Itga9 (integrin subunit alpha 9) - Rat Genome Database

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Gene: Itga9 (integrin subunit alpha 9) Rattus norvegicus
Analyze
Symbol: Itga9
Name: integrin subunit alpha 9
RGD ID: 1311191
Description: Enables collagen binding activity and laminin binding activity. Involved in wound healing. Located in membrane. Part of integrin alpha9-beta1 complex. Human ortholog(s) of this gene implicated in cerebral infarction; hypertension; and pancreatic cancer. Orthologous to human ITGA9 (integrin subunit alpha 9); PARTICIPATES IN altered integrin mediated signaling pathway; integrin mediated signaling pathway; pancreatic cancer pathway; INTERACTS WITH 2,2',4,4'-Tetrabromodiphenyl ether; 2,3,7,8-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran.
Type: protein-coding
RefSeq Status: MODEL
Also known as: integrin alpha 9; integrin alpha 9-like; integrin alpha-9; integrin, alpha 9; Itga9l; LOC316055; LOC685004; similar to integrin alpha 9
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Allele / Splice: Itga9em1Mcwi  
Genetic Models: SS-Itga9em1Mcwi
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.28118,307,424 - 118,615,527 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl8118,307,381 - 118,613,754 (+)Ensembl
Rnor_6.08127,271,029 - 127,576,709 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl8127,271,289 - 127,572,988 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.08126,493,359 - 126,795,566 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.48123,526,904 - 123,838,241 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.18123,387,039 - 123,857,990 (+)NCBI
Celera8117,492,541 - 117,791,124 (+)NCBICelera
Cytogenetic Map8q32NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

References

Additional References at PubMed
PMID:7534781   PMID:8889548   PMID:12947022   PMID:18778724   PMID:21060781   PMID:21321126   PMID:27031437  


Genomics

Comparative Map Data
Itga9
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.28118,307,424 - 118,615,527 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl8118,307,381 - 118,613,754 (+)Ensembl
Rnor_6.08127,271,029 - 127,576,709 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl8127,271,289 - 127,572,988 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.08126,493,359 - 126,795,566 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.48123,526,904 - 123,838,241 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.18123,387,039 - 123,857,990 (+)NCBI
Celera8117,492,541 - 117,791,124 (+)NCBICelera
Cytogenetic Map8q32NCBI
ITGA9
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl337,452,115 - 37,823,507 (+)EnsemblGRCh38hg38GRCh38
GRCh38337,452,141 - 37,823,507 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37337,493,632 - 37,864,998 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36337,468,817 - 37,836,285 (+)NCBINCBI36hg18NCBI36
Build 34337,468,816 - 37,836,285NCBI
Celera337,427,381 - 37,795,659 (+)NCBI
Cytogenetic Map3p22.2NCBI
HuRef337,453,524 - 37,803,820 (+)NCBIHuRef
CHM1_1337,445,418 - 37,812,994 (+)NCBICHM1_1
Itga9
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm399118,435,777 - 118,730,071 (+)NCBIGRCm39mm39
GRCm39 Ensembl9118,435,758 - 118,730,071 (+)Ensembl
GRCm389118,606,709 - 118,901,003 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl9118,606,690 - 118,901,003 (+)EnsemblGRCm38mm10GRCm38
MGSCv379118,515,827 - 118,810,121 (+)NCBIGRCm37mm9NCBIm37
MGSCv369118,455,407 - 118,747,637 (+)NCBImm8
Celera9119,076,746 - 119,369,133 (+)NCBICelera
Cytogenetic Map9F3NCBI
cM Map970.32NCBI
Itga9
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554214,331,048 - 4,663,092 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554214,331,053 - 4,663,101 (+)NCBIChiLan1.0ChiLan1.0
ITGA9
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1337,635,563 - 38,006,363 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl337,651,395 - 38,006,363 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0337,349,120 - 37,722,572 (+)NCBIMhudiblu_PPA_v0panPan3
CTDSPL
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1237,616,264 - 7,760,595 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl237,725,446 - 7,758,067 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha237,687,460 - 7,802,513 (+)NCBI
ROS_Cfam_1.0237,934,233 - 8,049,568 (+)NCBI
UMICH_Zoey_3.1237,748,828 - 7,863,990 (+)NCBI
UNSW_CanFamBas_1.0237,889,843 - 8,005,071 (+)NCBI
UU_Cfam_GSD_1.0237,882,182 - 7,997,474 (+)NCBI
Itga9
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118193,736,764 - 194,050,174 (+)NCBI
SpeTri2.0NW_00493647326,875,337 - 27,188,747 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
ITGA9
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1322,182,321 - 22,655,704 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11322,298,497 - 22,655,717 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21324,631,116 - 24,724,457 (+)NCBISscrofa10.2Sscrofa10.2susScr3
ITGA9
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1151,585,811 - 1,961,798 (-)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl151,581,676 - 1,961,435 (-)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366606310,313,062 - 10,698,298 (-)NCBIVero_WHO_p1.0
Itga9
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462477320,336,975 - 20,735,081 (-)NCBIHetGla_female_1.0hetGla2

