Ciita (class II, major histocompatibility complex, transactivator) - Rat Genome Database
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Gene: Ciita (class II, major histocompatibility complex, transactivator) Rattus norvegicus
Analyze
Symbol: Ciita
Name: class II, major histocompatibility complex, transactivator
RGD ID: 619813
Description: Predicted to have activating transcription factor binding activity; protein C-terminus binding activity; and transcription regulatory region sequence-specific DNA binding activity. Involved in several processes, including cellular response to electrical stimulus; cellular response to exogenous dsRNA; and regulation of macromolecule biosynthetic process. Localizes to cell surface. Used to study periapical periodontitis. Human ortholog(s) of this gene implicated in Addison's disease; MHC class II deficiency; autoimmune disease (multiple); and myocardial infarction. Orthologous to human CIITA (class II major histocompatibility complex transactivator); PARTICIPATES IN antigen processing and presentation pathway; influenza A pathway; primary immunodeficiency pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; acetamide; ammonium chloride.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: C2ta; class II transactivator; MHC class II transactivator; MHC class II transactivator type IV; Mhc2ta
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2105,139,947 - 5,187,493 (-)NCBI
Rnor_6.0 Ensembl105,213,350 - 5,260,608 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0105,212,621 - 5,260,641 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0104,036,437 - 4,083,966 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4105,087,174 - 5,133,418 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1105,087,173 - 5,133,418 (-)NCBI
Celera104,158,435 - 4,205,434 (-)NCBICelera
Cytogenetic Map10q11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
1. Akkad DA, etal., Int J Immunogenet. 2006 Feb;33(1):59-61.
2. Bontron S, etal., Hum Genet. 1997 Apr;99(4):541-6.
3. Cai G, etal., J Mol Cell Cardiol. 2005 Apr;38(4):593-605.
4. Frank MG, etal., Neurobiol Aging. 2006 May;27(5):717-22.
5. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
6. GOA data from the GO Consortium
7. Harnesk K, etal., J Immunol. 2008 Mar 1;180(5):3289-96.
8. Kim TW, etal., J Korean Med Sci. 2006 Oct;21(5):877-82.
9. Koizumi K, etal., Ann Rheum Dis. 2005 Jun;64(6):947-50.
10. Lee PT, etal., Eur J Immunol 2001 Aug;31(8):2347-56.
11. Lee YL, etal., J Endod. 2010 Jun;36(6):1021-5. doi: 10.1016/j.joen.2010.03.009. Epub 2010 Apr 21.
12. Lindholm E, etal., PLoS One. 2006 Dec 20;1:e64.
13. Linga-Reddy MV, etal., Tissue Antigens. 2007 Nov;70(5):412-4. Epub 2007 Aug 17.
14. Martinez A, etal., Ann Rheum Dis. 2010 Jan;69(1):309-11. Epub .
15. MGD data from the GO Consortium
16. Mori-Aoki A, etal., Biochem Biophys Res Commun 2000 Nov 11;278(1):58-62.
17. NCBI rat LocusLink and RefSeq merged data July 26, 2002
18. O'Doherty C, etal., Tissue Antigens. 2007 Sep;70(3):247-51.
19. Okamoto H, etal., Ann Rheum Dis. 2007 Sep;66(9):1263-4.
20. Pipeline to import KEGG annotations from KEGG into RGD
21. Repique CJ, etal., Scand J Immunol. 2003 Jul;58(1):15-22.
22. RGD automated data pipeline
23. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
24. RGD automated import pipeline for gene-chemical interactions
25. RGD comprehensive gene curation
26. Sims TN, etal., Transplantation. 1997 Dec 27;64(12):1657-64.
27. Skinningsrud B, etal., J Clin Endocrinol Metab. 2008 Sep;93(9):3310-7. Epub 2008 Jul 1.
28. Suzuki K, etal., Proc Natl Acad Sci U S A. 1999 Mar 2;96(5):2285-90.
29. Swanberg M, etal., Nat Genet 2005 May;37(5):486-94. Epub 2005 Apr 10.
30. Takeuchi O, etal., J Am Soc Nephrol. 2003 Nov;14(11):2823-32.
31. Wiszniewski W, etal., J Immunol. 2001 Aug 1;167(3):1787-94.
32. Yang Y, etal., Biosci Trends. 2013 Feb;7(1):50-5.
33. Zuvich RL, etal., Hum Mol Genet. 2011 Sep 1;20(17):3517-24. Epub 2011 Jun 8.
Additional References at PubMed
PMID:107465   PMID:9171108   PMID:12748124   PMID:15100295   PMID:16280321   PMID:16600381   PMID:17493635   PMID:19041327   PMID:20639463   PMID:23007646   PMID:28736195  


