Fancc (FA complementation group C) - Rat Genome Database

Send us a Message



Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Gene: Fancc (FA complementation group C) Rattus norvegicus
Analyze
Symbol: Fancc
Name: FA complementation group C
RGD ID: 2593
Description: Predicted to be involved in cellular response to oxidative stress and nucleotide-excision repair. Predicted to act upstream of or within several processes, including brain morphogenesis; neuronal stem cell population maintenance; and removal of superoxide radicals. Located in chromatin. Human ortholog(s) of this gene implicated in several diseases, including Fanconi anemia (multiple); acute myeloid leukemia; aspirin-induced respiratory disease; pancreatic cancer; and pancytopenia. Orthologous to human FANCC (FA complementation group C); INTERACTS WITH (+)-schisandrin B; 2,2',4,4'-Tetrabromodiphenyl ether; ammonium chloride.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: Facc; Fanconi anemia group C; fanconi anemia group C protein homolog; Fanconi anemia, complementation group C; LOC103694020; uncharacterized LOC103694020
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
mRatBN7.2171,680,660 - 1,822,610 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl171,681,324 - 1,829,376 (+)Ensembl
Rnor_6.017826,512 - 955,703 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl17833,509 - 955,615 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.017819,325 - 948,712 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4177,254,528 - 7,341,500 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1177,254,527 - 7,341,497 (+)NCBI
Celera17719,268 - 841,089 (-)NCBICelera
RH 3.4 Map175.6RGD
Cytogenetic Map17p14NCBI
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

Cellular Component
chromatin  (IDA,ISO)
cytosol  (IEA,ISO)
Fanconi anaemia nuclear complex  (IBA,IEA,ISO,ISS)

Molecular Function

References

References - curated
1. Barber LM, etal., Br J Haematol. 2003 Apr;121(1):57-62.
2. Carreau M, etal., Blood. 1998 Apr 15;91(8):2737-44.
3. Chen M, etal., Nat Genet 1996 Apr;12(4):448-51.
4. Ching Ying Wong J, etal., Mamm Genome 1997 Jul;8(7):522-5.
5. Couch FJ, etal., Cancer Res. 2005 Jan 15;65(2):383-6.
6. Faivre L, etal., Blood. 2000 Dec 15;96(13):4064-70.
7. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
8. Gavish H, etal., Hum Mol Genet 1993 Feb;2(2):123-6.
9. GOA data from the GO Consortium
10. Gush KA, etal., Blood. 2000 Jan 15;95(2):700-4.
11. Kim JH, etal., Mol Biol Rep. 2012 Mar;39(3):2385-94. doi: 10.1007/s11033-011-0989-6. Epub 2011 Jun 14.
12. Kwitek AE, etal., Genome Res. 2004 Apr;14(4):750-7
13. Li J, etal., Antioxid Redox Signal. 2012 Oct 15;17(8):1083-98. doi: 10.1089/ars.2011.4417. Epub 2012 Jun 25.
14. MGD data from the GO Consortium
15. Mi J and Kupfer GM, Blood 2005 Jan 15;105(2):759-66. Epub 2004 Jul 15.
16. NCBI rat LocusLink and RefSeq merged data July 26, 2002
17. OMIM Disease Annotation Pipeline
18. RGD automated data pipeline
19. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
20. RGD automated import pipeline for gene-chemical interactions
21. RGD comprehensive gene curation
22. Sejas DP, etal., J Immunol. 2007 Apr 15;178(8):5277-87.
23. Tentative Sequence Data IDs. TIGR Gene Index, Rat Data
24. Thompson ER, etal., PLoS Genet. 2012 Sep;8(9):e1002894. doi: 10.1371/journal.pgen.1002894. Epub 2012 Sep 27.
25. van der Heijden MS, etal., Clin Cancer Res. 2005 Oct 15;11(20):7508-15.
26. Whitney MA, etal., Blood 1996 Jul 1;88(1):49-58.
27. Wreesmann VB, etal., ORL J Otorhinolaryngol Relat Spec. 2007;69(4):218-25. Epub 2007 Apr 4.
28. Yates J, etal., Hum Mutat. 2006 Feb;27(2):214.
Additional References at PubMed
PMID:9596688   PMID:11493445   PMID:12477932   PMID:20347428   PMID:22266823   PMID:24483844  


