Aasdh (aminoadipate-semialdehyde dehydrogenase) - Rat Genome Database

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Gene: Aasdh (aminoadipate-semialdehyde dehydrogenase) Rattus norvegicus
Analyze
Symbol: Aasdh
Name: aminoadipate-semialdehyde dehydrogenase
RGD ID: 1311135
Description: Predicted to act upstream of or within amino acid activation for nonribosomal peptide biosynthetic process and beta-alanine metabolic process. Orthologous to human AASDH (aminoadipate-semialdehyde dehydrogenase); INTERACTS WITH 17alpha-ethynylestradiol; all-trans-retinoic acid; bisphenol A.
Type: protein-coding
RefSeq Status: MODEL
Also known as: acyl-CoA synthetase family member 4; beta-alanine-activating enzyme; LOC364136; LOW QUALITY PROTEIN: acyl-CoA synthetase family member 4; RGD1311135; similar to 2-aminoadipic 6-semialdehyde dehydrogenase
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
mRatBN7.21431,255,019 - 31,281,802 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl1431,255,310 - 31,281,796 (+)Ensembl
Rnor_6.01433,619,990 - 33,647,268 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1433,624,390 - 33,647,180 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01433,410,917 - 33,438,181 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41433,553,214 - 33,575,421 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11433,553,200 - 33,575,421 (+)NCBI
Celera1430,569,108 - 30,595,707 (+)NCBICelera
Cytogenetic Map14p11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

References

References - curated
1. RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:24467666  


Genomics

Comparative Map Data
Aasdh
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21431,255,019 - 31,281,802 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl1431,255,310 - 31,281,796 (+)Ensembl
Rnor_6.01433,619,990 - 33,647,268 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1433,624,390 - 33,647,180 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01433,410,917 - 33,438,181 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41433,553,214 - 33,575,421 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11433,553,200 - 33,575,421 (+)NCBI
Celera1430,569,108 - 30,595,707 (+)NCBICelera
Cytogenetic Map14p11NCBI
AASDH
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl456,338,287 - 56,387,508 (-)EnsemblGRCh38hg38GRCh38
GRCh38456,337,687 - 56,389,418 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37457,204,456 - 57,253,657 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36456,899,213 - 56,948,395 (-)NCBINCBI36hg18NCBI36
Celera454,710,829 - 54,760,021 (-)NCBI
Cytogenetic Map4q12NCBI
HuRef453,158,378 - 53,207,773 (-)NCBIHuRef
CHM1_1457,239,570 - 57,288,751 (-)NCBICHM1_1
Aasdh
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39577,021,506 - 77,053,376 (-)NCBIGRCm39mm39
GRCm39 Ensembl577,021,506 - 77,053,361 (-)Ensembl
GRCm38576,873,659 - 76,905,529 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl576,873,659 - 76,905,514 (-)EnsemblGRCm38mm10GRCm38
MGSCv37577,304,960 - 77,334,539 (-)NCBIGRCm37mm9NCBIm37
MGSCv36577,950,713 - 77,993,728 (-)NCBImm8
Celera574,152,121 - 74,182,004 (-)NCBICelera
Cytogenetic Map5C3.3NCBI
Aasdh
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495544714,622,728 - 14,648,005 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495544714,623,532 - 14,648,121 (+)NCBIChiLan1.0ChiLan1.0
AASDH
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1474,107,854 - 74,159,927 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl474,110,736 - 74,159,809 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0467,536,000 - 67,591,204 (+)NCBIMhudiblu_PPA_v0panPan3
AASDH
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11348,574,839 - 48,611,770 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1348,572,220 - 48,611,775 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1348,465,553 - 48,502,540 (-)NCBI
ROS_Cfam_1.01349,189,413 - 49,226,415 (-)NCBI
UMICH_Zoey_3.11348,861,363 - 48,898,350 (-)NCBI
UNSW_CanFamBas_1.01348,390,337 - 48,427,317 (-)NCBI
UU_Cfam_GSD_1.01349,336,285 - 49,373,201 (-)NCBI
Aasdh
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440528527,707,855 - 27,739,043 (+)NCBI
SpeTri2.0NW_00493648218,558,789 - 18,591,709 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
AASDH
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl855,604,626 - 55,645,504 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1855,604,394 - 55,645,536 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2857,986,062 - 57,998,070 (+)NCBISscrofa10.2Sscrofa10.2susScr3
AASDH
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1712,248,193 - 12,292,027 (+)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl712,249,208 - 12,296,516 (+)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366606612,918,085 - 12,962,654 (+)NCBIVero_WHO_p1.0
Aasdh
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462476113,026,875 - 13,063,511 (+)NCBIHetGla_female_1.0hetGla2

