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 (Ensembl: LOC24906)
Name: LY6/PLAUR domain containing 8 like 1 (Ensembl:RoBo-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 Genes
More Info homologs ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81043,115,979 - 43,124,349 (+)NCBIGRCr8
mRatBN7.21042,615,555 - 42,623,925 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1042,615,555 - 42,623,784 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1047,279,475 - 47,287,867 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01046,769,916 - 46,778,308 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01042,273,427 - 42,281,820 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01043,871,628 - 43,880,549 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1043,871,613 - 43,880,055 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01043,664,011 - 43,672,910 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41044,072,418 - 44,080,785 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11044,086,040 - 44,094,408 (+)NCBI
Celera1041,907,921 - 41,916,361 (+)NCBICelera
Cytogenetic Map10q22NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


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
115 total Variants
miRNA Target Status

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 (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
70223Bp57Blood pressure QTL 575arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)10180676123Rat
10401803Kidm50Kidney mass QTL 50kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)1041834445418344Rat
631554Bp133Blood pressure QTL 1330.005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1074336463851208Rat
2313064Bmd71Bone mineral density QTL 710.90.0001tibia mineral mass (VT:1000283)compact volumetric bone mineral density (CMO:0001730)10538701450387014Rat
2313066Bss63Bone structure and strength QTL 631.40.0001tibia strength trait (VT:1000284)bone polar moment of inertia (CMO:0001558)10538701450387014Rat
2313081Bss64Bone structure and strength QTL 641.30.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)10538701450387014Rat
2313095Bss62Bone structure and strength QTL 621.50.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)10538701450387014Rat
2313104Bss61Bone structure and strength QTL 610.90.0001tibia area (VT:1000281)tibia midshaft cross-sectional area (CMO:0001717)10538701450387014Rat
2298544Neuinf9Neuroinflammation QTL 94.6nervous system integrity trait (VT:0010566)spinal cord complement component 1, q subcomponent, B chain mRNA level (CMO:0002126)10580199062146030Rat
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)10615418273453136Rat
61427Cia16Collagen induced arthritis QTL 163.2joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)10635789696121100Rat
1578761Stresp21Stress response QTL 213.3thymus mass (VT:0004954)thymus wet weight (CMO:0000855)10637574651375746Rat
2303118Mamtr7Mammary tumor resistance QTL 70.003mammary gland integrity trait (VT:0010552)mammary tumor growth rate (CMO:0000344)109658275104670812Rat
9590310Scort19Serum corticosterone level QTL 196.30.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)101147401056474010Rat
9590268Scort13Serum corticosterone level QTL 133.260.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)101147401056474010Rat
9589136Insul27Insulin level QTL 2710.460.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)101147401056474010Rat
2301967Cm73Cardiac mass QTL 734.55heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)101448701189062041Rat
631268Cia21Collagen induced arthritis QTL 213.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1014487011104060283Rat
2316949Gluco60Glucose level QTL 603.7blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1014487011107057807Rat
1354587Kidm21Kidney mass QTL 213.3kidney mass (VT:0002707)right kidney wet weight (CMO:0000082)101502851360430477Rat
631564Apr3Acute phase response QTL 33.9blood interleukin-6 amount (VT:0008595)plasma interleukin-6 level (CMO:0001927)101527595560275955Rat
6893350Bw99Body weight QTL 990.870.16body mass (VT:0001259)body weight (CMO:0000012)11590666560906665Rat
6893352Bw100Body weight QTL 1000.330.6body mass (VT:0001259)body weight (CMO:0000012)11590666560906665Rat
631532Cm50Cardiac mass QTL 506.6heart mass (VT:0007028)calculated heart weight (CMO:0000073)101790711351786432Rat
1598852Anxrr19Anxiety related response QTL 195.07body movement coordination trait (VT:0005424)number of rearing movements in an experimental apparatus (CMO:0001752)101816784163167841Rat
2313055Bw96Body weight QTL 963.60.0001body mass (VT:0001259)body weight (CMO:0000012)101960648364606483Rat
2313087Bmd80Bone mineral density QTL 803.20.0001tibia mineral mass (VT:1000283)total volumetric bone mineral density (CMO:0001728)101960648364606483Rat
1554317Bmd4Bone mineral density QTL 49.40.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)101981604299406971Rat
1581497Esta1Estrogen-induced thymic atrophy QTL 1thymus mass (VT:0004954)thymus wet weight (CMO:0000855)102132980561345413Rat
724556Pur2Proteinuria QTL 25.5urine protein amount (VT:0005160)urine protein level (CMO:0000591)102242750090627625Rat
61354Pia10Pristane induced arthritis QTL 100.01joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1023444813104060283Rat
631267Cia20Collagen induced arthritis QTL 203.2joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1023444813104060283Rat
61325Aia5Adjuvant induced arthritis QTL 50.01joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1023444813104060283Rat
70224Eae3Experimental allergic encephalomyelitis QTL 34.1nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)102652195761345413Rat
1298069Bp168Blood pressure QTL 1685.5blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)102652195798003205Rat
631542Bp82Blood pressure QTL 826.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)102652195798952741Rat
2300171Bmd58Bone mineral density QTL 584.90.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)102694462871944628Rat
10402859Bp381Blood pressure QTL 3810.002arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)102760646872606468Rat
2292441Bp308Blood pressure QTL 308arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)102760646872606468Rat
724527Bp148Blood pressure QTL 1480.0001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)102845313673453136Rat
1600371Mcs21Mammary carcinoma susceptibility QTL 213mammary gland integrity trait (VT:0010552)mammary tumor growth rate (CMO:0000344)102887565052200160Rat
1331762Rf40Renal function QTL 403.873kidney blood vessel physiology trait (VT:0100012)absolute change in renal vascular resistance (CMO:0001900)102929950464155584Rat
1331791Cm31Cardiac mass QTL 313.84606heart mass (VT:0007028)heart wet weight (CMO:0000069)1029299504107211142Rat
631557Bp136Blood pressure QTL 1360.003arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)103063205375632053Rat
1576311Pia26Pristane induced arthritis QTL 26joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)103122402675632053Rat
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)103129743976297439Rat
1576319Cia29Collagen induced arthritis QTL 29joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)103397392178973921Rat
61332Eau3Experimental allergic uveoretinitis QTL 30.004uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)103449055945579777Rat
1354614Hpcl1Hepatic cholesterol level QTL 13.3liver cholesterol amount (VT:0010498)liver cholesterol level (CMO:0001597)103539226751793994Rat
1358897Stresp6Stress response QTL 64.170.022blood norepinephrine amount (VT:0005663)plasma norepinephrine level (CMO:0001010)103539226764155584Rat
61441Btemp1Thermal response to stress QTL 14body temperature trait (VT:0005535)core body temperature (CMO:0001036)103539245763642539Rat
2317042Aia20Adjuvant induced arthritis QTL 203.38joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)103756507982565079Rat
2317043Aia7Adjuvant induced arthritis QTL 73.82joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)103756507982565079Rat
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)1040035094102359817Rat
631269Cia22Collagen induced arthritis QTL 228.9joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1040035094104060283Rat
631270Cia23Collagen induced arthritis QTL 233.9joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1040035094104060283Rat
631552Vetf2Vascular elastic tissue fragility QTL 24.50.0002aorta elastic tissue integrity trait (VT:0010556)artery internal elastic lamina non-tumorous lesion count (CMO:0001913)104114263386142633Rat
61463Bp12Blood pressure QTL 126.30.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)104133325886333258Rat
8552805Bw145Body weight QTL 1452.2body mass (VT:0001259)change in body weight to body weight ratio (CMO:0002216)104194452678307017Rat
1298078Stresp5Stress response QTL 52.990.00025blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)1042045676104670812Rat
70188BpQTLcluster1Blood pressure QTL cluster 14.864arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)14232313287323132Rat
70188BpQTLcluster1Blood pressure QTL cluster 14.864arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)14232313287323132Rat
70188BpQTLcluster1Blood pressure QTL cluster 14.864arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)14232313287323132Rat
70188BpQTLcluster1Blood pressure QTL cluster 14.864arterial blood pressure trait (VT:2000000)pulse pressure (CMO:0000292)14232313287323132Rat
70198BpQTLcluster9Blood pressure QTL cluster 92.94arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)104232313287323132Rat

