Cd1d1 (CD1d1 molecule) - Rat Genome Database
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Gene: Cd1d1 (CD1d1 molecule) Rattus norvegicus
Analyze
Symbol: Cd1d1
Name: CD1d1 molecule
RGD ID: 2296
Description: Predicted to have several functions, including T cell receptor binding activity; lipid antigen binding activity; and lipopeptide binding activity. Predicted to be involved in several processes, including T cell differentiation; positive regulation of cytokine production; and regulation of leukocyte activation. Predicted to localize to several cellular components, including endosome; external side of plasma membrane; and lysosome. Orthologous to human CD1D (CD1d molecule); PARTICIPATES IN Entamoebiasis pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,4-dinitrotoluene; 2-nitrofluorene.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: antigen-presenting glycoprotein CD1d; Cd1; Cd1d; CD1D antigen; CD1D antigen also localized to RNO7q32 but is presumably on chromosome 2; CD1d1 antigen; T-cell surface glycoprotein CD1d
RGD Orthologs
Human
Mouse
Bonobo
Dog
Green Monkey
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.02186,330,298 - 186,333,805 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2186,330,298 - 186,333,805 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02205,728,725 - 205,732,232 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42179,011,165 - 179,014,672 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.12178,961,270 - 178,964,778 (-)NCBI
Celera2166,382,474 - 166,385,981 (-)NCBICelera
Cytogenetic Map2q34NCBI
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

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:7538697   PMID:9133426   PMID:10201995   PMID:10523605   PMID:11550008   PMID:11754812   PMID:14557411   PMID:14722359   PMID:17082577   PMID:19124746   PMID:20363964   PMID:20927351  
PMID:21460847   PMID:22065767  


Genomics

Comparative Map Data
Cd1d1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.02186,330,298 - 186,333,805 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2186,330,298 - 186,333,805 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02205,728,725 - 205,732,232 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42179,011,165 - 179,014,672 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.12178,961,270 - 178,964,778 (-)NCBI
Celera2166,382,474 - 166,385,981 (-)NCBICelera
Cytogenetic Map2q34NCBI
CD1D
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1158,178,030 - 158,186,427 (+)EnsemblGRCh38hg38GRCh38
GRCh38.p13 Ensembl1158,179,947 - 158,184,896 (+)EnsemblGRCh38hg38GRCh38
GRCh381158,178,030 - 158,186,427 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371158,147,828 - 158,156,217 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361156,416,361 - 156,422,841 (+)NCBINCBI36hg18NCBI36
Build 341154,962,809 - 154,967,758NCBI
Celera1131,220,809 - 131,227,289 (+)NCBI
Cytogenetic Map1q23.1NCBI
HuRef1129,508,011 - 129,514,491 (+)NCBIHuRef
CHM1_11159,546,145 - 159,552,625 (+)NCBICHM1_1
Cd1d1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39386,903,141 - 86,919,665 (-)NCBIGRCm39mm39
GRCm38386,995,834 - 87,012,358 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl386,995,834 - 86,999,441 (-)EnsemblGRCm38mm10GRCm38
MGSCv37386,799,756 - 86,803,262 (-)NCBIGRCm37mm9NCBIm37
MGSCv36387,081,765 - 87,085,267 (-)NCBImm8
Celera387,021,305 - 87,024,811 (-)NCBICelera
Cytogenetic Map3F1NCBI
cM Map337.91NCBI
CD1D
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11137,339,774 - 137,348,173 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1137,341,690 - 137,348,173 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01133,549,258 - 133,557,752 (+)NCBIMhudiblu_PPA_v0panPan3
CD1D
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.13823,489,169 - 23,491,712 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CD1D
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1 Ensembl205,727,049 - 5,730,061 (-)Ensembl
ChlSab1.1205,726,307 - 5,733,355 (-)NCBI

