Timd2 (T-cell immunoglobulin and mucin domain containing 2) - Rat Genome Database

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Gene: Timd2 (T-cell immunoglobulin and mucin domain containing 2) Rattus norvegicus
Analyze
Symbol: Timd2
Name: T-cell immunoglobulin and mucin domain containing 2
RGD ID: 1359571
Description: Predicted to enable ferritin receptor activity; phosphatidylserine binding activity; and virus receptor activity. Predicted to be involved in phagocytosis, engulfment and positive regulation of mast cell activation. Predicted to act upstream of or within iron ion transport. Predicted to be located in plasma membrane. Predicted to be active in cell surface. Human ortholog(s) of this gene implicated in atopic dermatitis. Orthologous to human HAVCR1 (hepatitis A virus cellular receptor 1); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; amitrole; bisphenol A.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: MGC108812; T-cell immunoglobulin and mucin domain-containing protein 2; T-cell immunoglobulin mucin receptor 2; T-cell membrane protein 2; TIM-2; Tim2; TIMD-2
RGD Orthologs
Mouse
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81031,561,563 - 31,602,515 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1031,561,585 - 31,600,141 (-)EnsemblGRCr8
mRatBN7.21031,060,308 - 31,101,262 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1031,060,326 - 31,094,623 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1035,775,923 - 35,810,266 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0104,314,289 - 4,348,634 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01030,762,229 - 30,796,589 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01031,755,473 - 31,796,423 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1031,755,510 - 31,790,263 (-)Ensemblrn6Rnor6.0
Rnor_5.01031,564,992 - 31,616,025 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41031,766,451 - 31,800,721 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1030,505,266 - 30,539,551 (-)NCBICelera
RGSC_v3.11031,767,505 - 31,801,770 (-)NCBI
Cytogenetic Map10q21NCBI
JBrowse:




Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
cell surface  (IBA,ISO)
plasma membrane  (IEA)

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. 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.
2. GOA pipeline RGD automated data pipeline
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
4. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
Additional References at PubMed
PMID:15489334   PMID:21886823  


Genomics

Comparative Map Data
Timd2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81031,561,563 - 31,602,515 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1031,561,585 - 31,600,141 (-)EnsemblGRCr8
mRatBN7.21031,060,308 - 31,101,262 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1031,060,326 - 31,094,623 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1035,775,923 - 35,810,266 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0104,314,289 - 4,348,634 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01030,762,229 - 30,796,589 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01031,755,473 - 31,796,423 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1031,755,510 - 31,790,263 (-)Ensemblrn6Rnor6.0
Rnor_5.01031,564,992 - 31,616,025 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41031,766,451 - 31,800,721 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1030,505,266 - 30,539,551 (-)NCBICelera
RGSC_v3.11031,767,505 - 31,801,770 (-)NCBI
Cytogenetic Map10q21NCBI
Timd2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391146,559,787 - 46,597,934 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1146,559,787 - 46,597,888 (-)EnsemblGRCm39 EnsemblGRCm39
GRCm381146,668,960 - 46,707,107 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1146,668,960 - 46,707,061 (-)Ensemblmm10GRCm38
MGSCv371146,482,462 - 46,520,606 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv361146,513,437 - 46,550,484 (-)NCBIMGSCv36mm8
Celera1151,257,001 - 51,295,891 (-)NCBICelera
Cytogenetic Map11B1.1NCBI
cM Map1128.05NCBI