Genomics

Candidate Gene Status
Ciita is a candidate Gene for QTL Neuinf3
Comparative Map Data
Ciita
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2105,139,947 - 5,187,493 (-)NCBI
Rnor_6.0 Ensembl105,213,350 - 5,260,608 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0105,212,621 - 5,260,641 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0104,036,437 - 4,083,966 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4105,087,174 - 5,133,418 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1105,087,173 - 5,133,418 (-)NCBI
Celera104,158,435 - 4,205,434 (-)NCBICelera
Cytogenetic Map10q11NCBI
CIITA
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1610,866,222 - 10,943,021 (+)EnsemblGRCh38hg38GRCh38
GRCh381610,866,208 - 10,941,562 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371610,971,055 - 11,030,251 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361610,878,556 - 10,926,341 (+)NCBINCBI36hg18NCBI36
Build 341610,878,539 - 10,933,676NCBI
Celera1611,140,481 - 11,188,432 (+)NCBI
Cytogenetic Map16p13.13NCBI
HuRef1610,888,898 - 10,936,424 (+)NCBIHuRef
CHM1_11610,970,985 - 11,018,760 (+)NCBICHM1_1
Ciita
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391610,297,877 - 10,348,928 (+)NCBIGRCm39mm39
GRCm39 Ensembl1610,297,923 - 10,346,282 (+)Ensembl
GRCm381610,480,014 - 10,531,064 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1610,480,059 - 10,528,418 (+)EnsemblGRCm38mm10GRCm38
MGSCv371610,488,372 - 10,527,657 (+)NCBIGRCm37mm9NCBIm37
MGSCv361610,401,857 - 10,441,142 (+)NCBImm8
Celera1611,120,578 - 11,160,248 (+)NCBICelera
Cytogenetic Map16A1NCBI
Ciita
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554427,603,893 - 7,647,624 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554427,600,903 - 7,647,619 (-)NCBIChiLan1.0ChiLan1.0
CIITA
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11611,041,434 - 11,090,485 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1611,041,434 - 11,090,485 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0169,819,440 - 9,885,379 (+)NCBIMhudiblu_PPA_v0panPan3
CIITA
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl631,774,609 - 31,836,820 (-)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.1631,774,486 - 31,837,025 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Ciita
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_0049365309,033,510 - 9,073,341 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CIITA
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl332,172,214 - 32,230,780 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1332,171,706 - 32,230,775 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2333,109,119 - 33,117,697 (-)NCBISscrofa10.2Sscrofa10.2susScr3
CIITA
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1510,341,690 - 10,401,988 (+)NCBI
ChlSab1.1 Ensembl510,372,344 - 10,400,451 (+)Ensembl
Ciita
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248248,099,877 - 8,156,661 (+)NCBI