Position Markers
D2Wox42  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.02186,330,451 - 186,330,790NCBIRnor6.0
Rnor_5.02205,728,878 - 205,729,217UniSTSRnor5.0
RGSC_v3.42179,011,318 - 179,011,657UniSTSRGSC3.4
Celera2166,382,627 - 166,382,966UniSTS
Cytogenetic Map2q34UniSTS
RH133461  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.02186,330,420 - 186,330,600NCBIRnor6.0
Rnor_6.02186,330,420 - 186,330,707NCBIRnor6.0
Rnor_5.02205,728,847 - 205,729,027UniSTSRnor5.0
Rnor_5.02205,728,847 - 205,729,134UniSTSRnor5.0
RGSC_v3.42179,011,287 - 179,011,574UniSTSRGSC3.4
RGSC_v3.42179,011,287 - 179,011,467UniSTSRGSC3.4
Celera2166,382,596 - 166,382,883UniSTS
Celera2166,382,596 - 166,382,776UniSTS
Cytogenetic Map2q34UniSTS
RH 3.4 Map21129.1UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2293843Kiddil6Kidney dilation QTL 63.1kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)242776916195645082Rat
1598805Memor8Memory QTL 83exploratory behavior trait (VT:0010471)average horizontal distance in proximity to the target during voluntary locomotion in an experimental apparatus (CMO:0002674)2157914311204022555Rat
70175BpQTLCluster3Blood pressure QTL cluster 34.128arterial blood pressure trait (VT:2000000)absolute change in systolic blood pressure (CMO:0000607)2140566078217498545Rat
70175BpQTLCluster3Blood pressure QTL cluster 34.128arterial blood pressure trait (VT:2000000)pulse pressure (CMO:0000292)2140566078217498545Rat
70175BpQTLCluster3Blood pressure QTL cluster 34.128arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2140566078217498545Rat
70175BpQTLCluster3Blood pressure QTL cluster 34.128arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2140566078217498545Rat
70175BpQTLCluster3Blood pressure QTL cluster 34.128arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)2140566078217498545Rat
71113Cari2Carrageenan-induced inflammation QTL 22.70.009hypodermis integrity trait (VT:0010550)inflammatory exudate volume (CMO:0001429)2147522550217498710Rat
631266Bp132Blood pressure QTL 1320.0005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)246537589217498710Rat
61467Bp14Blood pressure QTL 142.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)243133606217498545Rat
61467Bp14Blood pressure QTL 142.2arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)243133606217498545Rat
61469Bp16Blood pressure QTL 165.64arterial blood pressure trait (VT:2000000)blood pressure measurement (CMO:0000003)2184730446229730446Rat
70162Bp63Blood pressure QTL 635.64arterial blood pressure trait (VT:2000000)blood pressure measurement (CMO:0000003)2184730446229730446Rat
724568Uae13Urinary albumin excretion QTL 134.4urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)2149114878225501939Rat
1331734Bp204Blood pressure QTL 2043.61192arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2181990297240020001Rat
1331760Bp206Blood pressure QTL 2063.62454arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)256244671217498710Rat
1298074Bp164Blood pressure QTL 1640.003arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)242776916217498710Rat
1298076Bp166Blood pressure QTL 1660.0009arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2141583337217498710Rat
1298080Bp163Blood pressure QTL 1630.02arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)266828049217498710Rat
1298085Bp165Blood pressure QTL 1650.0006arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)242776916217498710Rat
1331794Bp202Blood pressure QTL 2023.66819arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2147122993240020001Rat
1331805Cm29Cardiac mass QTL 293.50746heart mass (VT:0007028)heart wet weight (CMO:0000069)2147122993240020001Rat
2307174Activ3Activity QTL 34.830.000058locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)2183984665228984665Rat
1581502Esta3Estrogen-induced thymic atrophy QTL 3thymus mass (VT:0004954)thymus wet weight (CMO:0000855)2142053350204585731Rat
631501Bp101Blood pressure QTL 1012.4arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2157914409217498545Rat
631507Bp105Blood pressure QTL 1050.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2116075644228737869Rat
1302793Bw16Body weight QTL 1650.0001body mass (VT:0001259)body weight (CMO:0000012)2169852800217498545Rat
1641891Alcrsp17Alcohol response QTL 17response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)2155965557254121739Rat
1641925Alcrsp2Alcohol response QTL 2response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)2155965557237742948Rat
1598833Bp295Blood pressure QTL 2953.5arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2161745602206745602Rat
1598838Bp290Blood pressure QTL 2901.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2181522444226522444Rat
2301415Cm67Cardiac mass QTL 670.003heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)2172795683189857032Rat
634308Sach6Saccharin preference QTL 64.9taste sensitivity trait (VT:0001986)saccharin intake volume to total fluid intake volume ratio (CMO:0001601)2116075644228737869Rat
1358356Srcrt1Stress Responsive Cort QTL13.66blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)2175403337239166203Rat
1578648Bss11Bone structure and strength QTL 114.7femur morphology trait (VT:0000559)femoral neck cortical cross-sectional area (CMO:0001702)2118446646227707979Rat
1300165Rf9Renal function QTL 93.28kidney glomerulus integrity trait (VT:0010546)index of glomerular damage (CMO:0001135)2138901276217498710Rat
