Ly9 (lymphocyte antigen 9) - Rat Genome Database

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Gene: Ly9 (lymphocyte antigen 9) Rattus norvegicus
Analyze
Symbol: Ly9
Name: lymphocyte antigen 9
RGD ID: 1308341
Description: Predicted to be involved in T-helper 17 cell lineage commitment and positive regulation of interleukin-17 production. Predicted to be located in cell surface and plasma membrane. Predicted to be active in external side of plasma membrane. Orthologous to human LY9 (lymphocyte antigen 9); INTERACTS WITH 1-naphthyl isothiocyanate; acetamide; amphetamine.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC289227; T-lymphocyte surface antigen Ly-9
RGD Orthologs
Human
Mouse
Bonobo
Dog
Pig
Green Monkey
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81386,610,762 - 86,633,314 (-)NCBIGRCr8
mRatBN7.21384,079,345 - 84,100,783 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1384,079,458 - 84,100,823 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1386,587,072 - 86,606,550 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01387,984,908 - 88,004,379 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01385,184,633 - 85,203,854 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01390,002,779 - 90,022,346 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1390,002,783 - 90,022,269 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01394,624,495 - 94,644,219 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41387,581,203 - 87,600,810 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11387,769,871 - 87,789,694 (-)NCBI
Celera1383,711,096 - 83,730,526 (-)NCBICelera
Cytogenetic Map13q24NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

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. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
3. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
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
Additional References at PubMed
PMID:1506686   PMID:22184727  


Genomics

Comparative Map Data
Ly9
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81386,610,762 - 86,633,314 (-)NCBIGRCr8
mRatBN7.21384,079,345 - 84,100,783 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1384,079,458 - 84,100,823 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1386,587,072 - 86,606,550 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01387,984,908 - 88,004,379 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01385,184,633 - 85,203,854 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01390,002,779 - 90,022,346 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1390,002,783 - 90,022,269 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01394,624,495 - 94,644,219 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41387,581,203 - 87,600,810 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11387,769,871 - 87,789,694 (-)NCBI
Celera1383,711,096 - 83,730,526 (-)NCBICelera
Cytogenetic Map13q24NCBI
LY9
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381160,796,174 - 160,828,255 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1160,796,074 - 160,828,261 (+)EnsemblGRCh38hg38GRCh38
GRCh371160,765,964 - 160,798,045 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361159,032,552 - 159,064,669 (+)NCBINCBI36Build 36hg18NCBI36
Build 341157,579,000 - 157,611,116NCBI
Celera1133,834,603 - 133,866,716 (+)NCBICelera
Cytogenetic Map1q23.3NCBI
HuRef1132,122,027 - 132,154,181 (+)NCBIHuRef
CHM1_11162,161,240 - 162,193,425 (+)NCBICHM1_1
T2T-CHM13v2.01159,933,205 - 159,965,298 (+)NCBIT2T-CHM13v2.0
Ly9
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391171,416,172 - 171,434,917 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1171,416,192 - 171,434,978 (-)EnsemblGRCm39 Ensembl
GRCm381171,588,613 - 171,607,410 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1171,588,624 - 171,607,410 (-)EnsemblGRCm38mm10GRCm38
MGSCv371173,518,744 - 173,537,491 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361173,425,307 - 173,443,949 (-)NCBIMGSCv36mm8
Celera1174,446,275 - 174,464,989 (-)NCBICelera
Cytogenetic Map1H3NCBI
cM Map179.54NCBI
LY9
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2189,019,244 - 89,054,064 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1188,759,668 - 88,794,378 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01136,151,608 - 136,185,365 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11140,075,646 - 140,107,790 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1140,075,646 - 140,107,784 (+)Ensemblpanpan1.1panPan2
LY9
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.13821,522,898 - 21,554,652 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl3821,523,637 - 21,554,579 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha3821,595,867 - 21,627,680 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.03821,640,415 - 21,671,866 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl3821,640,585 - 21,671,783 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.13821,527,340 - 21,559,137 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.03821,941,122 - 21,972,926 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.03822,351,067 - 22,382,513 (-)NCBIUU_Cfam_GSD_1.0
LY9
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl489,701,359 - 89,729,855 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1489,701,806 - 89,728,848 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2497,518,786 - 97,545,794 (+)NCBISscrofa10.2Sscrofa10.2susScr3
LY9
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1203,140,059 - 3,145,818 (-)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_0236660382,180,473 - 2,209,597 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0

