Ly6al1 (lymphocyte antigen 6 complex, locus A like 1) - Rat Genome Database

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Gene: Ly6al1 (lymphocyte antigen 6 complex, locus A like 1) Rattus norvegicus
Analyze
Symbol: Ly6al1
Name: lymphocyte antigen 6 complex, locus A like 1
RGD ID: 1586182
Description: Predicted to enable acetylcholine receptor binding activity and acetylcholine receptor inhibitor activity. Predicted to be involved in acetylcholine receptor signaling pathway. Predicted to be located in side of membrane and synapse. Predicted to be active in plasma membrane. Orthologous to several human genes including LY6H (lymphocyte antigen 6 family member H); INTERACTS WITH bilirubin IXalpha (ortholog); nickel atom (ortholog); trichostatin A (ortholog).
Type: protein-coding
RefSeq Status: MODEL
Previously known as: LOC300024; Ly6-A antigen; lymphocyte antigen 6B; lymphocyte antigen 6B-like; similar to Ly6-B antigen gene
RGD Orthologs
Human
Bonobo
Green Monkey
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr87108,892,342 - 108,898,892 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl7108,892,339 - 108,895,989 (-)EnsemblGRCr8
mRatBN7.27107,011,585 - 107,018,125 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl7107,011,623 - 107,015,179 (-)EnsemblmRatBN7.2
Rnor_6.07116,373,318 - 116,377,259 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_5.07116,268,691 - 116,272,614 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.47113,242,197 - 113,245,765 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera7103,383,921 - 103,387,578 (-)NCBICelera
Cytogenetic Map7q34NCBI
JBrowse:




Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

References

Genomics

Comparative Map Data
Ly6al1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr87108,892,342 - 108,898,892 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl7108,892,339 - 108,895,989 (-)EnsemblGRCr8
mRatBN7.27107,011,585 - 107,018,125 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl7107,011,623 - 107,015,179 (-)EnsemblmRatBN7.2
Rnor_6.07116,373,318 - 116,377,259 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_5.07116,268,691 - 116,272,614 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.47113,242,197 - 113,245,765 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera7103,383,921 - 103,387,578 (-)NCBICelera
Cytogenetic Map7q34NCBI
LY6S
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh388143,040,839 - 143,076,471 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl8143,040,839 - 143,048,357 (-)Ensemblhg38GRCh38
GRCh378144,122,256 - 144,127,127 (-)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map8q24.3NCBI
T2T-CHM13v2.08144,184,770 - 144,189,740 (-)NCBIT2T-CHM13v2.0
LOC129398654
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v27160,501,883 - 160,504,468 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan18136,014,402 - 136,018,734 (-)NCBINHGRI_mPanPan1
LY6S
(Chlorocebus sabaeus - green monkey)		 No map positions available.