Genomics

Comparative Map Data
Fancc
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2171,680,660 - 1,822,610 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl171,681,324 - 1,829,376 (+)Ensembl
Rnor_6.017826,512 - 955,703 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl17833,509 - 955,615 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.017819,325 - 948,712 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4177,254,528 - 7,341,500 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1177,254,527 - 7,341,497 (+)NCBI
Celera17719,268 - 841,089 (-)NCBICelera
RH 3.4 Map175.6RGD
Cytogenetic Map17p14NCBI
FANCC
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl995,099,054 - 95,426,796 (-)EnsemblGRCh38hg38GRCh38
GRCh38995,099,054 - 95,317,730 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37997,861,336 - 98,079,991 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36996,901,157 - 97,119,812 (-)NCBINCBI36hg18NCBI36
Build 34994,940,890 - 95,159,546NCBI
Celera968,302,367 - 68,521,048 (-)NCBI
Cytogenetic Map9q22.32NCBI
HuRef967,470,857 - 67,689,280 (-)NCBIHuRef
CHM1_1998,007,791 - 98,226,463 (-)NCBICHM1_1
Fancc
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391363,452,519 - 63,645,126 (-)NCBIGRCm39mm39
GRCm39 Ensembl1363,432,857 - 63,645,092 (-)Ensembl
GRCm381363,301,334 - 63,497,292 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1363,285,043 - 63,497,278 (-)EnsemblGRCm38mm10GRCm38
MGSCv371363,406,017 - 63,533,053 (-)NCBIGRCm37mm9NCBIm37
MGSCv361363,320,977 - 63,440,947 (-)NCBImm8
Celera1364,958,890 - 65,084,928 (-)NCBICelera
Cytogenetic Map13B3NCBI
cM Map1332.8NCBI
Fancc
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495542222,032,258 - 22,247,044 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495542222,031,825 - 22,246,478 (-)NCBIChiLan1.0ChiLan1.0
FANCC
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1994,327,355 - 94,544,772 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl994,329,971 - 94,477,198 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0966,201,581 - 66,418,229 (-)NCBIMhudiblu_PPA_v0panPan3
FANCC
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1171,388,931 - 71,678,019 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl171,487,601 - 71,678,506 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha172,151,677 - 72,440,952 (+)NCBI
ROS_Cfam_1.0171,693,614 - 71,983,350 (+)NCBI
UMICH_Zoey_3.1171,505,368 - 71,794,755 (+)NCBI
UNSW_CanFamBas_1.0171,269,071 - 71,558,824 (+)NCBI
UU_Cfam_GSD_1.0171,975,513 - 72,265,108 (+)NCBI
Fancc
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_0244049444,751,995 - 4,931,679 (-)NCBI
SpeTri2.0NW_0049366263,980,311 - 4,147,042 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
FANCC
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.11026,796,546 - 27,055,271 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21031,282,173 - 31,315,897 (+)NCBISscrofa10.2Sscrofa10.2susScr3
FANCC
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.112107,780,087 - 107,991,828 (+)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl12107,845,135 - 107,991,237 (+)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366603896,155,447 - 96,377,196 (+)NCBIVero_WHO_p1.0
Fancc
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462475316,566,864 - 16,811,438 (-)NCBIHetGla_female_1.0hetGla2

Position Markers
D17Got229  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2171,779,376 - 1,779,497 (-)MAPPERmRatBN7.2
Rnor_6.017857,487 - 857,607NCBIRnor6.0
Rnor_5.017850,440 - 850,560UniSTSRnor5.0
RGSC_v3.4177,317,343 - 7,317,463UniSTSRGSC3.4
Celera17743,288 - 743,408UniSTS
Cytogenetic Map17p14UniSTS
RH94652  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2171,803,299 - 1,803,455 (-)MAPPERmRatBN7.2
Rnor_6.017833,529 - 833,684NCBIRnor6.0
Rnor_5.017826,342 - 826,497UniSTSRnor5.0
RGSC_v3.4177,341,322 - 7,341,477UniSTSRGSC3.4
Celera17719,291 - 719,446UniSTS
RH 3.4 Map175.6UniSTS
Cytogenetic Map17p14UniSTS
RH141857  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2171,803,246 - 1,803,432 (-)MAPPERmRatBN7.2
Rnor_6.017833,552 - 833,737NCBIRnor6.0
Rnor_5.017826,365 - 826,550UniSTSRnor5.0
RGSC_v3.4177,341,269 - 7,341,454UniSTSRGSC3.4
Celera17719,314 - 719,499UniSTS
RH 3.4 Map1723.2UniSTS
Cytogenetic Map17p14UniSTS
Fanccrgdv551196202-C  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.017946,321 - 946,321 (-)RGDRnor6.0
Rnor_5.017939,418 - 939,418 (-)RGDRnor5.0
RGSC_v3.4177,228,496 - 7,228,496 (+)RGDRGSC3.4