Position Markers
D5Mit306  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21431,275,488 - 31,275,729 (+)MAPPERmRatBN7.2
Rnor_6.01433,640,955 - 33,641,195NCBIRnor6.0
Rnor_5.01433,431,868 - 33,432,108UniSTSRnor5.0
RGSC_v3.41433,569,108 - 33,569,348UniSTSRGSC3.4
Cytogenetic Map14p11UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
619619Rf4Renal disease susceptibility QTL 44.10.002total urine protein amount (VT:0000032)urine protein excretion rate to body weight ratio (CMO:0001099)14132754612Rat
634352Apr6Acute phase response QTL 63.7blood interleukin-6 amount (VT:0008595)plasma interleukin-6 level (CMO:0001927)14141131407Rat
1581500Renag1Renal agenesis QTL 1kidney development trait (VT:0000527)percentage of study population developing unilateral renal agenesis during a period of time (CMO:0000940)14817066868298175Rat
1358296Ael3Aortic elastin QTL 33.70.00051aorta elastin amount (VT:0003905)aortic elastin14826709053267090Rat
2302045Pia39Pristane induced arthritis QTL 394.90.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin G2a level (CMO:0002116)14826709053267090Rat
731183Pia20Pristane induced arthritis QTL 203.55joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)14908897839057237Rat
631839Niddm37Non-insulin dependent diabetes mellitus QTL 373.37blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)141103062295876975Rat
71117Niddm17Non-insulin dependent diabetes mellitus QTL 172.35blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)141759376142336881Rat
631262Tcas4Tongue tumor susceptibility QTL 47.29tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)141762256142337007Rat
2313397Coatc1Coat color QTL1coat/hair pigmentation trait (VT:0010463)coat/hair color measurement (CMO:0001808)141854133263541332Rat
61420Pia6Pristane induced arthritis QTL 64.9joint integrity trait (VT:0010548)arthritic paw count (CMO:0001460)141863134542337007Rat
10755459Coatc15Coat color QTL 150.01681coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)141983694464836944Rat
70187Pancm5Pancreatic morphology QTL 516.7pancreas mass (VT:0010144)pancreas weight to body weight ratio (CMO:0000630)143032009280829842Rat
2324617Coatc2Coat color QTL 20.001coat/hair pigmentation trait (VT:0010463)pigmented coat/hair area to total coat/hair area ratio (CMO:0001810)143076702539153750Rat
1300154Bp189Blood pressure QTL 1893.04arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)143088377768757901Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:9
Count of miRNA genes:9
Interacting mature miRNAs:9
Transcripts:ENSRNOT00000002907
Prediction methods:Miranda, Rnahybrid
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 4 17 8 17 8 69 22 34 8
Low 3 39 40 33 2 33 8 11 5 13 7 3 8
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts XM_006250858 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008770110 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008770111 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017599441 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017599442 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017599443 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017599444 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017599445 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017599446 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017599447 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017604860 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039092928 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039092929 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039092930 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039092931 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039092932 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039092933 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039092934 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039092935 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039092936 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039092937 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide CH473981 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000252 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000002907   ⟹   ENSRNOP00000002907
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1431,255,310 - 31,281,796 (+)Ensembl
Rnor_6.0 Ensembl1433,624,390 - 33,647,180 (+)Ensembl
RefSeq Acc Id: XM_017599447   ⟹   XP_017454936
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21431,266,781 - 31,281,802 (+)NCBI
Rnor_6.01433,635,411 - 33,647,268 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039092928   ⟹   XP_038948856
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21431,255,282 - 31,281,802 (+)NCBI
RefSeq Acc Id: XM_039092929   ⟹   XP_038948857
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21431,255,282 - 31,281,802 (+)NCBI
RefSeq Acc Id: XM_039092930   ⟹   XP_038948858
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21431,255,170 - 31,281,802 (+)NCBI
RefSeq Acc Id: XM_039092931   ⟹   XP_038948859
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21431,255,282 - 31,281,802 (+)NCBI
RefSeq Acc Id: XM_039092932   ⟹   XP_038948860
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21431,255,019 - 31,281,802 (+)NCBI
RefSeq Acc Id: XM_039092933   ⟹   XP_038948861
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21431,255,282 - 31,281,802 (+)NCBI
RefSeq Acc Id: XM_039092934   ⟹   XP_038948862
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21431,255,282 - 31,281,802 (+)NCBI
RefSeq Acc Id: XM_039092935   ⟹   XP_038948863
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21431,255,282 - 31,281,802 (+)NCBI
RefSeq Acc Id: XM_039092936   ⟹   XP_038948864
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21431,255,282 - 31,281,802 (+)NCBI
RefSeq Acc Id: XM_039092937   ⟹   XP_038948865
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21431,255,282 - 31,274,639 (+)NCBI
Reference Sequences
RefSeq Acc Id: XP_017454936   ⟸   XM_017599447
- Peptide Label: isoform X5
- Sequence:
RefSeq Acc Id: ENSRNOP00000002907   ⟸   ENSRNOT00000002907
RefSeq Acc Id: XP_038948860   ⟸   XM_039092932
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038948858   ⟸   XM_039092930
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038948859   ⟸   XM_039092931
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038948857   ⟸   XM_039092929
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038948863   ⟸   XM_039092935
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038948856   ⟸   XM_039092928
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038948862   ⟸   XM_039092934
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038948861   ⟸   XM_039092933
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038948864   ⟸   XM_039092936
- Peptide Label: isoform X6
RefSeq Acc Id: XP_038948865   ⟸   XM_039092937
- Peptide Label: isoform X7
Protein Domains
Carrier

