Themis (thymocyte selection associated) - Rat Genome Database

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Gene: Themis (thymocyte selection associated) Rattus norvegicus
Analyze
Symbol: Themis
Name: thymocyte selection associated
RGD ID: 1560849
Description: Predicted to be involved in T cell receptor signaling pathway; negative T cell selection; and positive T cell selection. Predicted to be located in cell-cell junction. Predicted to be part of COP9 signalosome. Predicted to be active in cytoplasm and nucleus. Used to study inflammatory bowel disease. Orthologous to human THEMIS (thymocyte selection associated); INTERACTS WITH 1,2-dichloroethane (ortholog); 2,4-dibromophenyl 2,4,5-tribromophenyl ether (ortholog); 3,3',4,4'-tetrachlorobiphenyl (ortholog).
Type: protein-coding
RefSeq Status: MODEL
Previously known as: LOC498985; RGD1560849; similar to RIKEN cDNA E430004N04 gene
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Allele / Splice: Themism1Adej  
Genetic Models: BN-Themism1Adej
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2116,433,906 - 16,623,889 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl116,432,631 - 16,664,329 (-)EnsemblmRatBN7.2 Ensembl
Rnor_6.0117,152,973 - 17,378,225 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl117,171,631 - 17,378,047 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0118,308,043 - 18,532,366 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4117,032,677 - 17,226,924 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera114,851,097 - 15,078,338 (-)NCBICelera
Cytogenetic Map1p12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
cell-cell junction  (ISO)
COP9 signalosome  (ISO)
cytoplasm  (IBA,ISO)
nucleus  (IBA,ISO)

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. A spontaneous mutation of the rat Themis gene leads to impaired function of regulatory T cells linked to inflammatory bowel disease. Chabod M, etal., PLoS Genet. 2012 Jan;8(1):e1002461. doi: 10.1371/journal.pgen.1002461. Epub 2012 Jan 19.
2. 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.
3. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
4. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:19597497   PMID:19597498   PMID:19597499   PMID:19805304   PMID:20203423   PMID:22561606   PMID:23793062  


Genomics

Comparative Map Data
Themis
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2116,433,906 - 16,623,889 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl116,432,631 - 16,664,329 (-)EnsemblmRatBN7.2 Ensembl
Rnor_6.0117,152,973 - 17,378,225 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl117,171,631 - 17,378,047 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0118,308,043 - 18,532,366 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4117,032,677 - 17,226,924 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera114,851,097 - 15,078,338 (-)NCBICelera
Cytogenetic Map1p12NCBI
THEMIS
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh386127,696,628 - 127,918,595 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl6127,708,072 - 127,918,631 (-)EnsemblGRCh38hg38GRCh38
GRCh376128,029,339 - 128,239,740 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 366128,071,038 - 128,281,435 (-)NCBINCBI36Build 36hg18NCBI36
Celera6128,771,575 - 128,982,019 (-)NCBICelera
Cytogenetic Map6q22.33NCBI
HuRef6125,605,605 - 125,816,711 (-)NCBIHuRef
CHM1_16128,293,828 - 128,504,020 (-)NCBICHM1_1
T2T-CHM13v2.06128,897,128 - 129,107,550 (-)NCBIT2T-CHM13v2.0
Themis
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391028,544,356 - 28,759,816 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1028,544,356 - 28,759,814 (+)EnsemblGRCm39 Ensembl
GRCm381028,668,360 - 28,883,820 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1028,668,360 - 28,883,818 (+)EnsemblGRCm38mm10GRCm38
MGSCv371028,388,201 - 28,602,555 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361028,357,811 - 28,572,165 (+)NCBIMGSCv36mm8
Celera1029,586,196 - 29,816,300 (+)NCBICelera
Cytogenetic Map10A4NCBI
Themis
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_0049554368,743,835 - 8,909,040 (-)NCBIChiLan1.0ChiLan1.0
THEMIS
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.16129,601,170 - 129,814,542 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl6129,601,176 - 129,797,112 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v06125,489,491 - 125,685,995 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
THEMIS
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1166,363,172 - 66,540,272 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl166,363,125 - 66,540,327 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha167,190,331 - 67,279,926 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0166,571,969 - 66,748,404 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl166,571,954 - 66,748,440 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1166,494,735 - 66,676,345 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0166,282,091 - 66,458,649 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0166,921,859 - 67,104,609 (-)NCBIUU_Cfam_GSD_1.0
Themis
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404946116,589,828 - 116,679,894 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049366391,739,380 - 1,915,560 (+)EnsemblSpeTri2.0
SpeTri2.0NW_0049366391,739,380 - 1,915,545 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
THEMIS
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl135,333,465 - 35,519,870 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1135,333,210 - 35,530,710 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2138,931,867 - 38,999,233 (+)NCBISscrofa10.2Sscrofa10.2susScr3
THEMIS
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11345,665,494 - 45,886,672 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1345,682,663 - 45,884,856 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604017,911,702 - 18,107,125 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Themis
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247532,214,779 - 2,292,936 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Themis
1229 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:15
Count of miRNA genes:15
Interacting mature miRNAs:15
Transcripts:ENSRNOT00000020102
Prediction methods:Miranda, Rnahybrid
Result types:miRGate_prediction

