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
Alliance Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81168,164,926 - 68,239,266 (+)NCBIGRCr8
mRatBN7.21154,702,290 - 54,776,618 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1154,702,290 - 54,776,621 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1163,465,004 - 63,546,439 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01156,126,844 - 56,208,283 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01155,241,194 - 55,322,041 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01157,108,757 - 57,183,855 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1157,108,956 - 57,183,270 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01160,273,387 - 60,347,696 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41156,183,593 - 56,258,568 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1154,231,989 - 54,305,717 (+)NCBICelera
Cytogenetic Map11q21NCBI
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

Cellular Component
cytoplasm  (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 (+)NCBIGRCr8
mRatBN7.21154,702,290 - 54,776,618 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1154,702,290 - 54,776,621 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1163,465,004 - 63,546,439 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01156,126,844 - 56,208,283 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01155,241,194 - 55,322,041 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01157,108,757 - 57,183,855 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1157,108,956 - 57,183,270 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01160,273,387 - 60,347,696 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41156,183,593 - 56,258,568 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
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 - 111,665,750 (+)EnsemblGRCh38hg38GRCh38
GRCh373111,261,044 - 111,384,843 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 363112,743,616 - 112,853,896 (+)NCBINCBI36Build 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 Ensembl
GRCm381646,035,652 - 46,120,248 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1646,035,657 - 46,120,251 (-)EnsemblGRCm38mm10GRCm38
MGSCv371646,035,770 - 46,120,361 (-)NCBIGRCm37MGSCv37mm9NCBIm37
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 (+)EnsemblChiLan1.0
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 (+)Ensemblpanpan1.1panPan2
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 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha3316,333,066 - 16,427,734 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.03316,279,316 - 16,562,843 (+)NCBIROS_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_1.0
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 (+)EnsemblSpeTri2.0SpeTri2.0 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 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
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 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604197,235,943 - 97,339,499 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0

Variants

.
Variants in Cd96
434 total Variants
miRNA Target Status

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 (mRatBN7.2)
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)11169446234Rat
1558659Tescar1Testicular tumor resistance QTL 13.9testis integrity trait (VT:0010572)percentage of study population developing testis tumors during a period of time (CMO:0001261)11104193166113562Rat
724554Iddm17Insulin dependent diabetes mellitus QTL 170.001blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)111897620886241447Rat
10058952Gmadr6Adrenal mass QTL 62.290.0072adrenal gland mass (VT:0010420)both adrenal glands wet weight to body weight ratio (CMO:0002411)112295940367959403Rat
8694376Bw156Body weight QTL 1562.250.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)112328045668280456Rat
9590313Scort20Serum corticosterone level QTL 206.510.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)112328045668280456Rat
9589032Epfw10Epididymal fat weight QTL 109.290.001epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)112328045668280456Rat
8694424Bw162Body weight QTL 1623.80.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)112328045668280456Rat
724563Uae10Urinary albumin excretion QTL 106urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)112767241082846715Rat
1300130Rf20Renal function QTL 204.44kidney glomerulus integrity trait (VT:0010546)kidney glomerulus diameter (CMO:0001166)112952841860324829Rat
1300110Stl7Serum triglyceride level QTL 74.64blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)112952841882566702Rat
2298551Neuinf10Neuroinflammation QTL 103.7nervous system integrity trait (VT:0010566)spinal cord beta-2 microglobulin mRNA level (CMO:0002125)113123913478851519Rat
70180BpQTLcluster10Blood pressure QTL cluster 103.19arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)113491804179918041Rat
1300135Rf19Renal function QTL 193.38blood creatinine amount (VT:0005328)creatinine clearance (CMO:0000765)114094618882566702Rat
2312566Glom20Glomerulus QTL 203.60.001kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)114428575982566702Rat
1581565Pur10Proteinuria QTL 100.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)114480331882846466Rat
1581572Uae35Urinary albumin excretion QTL 350.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)114480331882846466Rat
4889859Pur28Proteinuria QTL 2819.50.001urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)114545932375190161Rat
724561Plsm4Polydactyly-luxate syndrome (PLS) morphotypes QTL 40.0003forelimb integrity trait (VT:0010562)front foot phalanges count (CMO:0001947)115445753486241447Rat

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
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 13 2
Low 3 11 8 5 6 5 12 20 11
Below cutoff 10 38 34 34 6 7 42 21 13 6

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000035485   ⟹   ENSRNOP00000034871
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1154,702,290 - 54,776,615 (+)Ensembl
Rnor_6.0 Ensembl1157,108,956 - 57,183,270 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000093728
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
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
  ENSRNOP00000081817.1
  ENSRNOP00065010678
GenBank Protein Q5BK49 (Get FASTA)   NCBI Sequence Viewer  
Reference Protein Sequences
RefSeq Acc Id: NP_001020203   ⟸   NM_001025032
- Peptide Label: precursor
- UniProtKB: Q5BK49 (UniProtKB/Swiss-Prot),   A6IQW9 (UniProtKB/TrEMBL)
- Sequence:
RefSeq 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, UniProtKB/TrEMBL
  ENSRNOG00065008922 UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000035485 ENTREZGENE
  ENSRNOT00000035485.8 UniProtKB/Swiss-Prot
  ENSRNOT00000093728.2 UniProtKB/TrEMBL
  ENSRNOT00065014258 UniProtKB/Swiss-Prot
Gene3D-CATH 2.60.40.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7380788 IMAGE-MGC_LOAD
InterPro CD80_C2-set UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  CD96 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  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_sub UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:498079 UniProtKB/Swiss-Prot
MGC_CLONE MGC:108908 IMAGE-MGC_LOAD
NCBI Gene 498079 ENTREZGENE
PANTHER PTHR15317 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  T-CELL SURFACE PROTEIN TACTILE UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam C2-set_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Cd96 PhenoGen
PROSITE IG_LIKE UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
RatGTEx ENSRNOG00000023030 RatGTEx
  ENSRNOG00065008922 RatGTEx
SMART SM00409 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF48726 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
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