LY6L (lymphocyte antigen 6 family member L) - Rat Genome Database

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Gene: LY6L (lymphocyte antigen 6 family member L) Homo sapiens
Analyze
Symbol: LY6L
Name: lymphocyte antigen 6 family member L
RGD ID: 11052114
HGNC Page HGNC
Description: Predicted to localize to plasma membrane; INTERACTS WITH 17beta-estradiol (ortholog); 17beta-estradiol 3-benzoate (ortholog); testosterone (ortholog).
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: Lymphocyte antigen 6 complex locus protein L; lymphocyte antigen 6 complex, locus L; lymphocyte antigen 6A-2/6E-1-like; Lymphocyte antigen 6L
RGD Orthologs
Mouse
Rat
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl8143,080,457 - 143,083,001 (+)EnsemblGRCh38hg38GRCh38
GRCh38.p13 Ensembl8143,080,630 - 143,083,486 (+)EnsemblGRCh38hg38GRCh38
GRCh388143,080,630 - 143,083,486 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh378144,162,047 - 144,164,903 (+)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map8q24.3NCBI
HuRef8139,415,909 - 139,418,742 (+)NCBIHuRef
CHM1_18144,203,236 - 144,205,658 (+)NCBICHM1_1
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
Additional References at PubMed
PMID:21873635  


Genomics

Comparative Map Data
LY6L
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl8143,080,457 - 143,083,001 (+)EnsemblGRCh38hg38GRCh38
GRCh38.p13 Ensembl8143,080,630 - 143,083,486 (+)EnsemblGRCh38hg38GRCh38
GRCh388143,080,630 - 143,083,486 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh378144,162,047 - 144,164,903 (+)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map8q24.3NCBI
HuRef8139,415,909 - 139,418,742 (+)NCBIHuRef
CHM1_18144,203,236 - 144,205,658 (+)NCBICHM1_1
Ly6l
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391575,321,301 - 75,323,662 (+)NCBIGRCm39mm39
GRCm39 Ensembl1575,321,306 - 75,323,255 (+)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
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.27107,220,285 - 107,222,907 (+)NCBI
Rnor_6.0 Ensembl7116,444,687 - 116,447,400 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.07116,444,786 - 116,447,400 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.07116,340,750 - 116,343,364 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera7103,508,980 - 103,511,714 (+)NCBICelera
Cytogenetic Map7q34NCBI
LY6L
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Mhudiblu_PPA_v08139,824,268 - 139,826,618 (+)NCBIMhudiblu_PPA_v0panPan3
LY6L
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Dog10K_Boxer_Tasha1336,914,398 - 36,917,433 (+)NCBI
ROS_Cfam_1.01337,433,340 - 37,436,378 (+)NCBI
UMICH_Zoey_3.11337,105,973 - 37,109,008 (+)NCBI
UNSW_CanFamBas_1.01337,224,428 - 37,227,463 (+)NCBI
UU_Cfam_GSD_1.01337,701,250 - 37,704,286 (+)NCBI
Ly6l
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_0244053031,433,096 - 1,435,720 (-)NCBI
LY6L
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl41,297,033 - 1,299,951 (-)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 - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.18137,316,369 - 137,319,956 (+)NCBI
Ly6l
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462473513,568,318 - 13,571,429 (-)NCBI

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:310
Count of miRNA genes:246
Interacting mature miRNAs:256
Transcripts:ENST00000562505
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.


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 sensory system adipose tissue appendage entire extraembryonic component
High
Medium 4 7 1
Low 2 2 17 1 7 1 147 3 93 146 22 5 2 1
Below cutoff 497 323 461 46 191 23 822 363 603 70 533 433 23 284 497

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000562505   ⟹   ENSP00000455811
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl8143,080,457 - 143,083,001 (+)Ensembl
RefSeq Acc Id: NM_001368160   ⟹   NP_001355089
RefSeq Status: VALIDATED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh388143,080,630 - 143,083,486 (+)NCBI
Protein Sequences
Protein RefSeqs NP_001355089 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein H3BQJ8 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001355089   ⟸   NM_001368160
- Peptide Label: preproprotein
RefSeq Acc Id: ENSP00000455811   ⟸   ENST00000562505
Protein Domains
UPAR/Ly6


Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 8p21.3-q24.3(chr8:21291522-145070385)x3 copy number gain See cases [RCV000142021] Chr8:21291522..145070385 [GRCh38]
Chr8:21149033..146295771 [GRCh37]
Chr8:21193313..146266575 [NCBI36]
Chr8:8p21.3-q24.3
pathogenic
GRCh38/hg38 8q21.13-24.3(chr8:78614077-145054634)x3 copy number gain See cases [RCV000142597] Chr8:78614077..145054634 [GRCh38]
Chr8:79526312..146280020 [GRCh37]
Chr8:79688867..146250824 [NCBI36]
Chr8:8q21.13-24.3
pathogenic
GRCh38/hg38 8p23.3-q24.3(chr8:226452-145068712)x3 copy number gain See cases [RCV000142858] Chr8:226452..145068712 [GRCh38]
Chr8:176452..146294098 [GRCh37]
Chr8:166452..146264902 [NCBI36]
Chr8:8p23.3-q24.3
pathogenic
GRCh38/hg38 8q24.3(chr8:142201468-144002730)x1 copy number loss See cases [RCV000135981] Chr8:142201468..144002730 [GRCh38]
Chr8:143282829..145076898 [GRCh37]
Chr8:143280736..145148886 [NCBI36]
Chr8:8q24.3
pathogenic
GRCh38/hg38 8q24.3(chr8:139004218-145049449)x3 copy number gain See cases [RCV000137340] Chr8:139004218..145049449 [GRCh38]
Chr8:140016461..146274835 [GRCh37]
Chr8:140085643..146245639 [NCBI36]
Chr8:8q24.3
likely pathogenic
GRCh38/hg38 8q21.2-24.3(chr8:85765999-145070385)x3 copy number gain See cases [RCV000143659] Chr8:85765999..145070385 [GRCh38]
Chr8:86778228..146295771 [GRCh37]
Chr8:86863079..146266575 [NCBI36]
Chr8:8q21.2-24.3
pathogenic
GRCh38/hg38 8q24.13-24.3(chr8:124498498-145068712)x3 copy number gain See cases [RCV000137346] Chr8:124498498..145068712 [GRCh38]
Chr8:125510739..146294098 [GRCh37]
Chr8:125579920..146264902 [NCBI36]
Chr8:8q24.13-24.3
pathogenic
GRCh38/hg38 8q24.3(chr8:139236824-145068712)x3 copy number gain See cases [RCV000137466] Chr8:139236824..145068712 [GRCh38]
Chr8:140249067..146294098 [GRCh37]
Chr8:140318249..146264902 [NCBI36]
Chr8:8q24.3
likely pathogenic
GRCh38/hg38 8q24.22-24.3(chr8:130639182-145068712)x3 copy number gain See cases [RCV000137644] Chr8:130639182..145068712 [GRCh38]
Chr8:131651428..146294098 [GRCh37]
Chr8:131720610..146264902 [NCBI36]
Chr8:8q24.22-24.3
pathogenic|conflicting data from submitters
GRCh38/hg38 8p23.3-q24.3(chr8:241530-145054634)x3 copy number gain See cases [RCV000148092] Chr8:241530..145054634 [GRCh38]
Chr8:191530..146280020 [GRCh37]
Chr8:181530..146250824 [NCBI36]
Chr8:8p23.3-q24.3
pathogenic
GRCh38/hg38 8q24.13-24.3(chr8:124514090-145054634)x3 copy number gain See cases [RCV000148117] Chr8:124514090..145054634 [GRCh38]
Chr8:125526331..146280020 [GRCh37]
Chr8:125595512..146250824 [NCBI36]
Chr8:8q24.13-24.3
pathogenic
GRCh38/hg38 8q21.3-24.3(chr8:87931152-145068712)x3 copy number gain See cases [RCV000138551] Chr8:87931152..145068712 [GRCh38]
Chr8:88943380..146294098 [GRCh37]
Chr8:89012496..146264902 [NCBI36]
Chr8:8q21.3-24.3
pathogenic
GRCh38/hg38 8p23.3-q24.3(chr8:241605-145054781)x3 copy number gain See cases [RCV000138643] Chr8:241605..145054781 [GRCh38]
Chr8:191605..146280167 [GRCh37]
Chr8:181605..146250971 [NCBI36]
Chr8:8p23.3-q24.3
pathogenic
GRCh38/hg38 8p23.3-q24.3(chr8:241530-145054634)x3 copy number gain See cases [RCV000053602] Chr8:241530..145054634 [GRCh38]
Chr8:191530..146280020 [GRCh37]
Chr8:181530..146250824 [NCBI36]
Chr8:8p23.3-q24.3
pathogenic
GRCh38/hg38 8q21.13-24.3(chr8:77480050-145068712)x3 copy number gain See cases [RCV000139036] Chr8:77480050..145068712 [GRCh38]
Chr8:78392286..146294098 [GRCh37]
Chr8:78554841..146264902 [NCBI36]
Chr8:8q21.13-24.3
pathogenic
GRCh38/hg38 8p23.3-q24.3(chr8:244417-145054775)x3 copy number gain Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000053604]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000053604]|See cases [RCV000053604] Chr8:244417..145054775 [GRCh38]
Chr8:194417..146280161 [GRCh37]
Chr8:184417..146250965 [NCBI36]
Chr8:8p23.3-q24.3
pathogenic