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)
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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/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
F344/NRrrc (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
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)
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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)
FHH/EurMcwi (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
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)
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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
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)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/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)
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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
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)
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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)
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)
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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)
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)
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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: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
14 33625291 33625292 G T snv LL/MavRrrc (RGD), SBN/Ygl (RGD), SR/JrHsd (RGD), F344/N (2020), FHH/EurMcwi (2019), FXLE16/Stm (2020), HXB20/IpcvMcwi (2020), LEXF4/Stm (2020), LH/MavRrrcAek (2020), LN/MavRrrcAek (2020), LEXF10A/StmMcwi (2020), SHR/OlalpcvMcwi (2019), SR/JrHsd (2020), CDR, ACI/EurMcwi (MCW), COP/CrCrl (MCW & UW), FHH/EurMcwi (MCW), FHL/EurMcwi (MCW), SBH/Ygl (MCW), SBN/Ygl (MCW), SR/JrHsd (MCW), SS/JrHsdMcwi (MCW), ACI/N (MCW), Buf/N (MCW), F344/NRrrc (MCW), M520/N (MCW), MR/N (MCW), WKY/N (MCW), WN/N (MCW), ACI/EurMcwi (RGD), BBDP/Wor (RGD), F344/NCrl (RGD), FHL/EurMcwi (RGD), GK/Ox (RGD), LEW/Crl (RGD), LH/MavRrrc (RGD), MNS/Gib (RGD), SBH/Ygl (RGD), SHR/NHsd (RGD), SHRSP/Gcrc (RGD), SS/Jr (RGD), SS/JrHsdMcwi (RGD), WAG/Rij (RGD), WKY/NCrl (RGD), WKY/Gcrc (RGD), ACI/EurMcwi (2019), ACI/N (2020), BUF/N (2020), F344/DuCrl (2019), F344/NCrl (2019), F344/Stm (2019), GK/FarMcwi (2019), HXB31/IpcvMcwi (2019), LEW/Crl (2019), LEXF1A/Stm (2019), LEXF2B/Stm (2019), LEXF3/Stm (2020), M520/N (2020), MWF/Hsd (2019), PVG/Seac (2019), SHRSP/A3NCrl (2019), SS/JrHsdMcwi (2019), WAG/RijCrl (2020), WKY/NCrl (2019), WKY/N (2020), WN/N (2020), LEW/NCrlBR (RGD), MHS/Gib (RGD), BXH3/CubMcwi (2020), FXLE18/Stm (2020), HXB2/IpcvMcwi (2019), LL/MavRrrcAek (2020), M520/NRrrcMcwi (2019), CDS, GH/OmrMcwi (MCW), FHH/EurMcwi (RGD), LN/MavRrrc (RGD)
