Lypd8l1 (LY6/PLAUR domain containing 8 like 1) - Rat Genome Database

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Gene: Lypd8l1 (LY6/PLAUR domain containing 8 like 1) Rattus norvegicus
Analyze
No known orthologs.
Symbol: Lypd8l1
Name: LY6/PLAUR domain containing 8 like 1
RGD ID: 3683
Description: Involved in bone remodeling. Predicted to be located in extracellular region.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: divalent metal transporter-1; DMT-1; Itg; LOC24906; protein RoBo-1; RoBo-1; rodent bone protein
RGD Orthologs
Alliance Orthologs
More Info homologs ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81043,115,979 - 43,124,349 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1043,117,891 - 43,124,875 (+)EnsemblGRCr8
mRatBN7.21042,615,555 - 42,623,925 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1042,615,555 - 42,623,784 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1047,279,475 - 47,287,867 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01046,769,916 - 46,778,308 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01042,273,427 - 42,281,820 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01043,871,628 - 43,880,549 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1043,871,613 - 43,880,055 (+)Ensemblrn6Rnor6.0
Rnor_5.01043,664,011 - 43,672,910 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41044,072,418 - 44,080,785 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1041,907,921 - 41,916,361 (+)NCBICelera
RGSC_v3.11044,086,040 - 44,094,408 (+)NCBI
Cytogenetic Map10q22NCBI
JBrowse:




Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

References

References - curated
# Reference Title Reference Citation
1. The genetic association database. Becker KG, etal., Nat Genet. 2004 May;36(5):431-2.
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. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
5. RoBo-1, a novel member of the urokinase plasminogen activator receptor/CD59/Ly-6/snake toxin family selectively expressed in rat bone and growth plate cartilage. Noel LS, etal., J Biol Chem 1998 Feb 13;273(7):3878-83.
6. GOA pipeline RGD automated data pipeline
7. Tentative Sequence Identification Numbers Tentative Sequence Data IDs. TIGR Gene Index, Rat Data
8. A light and electron microscopic study of divalent metal transporter-1 distribution in the rat hippocampus, after kainate-induced neuronal injury. Wang XS, etal., Exp Neurol 2002 Sep;177(1):193-201.
Additional References at PubMed
PMID:17614955  


