Cd99 (CD99 molecule (Xg blood group)) - Rat Genome Database

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Gene: Cd99 (CD99 molecule (Xg blood group)) Rattus norvegicus
Analyze
Symbol: Cd99
Name: CD99 molecule (Xg blood group)
RGD ID: 1594332
Description: Predicted to act upstream of or within several processes, including T cell extravasation; myeloid dendritic cell activation; and positive regulation of neutrophil extravasation. Predicted to be located in cell surface. Orthologous to human CD99 (CD99 molecule (Xg blood group)); INTERACTS WITH 2,2',4,4'-Tetrabromodiphenyl ether; 2,3,7,8-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: CD99 antigen; CD99 molecule
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr82056,000,494 - 56,005,140 (-)NCBIGRCr8
mRatBN7.22054,418,239 - 54,422,882 (-)NCBImRatBN7.2mRatBN7.2
UTH_Rnor_SHR_Utx2056,146,035 - 56,150,632 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.02055,795,712 - 55,800,309 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.02056,488,241 - 56,492,838 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.02056,192,426 - 56,196,961 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2056,192,390 - 56,197,025 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02057,779,372 - 57,783,907 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera2045,754,299 - 45,758,893 (+)NCBICelera
Cytogenetic Map20q13NCBI
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 surface  (ISO)

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. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:12477932   PMID:14970179   PMID:15978751   PMID:17344467   PMID:21423176   PMID:35352799  


Genomics

Comparative Map Data
Cd99
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr82056,000,494 - 56,005,140 (-)NCBIGRCr8
mRatBN7.22054,418,239 - 54,422,882 (-)NCBImRatBN7.2mRatBN7.2
UTH_Rnor_SHR_Utx2056,146,035 - 56,150,632 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.02055,795,712 - 55,800,309 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.02056,488,241 - 56,492,838 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.02056,192,426 - 56,196,961 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2056,192,390 - 56,197,025 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02057,779,372 - 57,783,907 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera2045,754,299 - 45,758,893 (+)NCBICelera
Cytogenetic Map20q13NCBI
CD99
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38Y2,691,295 - 2,741,309 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38X2,691,295 - 2,741,309 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 EnsemblX2,691,187 - 2,741,309 (+)EnsemblGRCh38hg38GRCh38
GRCh38.p14 EnsemblY2,691,187 - 2,741,309 (+)EnsemblGRCh38hg38GRCh38
GRCh37X2,609,336 - 2,659,350 (+)NCBIGRCh37GRCh37hg19GRCh37
GRCh37Y2,559,336 - 2,609,350 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36Y2,619,228 - 2,669,350 (+)NCBINCBI36Build 36hg18NCBI36
Build 36X2,619,228 - 2,669,350 (+)NCBINCBI36Build 36hg18NCBI36
Build 34Y2,602,588 - 2,652,709NCBI
CeleraX6,889,623 - 6,939,779 (+)NCBICelera
Cytogenetic MapX;YNCBI
HuRefX550,662 - 601,242 (+)NCBIHuRef
CHM1_1X2,639,584 - 2,689,681 (+)NCBICHM1_1
T2T-CHM13v2.0X2,304,268 - 2,354,297 (+)NCBIT2T-CHM13v2.0
T2T-CHM13v2.0Y2,368,252 - 2,418,268 (+)NCBIT2T-CHM13v2.0
Cd99
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Cytogenetic Map4 NCBI
Cd99
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_0049554991,607,382 - 1,646,172 (+)NCBIChiLan1.0ChiLan1.0
LOC100994485
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2Y44,439,873 - 44,492,027 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1-v2X2,433,098 - 2,484,973 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1X2,436,860 - 2,488,645 (+)NCBINHGRI_mPanPan1
NHGRI_mPanPan1Y2,434,971 - 2,487,126 (+)NCBINHGRI_mPanPan1
PanPan1.1X2,643,033 - 2,694,828 (+)NCBIpanpan1.1PanPan1.1panPan2
CD99
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1X1,369,316 - 1,430,527 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Dog10K_Boxer_TashaX1,346,278 - 1,381,038 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0X1,318,887 - 1,353,410 (+)NCBIROS_Cfam_1.0
UMICH_Zoey_3.1X1,309,594 - 1,344,332 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0X1,325,654 - 1,360,395 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0X1,362,108 - 1,396,897 (+)NCBIUU_Cfam_GSD_1.0
Cd99
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404953810,677 - 819,691 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049366443,557,048 - 3,566,046 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049366443,557,082 - 3,566,057 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CD99
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1Y5,946,851 - 5,983,610 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Cd99
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248341,165,420 - 1,195,438 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Cd99
52 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:49
Count of miRNA genes:45
Interacting mature miRNAs:49
Transcripts:ENSRNOT00000073028
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 (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2303587Bw93Body weight QTL 9313body mass (VT:0001259)body weight (CMO:0000012)202510672254435887Rat
7411652Foco24Food consumption QTL 240.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)201175751554435887Rat
1331747Hrtrt16Heart rate QTL 163.163heart pumping trait (VT:2000009)heart rate (CMO:0000002)202520973454435887Rat
2303626Vencon10Ventilatory control QTL 100.001respiration trait (VT:0001943)respiration rate (CMO:0000289)201919072154435887Rat
2303578Gluco50Glucose level QTL 502blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)202510672254435887Rat
2317880Alcrsp25Alcohol response QTL 252.3response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)201769755054435887Rat
1598869Memor6Memory QTL 63.1exploratory behavior trait (VT:0010471)total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)202924438854435887Rat
9590092Insglur9Insulin/glucose ratio QTL 918.380.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)201175751554435887Rat
2300188Bmd68Bone mineral density QTL 686.40.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)202510672254435887Rat


