Dcx (doublecortin) - Rat Genome Database

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Gene: Dcx (doublecortin) Rattus norvegicus
Analyze
Symbol: Dcx
Name: doublecortin
RGD ID: 620670
Description: Predicted to enable microtubule binding activity and protein kinase binding activity. Involved in nervous system development; positive regulation of endocytosis; and response to electrical stimulus. Located in dendrite; growth cone; and neuronal cell body. Colocalizes with microtubule. Used to study visual epilepsy. Biomarker of hypothyroidism and type 2 diabetes mellitus. Human ortholog(s) of this gene implicated in X-linked lissencephaly 1 and subcortical band heterotopia. Orthologous to human DCX (doublecortin); INTERACTS WITH 2,6-di-tert-butyl-4-methylphenol; 5-fluorouracil; 6-propyl-2-thiouracil.
Type: protein-coding
RefSeq Status: REVIEWED
Also known as: neuronal migration protein doublecortin
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2X107,430,767 - 107,573,612 (-)NCBImRatBN7.2
mRatBN7.2 EnsemblX107,430,767 - 107,507,476 (-)Ensembl
Rnor_6.0X115,098,675 - 115,175,515 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX115,098,675 - 115,175,299 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0X113,551,874 - 113,628,283 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X34,596,262 - 34,672,383 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1X34,649,730 - 34,718,439NCBI
CeleraX106,829,783 - 106,906,206 (-)NCBICelera
Cytogenetic MapXq33-q34NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
axon  (IDA)
axoneme  (IBA)
cytoplasm  (IEA,ISO)
dendrite  (IDA)
growth cone  (IDA)
microtubule  (IDA)
neuron projection  (IEA,ISO,ISS)
neuronal cell body  (IDA)

Molecular Function

Phenotype Annotations     Click to see Annotation Detail View

Mammalian Phenotype
References

References - curated
1. Aigner L, etal., Neuropediatrics. 2000 Aug;31(4):195-8.
2. Bai J, etal., Nat Neurosci 2003 Dec;6(12):1277-83. Epub 2003 Nov 16.
3. Corbo JC, etal., J Neurosci 2002 Sep 1;22(17):7548-57.
4. D'Alessio L, etal., Seizure. 2010 Nov;19(9):567-72. doi: 10.1016/j.seizure.2010.09.004.
5. des Portes V, etal., Hum Mol Genet. 1998 Jul;7(7):1063-70.
6. Fournier NM, etal., Hippocampus. 2009 Jun 4.
7. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
8. GOA data from the GO Consortium
9. Guerrini R, etal., Ann Neurol. 2003 Jul;54(1):30-7.
10. Haverfield EV, etal., Eur J Hum Genet. 2009 Jul;17(7):911-8. doi: 10.1038/ejhg.2008.213. Epub 2008 Dec 3.
11. Juhasova J, etal., Cell Mol Neurobiol. 2015 Jan;35(1):57-70. doi: 10.1007/s10571-014-0145-7. Epub 2014 Dec 9.
12. Kato M, etal., Hum Genet. 1999 Apr;104(4):341-4.
13. Kremer T, etal., PLoS One. 2013 May 14;8(5):e59269. doi: 10.1371/journal.pone.0059269. Print 2013.
14. Lapray D, etal., Cereb Cortex. 2010 Nov;20(11):2694-701. doi: 10.1093/cercor/bhq014. Epub 2010 Feb 17.
15. Manent JB, etal., Nat Med. 2009 Jan;15(1):84-90. doi: 10.1038/nm.1897. Epub 2008 Dec 21.
16. MGD data from the GO Consortium
17. NCBI rat LocusLink and RefSeq merged data July 26, 2002
18. Nosten-Bertrand M, etal., PLoS One. 2008 Jun 25;3(6):e2473. doi: 10.1371/journal.pone.0002473.
19. OMIM Disease Annotation Pipeline
20. RGD automated data pipeline
21. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
22. RGD automated import pipeline for gene-chemical interactions
23. Santra M, etal., Cancer Res. 2006 Dec 15;66(24):11726-35.
24. Santra M, etal., Cancer Sci. 2011 Jul;102(7):1350-7. doi: 10.1111/j.1349-7006.2011.01952.x. Epub 2011 May 10.
25. Santra M, etal., J Neurosci Res. 2010 Feb 1;88(2):304-14. doi: 10.1002/jnr.22207.
26. Tint I, etal., J Neurosci. 2009 Sep 2;29(35):10995-1010. doi: 10.1523/JNEUROSCI.3399-09.2009.
27. Tsai MH, etal., Eur J Paediatr Neurol. 2016 Sep;20(5):788-94. doi: 10.1016/j.ejpn.2016.05.010. Epub 2016 May 30.
28. Wang Y, etal., Arch Med Res. 2012 May;43(4):255-64. doi: 10.1016/j.arcmed.2012.05.002. Epub 2012 May 15.
29. Xu X, etal., Nan Fang Yi Ke Da Xue Xue Bao. 2013 Oct;33(10):1437-41.
30. Yap CC, etal., J Neurosci. 2012 May 30;32(22):7439-53. doi: 10.1523/JNEUROSCI.5318-11.2012.
31. Yi SS, etal., Neurochem Res. 2009 Jun;34(6):1039-46. doi: 10.1007/s11064-008-9870-y. Epub 2008 Nov 4.
Additional References at PubMed
PMID:12223548   PMID:14741102   PMID:15632090   PMID:15804431   PMID:16387638   PMID:16387639   PMID:17026970   PMID:17161913   PMID:17409252   PMID:18075265   PMID:18177494   PMID:18647639  
PMID:18803236   PMID:18854839   PMID:19342486   PMID:20857512   PMID:21689730   PMID:22038821   PMID:22197046   PMID:22198017   PMID:22198688   PMID:23001563   PMID:23447615   PMID:23852478  
PMID:23861879   PMID:24367100   PMID:25209608   PMID:27487661   PMID:29476059   PMID:32236698  