Genomics

Variants

.
Variants in Lypd8l1
111 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:195
Count of miRNA genes:134
Interacting mature miRNAs:146
Transcripts:ENSRNOT00000003797
Prediction methods:Microtar, 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
61441Btemp1Thermal response to stress QTL 14body temperature trait (VT:0005535)core body temperature (CMO:0001036)103589345164140567Rat
152025229Scl83Serum cholesterol level QTL 834.33blood cholesterol amount (VT:0000180)103621155669161158Rat
1578779Tcas10Tongue tumor susceptibility QTL 103.12tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)103179628176796281Rat
631564Apr3Acute phase response QTL 33.9blood interleukin-6 amount (VT:0008595)plasma interleukin-6 level (CMO:0001927)101577675460776754Rat
1298069Bp168Blood pressure QTL 1685.5blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)102702353598502431Rat
2293669Bmd33Bone mineral density QTL 334.50.0001femur strength trait (VT:0010010)femoral neck polar moment of inertia (CMO:0001670)102744378772443787Rat
631552Vetf2Vascular elastic tissue fragility QTL 24.50.0002aorta elastic tissue integrity trait (VT:0010556)artery internal elastic lamina non-tumorous lesion count (CMO:0001913)103550938391417879Rat
631554Bp133Blood pressure QTL 1330.005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)10125055464349221Rat
61325Aia5Adjuvant induced arthritis QTL 50.01joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1023948641107713808Rat
2293679Bmd30Bone mineral density QTL 303.50.0001femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)102744378772443787Rat
1298078Stresp5Stress response QTL 52.990.00025blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)1042546145107713808Rat
1578761Stresp21Stress response QTL 213.3thymus mass (VT:0004954)thymus wet weight (CMO:0000855)10687714251877142Rat
2298544Neuinf9Neuroinflammation QTL 94.6nervous system integrity trait (VT:0010566)spinal cord complement component 1, q subcomponent, B chain mRNA level (CMO:0002126)101993920764939207Rat
61332Eau3Experimental allergic uveoretinitis QTL 30.004uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)101803578263035782Rat
10401803Kidm50Kidney mass QTL 50kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)1092219745922197Rat
61463Bp12Blood pressure QTL 126.30.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)104183127886831278Rat
2317754Glom25Glomerulus QTL 253.5urine protein amount (VT:0005160)urine protein level (CMO:0000591)10210370847103708Rat
1598852Anxrr19Anxiety related response QTL 195.07body movement coordination trait (VT:0005424)number of rearing movements in an experimental apparatus (CMO:0001752)101866841963668419Rat
1581497Esta1Estrogen-induced thymic atrophy QTL 1thymus mass (VT:0004954)thymus wet weight (CMO:0000855)102183375861843633Rat
2313095Bss62Bone structure and strength QTL 621.50.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)10589381150893811Rat
724527Bp148Blood pressure QTL 1480.0001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)102895035373950353Rat
1358897Stresp6Stress response QTL 64.170.022blood norepinephrine amount (VT:0005663)plasma norepinephrine level (CMO:0001010)103589326364653589Rat
1331762Rf40Renal function QTL 403.873kidney blood vessel physiology trait (VT:0100012)absolute change in renal vascular resistance (CMO:0001900)102980091064653589Rat
2300171Bmd58Bone mineral density QTL 584.90.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)102744378772443787Rat
61354Pia10Pristane induced arthritis QTL 100.01joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1023948641107713808Rat
2301967Cm73Cardiac mass QTL 734.55heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)101499153586964295Rat
70188BpQTLcluster1Blood pressure QTL cluster 14.864arterial blood pressure trait (VT:2000000)pulse pressure (CMO:0000292)14282327487823274Rat
2313104Bss61Bone structure and strength QTL 610.90.0001tibia area (VT:1000281)tibia midshaft cross-sectional area (CMO:0001717)10589381150893811Rat
2316949Gluco60Glucose level QTL 603.7blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1014991535107556066Rat
2293652Bmd22Bone mineral density QTL 224.90.0001femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)102744378772443787Rat