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
nervous system
renal system
reproductive system
respiratory system
9 11 49 113 91 90 59 25 59 6 218 97 93 45 60 31

Sequence


Ensembl Acc Id: ENSRNOT00000073028   ⟹   ENSRNOP00000067281
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl2056,192,390 - 56,197,025 (-)Ensembl
RefSeq Acc Id: NM_001100804   ⟹   NP_001094274
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr82056,000,494 - 56,005,088 (-)NCBI
mRatBN7.22054,418,239 - 54,422,833 (-)NCBI
Rnor_6.02056,192,426 - 56,196,961 (-)NCBI
Rnor_5.02057,779,372 - 57,783,907 (-)NCBI
Celera2045,754,299 - 45,758,893 (+)RGD
Sequence:
RefSeq Acc Id: XM_039099056   ⟹   XP_038954984
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr82056,000,494 - 56,005,140 (-)NCBI
mRatBN7.22054,418,239 - 54,422,882 (-)NCBI
RefSeq Acc Id: XM_039099057   ⟹   XP_038954985
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr82056,000,494 - 56,005,140 (-)NCBI
mRatBN7.22054,418,239 - 54,422,882 (-)NCBI
RefSeq Acc Id: XM_063279500   ⟹   XP_063135570
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr82056,000,494 - 56,005,105 (-)NCBI
RefSeq Acc Id: XM_063279501   ⟹   XP_063135571
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr82056,001,991 - 56,005,105 (-)NCBI
RefSeq Acc Id: XM_063279502   ⟹   XP_063135572
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr82056,001,991 - 56,005,140 (-)NCBI
RefSeq Acc Id: NP_001094274   ⟸   NM_001100804
- Peptide Label: precursor
- UniProtKB: B4F7A5 (UniProtKB/TrEMBL),   Q4L2A2 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000067281   ⟸   ENSRNOT00000073028
RefSeq Acc Id: XP_038954985   ⟸   XM_039099057
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038954984   ⟸   XM_039099056
- Peptide Label: isoform X2
- UniProtKB: A6K6T0 (UniProtKB/TrEMBL),   Q4L2A2 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063135570   ⟸   XM_063279500
- Peptide Label: isoform X1
RefSeq Acc Id: XP_063135572   ⟸   XM_063279502
- Peptide Label: isoform X5
RefSeq Acc Id: XP_063135571   ⟸   XM_063279501
- Peptide Label: isoform X4
- UniProtKB: A6K6T1 (UniProtKB/TrEMBL)

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-B4F7A5-F1-model_v2 AlphaFold B4F7A5 1-165 view protein structure

Transcriptome

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

Promoters
RGD ID:13701688
Promoter ID:EPDNEW_R12211
Type:multiple initiation site
Name:Cd99_1
Description:CD99 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_6.02056,196,958 - 56,197,018EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1594332 AgrOrtholog
BioCyc Gene G2FUF-3217 BioCyc
Ensembl Genes ENSRNOG00000050735 Ensembl
InterPro CD99L2 UniProtKB/TrEMBL
KEGG Report rno:652929 UniProtKB/TrEMBL
NCBI Gene 652929 ENTREZGENE
PANTHER CD99 ANTIGEN UniProtKB/TrEMBL
  PTHR15076 UniProtKB/TrEMBL
Pfam CD99L2 UniProtKB/TrEMBL
PhenoGen Cd99 PhenoGen
RatGTEx ENSRNOG00000050735 RatGTEx
UniProt A6K6T0 ENTREZGENE, UniProtKB/TrEMBL
  A6K6T1 ENTREZGENE, UniProtKB/TrEMBL
  B4F7A5 ENTREZGENE, UniProtKB/TrEMBL
  Q4L2A2 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2017-03-27 Cd99  CD99 molecule (Xg blood group)  Cd99  CD99 molecule  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2013-08-01 Cd99  CD99 molecule  Cd99  CD99 antigen  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-11-20 Cd99  CD99 antigen      Symbol and Name status set to provisional 70820 PROVISIONAL