Position Markers
D2Mgh4  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.28118,377,666 - 118,378,107 (+)MAPPERmRatBN7.2
mRatBN7.28118,377,666 - 118,377,831 (+)MAPPERmRatBN7.2
mRatBN7.28118,377,781 - 118,377,831 (+)MAPPERmRatBN7.2
Rnor_6.08127,341,429 - 127,341,919NCBIRnor6.0
Rnor_6.08127,341,429 - 127,341,593NCBIRnor6.0
Rnor_5.08126,561,786 - 126,562,276UniSTSRnor5.0
Rnor_5.08126,561,786 - 126,561,950UniSTSRnor5.0
RGSC_v3.48123,595,751 - 123,595,915UniSTSRGSC3.4
RGSC_v3.18123,615,487 - 123,615,652RGD
Celera8117,561,112 - 117,561,259UniSTS
FHH x ACI Map230.8999RGD
FHH x ACI Map230.8999UniSTS
Cytogenetic Map8q32UniSTS
D8Got193  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.28118,302,732 - 118,302,888 (+)MAPPERmRatBN7.2
Rnor_6.08127,266,322 - 127,266,477NCBIRnor6.0
Rnor_5.08126,488,628 - 126,488,783UniSTSRnor5.0
RGSC_v3.48123,521,936 - 123,522,092RGDRGSC3.4
RGSC_v3.48123,521,937 - 123,522,092UniSTSRGSC3.4
RGSC_v3.18123,541,674 - 123,541,829RGD
Celera8117,487,834 - 117,487,989UniSTS
RH 3.4 Map81292.2UniSTS
RH 3.4 Map81292.2RGD
RH 2.0 Map81003.0RGD
Cytogenetic Map8q32UniSTS
D8Got195  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.28118,324,174 - 118,324,442 (+)MAPPERmRatBN7.2
Rnor_6.08127,287,773 - 127,288,040NCBIRnor6.0
Rnor_5.08126,510,079 - 126,510,346UniSTSRnor5.0
RGSC_v3.48123,543,384 - 123,543,652RGDRGSC3.4
RGSC_v3.48123,543,385 - 123,543,652UniSTSRGSC3.4
RGSC_v3.18123,563,122 - 123,563,389RGD
Celera8117,509,265 - 117,509,540UniSTS
RH 3.4 Map81312.8UniSTS
RH 3.4 Map81312.8RGD
RH 2.0 Map81029.9RGD
Cytogenetic Map8q32UniSTS
D8Got167  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.28118,324,105 - 118,324,310 (+)MAPPERmRatBN7.2
Rnor_6.08127,287,704 - 127,287,908NCBIRnor6.0
Rnor_5.08126,510,010 - 126,510,214UniSTSRnor5.0
RGSC_v3.48123,543,315 - 123,543,520RGDRGSC3.4
RGSC_v3.48123,543,316 - 123,543,520UniSTSRGSC3.4
RGSC_v3.18123,563,053 - 123,563,257RGD
Celera8117,509,196 - 117,509,408UniSTS
RH 3.4 Map81303.4RGD
RH 3.4 Map81303.4UniSTS
Cytogenetic Map8q32UniSTS
AU047111  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.28118,322,812 - 118,322,984 (+)MAPPERmRatBN7.2
Rnor_6.08127,286,411 - 127,286,582NCBIRnor6.0
Rnor_5.08126,508,717 - 126,508,888UniSTSRnor5.0
RGSC_v3.48123,542,023 - 123,542,194UniSTSRGSC3.4
Celera8117,507,903 - 117,508,074UniSTS
Cytogenetic Map8q32UniSTS
D9Ertd428e  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.28118,611,924 - 118,612,144 (+)MAPPERmRatBN7.2
Rnor_6.08127,573,108 - 127,573,327NCBIRnor6.0
Rnor_5.08126,791,965 - 126,792,184UniSTSRnor5.0
RGSC_v3.48123,837,966 - 123,838,185UniSTSRGSC3.4
Celera8117,787,521 - 117,787,740UniSTS
Cytogenetic Map8q32UniSTS
RH132998  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.28118,311,842 - 118,312,042 (+)MAPPERmRatBN7.2
Rnor_6.08127,275,432 - 127,275,631NCBIRnor6.0
Rnor_5.08126,497,738 - 126,497,937UniSTSRnor5.0
RGSC_v3.48123,531,047 - 123,531,246UniSTSRGSC3.4
Celera8117,496,946 - 117,497,145UniSTS
RH 3.4 Map81292.1UniSTS
Cytogenetic Map8q32UniSTS
RH144307  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.28118,308,441 - 118,308,596 (+)MAPPERmRatBN7.2
Rnor_6.08127,272,031 - 127,272,185NCBIRnor6.0
Rnor_5.08126,494,337 - 126,494,491UniSTSRnor5.0
RGSC_v3.48123,527,646 - 123,527,800UniSTSRGSC3.4
Celera8117,493,543 - 117,493,697UniSTS
