Cd96 (CD96 molecule) - Rat Genome Database

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Gene: Cd96 (CD96 molecule) Rattus norvegicus
Analyze
Symbol: Cd96
Name: CD96 molecule
RGD ID: 1565249
Description: Predicted to be involved in cell-matrix adhesion and inflammatory response. Predicted to act upstream of or within negative regulation of natural killer cell cytokine production; negative regulation of type II interferon production; and response to lipopolysaccharide. Predicted to be located in cytoplasm. Human ortholog(s) of this gene implicated in C syndrome. Orthologous to human CD96 (CD96 molecule); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 6-propyl-2-thiouracil; alpha-Zearalanol.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: CD96 antigen; cell surface antigen CD96; t cell-activated increased late expression protein; T-cell surface protein tactile
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81168,164,926 - 68,239,266 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1168,164,872 - 68,241,937 (+)EnsemblGRCr8
mRatBN7.21154,702,290 - 54,776,618 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1154,702,290 - 54,776,621 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1163,465,004 - 63,546,439 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01156,126,844 - 56,208,283 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01155,241,194 - 55,322,041 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01157,108,757 - 57,183,855 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1157,108,956 - 57,183,270 (+)Ensemblrn6Rnor6.0
Rnor_5.01160,273,387 - 60,347,696 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41156,183,593 - 56,258,568 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1154,231,989 - 54,305,717 (+)NCBICelera
Cytogenetic Map11q21NCBI
JBrowse:




Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
cytoplasm  (IEA,ISO)
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. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
3. GOA pipeline RGD automated data pipeline
4. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
5. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
6. 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:17847009   PMID:24658051  


Genomics

Comparative Map Data
Cd96
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81168,164,926 - 68,239,266 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1168,164,872 - 68,241,937 (+)EnsemblGRCr8
mRatBN7.21154,702,290 - 54,776,618 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1154,702,290 - 54,776,621 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1163,465,004 - 63,546,439 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01156,126,844 - 56,208,283 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01155,241,194 - 55,322,041 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01157,108,757 - 57,183,855 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1157,108,956 - 57,183,270 (+)Ensemblrn6Rnor6.0
Rnor_5.01160,273,387 - 60,347,696 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41156,183,593 - 56,258,568 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1154,231,989 - 54,305,717 (+)NCBICelera
Cytogenetic Map11q21NCBI
CD96
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh383111,542,197 - 111,665,996 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl3111,292,719 - 111,665,996 (+)Ensemblhg38GRCh38
GRCh373111,261,044 - 111,384,843 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 363112,743,616 - 112,853,896 (+)NCBIBuild 36Build 36hg18NCBI36
Build 343112,743,545 - 112,853,906NCBI
Celera3109,660,587 - 109,770,891 (+)NCBICelera
Cytogenetic Map3q13.13-q13.2NCBI
HuRef3108,635,962 - 108,746,199 (+)NCBIHuRef
CHM1_13111,225,192 - 111,335,543 (+)NCBICHM1_1
T2T-CHM13v2.03114,263,009 - 114,386,816 (+)NCBIT2T-CHM13v2.0
Cd96
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391645,856,015 - 45,940,611 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1645,856,020 - 45,940,614 (-)EnsemblGRCm39 EnsemblGRCm39
GRCm381646,035,652 - 46,120,248 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1646,035,657 - 46,120,251 (-)Ensemblmm10GRCm38
MGSCv371646,035,770 - 46,120,361 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv361645,954,989 - 46,039,446 (-)NCBIMGSCv36mm8
Celera1646,412,471 - 46,501,450 (-)NCBICelera
Cytogenetic Map16B5NCBI
cM Map1630.45NCBI
Cd96
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495542711,971,021 - 12,059,171 (+)Ensembl
ChiLan1.0NW_00495542711,971,051 - 12,057,185 (+)NCBIChiLan1.0ChiLan1.0
CD96
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v22109,544,305 - 109,651,004 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan13109,549,085 - 109,655,784 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v03108,694,670 - 108,798,114 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.13115,619,322 - 115,720,858 (+)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl3115,619,374 - 115,720,858 (+)EnsemblpanPan2panpan1.1
CD96
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.13316,231,244 - 16,327,670 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl3316,231,994 - 16,325,572 (+)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha3316,333,066 - 16,427,734 (+)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.03316,279,316 - 16,562,843 (+)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl3316,470,540 - 16,563,394 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.13316,278,454 - 16,373,916 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.03316,324,781 - 16,421,426 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.03316,870,215 - 16,964,480 (+)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Cd96
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405602138,061,834 - 138,151,507 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936834434,877 - 522,411 (+)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_004936834432,538 - 522,118 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CD96
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl13148,090,630 - 148,192,232 (-)EnsemblsusScr11Sscrofa11.1
Sscrofa11.113148,103,424 - 148,192,272 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.213158,860,932 - 158,952,300 (-)NCBISscrofa10.2Sscrofa10.2susScr3
CD96
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12269,141,470 - 69,245,962 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2269,140,288 - 69,244,097 (-)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_02366604197,235,943 - 97,339,499 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Cd96
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v1430,765,863 - 30,838,968 (-)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Cd96
513 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:58
Count of miRNA genes:52
Interacting mature miRNAs:56
Transcripts:ENSRNOT00000035485
Prediction methods:Miranda, Rnahybrid, 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.