GRCh38/hg38 8q22.1-24.3(chr8:95606052-145054775)x3 copy number gain Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000053677]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000053677]|See cases [RCV000053677] Chr8:95606052..145054775 [GRCh38]
Chr8:96618280..146280161 [GRCh37]
Chr8:96687456..146250965 [NCBI36]
Chr8:8q22.1-24.3
pathogenic
GRCh38/hg38 8q24.13-24.3(chr8:124514090-145054634)x3 copy number gain See cases [RCV000053678] Chr8:124514090..145054634 [GRCh38]
Chr8:125526331..146280020 [GRCh37]
Chr8:125595512..146250824 [NCBI36]
Chr8:8q24.13-24.3
pathogenic
GRCh38/hg38 8q24.3(chr8:139447227-145054775)x3 copy number gain Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000053701]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000053701]|See cases [RCV000053701] Chr8:139447227..145054775 [GRCh38]
Chr8:140459470..146280161 [GRCh37]
Chr8:140528652..146250965 [NCBI36]
Chr8:8q24.3
pathogenic
GRCh38/hg38 8q23.3-24.3(chr8:113580402-145054634)x3 copy number gain See cases [RCV000050638] Chr8:113580402..145054634 [GRCh38]
Chr8:114592631..146280020 [GRCh37]
Chr8:114661807..146250824 [NCBI36]
Chr8:8q23.3-24.3
pathogenic
GRCh38/hg38 8q22.1-24.3(chr8:97382873-145070385)x3 copy number gain See cases [RCV000140447] Chr8:97382873..145070385 [GRCh38]
Chr8:98395101..146295771 [GRCh37]
Chr8:98464277..146266575 [NCBI36]
Chr8:8q22.1-24.3
pathogenic
GRCh38/hg38 8q24.21-24.3(chr8:128220912-145049449)x3 copy number gain See cases [RCV000050830] Chr8:128220912..145049449 [GRCh38]
Chr8:129233158..146274835 [GRCh37]
Chr8:129302340..146245639 [NCBI36]
Chr8:8q24.21-24.3
pathogenic
GRCh38/hg38 8q24.3(chr8:141738068-144140607)x1 copy number loss See cases [RCV000140913] Chr8:141738068..144140607 [GRCh38]
Chr8:142764538..145195510 [GRCh37]
Chr8:142823655..145267498 [NCBI36]
Chr8:8q24.3
pathogenic
GRCh38/hg38 8p23.3-q24.3(chr8:241530-145049449)x3 copy number gain See cases [RCV000051206] Chr8:241530..145049449 [GRCh38]
Chr8:191530..146274835 [GRCh37]
Chr8:181530..146245639 [NCBI36]
Chr8:8p23.3-q24.3
pathogenic
GRCh38/hg38 8q22.1-24.3(chr8:94682154-145068656)x3 copy number gain See cases [RCV000134353] Chr8:94682154..145068656 [GRCh38]
Chr8:95694382..146294042 [GRCh37]
Chr8:95763558..146264846 [NCBI36]
Chr8:8q22.1-24.3
pathogenic
GRCh38/hg38 8q22.3-24.3(chr8:100867343-145070385)x3 copy number gain See cases [RCV000141694] Chr8:100867343..145070385 [GRCh38]
Chr8:101879571..146295771 [GRCh37]
Chr8:101948747..146266575 [NCBI36]
Chr8:8q22.3-24.3
pathogenic
GRCh38/hg38 8p23.3-q24.3(chr8:208048-145070385)x3 copy number gain See cases [RCV000141808] Chr8:208048..145070385 [GRCh38]
Chr8:158048..146295771 [GRCh37]
Chr8:148048..146266575 [NCBI36]
Chr8:8p23.3-q24.3
pathogenic
GRCh38/hg38 8q22.3-24.3(chr8:103306336-145068712)x3 copy number gain See cases [RCV000142810] Chr8:103306336..145068712 [GRCh38]
Chr8:104318564..146294098 [GRCh37]
Chr8:104387740..146264902 [NCBI36]
Chr8:8q22.3-24.3
pathogenic|likely pathogenic

Additional Information

Database Acc Id Source(s)
AGR Gene HGNC:52284 AgrOrtholog
COSMIC LY6L COSMIC
Ensembl Genes ENSG00000261667 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
  ENSG00000282693 UniProtKB/Swiss-Prot
Ensembl Protein ENSP00000455811 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSP00000487842 UniProtKB/Swiss-Prot
Ensembl Transcript ENST00000562505 ENTREZGENE, UniProtKB/Swiss-Prot
  ENST00000631950 UniProtKB/Swiss-Prot
GTEx ENSG00000261667 GTEx
  ENSG00000282693 GTEx
HGNC ID HGNC:52284 ENTREZGENE
Human Proteome Map LY6L Human Proteome Map
InterPro LY6_UPA_recep-like UniProtKB/Swiss-Prot
NCBI Gene LY6L ENTREZGENE
Pfam UPAR_LY6 UniProtKB/Swiss-Prot
PharmGKB PA166181554 PharmGKB
SMART SM00134 UniProtKB/Swiss-Prot
UniProt H3BQJ8 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2017-01-31 LY6L  lymphocyte antigen 6 family member L    lymphocyte antigen 6 complex, locus L  Symbol and/or name change 5135510 APPROVED