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 enable DNA-binding transcription factor binding activity and transcription cis-regulatory region binding activity. Involved in several processes, including cellular response to electrical stimulus; cellular response to exogenous dsRNA; and regulation of transcription by RNA polymerase II. Located in 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 17beta-estradiol; 17beta-estradiol 3-benzoate; 2,3,7,8-tetrachlorodibenzodioxine.
Type: protein-coding
RefSeq Status: VALIDATED
Previously 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 Orthologs
More Info more info ...
Candidate Gene For: Neuinf3
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8105,646,854 - 5,694,393 (-)NCBIGRCr8
mRatBN7.2105,139,947 - 5,187,493 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl105,140,178 - 5,187,440 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx109,836,592 - 9,883,847 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0109,357,706 - 9,404,970 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0104,995,977 - 5,043,240 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0105,212,621 - 5,260,641 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl105,213,350 - 5,260,608 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0104,036,437 - 4,083,966 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4105,087,174 - 5,133,418 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
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


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
17beta-estradiol  (EXP)
17beta-estradiol 3-benzoate  (EXP)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2-(3,4-dimethoxyphenyl)-5-\{[2-(3,4-dimethoxyphenyl)ethyl](methyl)amino\}-2-(propan-2-yl)pentanenitrile  (ISO)
4,4'-sulfonyldiphenol  (ISO)
4-hydroxyphenyl retinamide  (ISO)
5-aza-2'-deoxycytidine  (ISO)
5-azacytidine  (ISO)
9-cis-retinoic acid  (ISO)
acetamide  (EXP)
aflatoxin B1  (ISO)
Aflatoxin B2 alpha  (ISO)
all-trans-retinoic acid  (ISO)
allethrin  (EXP)
alpha-Zearalanol  (EXP)
ammonium chloride  (EXP)
amphetamine  (EXP)
antirheumatic drug  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenous acid  (ISO)
atrazine  (EXP)
benzo[a]pyrene  (ISO)
bis(2-chloroethyl) sulfide  (ISO)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
buta-1,3-diene  (ISO)
butanal  (ISO)
capsaicin  (ISO)
carbon nanotube  (ISO)
chloroprene  (ISO)
copper(II) chloride  (ISO)
Cuprizon  (EXP)
cyhalothrin  (EXP)
cypermethrin  (EXP)
diarsenic trioxide  (ISO)
dichloromethane  (EXP)
dimethyl fumarate  (ISO)
dimethylarsinic acid  (ISO)
ethylbenzene  (EXP)
fenvalerate  (EXP)
folic acid  (ISO)
gentamycin  (EXP)
lipopolysaccharide  (ISO)
manganese(II) chloride  (EXP)
melphalan  (ISO)
methoxychlor  (EXP)
methyl methanesulfonate  (ISO)
methylarsonic acid  (ISO)
mono(2-ethylhexyl) phthalate  (ISO)
nevirapine  (ISO)
nickel atom  (ISO)
Nor-9-carboxy-delta9-THC  (ISO)
ozone  (ISO)
paracetamol  (EXP)
paraquat  (EXP)
perfluorononanoic acid  (ISO)
perfluorooctane-1-sulfonic acid  (ISO)
perfluorooctanoic acid  (ISO)
pirinixic acid  (ISO)
pregnenolone 16alpha-carbonitrile  (ISO)
pyrethrins  (EXP)
ritonavir  (ISO)
S-(1,2-dichlorovinyl)-L-cysteine  (ISO)
simvastatin  (ISO)
sodium arsenate  (ISO)
sodium arsenite  (ISO)
sodium dichromate  (ISO)
T-2 toxin  (ISO)
tamibarotene  (ISO)
testosterone  (EXP)
thioacetamide  (EXP)
titanium dioxide  (ISO)
trichloroethene  (EXP)
triptonide  (ISO)
tungsten  (ISO)
valproic acid  (ISO)
verapamil  (ISO)
zinc atom  (ISO)
zinc(0)  (ISO)
zoledronic acid  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
cell surface  (IDA)
cytosol  (IEA,ISO)
nucleoplasm  (ISO)
PML body  (ISO)