Position Markers
D10Mgh25  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0105,217,199 - 5,217,339NCBIRnor6.0
Rnor_5.0104,040,517 - 4,040,657UniSTSRnor5.0
RGSC_v3.4105,090,008 - 5,090,149RGDRGSC3.4
RGSC_v3.4105,090,009 - 5,090,149UniSTSRGSC3.4
RGSC_v3.1105,090,008 - 5,090,149RGD
Celera104,162,284 - 4,162,424UniSTS
Cytogenetic Map10q11UniSTS
D10Got7  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0105,255,322 - 5,255,555NCBIRnor6.0
Rnor_5.0104,078,682 - 4,078,915UniSTSRnor5.0
RGSC_v3.4105,128,131 - 5,128,365RGDRGSC3.4
RGSC_v3.4105,128,132 - 5,128,365UniSTSRGSC3.4
RGSC_v3.1105,128,131 - 5,128,365RGD
Celera104,200,148 - 4,200,381UniSTS
RH 2.0 Map100.0RGD
Cytogenetic Map10q11UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
7387235Uae41Urinary albumin excretion QTL 415.260.1874urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)10129592136Rat
2293680Bss40Bone structure and strength QTL 405.660.0001femur strength trait (VT:0010010)femur total energy absorbed before break (CMO:0001677)10135538813Rat
634327Hc4Hypercalciuria QTL 42.4urine calcium amount (VT:0002985)urine calcium excretion rate (CMO:0000763)10138594330Rat
7411611Foco17Food consumption QTL 1718.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)10142669970Rat
10401803Kidm50Kidney mass QTL 50kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)10144902893Rat
631554Bp133Blood pressure QTL 1330.005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1076442166221621Rat
1549898Neuinf3Neuroinflammation QTL 326.4nervous system integrity trait (VT:0010566)MHC Class II RT1A-positive spinal cord ventral horn area to total spinal cord ventral horn area ratio (CMO:0001980)1028476255460218Rat
1576304Schws7Schwannoma susceptibility QTL 70.0115nervous system integrity trait (VT:0010566)percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)10483563820170031Rat
631828Alc5Alcohol consumption QTL 52.4consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)10521719917555534Rat
737820Alc9Alcohol consumption QTL 92.2consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)10521719919591669Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:245
Count of miRNA genes:155
Interacting mature miRNAs:164
Transcripts:ENSRNOT00000003572
Prediction methods:Microtar, 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 2 6 17 2
Low 1 13 26 17 2 17 6 9 23 12 9 6
Below cutoff 20 17 16 16 2 2 50 12 29 2

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000003572   ⟹   ENSRNOP00000003572
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl105,213,350 - 5,260,608 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000085310   ⟹   ENSRNOP00000075087
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl105,213,350 - 5,253,336 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000085479   ⟹   ENSRNOP00000069553
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl105,213,350 - 5,251,809 (-)Ensembl
RefSeq Acc Id: NM_001270803   ⟹   NP_001257732
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2105,140,178 - 5,180,166 (-)NCBI
Rnor_6.0105,213,350 - 5,253,336 (-)NCBI
Rnor_5.0104,036,437 - 4,083,966 (-)NCBI
Celera104,158,435 - 4,198,162 (-)NCBI
Sequence:
RefSeq Acc Id: NM_001270804   ⟹   NP_001257733
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2105,140,178 - 5,178,639 (-)NCBI
Rnor_6.0105,213,350 - 5,251,809 (-)NCBI
Rnor_5.0104,036,437 - 4,083,966 (-)NCBI
Celera104,158,435 - 4,196,635 (-)NCBI
Sequence:
RefSeq Acc Id: NM_053529   ⟹   NP_445981
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2105,140,178 - 5,187,440 (-)NCBI
Rnor_6.0105,213,350 - 5,260,608 (-)NCBI
Rnor_5.0104,036,437 - 4,083,966 (-)NCBI
RGSC_v3.4105,087,174 - 5,133,418 (-)RGD
Celera104,158,435 - 4,205,434 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006245738   ⟹   XP_006245800
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2105,139,947 - 5,187,493 (-)NCBI
Rnor_6.0105,212,621 - 5,260,641 (-)NCBI
Rnor_5.0104,036,437 - 4,083,966 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008767501   ⟹   XP_008765723
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0105,212,621 - 5,253,184 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039087000   ⟹   XP_038942928
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2105,139,947 - 5,164,416 (-)NCBI
RefSeq Acc Id: XR_005489960
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2105,139,947 - 5,187,493 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_445981   ⟸   NM_053529
- Peptide Label: isoform 1
- UniProtKB: G3V6C0 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: NP_001257732   ⟸   NM_001270803
- Peptide Label: isoform 2
- UniProtKB: A0A0G2K9Q5 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: NP_001257733   ⟸   NM_001270804
- Peptide Label: isoform 3
- UniProtKB: A0A0G2JVN3 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006245800   ⟸   XM_006245738
- Peptide Label: isoform X1
- UniProtKB: G3V6C0 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008765723   ⟸   XM_008767501
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: ENSRNOP00000075087   ⟸   ENSRNOT00000085310
RefSeq Acc Id: ENSRNOP00000069553   ⟸   ENSRNOT00000085479
RefSeq Acc Id: ENSRNOP00000003572   ⟸   ENSRNOT00000003572
RefSeq Acc Id: XP_038942928   ⟸   XM_039087000
- Peptide Label: isoform X2
Protein Domains
NACHT