Variants

.
Variants in Timd2
193 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:141
Count of miRNA genes:117
Interacting mature miRNAs:122
Transcripts:ENSRNOT00000059468
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 (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
631564Apr3Acute phase response QTL 33.9blood interleukin-6 amount (VT:0008595)plasma interleukin-6 level (CMO:0001927)101577675460776754Rat
1298069Bp168Blood pressure QTL 1685.5blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)102702353598502431Rat
2293669Bmd33Bone mineral density QTL 334.50.0001femur strength trait (VT:0010010)femoral neck polar moment of inertia (CMO:0001670)102744378772443787Rat
631554Bp133Blood pressure QTL 1330.005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)10125055464349221Rat
61325Aia5Adjuvant induced arthritis QTL 50.01joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1023948641107713808Rat
2293679Bmd30Bone mineral density QTL 303.50.0001femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)102744378772443787Rat
1578761Stresp21Stress response QTL 213.3thymus mass (VT:0004954)thymus wet weight (CMO:0000855)10687714251877142Rat
2293680Bss40Bone structure and strength QTL 405.660.0001femur strength trait (VT:0010010)femur total energy absorbed before break (CMO:0001677)10135730538Rat
2298544Neuinf9Neuroinflammation QTL 94.6nervous system integrity trait (VT:0010566)spinal cord complement component 1, q subcomponent, B chain mRNA level (CMO:0002126)101993920764939207Rat
61332Eau3Experimental allergic uveoretinitis QTL 30.004uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)101803578263035782Rat
10401803Kidm50Kidney mass QTL 50kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)1092219745922197Rat
2317754Glom25Glomerulus QTL 253.5urine protein amount (VT:0005160)urine protein level (CMO:0000591)10210370847103708Rat
1598852Anxrr19Anxiety related response QTL 195.07body movement coordination trait (VT:0005424)number of rearing movements in an experimental apparatus (CMO:0001752)101866841963668419Rat
1581497Esta1Estrogen-induced thymic atrophy QTL 1thymus mass (VT:0004954)thymus wet weight (CMO:0000855)102183375861843633Rat
2313095Bss62Bone structure and strength QTL 621.50.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)10589381150893811Rat
724527Bp148Blood pressure QTL 1480.0001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)102895035373950353Rat
1331762Rf40Renal function QTL 403.873kidney blood vessel physiology trait (VT:0100012)absolute change in renal vascular resistance (CMO:0001900)102980091064653589Rat
2300171Bmd58Bone mineral density QTL 584.90.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)102744378772443787Rat
61354Pia10Pristane induced arthritis QTL 100.01joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1023948641107713808Rat
2301967Cm73Cardiac mass QTL 734.55heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)101499153586964295Rat
2313104Bss61Bone structure and strength QTL 610.90.0001tibia area (VT:1000281)tibia midshaft cross-sectional area (CMO:0001717)10589381150893811Rat
2316949Gluco60Glucose level QTL 603.7blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1014991535107556066Rat
2293652Bmd22Bone mineral density QTL 224.90.0001femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)102744378772443787Rat
724556Pur2Proteinuria QTL 25.5urine protein amount (VT:0005160)urine protein level (CMO:0000591)102293137391127454Rat
8662860Vetf10Vascular elastic tissue fragility QTL 10artery integrity trait (VT:0010639)number of ruptures of the internal elastic lamina of the abdominal aorta and iliac arteries (CMO:0002562)10666092373950353Rat
2313066Bss63Bone structure and strength QTL 631.40.0001tibia strength trait (VT:1000284)bone polar moment of inertia (CMO:0001558)10589381150893811Rat
2313064Bmd71Bone mineral density QTL 710.90.0001tibia mineral mass (VT:1000283)compact volumetric bone mineral density (CMO:0001730)10589381150893811Rat
70223Bp57Blood pressure QTL 575arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)101465354159653541Rat
1354587Kidm21Kidney mass QTL 213.3kidney mass (VT:0002707)right kidney wet weight (CMO:0000082)101553301273695498Rat
634329Pia15Pristane induced arthritis QTL 153.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)102466212373695339Rat
70224Eae3Experimental allergic encephalomyelitis QTL 34.1nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)102702353561843633Rat
2313081Bss64Bone structure and strength QTL 641.30.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)10589381150893811Rat
1331791Cm31Cardiac mass QTL 313.84606heart mass (VT:0007028)heart wet weight (CMO:0000069)102980091091417879Rat
2298495Eae23Experimental allergic encephalomyelitis QTL 2316.93nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis duration (CMO:0001424)101617552561175525Rat
2313087Bmd80Bone mineral density QTL 803.20.0001tibia mineral mass (VT:1000283)total volumetric bone mineral density (CMO:0001728)102011061465110614Rat
634327Hc4Hypercalciuria QTL 42.4urine calcium amount (VT:0002985)urine calcium excretion rate (CMO:0000763)10138832698Rat
631531Iresp2Immunoglobin response QTL26.3blood immunoglobulin E amount (VT:0002492)serum immunoglobulin E level (CMO:0002101)102342212132490778Rat
631530Tls3T-lymphoma susceptibility QTL 300.0001thymus integrity trait (VT:0010555)percentage of study population developing T-cell lymphomas during a period of time (CMO:0001911)102758722696099902Rat
2289985Bp305Blood pressure QTL 305arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)102907697874076978Rat
631660Hcar1Hepatocarcinoma resistance QTL 13.40.0001liver integrity trait (VT:0010547)volume of individual liver tumorous lesion (CMO:0001078)10666111835509383Rat
631532Cm50Cardiac mass QTL 506.6heart mass (VT:0007028)calculated heart weight (CMO:0000073)101803578263035782Rat
631267Cia20Collagen induced arthritis QTL 203.2joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1023948641107713808Rat
2293705Bmd25Bone mineral density QTL 257.10.0001femur mineral mass (VT:0010011)compact volumetric bone mineral density (CMO:0001730)102744378772443787Rat
1600371Mcs21Mammary carcinoma susceptibility QTL 213mammary gland integrity trait (VT:0010552)mammary tumor growth rate (CMO:0000344)102937704652699134Rat
631268Cia21Collagen induced arthritis QTL 213.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1014991535107713808Rat
1576311Pia26Pristane induced arthritis QTL 26joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)103112911376129113Rat
61427Cia16Collagen induced arthritis QTL 163.2joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)10686461896620484Rat
2313055Bw96Body weight QTL 963.60.0001body mass (VT:0001259)body weight (CMO:0000012)102011061465110614Rat
631542Bp82Blood pressure QTL 826.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)102702353599451848Rat