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. Promoter polymorphism rs3087456 in the MHC class II transactivator gene is not associated with susceptibility for selected autoimmune diseases in German patient groups. Akkad DA, etal., Int J Immunogenet. 2006 Feb;33(1):59-61.
2. Two novel mutations in the MHC class II transactivator CIITA in a second patient from MHC class II deficiency complementation group A. Bontron S, etal., Hum Genet. 1997 Apr;99(4):541-6.
3. Successful treatment of experimental autoimmune myocarditis by adenovirus-mediated gene transfer of antisense CIITA. Cai G, etal., J Mol Cell Cardiol. 2005 Apr;38(4):593-605.
4. mRNA up-regulation of MHC II and pivotal pro-inflammatory genes in normal brain aging. Frank MG, etal., Neurobiol Aging. 2006 May;27(5):717-22.
5. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
6. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
7. Vra4 congenic rats with allelic differences in the class II transactivator gene display altered susceptibility to experimental autoimmune encephalomyelitis. Harnesk K, etal., J Immunol. 2008 Mar 1;180(5):3289-96.
8. Overexpression of CIITA in T cells aggravates Th2-mediated colitis in mice. Kim TW, etal., J Korean Med Sci. 2006 Oct;21(5):877-82.
9. Single nucleotide polymorphisms in the gene encoding the major histocompatibility complex class II transactivator (CIITA) in systemic lupus erythematosus. Koizumi K, etal., Ann Rheum Dis. 2005 Jun;64(6):947-50.
10. Failure of MHC class II expression in neonatal alveolar macrophages: potential role of class II transactivator. Lee PT, etal., Eur J Immunol 2001 Aug;31(8):2347-56.
11. Major histocompatibility complex class II transactivator inhibits cysteine-rich 61 expression in osteoblastic cells and its implication in the pathogenesis of periapical lesions. Lee YL, etal., J Endod. 2010 Jun;36(6):1021-5. doi: 10.1016/j.joen.2010.03.009. Epub 2010 Apr 21.
12. Polymorphism in the MHC2TA gene is associated with features of the metabolic syndrome and cardiovascular mortality. Lindholm E, etal., PLoS One. 2006 Dec 20;1:e64.
13. A polymorphic variant in the MHC2TA gene is not associated with systemic lupus erythematosus. Linga-Reddy MV, etal., Tissue Antigens. 2007 Nov;70(5):412-4. Epub 2007 Aug 17.
14. Chromosomal region 16p13: further evidence of increased predisposition to immune diseases. Martinez A, etal., Ann Rheum Dis. 2010 Jan;69(1):309-11. Epub .
15. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
16. Class II transactivator suppresses transcription of thyroid-specific genes. Mori-Aoki A, etal., Biochem Biophys Res Commun 2000 Nov 11;278(1):58-62.
17. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
18. The MHC2TA-168A/G and +1614G/C polymorphisms and risk for multiple sclerosis or chronic inflammatory arthropathies. O'Doherty C, etal., Tissue Antigens. 2007 Sep;70(3):247-51.
19. Protective effect of A at position - 168 in the type III promoter of the MHCIITA gene in systemic lupus erythematosus. Okamoto H, etal., Ann Rheum Dis. 2007 Sep;66(9):1263-4.
20. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
21. Susceptibility of mice deficient in the MHC class II transactivator to infection with Mycobacterium tuberculosis. Repique CJ, etal., Scand J Immunol. 2003 Jul;58(1):15-22.
22. GOA pipeline RGD automated data pipeline
23. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
24. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
25. Comprehensive gene review and curation RGD comprehensive gene curation
26. In vivo class II transactivator expression in mice is induced by a non-interferon-gamma mechanism in response to local injury. Sims TN, etal., Transplantation. 1997 Dec 27;64(12):1657-64.
27. Polymorphisms in CLEC16A and CIITA at 16p13 are associated with primary adrenal insufficiency. Skinningsrud B, etal., J Clin Endocrinol Metab. 2008 Sep;93(9):3310-7. Epub 2008 Jul 1.
28. Activation of target-tissue immune-recognition molecules by double-stranded polynucleotides. Suzuki K, etal., Proc Natl Acad Sci U S A. 1999 Mar 2;96(5):2285-90.
29. MHC2TA is associated with differential MHC molecule expression and susceptibility to rheumatoid arthritis, multiple sclerosis and myocardial infarction. Swanberg M, etal., Nat Genet 2005 May;37(5):486-94. Epub 2005 Apr 10.
30. Differential usage of class II transactivator promoters PI and PIV during inflammation and injury in kidney. Takeuchi O, etal., J Am Soc Nephrol. 2003 Nov;14(11):2823-32.
31. Mutation in the class II trans-activator leading to a mild immunodeficiency. Wiszniewski W, etal., J Immunol. 2001 Aug 1;167(3):1787-94.
32. Downregulating immunogenicity of Schwann cells via inhibiting a potential target of class II transactivator (CIITA) gene. Yang Y, etal., Biosci Trends. 2013 Feb;7(1):50-5.
33. Interrogating the complex role of chromosome 16p13.13 in multiple sclerosis susceptibility: independent genetic signals in the CIITA-CLEC16A-SOCS1 gene complex. 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   PMID:32770803  
PMID:33223048   PMID:38115045   PMID:38728204  