QTLs in Region (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1300147Bp187Blood pressure QTL 1873.67arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)112252474682951192Rat
1598841Memor7Memory QTL 7exploratory behavior trait (VT:0010471)total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)113330600878306008Rat
724554Iddm17Insulin dependent diabetes mellitus QTL 170.001blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)114644316891443168Rat
1598811Bp291Blood pressure QTL 2911.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)113330600878306008Rat
1581565Pur10Proteinuria QTL 100.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)115827236396350770Rat
4889859Pur28Proteinuria QTL 2819.50.001urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)115892833699753367Rat
8694376Bw156Body weight QTL 1562.250.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)113674945981749459Rat
10755497Bp388Blood pressure QTL 3882.76arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)113294306789836615Rat
1300130Rf20Renal function QTL 204.44kidney glomerulus integrity trait (VT:0010546)kidney glomerulus diameter (CMO:0001166)113191546976915469Rat
10058952Gmadr6Adrenal mass QTL 62.290.0072adrenal gland mass (VT:0010420)both adrenal glands wet weight to body weight ratio (CMO:0002411)113642841681428416Rat
1558659Tescar1Testicular tumor resistance QTL 13.9testis integrity trait (VT:0010572)percentage of study population developing testis tumors during a period of time (CMO:0001261)113461876079618760Rat
1300135Rf19Renal function QTL 193.38blood creatinine amount (VT:0005328)creatinine clearance (CMO:0000765)115441539196071021Rat
2298551Neuinf10Neuroinflammation QTL 103.7nervous system integrity trait (VT:0010566)spinal cord beta-2 microglobulin mRNA level (CMO:0002125)115893182292356038Rat
2312566Glom20Glomerulus QTL 203.60.001kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)115775483796071021Rat
724563Uae10Urinary albumin excretion QTL 106urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)112019354996351019Rat
9589032Epfw10Epididymal fat weight QTL 109.290.001epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)113674945981749459Rat
724561Plsm4Polydactyly-luxate syndrome (PLS) morphotypes QTL 40.0003forelimb integrity trait (VT:0010562)front foot phalanges count (CMO:0001947)116796218499753367Rat
9590313Scort20Serum corticosterone level QTL 206.510.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)113674945981749459Rat
8694424Bw162Body weight QTL 1623.80.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)113674945981749459Rat
1581572Uae35Urinary albumin excretion QTL 350.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)115827236396350770Rat
1300110Stl7Serum triglyceride level QTL 74.64blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)115107102196071021Rat
631510Spl2Serum phospholipid level QTL 24.1blood phospholipid amount (VT:0006084)serum phospholipid level (CMO:0001171)112755668572556685Rat

Markers in Region
AI178367  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21154,776,399 - 54,776,519 (+)MAPPERmRatBN7.2
Rnor_6.01157,183,047 - 57,183,166NCBIRnor6.0
Rnor_5.01160,347,478 - 60,347,597UniSTSRnor5.0
RGSC_v3.41156,258,350 - 56,258,469UniSTSRGSC3.4
Celera1154,305,499 - 54,305,618UniSTS
RH 3.4 Map4581.3UniSTS
Cytogenetic Map11q21UniSTS