Variants

.
Variants in Ly6al1
16 total Variants

QTLs in Region (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1300179Kidm5Kidney mass QTL 53.51kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)792388565119280177Rat
1331728Bp214Blood pressure QTL 2142.825arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)782111245123048330Rat
1331731Bp216Blood pressure QTL 2162.851arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)7104186212135371468Rat
1358361Sradr5Stress Responsive Adrenal Weight QTL 55.55adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)731770293110435881Rat
1357338Stl17Serum triglyceride level QTL 173.23blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)771621154114982716Rat
70159Bp61Blood pressure QTL 610.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)773618702118618702Rat
631687Hcas1Hepatocarcinoma susceptibility QTL 13.90.001liver integrity trait (VT:0010547)liver tumorous lesion volume to total liver volume ratio (CMO:0001082)793302009131686183Rat
61397Bw17Body weight QTL 176.3body mass (VT:0001259)body weight (CMO:0000012)795485047137014596Rat
631504Cm27Cardiac mass QTL 273.45heart left ventricle mass (VT:0007031)heart left ventricle wet weight (CMO:0000071)746307490127866166Rat
634322Bw12Body weight QTL 120body mass (VT:0001259)body weight (CMO:0000012)785043242130043242Rat
70173Niddm19Non-insulin dependent diabetes mellitus QTL 194.330.00005blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)785497398130497398Rat
1549899Stresp8Stress response QTL 84.370.0008stress-related behavior trait (VT:0010451)defensive burying duration (CMO:0001961)792362341137014596Rat
2317052Aia17Adjuvant induced arthritis QTL 172.13joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)783626689128626689Rat
1331723Bw25Body weight QTL 253.348body mass (VT:0001259)body weight (CMO:0000012)796700404111672180Rat
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)782111382132099989Rat
731176Glom5Glomerulus QTL 52.50.0035kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)798549867137014596Rat
7411607Foco15Food consumption QTL 150.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)777807807122807807Rat
631201Panci1Pancreas inflammation QTL 100.001pancreas integrity trait (VT:0010560)percentage of study population displaying chronic pancreatitis at a point in time (CMO:0001214)773557047118557047Rat
634336Anxrr17Anxiety related response QTL 173.66locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)71509236116977875Rat
1331768Kidm10Kidney mass QTL 104.62096kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)782111245123048330Rat
61357Bp38Blood pressure QTL 381.60.052arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)740540077123682549Rat
2313102Bmd79Bone mineral density QTL 792.30.0001tibia mineral mass (VT:1000283)total volumetric bone mineral density (CMO:0001728)796700404118618702Rat
2316947Rf58Renal function QTL 587.8kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)749682832115766396Rat
10450862Kidm55Kidney mass QTL 554.9kidney mass (VT:0002707)kidney weight (CMO:0000081)772725037117725037Rat
61428Scl3Serum cholesterol level QTL 33.2blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)7100548246137014596Rat
1331746Kidm9Kidney mass QTL 93.934kidney mass (VT:0002707)right kidney wet weight (CMO:0000082)782111245134948181Rat
10450856Livw4Liver weight QTL 43.8liver mass (VT:0003402)liver weight (CMO:0000092)772725037117725037Rat
7411654Foco25Food consumption QTL 259.30.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)777807807122807807Rat
2316955Stl24Serum triglyceride level QTL 247.1blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)749682832115766396Rat
10402855Bp379Blood pressure QTL 3790.21arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)778682549123682549Rat
2316952Pur22Proteinuria QTL 225.2urine protein amount (VT:0005160)urine protein level (CMO:0000591)749682832115766396Rat
631540Bw9Body weight QTL 94.5body mass (VT:0001259)body weight (CMO:0000012)771621154119349044Rat
1358891Bp265Blood pressure QTL 2652.21arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)771827901136544683Rat

Markers in Region
RH127485  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.27107,011,671 - 107,011,862 (+)MAPPERmRatBN7.2
mRatBN7.27107,062,406 - 107,062,596 (+)MAPPERmRatBN7.2
Rnor_6.07116,419,660 - 116,419,849NCBIRnor6.0
Rnor_6.07116,373,405 - 116,373,595NCBIRnor6.0
Rnor_5.07116,315,624 - 116,315,813UniSTSRnor5.0
Rnor_5.07116,268,775 - 116,268,965UniSTSRnor5.0
RGSC_v3.47113,242,279 - 113,242,469UniSTSRGSC3.4
RGSC_v3.47113,306,093 - 113,306,282UniSTSRGSC3.4
Celera7103,432,551 - 103,432,740UniSTS
Celera7103,384,008 - 103,384,198UniSTS
RH 3.4 Map7770.7UniSTS
Cytogenetic Map7q34UniSTS
AI789751  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.27107,011,792 - 107,011,963 (+)MAPPERmRatBN7.2
Rnor_6.07116,373,526 - 116,373,696NCBIRnor6.0
Rnor_5.07116,268,896 - 116,269,066UniSTSRnor5.0
RGSC_v3.47113,242,400 - 113,242,570UniSTSRGSC3.4
RGSC_v3.47113,370,425 - 113,370,593UniSTSRGSC3.4
Celera7103,384,129 - 103,384,299UniSTS
Cytogenetic Map7q34UniSTS


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
hemolymphoid system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
sensory system
visual system
3 1 5 19 66 118 80 10 12 35 2 3 3

