344/NRrrc (KNAW), MR/N (KNAW), WKY/N (KNAW), SHR/OlaIpcv (KNAW), COP/CrCrl (MCW & UW), GH/OmrMcwi (MCW), ACI/EurMcwi (ICL), F344/NCrl (ICL), GK/Ox (ICL), SBN/Ygl (ICL), SHR/OlaIpcv (ICL), SHR/NHsd (ICL), SHRSP/Gcrc (ICL), WKY/NCrl (ICL), WKY/Gcrc (ICL), WKY/NHsd (ICL), DA/BklArbNsi (ICAHN), SHR/OlaIpcv (ICL)
13 23392461 23392462 G C snv ACI/EurMcwi (MCW), F344/NHsd (ICAHN), ACI/N (KNAW), BUF/N (KNAW), F344/NRrrc (KNAW), MR/N (KNAW), WKY/N (KNAW), SHR/OlaIpcv (KNAW), COP/CrCrl (MCW & UW), GH/OmrMcwi (MCW), ACI/EurMcwi (ICL), F344/NCrl (ICL), GK/Ox (ICL), SBN/Ygl (ICL), SHR/OlaIpcv (ICL), SHR/NHsd (ICL), SHRSP/Gcrc (ICL), WKY/NCrl (ICL), WKY/Gcrc (ICL), WKY/NHsd (ICL), SHRSP/Gcrc (MDC)
13 23431952 23431953 G T snv ACI/EurMcwi (MCW), SHR/OlaIpcv (ICL), SHRSP/Gcrc (MDC), ACI/N (KNAW), BUF/N (KNAW), F344/NRrrc (KNAW), MR/N (KNAW), WKY/N (KNAW), SHR/OlaIpcv (KNAW), COP/CrCrl (MCW & UW), GH/OmrMcwi (MCW), ACI/EurMcwi (ICL), F344/NCrl (ICL), GK/Ox (ICL), SBN/Ygl (ICL), SHR/OlaIpcv (ICL), SHR/NHsd (ICL), SHRSP/Gcrc (ICL), WKY/NCrl (ICL), WKY/Gcrc (ICL), WKY/NHsd (ICL), HCR/1Mco (UMich), LCR/1Mco (UMich), LCR/2Mco (UMich), DA/BklArbNsi (ICAHN), F344/NHsd (ICAHN)
13 23711807 23711808 G T snv WKY/NHsd (ICL), LCR/2Mco (UMich), WKY/NCrl (ICL), SHRSP/Gcrc (ICL), SHR/NHsd (ICL), SHR/OlaIpcv (ICL), SBN/Ygl (ICL), GK/Ox (ICL), F344/NCrl (ICL), ACI/EurMcwi (ICL), GH/OmrMcwi (MCW), COP/CrCrl (MCW & UW), SHR/OlaIpcv (KNAW), WKY/N (KNAW), MR/N (KNAW), F344/NRrrc (KNAW), BUF/N (KNAW), ACI/N (KNAW), SHRSP/Gcrc (MDC), SHR/OlaIpcv (ICL), ACI/EurMcwi (MCW), WKY/Gcrc (ICL)
13 23711808 23711809 C A snv LCR/2Mco (UMich), WKY/NHsd (ICL), WKY/Gcrc (ICL), WKY/NCrl (ICL), SHRSP/Gcrc (ICL), SHR/NHsd (ICL), SHR/OlaIpcv (ICL), SBN/Ygl (ICL), GK/Ox (ICL), F344/NCrl (ICL), ACI/EurMcwi (ICL), GH/OmrMcwi (MCW), COP/CrCrl (MCW & UW), SHR/OlaIpcv (KNAW), WKY/N (KNAW), MR/N (KNAW), F344/NRrrc (KNAW), BUF/N (KNAW), ACI/N (KNAW), SHRSP/Gcrc (MDC), ACI/EurMcwi (MCW), SHR/OlaIpcv (ICL)
13 23907411 23907412 C A snv ACI/EurMcwi (MCW), F344/NHsd (ICAHN), SHRSP/Gcrc (MDC), ACI/N (KNAW), BUF/N (KNAW), F344/NRrrc (KNAW), MR/N (KNAW), WKY/N (KNAW), SHR/OlaIpcv (KNAW), COP/CrCrl (MCW & UW), GH/OmrMcwi (MCW), ACI/EurMcwi (ICL), F344/NCrl (ICL), GK/Ox (ICL), SBN/Ygl (ICL), SHR/OlaIpcv (ICL), SHR/NHsd (ICL), SHRSP/Gcrc (ICL), WKY/NCrl (ICL), WKY/Gcrc (ICL), WKY/NHsd (ICL), HCR/1Mco (UMich), LCR/2Mco (UMich), DA/BklArbNsi (ICAHN), SHR/OlaIpcv (ICL)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1566343 AgrOrtholog
Ensembl Genes ENSRNOG00000043185 Ensembl, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000062287 UniProtKB/TrEMBL
  ENSRNOP00000076029 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000067198 UniProtKB/TrEMBL
  ENSRNOT00000092965 UniProtKB/TrEMBL
InterPro Caspr5 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ConA-like_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  EGF-like_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  FA58C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Fibrinogen-like_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Fibrinogen_a/b/g_C_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Galactose-bd-like_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Laminin_G UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:297846 UniProtKB/Swiss-Prot
NCBI Gene 297846 ENTREZGENE
PANTHER PTHR15036:SF70 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam F5_F8_type_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Laminin_G_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Cntnap5c PhenoGen
PROSITE EGF_3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  FA58C_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  FA58C_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  FA58C_3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  FIBRINOGEN_C_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  LAM_G_DOMAIN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART EGF UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  FA58C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  LamG UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF49785 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF49899 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF56496 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A1B0GWV0_RAT UniProtKB/TrEMBL
  CTP5D_RAT UniProtKB/Swiss-Prot
  F1LMS4_RAT UniProtKB/TrEMBL
  Q0V8T3 ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2012-07-16 Cntnap5c  contactin associated protein-like 5C  Cntnap5  contactin associated protein-like 5  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2010-05-05 Cntnap5  contactin associated protein-like 5  RGD1566343  similar to contactin associated protein-like 5 isoform 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-09-30 RGD1566343  similar to contactin associated protein-like 5 isoform 1  Cntnap5b  contactin associated protein-like 5B  Symbol and Name updated 1299863 APPROVED
2008-09-30 Cntnap5b  contactin associated protein-like 5B  RGD1566343  similar to contactin associated protein-like 5 isoform 1   Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 RGD1566343  similar to contactin associated protein-like 5 isoform 1   RGD1566343_predicted  similar to contactin associated protein-like 5 isoform 1 (predicted)  'predicted' is removed 2292626 APPROVED
2006-03-07 RGD1566343_predicted  similar to contactin associated protein-like 5 isoform 1 (predicted)  LOC297846  similar to contactin associated protein-like 5 isoform 1  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC297846  similar to contactin associated protein-like 5 isoform 1      Symbol and Name status set to provisional 70820 PROVISIONAL