Genomics

Comparative Map Data
Ciita
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8105,646,854 - 5,694,393 (-)NCBIGRCr8
mRatBN7.2105,139,947 - 5,187,493 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl105,140,178 - 5,187,440 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx109,836,592 - 9,883,847 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0109,357,706 - 9,404,970 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0104,995,977 - 5,043,240 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0105,212,621 - 5,260,641 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl105,213,350 - 5,260,608 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0104,036,437 - 4,083,966 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4105,087,174 - 5,133,418 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
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
GRCh381610,866,206 - 10,943,021 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1610,866,222 - 10,943,021 (+)EnsemblGRCh38hg38GRCh38
GRCh371610,971,055 - 11,030,251 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361610,878,556 - 10,926,341 (+)NCBINCBI36Build 36hg18NCBI36
Build 341610,878,539 - 10,933,676NCBI
Celera1611,140,481 - 11,188,432 (+)NCBICelera
Cytogenetic Map16p13.13NCBI
HuRef1610,888,898 - 10,936,424 (+)NCBIHuRef
CHM1_11610,970,985 - 11,018,760 (+)NCBICHM1_1
T2T-CHM13v2.01610,902,173 - 10,978,992 (+)NCBIT2T-CHM13v2.0
Ciita
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391610,297,877 - 10,348,928 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1610,297,923 - 10,346,282 (+)EnsemblGRCm39 Ensembl
GRCm381610,480,014 - 10,531,064 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1610,480,059 - 10,528,418 (+)EnsemblGRCm38mm10GRCm38
MGSCv371610,488,372 - 10,527,657 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361610,401,857 - 10,441,142 (+)NCBIMGSCv36mm8
Celera1611,120,578 - 11,160,248 (+)NCBICelera
Cytogenetic Map16A1NCBI
cM Map165.65NCBI
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
NHGRI_mPanPan1-v21811,426,662 - 11,492,167 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11615,201,913 - 15,267,425 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0169,819,440 - 9,885,379 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11611,041,434 - 11,090,485 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1611,041,434 - 11,090,485 (+)Ensemblpanpan1.1panPan2
CIITA
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1631,774,486 - 31,837,025 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl631,774,609 - 31,836,820 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha633,156,962 - 33,219,510 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0631,956,967 - 32,019,399 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl631,956,967 - 31,996,000 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1631,770,183 - 31,832,926 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0631,644,456 - 31,706,901 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0632,068,973 - 32,131,721 (-)NCBIUU_Cfam_GSD_1.0
Ciita
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024409344111,196,647 - 111,229,034 (+)NCBIHiC_Itri_2
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 - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1510,341,690 - 10,401,988 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl510,372,344 - 10,400,451 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366606819,764,657 - 19,814,384 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Ciita
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248248,116,537 - 8,153,482 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248248,099,877 - 8,156,661 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Ciita
293 total Variants
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.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
634329Pia15Pristane induced arthritis QTL 153.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)10124158324Rat
2293680Bss40Bone structure and strength QTL 405.660.0001femur strength trait (VT:0010010)femur total energy absorbed before break (CMO:0001677)10135225947Rat
7387235Uae41Urinary albumin excretion QTL 415.260.1874urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)10129497586Rat
10401803Kidm50Kidney mass QTL 50kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)1041834445418344Rat
737820Alc9Alcohol consumption QTL 92.2consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)10514402719233348Rat
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)10476552719816042Rat
7411611Foco17Food consumption QTL 1718.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)10142315980Rat
631554Bp133Blood pressure QTL 1330.005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1074336463851208Rat
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)1034063205387112Rat
631828Alc5Alcohol consumption QTL 52.4consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)10514402717245662Rat
70223Bp57Blood pressure QTL 575arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)10180676123Rat
634327Hc4Hypercalciuria QTL 42.4urine calcium amount (VT:0002985)urine calcium excretion rate (CMO:0000763)10138328221Rat

Markers in Region
D10Mgh25  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2105,144,027 - 5,144,168 (+)MAPPERmRatBN7.2
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
mRatBN7.2105,182,151 - 5,182,387 (+)MAPPERmRatBN7.2
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


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
nervous system
renal system
reproductive system
respiratory system
9 11 39 89 83 82 51 25 51 6 200 87 69 45 60 31