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
9590316Scort21Serum corticosterone level QTL 214.750.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)17122871563Rat
10401807Kidm52Kidney mass QTL 52kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)17131701463Rat
70184BpQTLcluster14Blood pressure QTL cluster 143.38arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)17131990913Rat
631207Niddm41Non-insulin dependent diabetes mellitus QTL 41blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)17137830672Rat
1354658Spl8Serum phospholipid level QTL 83.8blood VLDL phospholipid amount (VT:0010507)blood very low density lipoprotein phospholipid level (CMO:0001571)17160781592Rat
1354581Bp247Blood pressure QTL 2474.5arterial blood pressure trait (VT:2000000)pulse pressure (CMO:0000292)17169599340Rat
1354662Rf49Renal function QTL 492.9blood creatinine amount (VT:0005328)plasma creatinine level (CMO:0000537)17169599340Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:98
Count of miRNA genes:82
Interacting mature miRNAs:92
Transcripts:ENSRNOT00000022884
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 4 11 4 9 4 14 22 28 2
Low 3 39 46 37 10 37 8 11 60 13 13 9 8
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_012557 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006253488 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006253489 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006253490 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006253491 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008771423 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039095340 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039095341 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_001841732 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_005495234 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_005495235 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_005495236 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AC134760 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC168147 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH474087 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000284 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  U73586 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000022884   ⟹   ENSRNOP00000022884
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl171,681,324 - 1,803,468 (+)Ensembl
Rnor_6.0 Ensembl17833,509 - 955,615 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000094085   ⟹   ENSRNOP00000092010
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl171,681,324 - 1,803,468 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000095403   ⟹   ENSRNOP00000084889
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl171,681,324 - 1,829,376 (+)Ensembl
RefSeq Acc Id: NM_012557   ⟹   NP_036689
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2171,681,361 - 1,803,478 (+)NCBI
Rnor_6.017833,506 - 955,615 (-)NCBI
Rnor_5.017819,325 - 948,712 (-)NCBI
RGSC_v3.4177,254,528 - 7,341,500 (+)RGD
Celera17719,268 - 841,089 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006253488   ⟹   XP_006253550
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2171,681,642 - 1,810,500 (+)NCBI
Rnor_6.017826,512 - 923,430 (-)NCBI
Rnor_5.017819,325 - 948,712 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006253489   ⟹   XP_006253551
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2171,680,663 - 1,810,500 (+)NCBI
Rnor_6.017826,512 - 923,430 (-)NCBI
Rnor_5.017819,325 - 948,712 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006253491   ⟹   XP_006253553
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2171,739,766 - 1,810,500 (+)NCBI
Rnor_6.017826,512 - 897,149 (-)NCBI
Rnor_5.017819,325 - 948,712 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008771423   ⟹   XP_008769645
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2171,681,110 - 1,810,500 (+)NCBI
Rnor_6.017826,512 - 955,703 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039095340   ⟹   XP_038951268
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2171,680,660 - 1,810,500 (+)NCBI
RefSeq Acc Id: XM_039095341   ⟹   XP_038951269
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2171,681,110 - 1,810,500 (+)NCBI
RefSeq Acc Id: XR_001841732
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2171,680,661 - 1,822,610 (+)NCBI
Rnor_6.017826,512 - 923,430 (-)NCBI
Sequence:
RefSeq Acc Id: XR_005495234
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2171,680,661 - 1,822,610 (+)NCBI
RefSeq Acc Id: XR_005495235
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2171,680,661 - 1,822,610 (+)NCBI
RefSeq Acc Id: XR_005495236
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2171,680,661 - 1,822,610 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_036689   ⟸   NM_012557
- UniProtKB: B4F762 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006253551   ⟸   XM_006253489
- Peptide Label: isoform X2
- UniProtKB: B4F762 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006253550   ⟸   XM_006253488
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_006253553   ⟸   XM_006253491
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_008769645   ⟸   XM_008771423
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: ENSRNOP00000022884   ⟸   ENSRNOT00000022884
RefSeq Acc Id: XP_038951268   ⟸   XM_039095340
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038951269   ⟸   XM_039095341
- Peptide Label: isoform X5
RefSeq Acc Id: ENSRNOP00000084889   ⟸   ENSRNOT00000095403
RefSeq Acc Id: ENSRNOP00000092010   ⟸   ENSRNOT00000094085

Transcriptome

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


Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN-Lx/CubMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BUF/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
DA/OlaHsd (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
F344/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FXLE16/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GH/OmrMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/FarMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GK/Ox (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
HXB10/IpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
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)
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
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)
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
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)
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
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)
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
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)
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: 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:2593 AgrOrtholog
Ensembl Genes ENSRNOG00000016889 Ensembl, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000022884 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000022884 UniProtKB/TrEMBL
InterPro FANCC UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:24361 UniProtKB/TrEMBL
NCBI Gene 24361 ENTREZGENE
PANTHER PTHR16798 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Fanconi_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Fancc PhenoGen
PIRSF FACC_protein UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PRINTS FANCONICGENE UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
TIGR TC235798
UniProt B4F762 ENTREZGENE, UniProtKB/TrEMBL
  FANCC_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2021-03-09 Fancc  FA complementation group C  LOC103694020  uncharacterized LOC103694020  Data Merged 737654 PROVISIONAL
2018-05-25 Fancc  FA complementation group C  Fancc  Fanconi anemia, complementation group C  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2014-08-25 LOC103694020  uncharacterized LOC103694020      Symbol and Name status set to provisional 70820 PROVISIONAL
2002-06-10 Fancc  Fanconi anemia group C      Symbol and Name status set to approved 70586 APPROVED