70198BpQTLcluster9Blood pressure QTL cluster 92.94arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)104282327487823274Rat
724556Pur2Proteinuria QTL 25.5urine protein amount (VT:0005160)urine protein level (CMO:0000591)102293137391127454Rat
8662860Vetf10Vascular elastic tissue fragility QTL 10artery integrity trait (VT:0010639)number of ruptures of the internal elastic lamina of the abdominal aorta and iliac arteries (CMO:0002562)10666092373950353Rat
2313066Bss63Bone structure and strength QTL 631.40.0001tibia strength trait (VT:1000284)bone polar moment of inertia (CMO:0001558)10589381150893811Rat
2313064Bmd71Bone mineral density QTL 710.90.0001tibia mineral mass (VT:1000283)compact volumetric bone mineral density (CMO:0001730)10589381150893811Rat
70223Bp57Blood pressure QTL 575arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)101465354159653541Rat
1354587Kidm21Kidney mass QTL 213.3kidney mass (VT:0002707)right kidney wet weight (CMO:0000082)101553301273695498Rat
634329Pia15Pristane induced arthritis QTL 153.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)102466212373695339Rat
70224Eae3Experimental allergic encephalomyelitis QTL 34.1nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)102702353561843633Rat
2298480Eau7Experimental allergic uveoretinitis QTL 70.0049uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)103550938380509383Rat
2313081Bss64Bone structure and strength QTL 641.30.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)10589381150893811Rat
1331791Cm31Cardiac mass QTL 313.84606heart mass (VT:0007028)heart wet weight (CMO:0000069)102980091091417879Rat
2298495Eae23Experimental allergic encephalomyelitis QTL 2316.93nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis duration (CMO:0001424)101617552561175525Rat
2313087Bmd80Bone mineral density QTL 803.20.0001tibia mineral mass (VT:1000283)total volumetric bone mineral density (CMO:0001728)102011061465110614Rat
1354614Hpcl1Hepatic cholesterol level QTL 13.3liver cholesterol amount (VT:0010498)liver cholesterol level (CMO:0001597)103589326352293000Rat
631530Tls3T-lymphoma susceptibility QTL 300.0001thymus integrity trait (VT:0010555)percentage of study population developing T-cell lymphomas during a period of time (CMO:0001911)102758722696099902Rat
2289985Bp305Blood pressure QTL 305arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)102907697874076978Rat
631532Cm50Cardiac mass QTL 506.6heart mass (VT:0007028)calculated heart weight (CMO:0000073)101803578263035782Rat
631267Cia20Collagen induced arthritis QTL 203.2joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1023948641107713808Rat
2293705Bmd25Bone mineral density QTL 257.10.0001femur mineral mass (VT:0010011)compact volumetric bone mineral density (CMO:0001730)102744378772443787Rat
1600371Mcs21Mammary carcinoma susceptibility QTL 213mammary gland integrity trait (VT:0010552)mammary tumor growth rate (CMO:0000344)102937704652699134Rat
631269Cia22Collagen induced arthritis QTL 228.9joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1040535708107713808Rat
1576308Schws1Schwannoma susceptibility QTL 10.0041nervous system integrity trait (VT:0010566)percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)1040535708107713808Rat
631268Cia21Collagen induced arthritis QTL 213.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1014991535107713808Rat
1576311Pia26Pristane induced arthritis QTL 26joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)103112911376129113Rat
631270Cia23Collagen induced arthritis QTL 233.9joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1040535708107713808Rat
61427Cia16Collagen induced arthritis QTL 163.2joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)10686461896620484Rat
12880050Am10Aortic mass QTL 100.016aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)103950348784503487Rat
6893342Cm78Cardiac mass QTL 780.10.88heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)103550938388177745Rat
2313055Bw96Body weight QTL 963.60.0001body mass (VT:0001259)body weight (CMO:0000012)102011061465110614Rat
631542Bp82Blood pressure QTL 826.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)102702353599451848Rat

