Chrdl1 (chordin-like 1) - Rat Genome Database

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Gene: Chrdl1 (chordin-like 1) Rattus norvegicus
Analyze
Symbol: Chrdl1
Name: chordin-like 1
RGD ID: 735215
Description: Involved in cell fate determination and neuron differentiation. Predicted to localize to extracellular region. Human ortholog(s) of this gene implicated in megalocornea. Orthologous to human CHRDL1 (chordin like 1); PARTICIPATES IN Bone morphogenetic proteins signaling pathway; INTERACTS WITH 3,7-dihydropurine-6-thione; 6-propyl-2-thiouracil; acrylamide.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: chordin-like protein 1; Kjr; kohjirin; neuralin-1; neurogenesin 1; Neurogenesin-1; Ng1; ventroptin
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
mRatBN7.2X106,889,125 - 106,992,937 (-)NCBI
Rnor_6.0 EnsemblX114,554,359 - 114,658,931 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0X114,554,359 - 114,658,975 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0X112,998,868 - 113,103,004 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X35,143,324 - 35,246,363 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1X35,196,792 - 35,299,832 (+)NCBI
CeleraX106,298,521 - 106,402,293 (-)NCBICelera
Cytogenetic MapXq33NCBI
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
1,2-dichloroethane  (ISO)
17beta-estradiol  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
3,7-dihydropurine-6-thione  (EXP)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
4-hydroxyphenyl retinamide  (ISO)
6-propyl-2-thiouracil  (EXP)
acrylamide  (EXP,ISO)
aflatoxin B1  (EXP,ISO)
all-trans-retinoic acid  (ISO)
antirheumatic drug  (ISO)
arsenous acid  (ISO)
benzo[a]pyrene  (EXP,ISO)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
bromobenzene  (EXP)
Butylparaben  (EXP)
cadmium atom  (ISO)
carbamazepine  (ISO)
carbon nanotube  (ISO)
chromium atom  (ISO)
copper atom  (ISO)
copper(0)  (ISO)
dexamethasone  (ISO)
diarsenic trioxide  (ISO)
dioxygen  (ISO)
dorsomorphin  (ISO)
entinostat  (ISO)
enzacamene  (EXP)
ethanol  (ISO)
folic acid  (ISO)
indometacin  (ISO)
mercaptopurine  (EXP)
mercury dibromide  (ISO)
methimazole  (EXP)
methylmercury chloride  (ISO)
mitoxantrone  (ISO)
N-methyl-4-phenylpyridinium  (ISO)
N-nitrosodiethylamine  (EXP)
N-Nitrosopyrrolidine  (ISO)
nickel sulfate  (ISO)
p-chloromercuribenzoic acid  (ISO)
paracetamol  (EXP,ISO)
phenylmercury acetate  (ISO)
potassium chromate  (ISO)
potassium dichromate  (ISO)
profenofos  (EXP)
progesterone  (ISO)
purine-6-thiol  (EXP)
rotenone  (EXP)
SB 431542  (ISO)
silver atom  (ISO)
silver(0)  (ISO)
sodium arsenate  (ISO)
sodium arsenite  (ISO)
Soman  (EXP)
tert-butyl hydroperoxide  (ISO)
tetrachloromethane  (EXP)
titanium dioxide  (ISO)
trichostatin A  (ISO)
uranium atom  (ISO)
valproic acid  (ISO)
XL147  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Pathway Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:20459000   PMID:22284829   PMID:23404565   PMID:23676271   PMID:32446365  


Genomics

Comparative Map Data
Chrdl1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2X106,889,125 - 106,992,937 (-)NCBI
Rnor_6.0 EnsemblX114,554,359 - 114,658,931 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0X114,554,359 - 114,658,975 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0X112,998,868 - 113,103,004 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X35,143,324 - 35,246,363 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1X35,196,792 - 35,299,832 (+)NCBI
CeleraX106,298,521 - 106,402,293 (-)NCBICelera
Cytogenetic MapXq33NCBI
CHRDL1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 EnsemblX110,673,856 - 110,795,819 (-)EnsemblGRCh38hg38GRCh38
GRCh38X110,673,856 - 110,795,817 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37X109,917,084 - 110,039,045 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36X109,805,129 - 109,925,649 (-)NCBINCBI36hg18NCBI36
Build 34X109,724,618 - 109,845,138NCBI
CeleraX110,396,687 - 110,518,880 (-)NCBI
Cytogenetic MapXq23NCBI
HuRefX99,536,440 - 99,658,656 (-)NCBIHuRef
CHM1_1X109,828,368 - 109,950,621 (-)NCBICHM1_1
Chrdl1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39X142,068,670 - 142,177,282 (-)NCBIGRCm39mm39
GRCm39 EnsemblX142,068,670 - 142,177,258 (-)Ensembl
GRCm38X143,285,674 - 143,394,263 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblX143,285,674 - 143,394,262 (-)EnsemblGRCm38mm10GRCm38
MGSCv37X139,720,217 - 139,828,805 (-)NCBIGRCm37mm9NCBIm37
MGSCv36X138,544,347 - 138,640,552 (-)NCBImm8
CeleraX127,242,501 - 127,351,024 (-)NCBICelera
Cytogenetic MapXF2NCBI
Chrdl1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554905,108,308 - 5,257,445 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554905,108,308 - 5,218,679 (+)NCBIChiLan1.0ChiLan1.0
CHRDL1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1X110,251,525 - 110,375,068 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 EnsemblX110,251,525 - 110,375,289 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0X99,781,730 - 99,915,778 (-)NCBIMhudiblu_PPA_v0panPan3
CHRDL1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1X83,816,131 - 83,936,497 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 EnsemblX83,817,880 - 83,936,949 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_TashaX69,902,330 - 70,023,049 (-)NCBI
ROS_Cfam_1.0X85,474,229 - 85,594,632 (-)NCBI
UMICH_Zoey_3.1X82,954,985 - 83,076,135 (-)NCBI
UNSW_CanFamBas_1.0X84,638,644 - 84,759,034 (-)NCBI
UU_Cfam_GSD_1.0X84,466,847 - 84,587,260 (-)NCBI
Chrdl1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2X83,070,399 - 83,183,059 (-)NCBI
SpeTri2.0NW_0049364994,474,899 - 4,587,563 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CHRDL1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 EnsemblX90,703,422 - 90,827,210 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1X90,703,422 - 90,827,216 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2X104,266,419 - 104,398,294 (+)NCBISscrofa10.2Sscrofa10.2susScr3
CHRDL1
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1X98,490,291 - 98,611,811 (-)NCBI
ChlSab1.1 EnsemblX98,489,874 - 98,611,951 (-)Ensembl
Chrdl1
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248035,011,132 - 5,144,899 (+)NCBI