Genomics

Comparative Map Data
Dcx
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2X107,430,767 - 107,573,612 (-)NCBImRatBN7.2
mRatBN7.2 EnsemblX107,430,767 - 107,507,476 (-)Ensembl
Rnor_6.0X115,098,675 - 115,175,515 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX115,098,675 - 115,175,299 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0X113,551,874 - 113,628,283 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X34,596,262 - 34,672,383 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1X34,649,730 - 34,718,439NCBI
CeleraX106,829,783 - 106,906,206 (-)NCBICelera
Cytogenetic MapXq33-q34NCBI
DCX
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 EnsemblX111,293,779 - 111,412,429 (-)EnsemblGRCh38hg38GRCh38
GRCh38X111,293,779 - 111,412,205 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37X110,537,007 - 110,655,420 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36X110,423,663 - 110,542,062 (-)NCBINCBI36hg18NCBI36
Build 34X110,343,151 - 110,461,551NCBI
CeleraX111,016,623 - 111,134,992 (-)NCBI
Cytogenetic MapXq23NCBI
HuRefX100,159,414 - 100,278,099 (-)NCBIHuRef
CHM1_1X110,448,522 - 110,566,950 (-)NCBICHM1_1
Dcx
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39X142,638,838 - 142,716,392 (-)NCBIGRCm39mm39
GRCm39 EnsemblX142,638,838 - 142,716,307 (-)Ensembl
GRCm38X143,855,842 - 143,933,396 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblX143,855,842 - 143,933,311 (-)EnsemblGRCm38mm10GRCm38
MGSCv37X140,290,385 - 140,367,762 (-)NCBIGRCm37mm9NCBIm37
MGSCv36X139,102,210 - 139,179,587 (-)NCBImm8
CeleraX127,810,174 - 127,886,575 (-)NCBICelera
Cytogenetic MapXF2NCBI
Dcx
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554904,354,307 - 4,469,055 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554904,354,307 - 4,469,055 (+)NCBIChiLan1.0ChiLan1.0
DCX
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1X110,878,060 - 110,988,303 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 EnsemblX110,875,032 - 110,988,582 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0X100,411,871 - 100,529,833 (-)NCBIMhudiblu_PPA_v0panPan3
DCX
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1X84,408,762 - 84,541,157 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 EnsemblX84,408,895 - 84,517,827 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_TashaX70,501,790 - 70,641,477 (-)NCBI
ROS_Cfam_1.0X86,062,412 - 86,202,409 (-)NCBI
UMICH_Zoey_3.1X83,553,159 - 83,685,002 (-)NCBI
UNSW_CanFamBas_1.0X85,222,965 - 85,362,879 (-)NCBI
UU_Cfam_GSD_1.0X85,051,446 - 85,192,159 (-)NCBI
Dcx
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2X83,645,350 - 83,761,221 (-)NCBI
SpeTri2.0NW_0049364993,905,262 - 4,004,457 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
DCX
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 EnsemblX91,323,768 - 91,644,567 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1X91,317,671 - 91,644,572 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2X105,739,468 - 106,059,734 (-)NCBISscrofa10.2Sscrofa10.2susScr3
DCX
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1X99,106,291 - 99,220,479 (-)NCBI
ChlSab1.1 EnsemblX99,120,505 - 99,220,237 (-)Ensembl
Vero_WHO_p1.0NW_02366606524,340,271 - 24,459,762 (-)NCBI
Dcx
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248034,168,556 - 4,304,642 (+)NCBI


