Ly6l (lymphocyte antigen 6 family member L) - Rat Genome Database

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Gene: Ly6l (lymphocyte antigen 6 family member L) Rattus norvegicus
Analyze
Symbol: Ly6l
Name: lymphocyte antigen 6 family member L
RGD ID: 1597652
Description: Orthologous to human LY6L (lymphocyte antigen 6 family member L); INTERACTS WITH 17beta-estradiol; 17beta-estradiol 3-benzoate; Cuprizon.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: hypothetical protein LOC686432; LOC686432; lymphocyte antigen 6 complex, locus L; lymphocyte antigen 6H; lymphocyte antigen 6L
RGD Orthologs
Human
Mouse
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr87109,101,360 - 109,103,440 (+)NCBIGRCr8
mRatBN7.27107,220,612 - 107,222,692 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl7107,141,903 - 107,143,843 (+)EnsemblmRatBN7.2 Ensembl
Rnor_6.07116,444,786 - 116,447,400 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl7116,444,687 - 116,447,400 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.07116,340,750 - 116,343,364 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera7103,508,980 - 103,511,714 (+)NCBICelera
Cytogenetic Map7q34NCBI
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

Cellular Component

References

Genomics

Comparative Map Data
Ly6l
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr87109,101,360 - 109,103,440 (+)NCBIGRCr8
mRatBN7.27107,220,612 - 107,222,692 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl7107,141,903 - 107,143,843 (+)EnsemblmRatBN7.2 Ensembl
Rnor_6.07116,444,786 - 116,447,400 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl7116,444,687 - 116,447,400 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.07116,340,750 - 116,343,364 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera7103,508,980 - 103,511,714 (+)NCBICelera
Cytogenetic Map7q34NCBI
LY6L
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh388143,080,630 - 143,083,486 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl8143,080,630 - 143,083,486 (+)EnsemblGRCh38hg38GRCh38
GRCh378144,162,047 - 144,164,903 (+)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map8q24.3NCBI
HuRef8139,415,909 - 139,418,742 (+)NCBIHuRef
CHM1_18144,202,836 - 144,205,669 (+)NCBICHM1_1
T2T-CHM13v2.08144,224,950 - 144,227,806 (+)NCBIT2T-CHM13v2.0
Ly6l
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391575,321,301 - 75,323,662 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1575,321,306 - 75,323,255 (+)EnsemblGRCm39 Ensembl
GRCm381575,449,452 - 75,451,813 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1575,449,457 - 75,451,406 (+)EnsemblGRCm38mm10GRCm38
Celera1576,948,561 - 76,953,991 (+)NCBICelera
Cytogenetic Map15D3NCBI
cM Map1534.37NCBI
LY6L
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v27160,554,025 - 160,556,307 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan18136,071,302 - 136,073,512 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v08139,824,268 - 139,826,618 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
LY6L
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Dog10K_Boxer_Tasha1336,914,398 - 36,917,433 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01337,433,340 - 37,436,378 (+)NCBIROS_Cfam_1.0
UMICH_Zoey_3.11337,105,973 - 37,109,008 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01337,224,428 - 37,227,463 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01337,701,250 - 37,704,286 (+)NCBIUU_Cfam_GSD_1.0
Ly6l
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_0244053031,433,096 - 1,435,720 (-)NCBIHiC_Itri_2
LY6L
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl41,296,032 - 1,299,886 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.141,296,421 - 1,300,185 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.241,386,483 - 1,390,063 (-)NCBISscrofa10.2Sscrofa10.2susScr3
LY6L
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.18137,316,369 - 137,319,956 (+)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_0236660392,623,981 - 2,626,492 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Ly6l
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462473513,568,318 - 13,571,429 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Ly6l
8 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:75
Count of miRNA genes:66
Interacting mature miRNAs:67
Transcripts:ENSRNOT00000071091
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
634336Anxrr17Anxiety related response QTL 173.66locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)7924703115097879Rat
61357Bp38Blood pressure QTL 381.60.052arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)741333674119109060Rat
1358361Sradr5Stress Responsive Adrenal Weight QTL 55.55adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)743747012108555253Rat
1300179Kidm5Kidney mass QTL 53.51kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)743747012135012528Rat
631504Cm27Cardiac mass QTL 273.45heart left ventricle mass (VT:0007031)heart left ventricle wet weight (CMO:0000071)744421311118198041Rat
70173Niddm19Non-insulin dependent diabetes mellitus QTL 194.330.00005blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)764002457135012528Rat
2316947Rf58Renal function QTL 587.8kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)768938720113886318Rat
2316952Pur22Proteinuria QTL 225.2urine protein amount (VT:0005160)urine protein level (CMO:0000591)768938720113886318Rat
2316955Stl24Serum triglyceride level QTL 247.1blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)768938720113886318Rat
631540Bw9Body weight QTL 94.5body mass (VT:0001259)body weight (CMO:0000012)769736226117455174Rat
1357338Stl17Serum triglyceride level QTL 173.23blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)769736356112729554Rat
634331Pia17Pristane induced arthritis QTL 174.7joint integrity trait (VT:0010548)arthritic paw count (CMO:0001460)773829340130221005Rat
7411654Foco25Food consumption QTL 259.30.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)775918751120918751Rat
7411607Foco15Food consumption QTL 150.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)775918751120918751Rat
631529Tls2T-lymphoma susceptibility QTL 200.001thymus integrity trait (VT:0010555)percentage of study population developing T-cell lymphomas during a period of time (CMO:0001911)780221299109401111Rat
1331746Kidm9Kidney mass QTL 93.934kidney mass (VT:0002707)right kidney wet weight (CMO:0000082)780221299112308525Rat
1331728Bp214Blood pressure QTL 2142.825arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)780221299124373579Rat
1331768Kidm10Kidney mass QTL 104.62096kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)780221299125221299Rat
2317052Aia17Adjuvant induced arthritis QTL 172.13joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)781737938126737938Rat
634322Bw12Body weight QTL 120body mass (VT:0001259)body weight (CMO:0000012)783153392128153392Rat
1358891Bp265Blood pressure QTL 2652.21arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)783591953134666232Rat
1358914Bp266Blood pressure QTL 266arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)783591953134666232Rat
71114Niddm14Non-insulin dependent diabetes mellitus QTL 144.5blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)784257275129257275Rat
2298475Eau6Experimental allergic uveoretinitis QTL 60.0029uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)784257275129257275Rat
1558655Swd4Spike wave discharge measurement QTL 43.680.0002brain electrophysiology trait (VT:0010557)brain spike-and-wave discharge severity grade (CMO:0001988)786983365131983365Rat
1549899Stresp8Stress response QTL 84.370.0008stress-related behavior trait (VT:0010451)defensive burying duration (CMO:0001961)790482196135012528Rat
2299163Iddm34Insulin dependent diabetes mellitus QTL 342.71blood glucose amount (VT:0000188)age at onset/diagnosis of type 1 diabetes mellitus (CMO:0001140)791281130135012528Rat
631687Hcas1Hepatocarcinoma susceptibility QTL 13.90.001liver integrity trait (VT:0010547)liver tumorous lesion volume to total liver volume ratio (CMO:0001082)791412594129807172Rat
2313102Bmd79Bone mineral density QTL 792.30.0001tibia mineral mass (VT:1000283)total volumetric bone mineral density (CMO:0001728)794811085116738842Rat
1357336Gluco6Glucose level QTL 63.4blood glucose amount (VT:0000188)serum glucose level (CMO:0000543)794811326116294265Rat
731176Glom5Glomerulus QTL 52.50.0035kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)796670164135012528Rat
1331731Bp216Blood pressure QTL 2162.851arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)7102297359133492884Rat
70159Bp61Blood pressure QTL 610.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)7103146217116738842Rat
731174Uae23Urinary albumin excretion QTL 232.40.0042urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)7104603555135012528Rat
2306821Bp335Blood pressure QTL 3350.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)7106571501135012528Rat