RH 3.4 Map81302.6UniSTS
Cytogenetic Map8q32UniSTS
BE102516  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.28118,583,600 - 118,583,778 (+)MAPPERmRatBN7.2
Rnor_6.08127,544,784 - 127,544,961NCBIRnor6.0
Rnor_5.08126,763,641 - 126,763,818UniSTSRnor5.0
RGSC_v3.48123,809,643 - 123,809,820UniSTSRGSC3.4
Celera8117,759,198 - 117,759,375UniSTS
RH 3.4 Map81302.1UniSTS
Cytogenetic Map8q32UniSTS
AU048253  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.28118,348,837 - 118,348,960 (+)MAPPERmRatBN7.2
Rnor_6.08127,312,516 - 127,312,638NCBIRnor6.0
Rnor_5.08126,533,351 - 126,533,473UniSTSRnor5.0
RGSC_v3.48123,566,695 - 123,566,817UniSTSRGSC3.4
Celera8117,532,112 - 117,532,234UniSTS
Cytogenetic Map8q32UniSTS
AU049476  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.28118,506,481 - 118,506,771 (+)MAPPERmRatBN7.2
Rnor_6.08127,471,197 - 127,471,486NCBIRnor6.0
Rnor_5.08126,690,240 - 126,690,529UniSTSRnor5.0
RGSC_v3.48123,733,215 - 123,733,504UniSTSRGSC3.4
Celera8117,688,799 - 117,689,088UniSTS
Cytogenetic Map8q32UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1554321Bmd3Bone mineral density QTL 37.90.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)840952565123900184Rat
70197BpQTLcluster8Blood pressure QTL cluster 83.482arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)846531639119088624Rat
70197BpQTLcluster8Blood pressure QTL cluster 83.482arterial blood pressure trait (VT:2000000)absolute change in systolic blood pressure (CMO:0000607)846531639119088624Rat
70197BpQTLcluster8Blood pressure QTL cluster 83.482arterial blood pressure trait (VT:2000000)pulse pressure (CMO:0000292)846531639119088624Rat
70197BpQTLcluster8Blood pressure QTL cluster 83.482arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)846531639119088624Rat
2303171Bp331Blood pressure QTL 3315.570.005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)861290298119084929Rat
1549909Stresp11Stress response QTL 116.830.0019stress-related behavior trait (VT:0010451)number of approaches toward negative stimulus before onset of defensive burying response (CMO:0001960)873473045118473045Rat
2300181Bmd55Bone mineral density QTL 555.70.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)876468691121468691Rat
61437Cia6Collagen induced arthritis QTL 6joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)882460758122812818Rat
738011Anxrr9Anxiety related response QTL 96.1exploratory behavior trait (VT:0010471)number of entries into a discrete space in an experimental apparatus (CMO:0000960)893535351123900184Rat
1358893Bp263Blood pressure QTL 2635.01arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)893965141123900184Rat
1358903Bp252Blood pressure QTL 25270.0001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)893965141123900184Rat
738014Anxrr15Anxiety related response QTL 153.60.005locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)895718998123900184Rat
2300182Bmd56Bone mineral density QTL 565.4femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)895718998123900184Rat
724539Cm19Cardiac mass QTL 192.6heart mass (VT:0007028)calculated heart weight (CMO:0000073)8100149864120994388Rat
1599689Iddm24Insulin dependent diabetes mellitus QTL 244.720.001blood glucose amount (VT:0000188)age at onset/diagnosis of type 1 diabetes mellitus (CMO:0001140)8112834440118649220Rat