QTLs in Region (mRatBN7.2)
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)X14843113120568734Rat
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)X41052407146860749Rat
738035Stresp1Stress response QTL 14.960.000011stress-related behavior trait (VT:0010451)defensive burying - copingX41304447112935181Rat
61431Cia19Collagen induced arthritis QTL 194.4joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)X65612192120568734Rat
724551Glom1Glomerulus QTL 12.80.0004kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)X75294106120294106Rat
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)X93956491138956491Rat
738025Stresp3Stress response QTL 34.610.0066stress-related behavior trait (VT:0010451)defensive burying - approachX100567703150256146Rat
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)X103312877148312877Rat
1598856Memor1Memory QTL 11.9exploratory behavior trait (VT:0010471)total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)X103312877148312877Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:1949
Count of miRNA genes:396
Interacting mature miRNAs:604
Transcripts:ENSRNOT00000074322
Prediction methods: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 69 12
Low 21 15 7 7 5 5 5 18 27 4 5
Below cutoff 3 20 32 24 19 24 3 6 11 2 6 3

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_053379 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006257382 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006257383 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006257384 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006257385 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006257386 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017602167 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039100106 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039100107 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039100108 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039100109 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039100110 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039100112 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AF155959 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH474047 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000448 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000074322   ⟹   ENSRNOP00000065381
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX107,430,767 - 107,507,476 (-)Ensembl
Rnor_6.0 EnsemblX115,098,675 - 115,175,299 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000103733   ⟹   ENSRNOP00000083258
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX107,445,120 - 107,507,476 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000107008   ⟹   ENSRNOP00000095915
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX107,433,107 - 107,507,476 (-)Ensembl
RefSeq Acc Id: NM_053379   ⟹   NP_445831
RefSeq Status: REVIEWED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X107,430,767 - 107,507,476 (-)NCBI
Rnor_6.0X115,098,675 - 115,175,299 (-)NCBI
Rnor_5.0X113,551,874 - 113,628,283 (-)NCBI
RGSC_v3.4X34,596,262 - 34,672,383 (+)RGD
CeleraX106,829,783 - 106,906,206 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006257382   ⟹   XP_006257444
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X107,430,767 - 107,507,424 (-)NCBI
Rnor_6.0X115,098,675 - 115,175,248 (-)NCBI
Rnor_5.0X113,551,874 - 113,628,283 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006257385   ⟹   XP_006257447
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X107,430,767 - 107,507,744 (-)NCBI
Rnor_6.0X115,098,675 - 115,175,514 (-)NCBI
Rnor_5.0X113,551,874 - 113,628,283 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006257386   ⟹   XP_006257448
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X107,430,767 - 107,507,584 (-)NCBI
Rnor_6.0X115,098,675 - 115,175,515 (-)NCBI
Rnor_5.0X113,551,874 - 113,628,283 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017602167   ⟹   XP_017457656
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X107,430,767 - 107,507,165 (-)NCBI
Rnor_6.0X115,098,675 - 115,175,070 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039100106   ⟹   XP_038956034
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X107,430,767 - 107,573,612 (-)NCBI
RefSeq Acc Id: XM_039100107   ⟹   XP_038956035
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X107,430,767 - 107,507,424 (-)NCBI
RefSeq Acc Id: XM_039100108   ⟹   XP_038956036
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X107,430,767 - 107,507,425 (-)NCBI
RefSeq Acc Id: XM_039100109   ⟹   XP_038956037
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X107,430,767 - 107,507,425 (-)NCBI
RefSeq Acc Id: XM_039100110   ⟹   XP_038956038
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X107,430,767 - 107,507,424 (-)NCBI
RefSeq Acc Id: XM_039100112   ⟹   XP_038956040
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X107,430,767 - 107,507,425 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_445831   ⟸   NM_053379
- UniProtKB: G3V997 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006257448   ⟸   XM_006257386
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_006257447   ⟸   XM_006257385
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_006257444   ⟸   XM_006257382
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017457656   ⟸   XM_017602167
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000065381   ⟸   ENSRNOT00000074322
RefSeq Acc Id: XP_038956034   ⟸   XM_039100106
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038956040   ⟸   XM_039100112
- Peptide Label: isoform X6
RefSeq Acc Id: XP_038956037   ⟸   XM_039100109
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038956036   ⟸   XM_039100108
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038956038   ⟸   XM_039100110
- Peptide Label: isoform X5
RefSeq Acc Id: XP_038956035   ⟸   XM_039100107
- Peptide Label: isoform X2
RefSeq Acc Id: ENSRNOP00000083258   ⟸   ENSRNOT00000103733
RefSeq Acc Id: ENSRNOP00000095915   ⟸   ENSRNOT00000107008
Protein Domains
Doublecortin

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)
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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