Variants

.
Variants in Ly9
206 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:148
Count of miRNA genes:120
Interacting mature miRNAs:125
Transcripts:ENSRNOT00000035498
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 (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1354666Bp244Blood pressure QTL 2444.9arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)131101056920Rat
1354666Bp244Blood pressure QTL 2444.9arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)131101056920Rat
1354666Bp244Blood pressure QTL 2444.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)131101056920Rat
1581570Eae17Experimental allergic encephalomyelitis QTL 174.1nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)138897350101631289Rat
7207885Glom27Glomerulus QTL 273.9kidney glomerulus integrity trait (VT:0010546)kidney crescentic glomeruli count to kidney normal glomeruli count ratio (CMO:0002139)1320605871101339738Rat
1354621Rf47Renal function QTL 473.7kidney renin amount (VT:0010559)kidney renin level (CMO:0002166)1330395351101056920Rat
70181BpQTLcluster11Blood pressure QTL cluster 116.922arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)133124133193395974Rat
70181BpQTLcluster11Blood pressure QTL cluster 116.922arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)133124133193395974Rat
70181BpQTLcluster11Blood pressure QTL cluster 116.922arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)133124133193395974Rat
70181BpQTLcluster11Blood pressure QTL cluster 116.922arterial blood pressure trait (VT:2000000)absolute change in mean arterial blood pressure (CMO:0000533)133124133193395974Rat
619615Bp80Blood pressure QTL 800.0354arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)133975454484754544Rat
12879444Bp397Blood pressure QTL 397arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)134504940490049404Rat
12879471Bp398Blood pressure QTL 398arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)134551471990514719Rat
12879441Bp396Blood pressure QTL 396arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)134569998390699983Rat
1298066Bp159Blood pressure QTL 1590.004arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)134608804691088046Rat
71119Thym2Thymus enlargement QTL 23.8thymus mass (VT:0004954)thymus weight to body weight ratio (CMO:0000612)134619797684753113Rat
1641901Alcrsp6Alcohol response QTL 6response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)135236217197362171Rat
1354655Bp241Blood pressure QTL 2413.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1356056920101056920Rat
738026Lnnr5Liver neoplastic nodule remodeling QTL 53.29liver integrity trait (VT:0010547)liver remodeling tumorous lesion number (CMO:0001461)135987440885581182Rat
12879475Bp400Blood pressure QTL 400arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1361825626106807694Rat
2293702Bss34Bone structure and strength QTL 344.610.0001femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)1365103704106807694Rat
2293687Bss26Bone structure and strength QTL 264.60.0001femur morphology trait (VT:0000559)femur cross-sectional area (CMO:0001661)1365103704106807694Rat
8655945Rf61Renal function QTL 613.6blood creatinine amount (VT:0005328)creatinine clearance (CMO:0000765)136906051986800898Rat
1331783Bp221Blood pressure QTL 2213.72886arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)136906051986800898Rat
1300166Kidm6Kidney mass QTL 63.93kidney mass (VT:0002707)single kidney wet weight to body weight ratio (CMO:0000622)136906051986800898Rat
8655959Pur32Proteinuria QTL 328.4urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)137402391897213863Rat
738027Lnnr6Liver neoplastic nodule remodeling QTL 63.3liver integrity trait (VT:0010547)liver remodeling tumorous lesion number (CMO:0001461)137486211785581182Rat
2293341Glom15Glomerulus QTL 159.1kidney glomerulus integrity trait (VT:0010546)kidney sclerotic glomeruli count to total glomeruli count ratio (CMO:0001269)1374862117101339893Rat
4889606Gluco63Glucose level QTL 632.860.003blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)1380753256106807694Rat

Markers in Region
G42060  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21384,099,761 - 84,099,910 (+)MAPPERmRatBN7.2
Rnor_6.01390,021,262 - 90,021,410NCBIRnor6.0
Rnor_5.01394,643,553 - 94,643,701UniSTSRnor5.0
RGSC_v3.41387,599,682 - 87,599,830UniSTSRGSC3.4
Celera1383,729,573 - 83,729,721UniSTS
Cytogenetic Map13q24UniSTS


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 1 8 19 5
Low 1 7 13 5 5 4 16 11
Below cutoff 1 22 26 26 26 8 9 26 17 6 8