Markers in Region
AA893273  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.27107,143,928 - 107,144,019 (+)MAPPERmRatBN7.2
mRatBN7.27107,222,585 - 107,222,676 (+)MAPPERmRatBN7.2
Rnor_6.07116,447,079 - 116,447,169NCBIRnor6.0
Rnor_5.07116,343,043 - 116,343,133UniSTSRnor5.0
RGSC_v3.47113,394,685 - 113,394,775UniSTSRGSC3.4
Celera7103,511,393 - 103,511,483UniSTS
RH 3.4 Map7770.7UniSTS
BQ206735  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.27107,227,557 - 107,227,708 (+)MAPPERmRatBN7.2
Rnor_6.07116,452,145 - 116,452,295NCBIRnor6.0
Rnor_5.07116,348,109 - 116,348,259UniSTSRnor5.0
RGSC_v3.47113,478,774 - 113,478,924UniSTSRGSC3.4
Celera7103,590,969 - 103,591,119UniSTS
Celera7103,514,619 - 103,514,770UniSTS
RH 3.4 Map7772.3UniSTS


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 2 7 5 11
Low 1 4 16 16 3 16 58 28 35
Below cutoff 32 27 12 16 12 8 9 15 1 8

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000071091
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl7107,141,903 - 107,143,843 (+)Ensembl
Rnor_6.0 Ensembl7116,444,687 - 116,446,993 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000076154
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl7116,444,805 - 116,447,400 (+)Ensembl
RefSeq Acc Id: NM_001408784   ⟹   NP_001395713
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr87109,101,360 - 109,103,440 (+)NCBI
mRatBN7.27107,220,612 - 107,222,692 (+)NCBI
Protein Sequences
Protein RefSeqs NP_001395713 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000080367.1
Reference Protein Sequences
RefSeq Acc Id: NP_001395713   ⟸   NM_001408784
- Peptide Label: precursor
- UniProtKB: A0A8I6G6H8 (UniProtKB/TrEMBL)
Protein Domains
UPAR/Ly6

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:1597652 AgrOrtholog
BioCyc Gene G2FUF-32992 BioCyc
Ensembl Genes ENSRNOG00000048148 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000071091.2 UniProtKB/TrEMBL
Gene3D-CATH 2.10.60.10 UniProtKB/TrEMBL
InterPro LY6_UPA_recep-like UniProtKB/TrEMBL
  Snake_toxin-like_sf UniProtKB/TrEMBL
NCBI Gene 686432 ENTREZGENE
PANTHER LYMPHOCYTE ANTIGEN 6H UniProtKB/TrEMBL
  LYMPHOCYTE ANTIGEN 6L UniProtKB/TrEMBL
Pfam UPAR_LY6 UniProtKB/TrEMBL
PhenoGen Ly6l PhenoGen
RatGTEx ENSRNOG00000048148 RatGTEx
Superfamily-SCOP SSF57302 UniProtKB/TrEMBL
UniProt A0A8I6G6H8 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2017-02-01 Ly6l  lymphocyte antigen 6 family member L  Ly6l  lymphocyte antigen 6 complex, locus L  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2016-04-15 Ly6l  lymphocyte antigen 6 complex, locus L  LOC686432  hypothetical protein LOC686432  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-11-20 LOC686432  hypothetical protein LOC686432      Symbol and Name status set to provisional 70820 PROVISIONAL