Markers in Region
D9Arb3  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2975,949,626 - 75,949,750 (+)MAPPERmRatBN7.2
Rnor_6.0981,648,009 - 81,648,132NCBIRnor6.0
Rnor_5.0981,412,948 - 81,413,071UniSTSRnor5.0
RGSC_v3.4973,707,004 - 73,707,128RGDRGSC3.4
RGSC_v3.4973,707,005 - 73,707,128UniSTSRGSC3.4
Celera973,523,345 - 73,523,468UniSTS
RGSC_v3.1973,853,986 - 73,854,110RGD
Cytogenetic Map9q33UniSTS
Cytogenetic Map10q22UniSTS


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
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
16 12 67 147 91 90 59 92 59 6 355 192 11 123 80 91 31 9 9

Sequence


Ensembl Acc Id: ENSRNOT00000003797   ⟹   ENSRNOP00000003797
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1043,117,891 - 43,124,168 (+)Ensembl
mRatBN7.2 Ensembl1042,615,555 - 42,623,784 (+)Ensembl
Rnor_6.0 Ensembl1043,871,682 - 43,880,049 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000080540   ⟹   ENSRNOP00000071561
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1043,871,613 - 43,880,055 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000172266   ⟹   ENSRNOP00000110292
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1043,117,891 - 43,124,875 (+)Ensembl
RefSeq Acc Id: NM_031537   ⟹   NP_113725
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81043,115,979 - 43,124,346 (+)NCBI
mRatBN7.21042,615,555 - 42,623,922 (+)NCBI
Rnor_6.01043,871,682 - 43,880,049 (+)NCBI
Rnor_5.01043,664,011 - 43,672,910 (+)NCBI
RGSC_v3.41044,072,418 - 44,080,785 (+)RGD
Celera1041,907,921 - 41,916,361 (+)RGD
Sequence:
RefSeq Acc Id: XM_006246377   ⟹   XP_006246439
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81043,116,112 - 43,124,349 (+)NCBI
mRatBN7.21042,615,688 - 42,623,925 (+)NCBI
Rnor_6.01043,871,781 - 43,880,549 (+)NCBI
Rnor_5.01043,664,011 - 43,672,910 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_113725 (Get FASTA)   NCBI Sequence Viewer  
  XP_006246439 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAC40033 (Get FASTA)   NCBI Sequence Viewer  
  EDM04544 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000003797
  ENSRNOP00000003797.2
GenBank Protein O55006 (Get FASTA)   NCBI Sequence Viewer  
RefSeq Acc Id: NP_113725   ⟸   NM_031537
- Peptide Label: precursor
- UniProtKB: O55006 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006246439   ⟸   XM_006246377
- Peptide Label: isoform X1
- UniProtKB: O55006 (UniProtKB/Swiss-Prot)
- Sequence:
Ensembl Acc Id: ENSRNOP00000071561   ⟸   ENSRNOT00000080540
Ensembl Acc Id: ENSRNOP00000003797   ⟸   ENSRNOT00000003797
Ensembl Acc Id: ENSRNOP00000110292   ⟸   ENSRNOT00000172266

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-O55006-F1-model_v2 AlphaFold O55006 1-240 view protein structure

Transcriptome

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

Promoters
RGD ID:13697219
Promoter ID:EPDNEW_R7741
Type:multiple initiation site
Name:LOC24906_1
Description:RoBo-1
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_6.01043,871,664 - 43,871,724EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:3683 AgrOrtholog
BioCyc Gene G2FUF-24985 BioCyc
Ensembl Genes ENSRNOG00000002820 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000003797 ENTREZGENE
  ENSRNOT00000003797.5 UniProtKB/Swiss-Prot
Gene3D-CATH 2.10.60.10 UniProtKB/Swiss-Prot
InterPro CNF-like_PLA2_Inhibitor UniProtKB/Swiss-Prot
  Snake_toxin-like_sf UniProtKB/Swiss-Prot
KEGG Report rno:24906 UniProtKB/Swiss-Prot
NCBI Gene 24906 ENTREZGENE
PANTHER GENE 12253-RELATED UniProtKB/Swiss-Prot
  LY6/PLAUR DOMAIN-CONTAINING PROTEIN 8 UniProtKB/Swiss-Prot
PhenoGen Lypd8l1 PhenoGen
RatGTEx ENSRNOG00000002820 RatGTEx
Superfamily-SCOP SSF57302 UniProtKB/Swiss-Prot
TIGR TC216701
UniProt A0ABK0M7F8_RAT UniProtKB/TrEMBL
  O55006 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2023-09-19 Lypd8l1  LY6/PLAUR domain containing 8 like 1  LOC24906  RoBo-1  Symbol and Name Changed 1299863 APPROVED
2006-12-01 LOC24906  RoBo-1  Slc11a1  solute carrier family 11 (proton-coupled divalent metal ion transporters), member 1  Symbol and Name updated 1299863 PENDING
2004-09-10 Slc11a1  solute carrier family 11 (proton-coupled divalent metal ion transporters), member 1    solute carrier family 11 member 1  Name updated 1299863 APPROVED
2001-06-20 Nramp1  Natural resistance-associated macrophage protein      Symbol withdrawn, duplicate of Slc11a1 (RGD:3683) 67952 WITHDRAWN
2001-06-20 Slc11a1  Solute carrier family 11 member 1      Name updated 67952 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_process mouse homolog is a macrophage protein associated with resistance or susceptibility to intracellular pathogens 704404