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000035498   ⟹   ENSRNOP00000036230
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1384,082,824 - 84,100,823 (-)Ensembl
Rnor_6.0 Ensembl1390,002,783 - 90,022,269 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000096361   ⟹   ENSRNOP00000087223
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1384,079,458 - 84,100,823 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000100394   ⟹   ENSRNOP00000088162
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1384,079,458 - 84,100,757 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000103580   ⟹   ENSRNOP00000092458
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1384,079,458 - 84,100,823 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000113721   ⟹   ENSRNOP00000081109
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1384,079,458 - 84,100,823 (-)Ensembl
RefSeq Acc Id: NM_001191673   ⟹   NP_001178602
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81386,611,755 - 86,633,190 (-)NCBI
mRatBN7.21384,079,345 - 84,100,783 (-)NCBI
Rnor_6.01390,002,783 - 90,022,269 (-)NCBI
Rnor_5.01394,624,495 - 94,644,219 (-)NCBI
Celera1383,711,096 - 83,730,526 (-)NCBI
Sequence:
RefSeq Acc Id: XM_063272129   ⟹   XP_063128199
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81386,610,762 - 86,633,314 (-)NCBI
Protein Sequences
Protein RefSeqs NP_001178602 (Get FASTA)   NCBI Sequence Viewer  
  XP_063128199 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL94660 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000036230.6
  ENSRNOP00000081109.1
  ENSRNOP00000087223.1
  ENSRNOP00000088162.1
  ENSRNOP00000092458
  ENSRNOP00000092458.1
Reference Protein Sequences
RefSeq Acc Id: NP_001178602   ⟸   NM_001191673
- UniProtKB: A0A8I6GJS8 (UniProtKB/TrEMBL),   A0A8I5ZS62 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000036230   ⟸   ENSRNOT00000035498
RefSeq Acc Id: ENSRNOP00000087223   ⟸   ENSRNOT00000096361
RefSeq Acc Id: ENSRNOP00000088162   ⟸   ENSRNOT00000100394
RefSeq Acc Id: ENSRNOP00000081109   ⟸   ENSRNOT00000113721
RefSeq Acc Id: ENSRNOP00000092458   ⟸   ENSRNOT00000103580
RefSeq Acc Id: XP_063128199   ⟸   XM_063272129
- Peptide Label: isoform X1
- UniProtKB: A0A8I6A5H0 (UniProtKB/TrEMBL)
Protein Domains
Ig-like

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZEF7-F1-model_v2 AlphaFold D3ZEF7 1-655 view protein structure

Transcriptome

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

Promoters
RGD ID:13699012
Promoter ID:EPDNEW_R9537
Type:single initiation site
Name:Ly9_1
Description:lymphocyte antigen 9
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_6.01390,022,295 - 90,022,355EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1308341 AgrOrtholog
BioCyc Gene G2FUF-17356 BioCyc
Ensembl Genes ENSRNOG00000025069 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000035498.6 UniProtKB/TrEMBL
  ENSRNOT00000096361.1 UniProtKB/TrEMBL
  ENSRNOT00000100394.1 UniProtKB/TrEMBL
  ENSRNOT00000103580 ENTREZGENE
  ENSRNOT00000103580.1 UniProtKB/TrEMBL
  ENSRNOT00000113721.1 UniProtKB/TrEMBL
Gene3D-CATH 2.60.40.10 UniProtKB/TrEMBL
InterPro Ig-like UniProtKB/TrEMBL
  Ig-like_dom_sf UniProtKB/TrEMBL
  Ig-like_fold UniProtKB/TrEMBL
  Ig_sub UniProtKB/TrEMBL
  Ig_V-set UniProtKB/TrEMBL
KEGG Report rno:289227 UniProtKB/TrEMBL
NCBI Gene 289227 ENTREZGENE
PANTHER SIGNALING LYMPHOCYTIC ACTIVATION MOLECULE UniProtKB/TrEMBL
  T-LYMPHOCYTE SURFACE ANTIGEN LY-9 UniProtKB/TrEMBL
Pfam Ig_2 UniProtKB/TrEMBL
  V-set UniProtKB/TrEMBL
PhenoGen Ly9 PhenoGen
PROSITE IG_LIKE UniProtKB/TrEMBL
RatGTEx ENSRNOG00000025069 RatGTEx
SMART SM00409 UniProtKB/TrEMBL
Superfamily-SCOP SSF48726 UniProtKB/TrEMBL
UniProt A0A8I5ZS62 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I6A4J1_RAT UniProtKB/TrEMBL
  A0A8I6A5H0 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I6GJS8 ENTREZGENE, UniProtKB/TrEMBL
  D3ZEF7_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-04-30 Ly9  lymphocyte antigen 9   Ly9_predicted  lymphocyte antigen 9 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Ly9_predicted  lymphocyte antigen 9 (predicted)      Symbol and Name status set to approved 70820 APPROVED