Lypd2 (Ly6/Plaur domain containing 2) - Rat Genome Database

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Gene: Lypd2 (Ly6/Plaur domain containing 2) Rattus norvegicus
Analyze
Symbol: Lypd2
Name: Ly6/Plaur domain containing 2
RGD ID: 1307892
Description: Predicted to be located in plasma membrane. Orthologous to human LYPD2 (LY6/PLAUR domain containing 2); INTERACTS WITH 6-propyl-2-thiouracil; bisphenol A; C60 fullerene.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC300017; ly6/PLAUR domain-containing protein 2; RGD1307892; similar to Ars component B
RGD Orthologs
Human
Mouse
Bonobo
Dog
Squirrel
Pig
Green Monkey
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr87108,506,545 - 108,508,582 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl7108,506,545 - 108,508,582 (-)EnsemblGRCr8
mRatBN7.27106,617,561 - 106,619,598 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl7106,617,561 - 106,619,598 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx7108,375,790 - 108,377,833 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.07110,599,470 - 110,601,513 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.07110,545,399 - 110,547,442 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.07115,967,267 - 115,969,304 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl7115,967,273 - 115,969,304 (-)Ensemblrn6Rnor6.0
Rnor_5.07115,872,656 - 115,874,781 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.47112,846,293 - 112,848,330 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera7103,018,710 - 103,020,747 (-)NCBICelera
RGSC_v3.17112,880,530 - 112,885,063 (-)NCBI
Cytogenetic Map7q34NCBI
JBrowse:




Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:23376485  


Genomics

Comparative Map Data
Lypd2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr87108,506,545 - 108,508,582 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl7108,506,545 - 108,508,582 (-)EnsemblGRCr8
mRatBN7.27106,617,561 - 106,619,598 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl7106,617,561 - 106,619,598 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx7108,375,790 - 108,377,833 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.07110,599,470 - 110,601,513 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.07110,545,399 - 110,547,442 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.07115,967,267 - 115,969,304 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl7115,967,273 - 115,969,304 (-)Ensemblrn6Rnor6.0
Rnor_5.07115,872,656 - 115,874,781 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.47112,846,293 - 112,848,330 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera7103,018,710 - 103,020,747 (-)NCBICelera
RGSC_v3.17112,880,530 - 112,885,063 (-)NCBI
Cytogenetic Map7q34NCBI
LYPD2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh388142,750,150 - 142,752,532 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl8142,750,150 - 142,752,532 (-)Ensemblhg38GRCh38
GRCh378143,831,568 - 143,833,950 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 368143,828,630 - 143,830,954 (-)NCBIBuild 36Build 36hg18NCBI36
Build 348143,828,630 - 143,830,954NCBI
Celera8140,142,653 - 140,144,977 (-)NCBICelera
Cytogenetic Map8q24.3NCBI
HuRef8139,084,025 - 139,086,349 (-)NCBIHuRef
CHM1_18143,871,901 - 143,874,225 (-)NCBICHM1_1
T2T-CHM13v2.08143,893,543 - 143,895,925 (-)NCBIT2T-CHM13v2.0
Lypd2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391574,604,095 - 74,606,644 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1574,604,096 - 74,606,178 (-)EnsemblGRCm39 EnsemblGRCm39
GRCm381574,732,246 - 74,734,795 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1574,732,247 - 74,734,329 (-)Ensemblmm10GRCm38
MGSCv371574,562,682 - 74,564,743 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv361574,559,502 - 74,561,584 (-)NCBIMGSCv36mm8
Celera1576,237,258 - 76,239,319 (-)NCBICelera
Cytogenetic Map15D3NCBI
cM Map1534.26NCBI
LYPD2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v27160,186,224 - 160,188,595 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan18135,712,429 - 135,714,800 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v08139,462,128 - 139,464,461 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.18142,505,939 - 142,508,272 (-)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl8142,505,939 - 142,508,272 (-)EnsemblpanPan2panpan1.1
LYPD2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11336,794,662 - 36,796,706 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1336,670,267 - 36,672,315 (-)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.01337,197,689 - 37,199,737 (-)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1337,197,684 - 37,199,754 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11336,916,403 - 36,918,451 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01337,006,042 - 37,008,090 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01337,428,138 - 37,430,186 (-)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
LOC101969996
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_0244053031,700,742 - 1,702,709 (+)NCBIHiC_Itri_2
SpeTri2.0NW_0049364709,126,833 - 9,128,808 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
LOC110260198
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl41,461,588 - 1,465,796 (+)EnsemblsusScr11Sscrofa11.1
Sscrofa11.141,461,565 - 1,463,707 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
LYPD2
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.18137,002,203 - 137,010,702 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl8137,002,571 - 137,004,668 (-)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_0236660392,944,928 - 2,947,113 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Lypd2
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v11247,475,028 - 247,477,057 (-)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Lypd2
4 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:35
Count of miRNA genes:32
Interacting mature miRNAs:34
Transcripts:ENSRNOT00000007958
Prediction methods:Miranda, Rnahybrid, Targetscan
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
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
1559283Emca4Estrogen-induced mammary cancer QTL 43.7mammary gland integrity trait (VT:0010552)percentage of study population developing mammary tumors during a period of time (CMO:0000948)763889858108889858Rat
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
1576303Ept7Estrogen-induced pituitary tumorigenesis QTL 73.7pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)763889858108889858Rat
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
D7Mco21  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.27106,618,511 - 106,618,736 (+)MAPPERmRatBN7.2
Rnor_6.07115,968,218 - 115,968,442NCBIRnor6.0
Rnor_5.07115,873,607 - 115,873,831UniSTSRnor5.0
RGSC_v3.47112,847,244 - 112,847,468UniSTSRGSC3.4
Celera7103,019,661 - 103,019,885UniSTS
Cytogenetic Map7q34UniSTS