Position Markers
RH127629  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0X114,566,339 - 114,566,556NCBIRnor6.0
Rnor_5.0X113,010,848 - 113,011,065UniSTSRnor5.0
RGSC_v3.4X35,234,368 - 35,234,585UniSTSRGSC3.4
CeleraX106,310,292 - 106,310,509UniSTS
RH 3.4 Map71133.12UniSTS
Cytogenetic MapXq14UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
61430Cia18Collagen induced arthritis QTL 183.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)X15688119127888215Rat
1598837Memor13Memory QTL 133.2exploratory behavior trait (VT:0010471)difference between time of physical contact/close proximity of test subject and social stimulus during sample phase and test phase (CMO:0002678)X44320616158345622Rat
738035Stresp1Stress response QTL 14.960.000011stress-related behavior trait (VT:0010451)defensive burying - copingX44557974120045269Rat
61431Cia19Collagen induced arthritis QTL 194.4joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)X70352120127888215Rat
724551Glom1Glomerulus QTL 12.80.0004kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)X82930791127930791Rat
1598872Memor14Memory QTL 144.5exploratory behavior trait (VT:0010471)difference between time of physical contact/close proximity of test subject and social stimulus during sample phase and test phase (CMO:0002678)X101333032146333032Rat
738025Stresp3Stress response QTL 34.610.0066stress-related behavior trait (VT:0010451)defensive burying - approachX107886746152409805Rat
1598809Memor15Memory QTL 154.4exploratory behavior trait (VT:0010471)difference between time of physical contact/close proximity of test subject and social stimulus during sample phase and test phase (CMO:0002678)X110957467155957467Rat
1598856Memor1Memory QTL 11.9exploratory behavior trait (VT:0010471)total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)X110957467155957467Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:945
Count of miRNA genes:335
Interacting mature miRNAs:460
Transcripts:ENSRNOT00000006008
Prediction methods:Microtar, Miranda, Pita, 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 5 1
Low 3 31 29 13 17 13 8 10 74 28 34 10 8
Below cutoff 12 26 26 2 26 1 7 2

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000006008   ⟹   ENSRNOP00000006008
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 EnsemblX114,554,359 - 114,658,931 (-)Ensembl
RefSeq Acc Id: NM_199502   ⟹   NP_955796
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X106,889,125 - 106,992,921 (-)NCBI
Rnor_6.0X114,554,359 - 114,658,931 (-)NCBI
Rnor_5.0X112,998,868 - 113,103,004 (-)NCBI
RGSC_v3.4X35,143,324 - 35,246,363 (+)RGD
CeleraX106,298,521 - 106,402,293 (-)RGD
Sequence:
RefSeq Acc Id: XM_006257373   ⟹   XP_006257435
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X106,889,125 - 106,992,937 (-)NCBI
Rnor_6.0X114,554,359 - 114,658,975 (-)NCBI
Rnor_5.0X112,998,868 - 113,103,004 (-)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_955796 (Get FASTA)   NCBI Sequence Viewer  
  XP_006257435 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein BAD06447 (Get FASTA)   NCBI Sequence Viewer  
  EDL85198 (Get FASTA)   NCBI Sequence Viewer  
  EDL85199 (Get FASTA)   NCBI Sequence Viewer  
  Q76LD0 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_955796   ⟸   NM_199502
- Sequence:
RefSeq Acc Id: XP_006257435   ⟸   XM_006257373
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000006008   ⟸   ENSRNOT00000006008
Protein Domains
VWFC

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)
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
MNS/Gib (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
MR/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
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
X 113040618 113040619 A G snv DOB/Oda (KyushuU)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:735215 AgrOrtholog
Ensembl Genes ENSRNOG00000004330 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000006008 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000006008 ENTREZGENE, UniProtKB/TrEMBL
InterPro VWF_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:363455 UniProtKB/Swiss-Prot
NCBI Gene 363455 ENTREZGENE
Pfam VWC UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Chrdl1 PhenoGen
PROSITE VWFC_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  VWFC_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART VWC UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt CRDL1_RAT UniProtKB/Swiss-Prot
  F1LQZ2_RAT UniProtKB/TrEMBL
  Q76LD0 ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2012-07-16 Chrdl1  chordin-like 1  Chrdl1  kohjirin  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2004-09-10 Chrdl1  kohjirin  Ng1    Symbol and Name updated 1299863 APPROVED