1354601Slep1Serum leptin concentration QTL 15.39blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)243149788198704485Rat
1354605Rf48Renal function QTL 482.9blood creatinine amount (VT:0005328)plasma creatinine level (CMO:0000537)275687495221880419Rat
1354609Niddm62Non-insulin dependent diabetes mellitus QTL 624.720.000006insulin secretion trait (VT:0003564)plasma insulin level (CMO:0000342)2158159186217498710Rat
1354622Kidm16Kidney mass QTL 163kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)283819608239166203Rat
1354648Bp239Blood pressure QTL 2390.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)266828236243550655Rat
1354649Kidm17Kidney mass QTL 172.9kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)283819608243901375Rat
2301966Bp322Blood pressure QTL 3223.58arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2158159186217498710Rat
1359022Ppulsi1Prepulse inhibition QTL 13.63prepulse inhibition trait (VT:0003088)acoustic startle response measurement (CMO:0001519)2142053350228984665Rat
1549833Bp257Blood pressure QTL 2570.003arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2181987080199696953Rat
1554319Bmd2Bone mineral density QTL 213.40.0001lumbar vertebra area (VT:0010570)lumbar vertebra cross-sectional area (CMO:0001689)2118446793228582621Rat
2306901Bp337Blood pressure QTL 3370.01arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2177680772243901375Rat
1358913Cm41Cardiac mass QTL 412.73heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)223837491218957222Rat
1358917Cm42Cardiac mass QTL 422.82heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)223837491218957222Rat
1359030Bp277Blood pressure QTL 277arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)2118446646200453484Rat
1359030Bp277Blood pressure QTL 277arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2118446646200453484Rat
1359032Hrtrt18Heart rate QTL 18heart pumping trait (VT:2000009)heart rate (CMO:0000002)2169852670207612467Rat
61374Edpm2Estrogen-dependent pituitary mass QTL 24.420.86pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)278321410217498710Rat
61401Niddm2Non-insulin dependent diabetes mellitus QTL 24.54blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)2159585731204585731Rat
6903312Bw112Body weight QTL 1123.20.0013body mass (VT:0001259)body weight (CMO:0000012)2149614623198704357Rat
6907363Bp357Blood pressure QTL 3574.10.002arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)2143447078188447078Rat
7488925Bp364Blood pressure QTL 3640.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2174160958219160958Rat
7488927Bp365Blood pressure QTL 3650.008arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2177339806222339806Rat
7771603Bp371Blood pressure QTL 3710.00001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2183864092187196901Rat
7771605Memor19Memory QTL 190.00001exploratory behavior trait (VT:0010471)measurement of voluntary locomotion into, out of or within a discrete space in an experimental apparatus (CMO:0000957)2183864092187196901Rat
8662843Vetf9Vascular elastic tissue fragility QTL 92.05thoracic aorta molecular composition trait (VT:0010568)aorta wall extracellular elastin dry weight to aorta wall extracellular collagen weight ratio (CMO:0002003)2169852670243026643Rat
8662832Vetf7Vascular elastic tissue fragility QTL 73.5aorta elastin amount (VT:0003905)aorta wall extracellular elastin dry weight to aorta wall dry weight ratio (CMO:0002002)283754907237610852Rat
10043136Iddm54Insulin dependent diabetes mellitus QTL 543.40.0001blood glucose amount (VT:0000188)age at onset/diagnosis of type 1 diabetes mellitus (CMO:0001140)2149614466205573168Rat
10043136Iddm54Insulin dependent diabetes mellitus QTL 543.40.0001blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)2149614466205573168Rat
12879846Cm90Cardiac mass QTL 900.011heart right ventricle mass (VT:0007033)heart right ventricle weight to body weight ratio (CMO:0000914)2172795683189857032Rat
12879836Kidm61Kidney mass QTL 610.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)2172795683199696953Rat
10755499Bp389Blood pressure QTL 3892.61arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)216679272245624402Rat
12879839Cm85Cardiac mass QTL 850.001heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)2172795683199696953Rat
11565181Bw176Body weight QTL 1760.002body mass (VT:0001259)body weight (CMO:0000012)2172795683189857032Rat
12879838Cm86Cardiac mass QTL 860.002heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)2172795683199696953Rat
12879840Bw179Body weight QTL 1790.005body mass (VT:0001259)body weight (CMO:0000012)2172795683199696953Rat
12879845Cm89Cardiac mass QTL 890.008heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)2172795683189857032Rat
11565180Kidm56Kidney mass QTL 560.003kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)2172795683189857032Rat
12879837Am2Aortic mass QTL 20.001aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)2172795683199696953Rat
12879847Am4Aortic mass QTL 40.001aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)2172795683189857032Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:177
Count of miRNA genes:127
Interacting mature miRNAs:141
Transcripts:ENSRNOT00000022150
Prediction methods:Microtar, Miranda, 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 23 53 37 19 37 6 9 28 21 11 6
Low 3 20 4 4 4 2 2 74 7 18 2
Below cutoff 2