Sequence


Ensembl Acc Id: ENSRNOT00000003572   ⟹   ENSRNOP00000003572
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl105,140,178 - 5,187,440 (-)Ensembl
Rnor_6.0 Ensembl105,213,350 - 5,260,608 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000085310   ⟹   ENSRNOP00000075087
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl105,140,178 - 5,180,166 (-)Ensembl
Rnor_6.0 Ensembl105,213,350 - 5,253,336 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000085479   ⟹   ENSRNOP00000069553
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl105,140,178 - 5,168,808 (-)Ensembl
Rnor_6.0 Ensembl105,213,350 - 5,251,809 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000095982   ⟹   ENSRNOP00000076804
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl105,140,178 - 5,168,808 (-)Ensembl
RefSeq Acc Id: NM_001270803   ⟹   NP_001257732
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8105,647,085 - 5,687,070 (-)NCBI
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
GRCr8105,647,085 - 5,685,543 (-)NCBI
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
GRCr8105,647,085 - 5,694,342 (-)NCBI
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
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8105,646,854 - 5,694,393 (-)NCBI
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_039087000   ⟹   XP_038942928
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8105,646,854 - 5,671,320 (-)NCBI
mRatBN7.2105,139,947 - 5,164,416 (-)NCBI
RefSeq Acc Id: NP_445981   ⟸   NM_053529
- Peptide Label: isoform 1
- UniProtKB: A6K4J3 (UniProtKB/TrEMBL),   Q9GJE0 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: NP_001257732   ⟸   NM_001270803
- Peptide Label: isoform 2
- UniProtKB: A0A0G2K9Q5 (UniProtKB/TrEMBL),   A6K4J5 (UniProtKB/TrEMBL),   Q9GJD9 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: NP_001257733   ⟸   NM_001270804
- Peptide Label: isoform 3
- UniProtKB: A6K4J8 (UniProtKB/TrEMBL),   Q9GJD8 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006245800   ⟸   XM_006245738
- Peptide Label: isoform X1
- UniProtKB: A6K4J3 (UniProtKB/TrEMBL),   Q9GJE0 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000075087   ⟸   ENSRNOT00000085310
Ensembl Acc Id: ENSRNOP00000069553   ⟸   ENSRNOT00000085479
Ensembl Acc Id: ENSRNOP00000003572   ⟸   ENSRNOT00000003572
RefSeq Acc Id: XP_038942928   ⟸   XM_039087000
- Peptide Label: isoform X2
- UniProtKB: Q9GJD8 (UniProtKB/TrEMBL)
Ensembl Acc Id: ENSRNOP00000076804   ⟸   ENSRNOT00000095982
Protein Domains
NACHT

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-G3V6C0-F1-model_v2 AlphaFold G3V6C0 1-1153 view protein structure

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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:619813 AgrOrtholog
BioCyc Gene G2FUF-26135 BioCyc
Ensembl Genes ENSRNOG00000002659 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000003572.4 UniProtKB/TrEMBL
  ENSRNOT00000085310.2 UniProtKB/TrEMBL
  ENSRNOT00000085479.2 UniProtKB/TrEMBL
  ENSRNOT00000095982.1 UniProtKB/TrEMBL
Gene3D-CATH 3.40.50.300 UniProtKB/TrEMBL
  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
PANTHER MHC CLASS II TRANSACTIVATOR UniProtKB/TrEMBL
  MHC CLASS II TRANSACTIVATOR UniProtKB/TrEMBL
Pfam LRR_6 UniProtKB/TrEMBL
  NACHT UniProtKB/TrEMBL
PhenoGen Ciita PhenoGen
PRINTS MHCIIACTVATR UniProtKB/TrEMBL
PROSITE NACHT UniProtKB/TrEMBL
RatGTEx ENSRNOG00000002659 RatGTEx
SMART LRR_RI UniProtKB/TrEMBL
Superfamily-SCOP RNI-like UniProtKB/TrEMBL
  SSF52540 UniProtKB/TrEMBL
UniProt A0A0G2JVN3_RAT UniProtKB/TrEMBL
  A0A0G2K9Q5 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I5ZK58_RAT UniProtKB/TrEMBL
  A6K4J3 ENTREZGENE, UniProtKB/TrEMBL
  A6K4J5 ENTREZGENE, UniProtKB/TrEMBL
  A6K4J8 ENTREZGENE, UniProtKB/TrEMBL
  G3V6C0_RAT UniProtKB/TrEMBL
  Q9GJD8 ENTREZGENE, UniProtKB/TrEMBL
  Q9GJD9 ENTREZGENE, UniProtKB/TrEMBL
  Q9GJE0 ENTREZGENE, 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