Markers in Region
RH140465  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21031,060,549 - 31,060,658 (+)MAPPERmRatBN7.2
Rnor_6.01031,755,715 - 31,755,823NCBIRnor6.0
Rnor_5.01031,565,234 - 31,565,342UniSTSRnor5.0
RGSC_v3.41031,766,693 - 31,766,801UniSTSRGSC3.4
Celera1030,505,508 - 30,505,616UniSTS
RH 3.4 Map10341.4UniSTS
Cytogenetic Map10q21UniSTS


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
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
16 12 59 154 91 90 59 89 59 6 345 181 11 130 81 92 31 9 9

Sequence


Ensembl Acc Id: ENSRNOT00000059468   ⟹   ENSRNOP00000056223
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1031,561,585 - 31,595,876 (-)Ensembl
mRatBN7.2 Ensembl1031,060,326 - 31,094,623 (-)Ensembl
Rnor_6.0 Ensembl1031,755,510 - 31,790,263 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000125994   ⟹   ENSRNOP00000103961
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1031,561,585 - 31,600,141 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000155157   ⟹   ENSRNOP00000112410
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1031,561,585 - 31,588,428 (-)Ensembl
RefSeq Acc Id: NM_001013855   ⟹   NP_001013877
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81031,561,567 - 31,595,876 (-)NCBI
mRatBN7.21031,060,308 - 31,094,623 (-)NCBI
Rnor_6.01031,755,473 - 31,789,784 (-)NCBI
Rnor_5.01031,564,992 - 31,616,025 (-)NCBI
RGSC_v3.41031,766,451 - 31,800,721 (-)RGD
Celera1030,505,266 - 30,539,551 (-)RGD
Sequence:
RefSeq Acc Id: XM_006246168   ⟹   XP_006246230
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81031,561,563 - 31,602,515 (-)NCBI
mRatBN7.21031,060,367 - 31,101,262 (-)NCBI
Rnor_6.01031,755,603 - 31,796,423 (-)NCBI
Rnor_5.01031,564,992 - 31,616,025 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008767669   ⟹   XP_008765891
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81031,561,563 - 31,596,348 (-)NCBI
mRatBN7.21031,060,367 - 31,095,097 (-)NCBI
Rnor_6.01031,755,603 - 31,790,270 (-)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001013877 (Get FASTA)   NCBI Sequence Viewer  
  XP_006246230 (Get FASTA)   NCBI Sequence Viewer  
  XP_008765891 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAH89832 (Get FASTA)   NCBI Sequence Viewer  
  AAP06755 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000056223
  ENSRNOP00000056223.2
GenBank Protein Q5FVR0 (Get FASTA)   NCBI Sequence Viewer  
RefSeq Acc Id: NP_001013877   ⟸   NM_001013855
- Peptide Label: precursor
- UniProtKB: Q5FVR0 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006246230   ⟸   XM_006246168
- Peptide Label: isoform X1
- UniProtKB: Q5FVR0 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_008765891   ⟸   XM_008767669
- Peptide Label: isoform X1
- UniProtKB: Q5FVR0 (UniProtKB/Swiss-Prot)
- Sequence:
Ensembl Acc Id: ENSRNOP00000056223   ⟸   ENSRNOT00000059468
Ensembl Acc Id: ENSRNOP00000103961   ⟸   ENSRNOT00000125994
Ensembl Acc Id: ENSRNOP00000112410   ⟸   ENSRNOT00000155157
Protein Domains
Ig-like V-type