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000022150   ⟹   ENSRNOP00000022150
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl2186,330,298 - 186,333,805 (-)Ensembl
RefSeq Acc Id: NM_017079   ⟹   NP_058775
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.02186,330,298 - 186,333,805 (-)NCBI
Rnor_5.02205,728,725 - 205,732,232 (-)NCBI
RGSC_v3.42179,011,165 - 179,014,672 (-)RGD
Celera2166,382,474 - 166,385,981 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_058775 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein BAA05455 (Get FASTA)   NCBI Sequence Viewer  
  BAA82323 (Get FASTA)   NCBI Sequence Viewer  
  EDM00791 (Get FASTA)   NCBI Sequence Viewer  
  Q63493 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_058775   ⟸   NM_017079
- Peptide Label: precursor
- UniProtKB: Q63493 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000022150   ⟸   ENSRNOT00000022150
Protein Domains
Ig-like

Transcriptome

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

Promoters
RGD ID:13691413
Promoter ID:EPDNEW_R1937
Type:initiation region
Name:Cd1d1_1
Description:CD1d1 molecule
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_6.02186,333,748 - 186,333,808EPDNEW

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)
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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)
FHH/EurMcwi (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
FHL/EurMcwi (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)
FHL/EurMcwi (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
GH/OmrMcwi (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)
GK/Ox (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
LE/Stm (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/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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:2296 AgrOrtholog
Ensembl Genes ENSRNOG00000016451 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000022150 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000022150 ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH 2.60.40.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  3.30.500.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro Ig-like_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ig-like_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ig-like_fold UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ig_C1-set UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  MHC_I-like_Ag-recog UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  MHC_I-like_Ag-recog_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  MHC_I/II-like_Ag-recog UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:25109 UniProtKB/Swiss-Prot
NCBI Gene 25109 ENTREZGENE
Pfam C1-set UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  MHC_I_3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Cd1d1 PhenoGen
PROSITE IG_LIKE UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART IGc1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF48726 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF54452 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
TIGR TC233314
UniGene Rn.11120 ENTREZGENE
UniProt CD1D_RAT UniProtKB/Swiss-Prot
  G3V837_RAT UniProtKB/TrEMBL
  Q63493 ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-06-27 Cd1d1  Cd1d1 molecule  Cd1d1  CD1d1 antigen  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-06-27 Cd1d1  CD1d1 molecule  Cd1d1  Cd1d1 molecule  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2002-11-06 Cd1d1  CD1d1 antigen  Cd1d  CD1D antigen  Symbol and Name updated 625702 APPROVED
2002-06-10 Cd1d  CD1D antigen      Symbol and Name status set to approved 70586 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_domains contains binding motifs for two cytokine-inducible transcription factors, NF-IL2-A and NF-IL6 632366