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

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


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1354647Despr8Despair related QTL 80.0000341locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)1124744506Rat
2298546Neuinf4Neuroinflammation QTL 45.1nervous system integrity trait (VT:0010566)spinal cord RT1-B protein level (CMO:0002132)1128736750Rat
2313053Bss51Bone structure and strength QTL 513.80.0001tibia length (VT:0004357)tibia length (CMO:0000450)1132356093Rat
2313070Bss52Bone structure and strength QTL 524.40.0001body length (VT:0001256)body length (CMO:0000013)1132356093Rat
2313090Bmd69Bone mineral density QTL 694.40.0001tibia mineral mass (VT:1000283)cortical volumetric bone mineral density (CMO:0001730)1132356093Rat
738020Pia8Pristane induced arthritis QTL 84.7joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1165833076Rat
1578650Bmd6Bone mineral density QTL 612.2femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)150910843284926Rat
1578651Bmd7Bone mineral density QTL 714.2femur mineral mass (VT:0010011)cortical volumetric bone mineral density (CMO:0001730)150910843284926Rat
1578669Bss9Bone structure and strength QTL 96.3femur morphology trait (VT:0000559)bone trabecular cross-sectional area (CMO:0002311)150910843284926Rat
1554320Bmd1Bone mineral density QTL 112.20.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)150910886060548Rat
1600360Mcs16Mammary carcinoma susceptibility QTL 162.4mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)1224439043433040Rat
7421626Bp360Blood pressure QTL 3600.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1439328949393289Rat
631688Hcas2Hepatocarcinoma susceptibility QTL 230.0001liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)15925874115540829Rat
4889451Eae29Experimental allergic encephalomyelitis QTL 295.51nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis severity score (CMO:0001419)1592587724697545Rat
631508Sald1Serum aldosterone level QTL 13.7blood aldosterone amount (VT:0005346)serum aldosterone level (CMO:0000487)1985600154856001Rat
2302038Pia31Pristane induced arthritis QTL 315.50.001blood autoantibody amount (VT:0003725)serum immunoglobulin M-type rheumatoid factor level relative to an arbitrary reference serum (CMO:0002111)11099206555992065Rat
1300167Hrtrt2Heart rate QTL 24.35heart pumping trait (VT:2000009)heart rate (CMO:0000002)11148131275088344Rat
2313062Bmd73Bone mineral density QTL 733.90.0001tibia mineral mass (VT:1000283)cortical volumetric bone mineral density (CMO:0001730)11148131282174945Rat
2313065Bss67Bone structure and strength QTL 673.10.0001tibia area (VT:1000281)tibia total energy absorbed before break (CMO:0001736)11148131282174945Rat
2313069Bss68Bone structure and strength QTL 682.90.0001tibia size trait (VT:0100001)tibia total energy absorbed before break (CMO:0001736)11148131282174945Rat
2313075Bss66Bone structure and strength QTL 663.40.0001tibia length (VT:0004357)tibia length (CMO:0000450)11148131282174945Rat
2313077Bss69Bone structure and strength QTL 693.50.0001tibia strength trait (VT:1000284)bone polar moment of inertia (CMO:0001558)11148131282174945Rat
2313092Bmd72Bone mineral density QTL 722.50.0001tibia mineral mass (VT:1000283)total volumetric bone mineral density (CMO:0001728)11148131282174945Rat
2313097Bss70Bone structure and strength QTL 703.50.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)11148131282174945Rat
2317755Glom22Glomerulus QTL 223.8urine protein amount (VT:0005160)urine protein level (CMO:0000591)11148148232355910Rat
1578756Iddm22Insulin dependent diabetes mellitus QTL 222.7blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)11183518156835181Rat
70179Xhs2X-ray hypersensitivity QTL 23.2intestine integrity trait (VT:0010554)post-insult time to onset of moribundity (CMO:0001896)11532110019121980Rat
5684998Bss101Bone structure and strength QTL 1013.6tibia strength trait (VT:1000284)tibia ultimate force (CMO:0001734)11543162149361612Rat
5684999Bss102Bone structure and strength QTL 1025.50.00000072tibia strength trait (VT:1000284)tibia stiffness (CMO:0001735)11543162149361612Rat
631494Bp95Blood pressure QTL 95400.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)11620621049268520Rat