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q5FVR0-F1-model_v2 AlphaFold Q5FVR0 1-349 view protein structure

Transcriptome

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

Promoters
RGD ID:13697128
Promoter ID:EPDNEW_R7653
Type:initiation region
Name:Timd2_2
Description:T-cell immunoglobulin and mucin domain containing 2
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_R7654  
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01031,789,820 - 31,789,880EPDNEW
RGD ID:13697129
Promoter ID:EPDNEW_R7654
Type:multiple initiation site
Name:Timd2_1
Description:T-cell immunoglobulin and mucin domain containing 2
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_R7653  
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01031,790,248 - 31,790,308EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1359571 AgrOrtholog
BioCyc Gene G2FUF-25360 BioCyc
Ensembl Genes ENSRNOG00000021345 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000059468 ENTREZGENE
  ENSRNOT00000059468.4 UniProtKB/Swiss-Prot
Gene3D-CATH 2.60.40.10 UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:7324518 IMAGE-MGC_LOAD
InterPro Ig-like_dom UniProtKB/Swiss-Prot
  Ig-like_dom_sf UniProtKB/Swiss-Prot
  Ig-like_fold UniProtKB/Swiss-Prot
  Ig_sub UniProtKB/Swiss-Prot
  Ig_V-set UniProtKB/Swiss-Prot
  TIM_domain-containing_protein UniProtKB/Swiss-Prot
KEGG Report rno:287222 UniProtKB/Swiss-Prot
MGC_CLONE MGC:108812 IMAGE-MGC_LOAD
NCBI Gene 287222 ENTREZGENE
PANTHER HEPATITIS A VIRUS CELLULAR RECEPTOR 1 UniProtKB/Swiss-Prot
  HEPATITIS A VIRUS CELLULAR RECEPTOR 1 HOMOLOG UniProtKB/Swiss-Prot
Pfam V-set UniProtKB/Swiss-Prot
PhenoGen Timd2 PhenoGen
PROSITE IG_LIKE UniProtKB/Swiss-Prot
RatGTEx ENSRNOG00000021345 RatGTEx
SMART SM00409 UniProtKB/Swiss-Prot
Superfamily-SCOP SSF48726 UniProtKB/Swiss-Prot
UniProt A0ABK0LHX4_RAT UniProtKB/TrEMBL
  A0ABK0M8F0_RAT UniProtKB/TrEMBL
  Q5FVR0 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-03-04 Timd2  T-cell immunoglobulin and mucin domain containing 2  Tim2  T-cell immunoglobulin and mucin domain containing 2  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-07-29 Tim2  T-cell immunoglobulin and mucin domain containing 2      Symbol and Name status set to provisional 70820 PROVISIONAL