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
14 2 11 50 29 39 16 5 16 1 114 20 46 63 69 23

Sequence


Ensembl Acc Id: ENSRNOT00000007958   ⟹   ENSRNOP00000007958
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl7108,506,545 - 108,508,582 (-)Ensembl
mRatBN7.2 Ensembl7106,617,561 - 106,619,598 (-)Ensembl
Rnor_6.0 Ensembl7115,967,273 - 115,969,304 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000075999   ⟹   ENSRNOP00000068270
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl7115,967,273 - 115,969,064 (-)Ensembl
RefSeq Acc Id: NM_001130545   ⟹   NP_001124017
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr87108,506,545 - 108,508,582 (-)NCBI
mRatBN7.27106,617,561 - 106,619,598 (-)NCBI
Rnor_6.07115,967,267 - 115,969,304 (-)NCBI
Rnor_5.07115,872,656 - 115,874,781 (-)NCBI
RGSC_v3.47112,846,293 - 112,848,330 (-)RGD
Celera7103,018,710 - 103,020,747 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001124017 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDM16093 (Get FASTA)   NCBI Sequence Viewer  
  EDM16094 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000007958
  ENSRNOP00000007958.6
RefSeq Acc Id: NP_001124017   ⟸   NM_001130545
- Peptide Label: precursor
- UniProtKB: D4A707 (UniProtKB/TrEMBL),   A6HRX8 (UniProtKB/TrEMBL),   A6HRX9 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000068270   ⟸   ENSRNOT00000075999
Ensembl Acc Id: ENSRNOP00000007958   ⟸   ENSRNOT00000007958
Protein Domains
UPAR/Ly6

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D4A707-F1-model_v2 AlphaFold D4A707 1-127 view protein structure

Transcriptome

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

Promoters
RGD ID:13695378
Promoter ID:EPDNEW_R5899
Type:single initiation site
Name:Lypd2_1
Description:Ly6/Plaur domain containing 2
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_6.07115,969,279 - 115,969,339EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1307892 AgrOrtholog
BioCyc Gene G2FUF-33016 BioCyc
Ensembl Genes ENSRNOG00000006058 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000007958 ENTREZGENE
  ENSRNOT00000007958.8 UniProtKB/TrEMBL
Gene3D-CATH 2.10.60.10 UniProtKB/TrEMBL
InterPro Ly-6/neurotoxin-like_GPI-ap UniProtKB/TrEMBL
  LY6_UPA_recep-like UniProtKB/TrEMBL
  Snake_toxin-like_sf UniProtKB/TrEMBL
  Toxin/TOLIP UniProtKB/TrEMBL
KEGG Report rno:300017 UniProtKB/TrEMBL
NCBI Gene 300017 ENTREZGENE
PANTHER UPAR/LY6 DOMAIN-CONTAINING PROTEIN UniProtKB/TrEMBL
  UPAR/LY6 DOMAIN-CONTAINING PROTEIN UniProtKB/TrEMBL
Pfam Toxin_TOLIP UniProtKB/TrEMBL
PhenoGen Lypd2 PhenoGen
RatGTEx ENSRNOG00000006058 RatGTEx
SMART SM00134 UniProtKB/TrEMBL
Superfamily-SCOP SSF57302 UniProtKB/TrEMBL
UniProt A6HRX8 ENTREZGENE, UniProtKB/TrEMBL
  A6HRX9 ENTREZGENE, UniProtKB/TrEMBL
  D4A707 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-04-30 Lypd2  Ly6/Plaur domain containing 2   Lypd2_predicted  Ly6/Plaur domain containing 2 (predicted)  'predicted' is removed 2292626 APPROVED
2006-03-30 Lypd2_predicted  Ly6/Plaur domain containing 2 (predicted)  RGD1307892_predicted  similar to Ars component B (predicted)  Symbol and Name updated 1299863 APPROVED
2005-01-20 RGD1307892_predicted  similar to Ars component B (predicted)  LOC300017_predicted    Symbol and Name status set to approved 1331353 APPROVED
2005-01-12 LOC300017_predicted  similar to Ars component B (predicted)      Symbol and Name status set to provisional 70820 PROVISIONAL