Genetic Models
This gene Itga9 is modified in the following models/strains
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:41
Count of miRNA genes:38
Interacting mature miRNAs:41
Transcripts:ENSRNOT00000015113
Prediction methods:Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

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

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


Expression


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

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 42 20 12 6 12 1 1 6 29 34 11 1
Low 3 1 37 29 13 29 7 10 68 6 7 7
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000015113   ⟹   ENSRNOP00000015113
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl8118,307,381 - 118,613,754 (+)Ensembl
Rnor_6.0 Ensembl8127,271,289 - 127,572,988 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000095055   ⟹   ENSRNOP00000094362
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl8118,312,114 - 118,613,754 (+)Ensembl
RefSeq Acc Id: XM_039082699   ⟹   XP_038938627
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.28118,307,424 - 118,615,527 (+)NCBI
RefSeq Acc Id: XM_039082700   ⟹   XP_038938628
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.28118,309,952 - 118,611,805 (+)NCBI
RefSeq Acc Id: XM_039082701   ⟹   XP_038938629
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.28118,312,152 - 118,611,805 (+)NCBI
RefSeq Acc Id: XM_039082702   ⟹   XP_038938630
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.28118,307,424 - 118,519,159 (+)NCBI
RefSeq Acc Id: XM_039082703   ⟹   XP_038938631
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.28118,385,074 - 118,611,952 (+)NCBI
Reference Sequences
RefSeq Acc Id: ENSRNOP00000015113   ⟸   ENSRNOT00000015113
RefSeq Acc Id: XP_038938627   ⟸   XM_039082699
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038938630   ⟸   XM_039082702
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038938628   ⟸   XM_039082700
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038938629   ⟸   XM_039082701
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038938631   ⟸   XM_039082703
- Peptide Label: isoform X5
RefSeq Acc Id: ENSRNOP00000094362   ⟸   ENSRNOT00000095055
Protein Domains
Integrin_alpha2

Transcriptome

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

Promoters
RGD ID:13696363
Promoter ID:EPDNEW_R6888
Type:single initiation site
Name:Itga9_1
Description:integrin subunit alpha 9
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.08127,271,326 - 127,271,386EPDNEW

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)
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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
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)
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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)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
F344/Stm (2019)
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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)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
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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)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
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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)
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)
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
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:1311191 AgrOrtholog
Ensembl Genes ENSRNOG00000043167 Ensembl, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000015113 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000015113 UniProtKB/TrEMBL
Gene3D-CATH 2.130.10.130 UniProtKB/TrEMBL
InterPro FG-GAP UniProtKB/TrEMBL
  Int_alpha_beta-p UniProtKB/TrEMBL
  Integrin_alpha UniProtKB/TrEMBL
  Integrin_alpha-2 UniProtKB/TrEMBL
  Integrin_alpha_C_CS UniProtKB/TrEMBL
  Integrin_alpha_N UniProtKB/TrEMBL
  Integrin_dom UniProtKB/TrEMBL
NCBI Gene 685004 ENTREZGENE
Pfam FG-GAP UniProtKB/TrEMBL
  Integrin_alpha2 UniProtKB/TrEMBL
PhenoGen Itga9 PhenoGen
PRINTS INTEGRINA UniProtKB/TrEMBL
PROSITE FG_GAP UniProtKB/TrEMBL
  INTEGRIN_ALPHA UniProtKB/TrEMBL
SMART Int_alpha UniProtKB/TrEMBL
Superfamily-SCOP SSF69179 UniProtKB/TrEMBL
UniProt D3ZN51_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2009-09-09 Itga9l  integrin alpha 9-like  Itga9  integrin alpha 9  Data Merged 737654 APPROVED
2009-09-09 Itga9  integrin, alpha 9  Itga9l  integrin alpha 9-like  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-03-14 Itga9  integrin alpha 9  Itga9  integrin alpha 9  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-03-13 Itga9  integrin alpha 9  LOC685004  similar to integrin alpha 9  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-03-13 Itga9l  integrin alpha 9-like  Itga9  integrin alpha 9  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-01-09 LOC685004  similar to integrin alpha 9  LOC687154  similar to integrin alpha 9  Data Merged 1643240 APPROVED
2006-11-19 LOC685004  similar to integrin alpha 9      Symbol and Name status set to provisional 70820 PROVISIONAL
2006-11-19 LOC687154  similar to integrin alpha 9      Symbol and Name status set to provisional 70820 PROVISIONAL
2005-12-06 Itga9  integrin alpha 9  Itga9_predicted  integrin alpha 9 (predicted)  Symbol and Name updated 1559027 APPROVED
2005-01-12 Itga9_predicted  integrin alpha 9 (predicted)      Symbol and Name status set to approved 70820 APPROVED