Sequence


Ensembl Acc Id: ENSRNOT00000071792
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl7116,373,697 - 116,376,822 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000076148
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl7116,373,728 - 116,379,331 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000076236   ⟹   ENSRNOP00000085819
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl7108,892,339 - 108,895,989 (-)Ensembl
mRatBN7.2 Ensembl7107,011,623 - 107,015,179 (-)Ensembl
Rnor_6.0 Ensembl7116,373,323 - 116,376,897 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000082405
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl7116,373,324 - 116,504,853 (-)Ensembl
RefSeq Acc Id: XM_017595247   ⟹   XP_017450736
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr87108,892,342 - 108,896,141 (-)NCBI
mRatBN7.27107,011,585 - 107,015,388 (-)NCBI
Rnor_6.07116,373,318 - 116,376,971 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039080267   ⟹   XP_038936195
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr87108,892,342 - 108,898,892 (-)NCBI
mRatBN7.27107,011,585 - 107,018,125 (-)NCBI
RefSeq Acc Id: XM_039080268   ⟹   XP_038936196
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr87108,892,342 - 108,898,384 (-)NCBI
mRatBN7.27107,011,585 - 107,017,616 (-)NCBI
RefSeq Acc Id: XM_039080269   ⟹   XP_038936197
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr87108,892,342 - 108,896,144 (-)NCBI
mRatBN7.27107,011,585 - 107,015,391 (-)NCBI
Protein Sequences
Protein RefSeqs XP_017450736 (Get FASTA)   NCBI Sequence Viewer  
  XP_038936195 (Get FASTA)   NCBI Sequence Viewer  
  XP_038936196 (Get FASTA)   NCBI Sequence Viewer  
  XP_038936197 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAA41545 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000085819
  ENSRNOP00000085819.1
RefSeq Acc Id: XP_017450736   ⟸   XM_017595247
- Peptide Label: isoform X1
- UniProtKB: A0A8I6A377 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_038936195   ⟸   XM_039080267
- Peptide Label: isoform X2
- UniProtKB: Q63316 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038936196   ⟸   XM_039080268
- Peptide Label: isoform X2
- UniProtKB: Q63316 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038936197   ⟸   XM_039080269
- Peptide Label: isoform X2
- UniProtKB: Q63316 (UniProtKB/TrEMBL)
Ensembl Acc Id: ENSRNOP00000085819   ⟸   ENSRNOT00000076236
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:1586182 AgrOrtholog
BioCyc Gene G2FUF-33001 BioCyc
Ensembl Genes ENSRNOG00000048850 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000076236 ENTREZGENE
  ENSRNOT00000076236.4 UniProtKB/TrEMBL
Gene3D-CATH 2.10.60.10 UniProtKB/TrEMBL
InterPro LY6_UPA_recep-like UniProtKB/TrEMBL
  LY6H/LY6L_nAChR_modulators UniProtKB/TrEMBL
  Snake_toxin-like_sf UniProtKB/TrEMBL
KEGG Report rno:300024 UniProtKB/TrEMBL
NCBI Gene 300024 ENTREZGENE
PANTHER LYMPHOCYTE ANTIGEN 6 COMPLEX, LOCUS G2-RELATED UniProtKB/TrEMBL
  LYMPHOCYTE ANTIGEN 6H UniProtKB/TrEMBL
Pfam UPAR_LY6 UniProtKB/TrEMBL
PhenoGen Ly6al1 PhenoGen
RatGTEx ENSRNOG00000048850 RatGTEx
SMART SM00134 UniProtKB/TrEMBL
Superfamily-SCOP SSF57302 UniProtKB/TrEMBL
UniProt A0A8I6A377 ENTREZGENE, UniProtKB/TrEMBL
  Q63316 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2023-09-19 Ly6al1  lymphocyte antigen 6 complex, locus A like 1  LOC300024  similar to Ly6-B antigen gene  Symbol and Name Changed 1299863 APPROVED
2006-11-19 LOC300024  similar to Ly6-B antigen gene      Symbol and Name status set to provisional 70820 PROVISIONAL