14 33640679 33640680 A T snv ACI/EurMcwi (MCW), ACI/N (MCW), ACI/EurMcwi (RGD), LH/MavRrrc (RGD), ACI/EurMcwi (2019), ACI/N (2020), MWF/Hsd (2019), LN/MavRrrcAek (2020), CDS, GH/OmrMcwi (MCW), LN/MavRrrc (RGD), SR/JrHsd (RGD), SR/JrHsd (2020), SBH/Ygl (MCW), SBN/Ygl (MCW), SR/JrHsd (MCW), MR/N (MCW), SBH/Ygl (RGD), SBN/Ygl (RGD), LH/MavRrrcAek (2020)
14 33640683 33640684 G A snv CDR, SHR/OlalpcvMcwi (2019), FHH/EurMcwi (MCW), FHL/EurMcwi (MCW), SS/JrHsdMcwi (MCW), Buf/N (MCW), F344/NRrrc (MCW), M520/N (MCW), WKY/N (MCW), WN/N (MCW), BBDP/Wor (RGD), F344/NCrl (RGD), FHL/EurMcwi (RGD), GK/Ox (RGD), LEW/Crl (RGD), MNS/Gib (RGD), SHRSP/Gcrc (RGD), SS/Jr (RGD), SS/JrHsdMcwi (RGD), WAG/Rij (RGD), WKY/NCrl (RGD), WKY/Gcrc (RGD), BUF/N (2020), F344/DuCrl (2019), F344/NCrl (2019), F344/Stm (2019), GK/FarMcwi (2019), LEW/Crl (2019), LEXF1A/Stm (2019), LEXF2B/Stm (2019), M520/N (2020), PVG/Seac (2019), SHRSP/A3NCrl (2019), SS/JrHsdMcwi (2019), WAG/RijCrl (2020), WKY/NCrl (2019), WKY/N (2020), WN/N (2020), FHH/EurMcwi (RGD), LEW/NCrlBR (RGD), LL/MavRrrc (RGD), MHS/Gib (RGD), WKY/NHsd (RGD), BXH3/CubMcwi (2020), F344/N (2020), FHH/EurMcwi (2019), FXLE16/Stm (2020), FXLE18/Stm (2020), HXB20/IpcvMcwi (2020), HXB2/IpcvMcwi (2019), HXB31/IpcvMcwi (2019), LEXF3/Stm (2020), LEXF4/Stm (2020), LL/MavRrrcAek (2020), LEXF10A/StmMcwi (2020), M520/NRrrcMcwi (2019), COP/CrCrl (MCW & UW)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1311135 AgrOrtholog
Ensembl Genes ENSRNOG00000002137 Ensembl, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000002907 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000002907 UniProtKB/TrEMBL
Gene3D-CATH 2.130.10.10 UniProtKB/TrEMBL
  3.40.50.12780 UniProtKB/TrEMBL
InterPro Acyl_carrier_prot-like UniProtKB/TrEMBL
  AMP-binding_CS UniProtKB/TrEMBL
  AMP-dep_Synth/Lig UniProtKB/TrEMBL
  AMP-dep_Synthh-like_sf UniProtKB/TrEMBL
  PQQ-like_dom UniProtKB/TrEMBL
  PQQ_beta_propeller_repeat UniProtKB/TrEMBL
  PQQ_repeat UniProtKB/TrEMBL
  Quino_AlcDH-like UniProtKB/TrEMBL
  WD40/YVTN_repeat-like_dom_sf UniProtKB/TrEMBL
NCBI Gene 364136 ENTREZGENE
Pfam AMP-binding UniProtKB/TrEMBL
  PQQ_2 UniProtKB/TrEMBL
  PQQ_3 UniProtKB/TrEMBL
PhenoGen Aasdh PhenoGen
PROSITE ACP_DOMAIN UniProtKB/TrEMBL
  AMP_BINDING UniProtKB/TrEMBL
SMART PQQ UniProtKB/TrEMBL
Superfamily-SCOP Quin_alc_DH_like UniProtKB/TrEMBL
UniProt D4A5F5_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-02-27 Aasdh  aminoadipate-semialdehyde dehydrogenase  RGD1311135_predicted  similar to 2-aminoadipic 6-semialdehyde dehydrogenase (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-01-20 RGD1311135_predicted  similar to 2-aminoadipic 6-semialdehyde dehydrogenase (predicted)  LOC364136_predicted    Symbol and Name status set to approved 1331353 APPROVED
2005-01-12 LOC364136_predicted  similar to 2-aminoadipic 6-semialdehyde dehydrogenase (predicted)      Symbol and Name status set to provisional 70820 PROVISIONAL