Transcriptome

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

Promoters
RGD ID:13696944
Promoter ID:EPDNEW_R7469
Type:single initiation site
Name:Ciita_1
Description:class II, major histocompatibility complex, transactivator
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_6.0105,260,589 - 5,260,649EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
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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
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
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
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
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
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 (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
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Damaging Variants


Assembly: Rnor_5.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
10 4063295 4063296 C T snv SBH/Ygl (KNAW), SBH/Ygl (MCW)


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
10 5239977 5239978 C T snv SBH/Ygl (RGD), SBH/Ygl (MCW)


Assembly: RGSC_v3.4

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
10 5112787 5112788 C T snv SBH/Ygl (ICL)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:619813 AgrOrtholog
Ensembl Genes ENSRNOG00000002659 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000003572 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000069553 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000075087 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000003572 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000085310 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000085479 ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH 3.80.10.10 UniProtKB/TrEMBL
InterPro Leu-rich_rpt UniProtKB/TrEMBL
  LRR_dom_sf UniProtKB/TrEMBL
  MHC_II_transact UniProtKB/TrEMBL
  NACHT_NTPase UniProtKB/TrEMBL
  P-loop_NTPase UniProtKB/TrEMBL
KEGG Report rno:85483 UniProtKB/TrEMBL
NCBI Gene 85483 ENTREZGENE
Pfam LRR_6 UniProtKB/TrEMBL
  NACHT UniProtKB/TrEMBL
PhenoGen Ciita PhenoGen
PRINTS MHCIIACTVATR UniProtKB/TrEMBL
PROSITE NACHT UniProtKB/TrEMBL
Superfamily-SCOP SSF52540 UniProtKB/TrEMBL
UniProt A0A0G2JVN3 ENTREZGENE, UniProtKB/TrEMBL
  A0A0G2K9Q5 ENTREZGENE, UniProtKB/TrEMBL
  G3V6C0 ENTREZGENE, UniProtKB/TrEMBL
  Q9GJD8_RAT UniProtKB/TrEMBL
  Q9GJD9_RAT UniProtKB/TrEMBL
  Q9GJE0_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-04-07 Ciita  class II transactivator  C2ta  class II, major histocompatibility complex, transactivator  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-11-17 C2ta  class II, major histocompatibility complex, transactivator  Mhc2ta  MHC class II transactivator  Symbol and Name updated 1299863 APPROVED
2005-01-20 Mhc2ta  MHC class II transactivator  C2ta    Symbol updated 1299863 APPROVED
2002-08-07 C2ta  MHC class II transactivator      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_process may play a role in the inflammatory response 1358146
gene_regulation Following ventral root avulsion nerve injury, transcripts were upregulated more in DA rat than in PVG rats 1358146