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)
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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
BXH3/CubMcwi (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
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)
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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)
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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
F344/DuCrl (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
F344/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
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)
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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
FHH/EurMcwi (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
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)
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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)
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)
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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
FXLE18/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
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)
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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
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)
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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
HXB2/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
HXB20/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
HXB31/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
HXB4/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
LE/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
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 (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
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
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)
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
LEXF1A/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
LEXF1C/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
LEXF2B/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
LEXF3/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
LEXF4/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
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
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)
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/MavRrrcAek (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: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
LN/MavRrrcAek (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: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/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
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
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)
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 (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
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
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)
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
SBN/Ygl (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: SBN/Ygl sequenced by MCW
SBN/Ygl (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
SHR/NHsd (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
SHR/OlalpcvMcwi (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
SHRSP/A3NCrl (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
SHRSP/Gcrc (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
SR/JrHsd (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: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SR/JrHsd (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: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (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
SS/Jr (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
SS/JrHsdMcwi (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
SS/JrHsdMcwi (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)
SS/JrHsdMcwi (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
WAG/Rij (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
WAG/RijCrl (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: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/Gcrc (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
WKY/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
WKY/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
WKY/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
WKY/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
WKY/NHsd (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
WN/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
WN/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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:620670 AgrOrtholog
Ensembl Genes ENSRNOG00000047712 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000065381 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000074322 ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH 3.10.20.230 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro Doublecortin_chordata UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Doublecortin_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Doublecortin_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  RP1/RP1L1/DCX UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:84394 UniProtKB/TrEMBL
NCBI Gene 84394 ENTREZGENE
PANTHER PTHR23005 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam DCX UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Dcx PhenoGen
PIRSF Doublin UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE PS50309 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART DCX UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF89837 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt DCX_RAT UniProtKB/Swiss-Prot
  G3V997 ENTREZGENE, UniProtKB/TrEMBL
  Q9ESI7 ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2005-01-20 Dcx  doublecortin      Symbol and Name status set to approved 1299863 APPROVED
2002-08-07 Dcx  doublecortin      Symbol and Name status set to provisional 70820 PROVISIONAL