Markers in Region
D1Got11  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2116,534,806 - 16,534,956 (+)MAPPERmRatBN7.2
Rnor_6.0117,250,010 - 17,250,159NCBIRnor6.0
Rnor_5.0118,405,076 - 18,405,225UniSTSRnor5.0
RGSC_v3.4117,120,760 - 17,120,910RGDRGSC3.4
RGSC_v3.4117,120,761 - 17,120,910UniSTSRGSC3.4
RGSC_v3.1117,120,823 - 17,120,972RGD
Celera114,948,670 - 14,948,819UniSTS
RH 3.4 Map1157.3UniSTS
RH 3.4 Map1157.3RGD
RH 2.0 Map1106.0RGD
Cytogenetic Map1p12UniSTS


Genetic Models
This gene Themis is modified in the following models/strains

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 8 14
Low 2 1 8 4 5 4 3 7 11
Below cutoff 1 12 8 4 4 8 9 20 12 16 8

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000020102   ⟹   ENSRNOP00000020102
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl116,432,631 - 16,664,329 (-)Ensembl
Rnor_6.0 Ensembl117,171,631 - 17,378,047 (-)Ensembl
RefSeq Acc Id: XM_017589835   ⟹   XP_017445324
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2116,433,906 - 16,623,889 (-)NCBI
Rnor_6.0117,152,973 - 17,378,225 (-)NCBI
Sequence:
Protein Sequences
Protein RefSeqs XP_017445324 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL93818 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: XP_017445324   ⟸   XM_017589835
- Sequence:
RefSeq Acc Id: ENSRNOP00000020102   ⟸   ENSRNOT00000020102
Protein Domains
CABIT

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-F1M3E4-F1-model_v2 AlphaFold F1M3E4 1-631 view protein structure

Transcriptome

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

Promoters
RGD ID:13689521
Promoter ID:EPDNEW_R43
Type:single initiation site
Name:Themis_1
Description:thymocyte selection associated
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_6.0117,378,036 - 17,378,096EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1560849 AgrOrtholog
BioCyc Gene G2FUF-62177 BioCyc
Ensembl Genes ENSRNOG00000014979 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000020102 ENTREZGENE
  ENSRNOP00000020102.7 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000020102 ENTREZGENE
  ENSRNOT00000020102.8 UniProtKB/TrEMBL
InterPro CABIT_dom UniProtKB/TrEMBL
  THEMIS UniProtKB/TrEMBL
KEGG Report rno:498985 UniProtKB/TrEMBL
NCBI Gene 498985 ENTREZGENE
PANTHER PTHR15215 UniProtKB/TrEMBL
Pfam CABIT UniProtKB/TrEMBL
PhenoGen Themis PhenoGen
UniProt F1M3E4_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2013-11-25 Themis  thymocyte selection associated  RGD1560849  similar to RIKEN cDNA E430004N04 gene  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 RGD1560849  similar to RIKEN cDNA E430004N04 gene   RGD1560849_predicted  similar to RIKEN cDNA E430004N04 gene (predicted)  'predicted' is removed 2292626 APPROVED
2006-03-07 RGD1560849_predicted  similar to RIKEN cDNA E430004N04 gene (predicted)  LOC498985  similar to RIKEN cDNA E430004N04 gene  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC498985  similar to RIKEN cDNA E430004N04 gene      Symbol and Name status set to provisional 70820 PROVISIONAL