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 8 39 119 88 88 57 92 57 6 315 160 11 91 76 86 31 15 15

Sequence


Ensembl Acc Id: ENSRNOT00000035485   ⟹   ENSRNOP00000034871
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1168,164,872 - 68,239,176 (+)Ensembl
mRatBN7.2 Ensembl1154,702,290 - 54,776,615 (+)Ensembl
Rnor_6.0 Ensembl1157,108,956 - 57,183,270 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000093728
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1168,164,872 - 68,241,937 (+)Ensembl
mRatBN7.2 Ensembl1154,712,109 - 54,776,621 (+)Ensembl
Rnor_6.0 Ensembl1157,118,779 - 57,147,976 (+)Ensembl
RefSeq Acc Id: NM_001025032   ⟹   NP_001020203
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81168,164,926 - 68,239,246 (+)NCBI
mRatBN7.21154,702,290 - 54,776,618 (+)NCBI
Rnor_6.01157,108,956 - 57,183,265 (+)NCBI
Rnor_5.01160,273,387 - 60,347,696 (+)NCBI
RGSC_v3.41156,183,593 - 56,258,568 (+)RGD
Celera1154,231,989 - 54,305,717 (+)RGD
Sequence:
RefSeq Acc Id: XM_063270703   ⟹   XP_063126773
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81168,174,746 - 68,239,266 (+)NCBI
Protein Sequences
Protein RefSeqs NP_001020203 (Get FASTA)   NCBI Sequence Viewer  
  XP_063126773 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAH91206 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000034871
  ENSRNOP00000034871.5
GenBank Protein Q5BK49 (Get FASTA)   NCBI Sequence Viewer  
RefSeq Acc Id: NP_001020203   ⟸   NM_001025032
- Peptide Label: precursor
- UniProtKB: Q5BK49 (UniProtKB/Swiss-Prot),   A6IQW9 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000034871   ⟸   ENSRNOT00000035485
RefSeq Acc Id: XP_063126773   ⟸   XM_063270703
- Peptide Label: isoform X1
Protein Domains
Ig-like   Ig-like C2-type   Ig-like V-type

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q5BK49-F1-model_v2 AlphaFold Q5BK49 1-603 view protein structure

Transcriptome

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


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1565249 AgrOrtholog
BioCyc Gene G2FUF-21394 BioCyc
Ensembl Genes ENSRNOG00000023030 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000035485 ENTREZGENE
  ENSRNOT00000035485.8 UniProtKB/Swiss-Prot
Gene3D-CATH 2.60.40.10 UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:7380788 IMAGE-MGC_LOAD
InterPro CD80_C2-set UniProtKB/Swiss-Prot
  CD96 UniProtKB/Swiss-Prot
  Ig-like_dom UniProtKB/Swiss-Prot
  Ig-like_dom_sf UniProtKB/Swiss-Prot
  Ig-like_fold UniProtKB/Swiss-Prot
  Ig_sub UniProtKB/Swiss-Prot
KEGG Report rno:498079 UniProtKB/Swiss-Prot
MGC_CLONE MGC:108908 IMAGE-MGC_LOAD
NCBI Gene 498079 ENTREZGENE
PANTHER PTHR15317 UniProtKB/Swiss-Prot
  T-CELL SURFACE PROTEIN TACTILE UniProtKB/Swiss-Prot
Pfam C2-set_2 UniProtKB/Swiss-Prot
PhenoGen Cd96 PhenoGen
PROSITE IG_LIKE UniProtKB/Swiss-Prot
RatGTEx ENSRNOG00000023030 RatGTEx
SMART SM00409 UniProtKB/Swiss-Prot
Superfamily-SCOP SSF48726 UniProtKB/Swiss-Prot
UniProt A0A8I5ZTP5_RAT UniProtKB/TrEMBL
  A6IQW9 ENTREZGENE, UniProtKB/TrEMBL
  Q5BK49 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-09-26 Cd96  CD96 molecule  Cd96  CD96 antigen  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-02-09 Cd96  CD96 antigen      Symbol and Name status set to provisional 70820 PROVISIONAL