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
RGSC_v3.1973,853,986 - 73,854,110RGD
Celera973,523,345 - 73,523,468UniSTS
Cytogenetic Map9q33UniSTS
Cytogenetic Map10q22UniSTS


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 1 25 16 18 16 2 6 11
Low 2 25 30 23 1 23 8 11 19 31 33 8
Below cutoff 18 2 2 2 45 2 2

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000003797   ⟹   ENSRNOP00000003797
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1042,615,555 - 42,623,784 (+)Ensembl
Rnor_6.0 Ensembl1043,871,682 - 43,880,049 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000080540   ⟹   ENSRNOP00000071561
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1043,871,613 - 43,880,055 (+)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
  ENSRNOP00055041595
  ENSRNOP00060039956
  ENSRNOP00065008644
GenBank Protein O55006 (Get FASTA)   NCBI Sequence Viewer  
Reference Protein Sequences
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:
RefSeq Acc Id: ENSRNOP00000071561   ⟸   ENSRNOT00000080540
RefSeq Acc Id: ENSRNOP00000003797   ⟸   ENSRNOT00000003797

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
  ENSRNOG00055029163 UniProtKB/Swiss-Prot
  ENSRNOG00060027666 UniProtKB/Swiss-Prot
  ENSRNOG00065007550 UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000003797 ENTREZGENE
  ENSRNOT00000003797.5 UniProtKB/Swiss-Prot
  ENSRNOT00055050514 UniProtKB/Swiss-Prot
  ENSRNOT00060048012 UniProtKB/Swiss-Prot
  ENSRNOT00065011820 UniProtKB/Swiss-Prot
Gene3D-CATH 2.10.60.10 UniProtKB/Swiss-Prot
InterPro LY6_UPA_recep-like 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
Pfam UPAR_LY6 UniProtKB/Swiss-Prot
PhenoGen Lypd8l1 PhenoGen
RatGTEx ENSRNOG00000002820 RatGTEx
  ENSRNOG00055029163 RatGTEx
  ENSRNOG00060027666 RatGTEx
  ENSRNOG00065007550 RatGTEx
Superfamily-SCOP SSF57302 UniProtKB/Swiss-Prot
TIGR TC216701
UniProt 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