Ly75 (lymphocyte antigen 75) - Rat Genome Database

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Gene: Ly75 (lymphocyte antigen 75) Rattus norvegicus
Analyze
Symbol: Ly75
Name: lymphocyte antigen 75
RGD ID: 1565962
Description: Predicted to enable signaling receptor activity. Predicted to be involved in endocytosis. Predicted to be located in plasma membrane. Predicted to be active in external side of plasma membrane. Orthologous to several human genes including LY75 (lymphocyte antigen 75); INTERACTS WITH 17beta-estradiol; 2,3,7,8-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC499800; RGD1565962; similar to DEC-205
RGD Orthologs
Human
Mouse
Bonobo
Pig
Green Monkey
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8365,173,395 - 65,260,878 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl365,173,395 - 65,260,878 (-)EnsemblGRCr8
mRatBN7.2344,764,702 - 44,852,219 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl344,765,122 - 44,852,374 (-)EnsemblmRatBN7.2
Rnor_6.0346,369,749 - 46,457,182 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl346,365,165 - 46,457,201 (-)Ensemblrn6Rnor6.0
Rnor_5.0351,477,873 - 51,565,302 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4342,002,053 - 42,088,438 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera342,807,583 - 42,893,881 (-)NCBICelera
Cytogenetic Map3q21NCBI
JBrowse:




Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:10648399   PMID:20458337   PMID:20709950  


Genomics

Comparative Map Data
Ly75
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8365,173,395 - 65,260,878 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl365,173,395 - 65,260,878 (-)EnsemblGRCr8
mRatBN7.2344,764,702 - 44,852,219 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl344,765,122 - 44,852,374 (-)EnsemblmRatBN7.2
Rnor_6.0346,369,749 - 46,457,182 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl346,365,165 - 46,457,201 (-)Ensemblrn6Rnor6.0
Rnor_5.0351,477,873 - 51,565,302 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4342,002,053 - 42,088,438 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera342,807,583 - 42,893,881 (-)NCBICelera
Cytogenetic Map3q21NCBI
LY75
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh382159,803,355 - 159,904,756 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl2159,803,355 - 159,904,756 (-)Ensemblhg38GRCh38
GRCh372160,659,866 - 160,761,267 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 362160,368,112 - 160,469,508 (-)NCBIBuild 36Build 36hg18NCBI36
Build 342160,485,382 - 160,586,754NCBI
Celera2154,271,706 - 154,373,097 (-)NCBICelera
Cytogenetic Map2q24.2NCBI
HuRef2152,542,810 - 152,644,955 (-)NCBIHuRef
CHM1_12160,666,254 - 160,767,989 (-)NCBICHM1_1
T2T-CHM13v2.02160,260,710 - 160,363,008 (-)NCBIT2T-CHM13v2.0
Ly75
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39260,122,447 - 60,213,617 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl260,122,447 - 60,213,647 (-)EnsemblGRCm39 EnsemblGRCm39
GRCm38260,292,103 - 60,383,273 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl260,292,103 - 60,383,303 (-)Ensemblmm10GRCm38
MGSCv37260,131,817 - 60,221,288 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv36260,092,942 - 60,184,103 (-)NCBIMGSCv36mm8
Celera261,988,204 - 62,078,536 (-)NCBICelera
Cytogenetic Map2C1.1NCBI
cM Map234.54NCBI
LY75
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21362,494,125 - 62,596,312 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan12B62,509,098 - 62,611,283 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v02B47,095,026 - 47,196,905 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.12B164,469,059 - 164,568,413 (-)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2B164,469,343 - 164,568,677 (-)EnsemblpanPan2panpan1.1
LY75
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1566,740,071 - 66,847,605 (-)EnsemblsusScr11Sscrofa11.1
Sscrofa11.11566,741,623 - 66,847,527 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21573,977,289 - 74,019,902 (-)NCBISscrofa10.2Sscrofa10.2susScr3
LY75
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11045,178,819 - 45,299,698 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1045,208,333 - 45,299,608 (-)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_023666040154,276,613 - 154,375,884 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0

Variants

.
Variants in Ly75
618 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:129
Count of miRNA genes:108
Interacting mature miRNAs:114
Transcripts:ENSRNOT00000010683, ENSRNOT00000071468
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
10401810Kidm53Kidney mass QTL 53kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)32862533967641995Rat
2298542Neuinf11Neuroinflammation QTL 113.9nervous system integrity trait (VT:0010566)spinal cord complement component 1, q subcomponent, B chain mRNA level (CMO:0002126)33540319997383526Rat
1358362Srcrt2Stress Responsive Cort QTL 22.78blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)358601291153936591Rat
631832Sach1Saccharin preference QTL 12.70.02consumption behavior trait (VT:0002069)calculated saccharin drink intake volume (CMO:0001600)34790417292904172Rat
737818Hcar12Hepatocarcinoma resistance QTL 122.6liver integrity trait (VT:0010547)volume of individual liver tumorous lesion (CMO:0001078)349872657138829559Rat
9590286Uminl1Urine mineral level QTL 13.50.001urine mineral amount (VT:0015086)urine electrolyte level (CMO:0000593)34865774493657744Rat
10450816Scl75Serum cholesterol level QTL 754.40.001blood LDL cholesterol amount (VT:0000181)blood low density lipoprotein cholesterol level (CMO:0000053)35860129171157804Rat
4889966Bss95Bone structure and strength QTL 954.4tibia area (VT:1000281)tibia-fibula cross-sectional area (CMO:0001718)33779691982796919Rat
2313093Bmd77Bone mineral density QTL 772.20.0001tibia mineral mass (VT:1000283)compact volumetric bone mineral density (CMO:0001730)34790417270710963Rat
12879852Cm93Cardiac mass QTL 930.001heart right ventricle mass (VT:0007033)heart right ventricle weight to body weight ratio (CMO:0000914)33870893167641995Rat
12879853Am5Aortic mass QTL 50.001aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)33870893167641995Rat
12879854Kidm63Kidney mass QTL 630.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)33870893167641995Rat
61356Bp37Blood pressure QTL 373blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)35109256196092561Rat
1358905Hrtrt17Heart rate QTL 175.90.000014heart pumping trait (VT:2000009)heart rate (CMO:0000002)336721849110333156Rat
12879849Bw180Body weight QTL 1800.037body mass (VT:0001259)body weight (CMO:0000012)33870893167641995Rat
12879850Cm91Cardiac mass QTL 910.001heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)33870893167641995Rat
2313101Bmd76Bone mineral density QTL 763.60.0001tibia mineral mass (VT:1000283)total volumetric bone mineral density (CMO:0001728)34790417270710963Rat
12879851Cm92Cardiac mass QTL 920.001heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)33870893167641995Rat
731172Bp151Blood pressure QTL 1510.04arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)33870893167641995Rat
8694196Abfw2Abdominal fat weight QTL 216.580.001visceral adipose mass (VT:0010063)abdominal fat pad weight to body weight ratio (CMO:0000095)34865774493657744Rat
1358885Bp251Blood pressure QTL 2513.8arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)31141509147Rat
2290452Scl56Serum cholesterol level QTL 562.26blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)33610140381101403Rat
10450852Stl33Serum triglyceride level QTL 333.40.05blood LDL triglyceride amount (VT:0010699)blood lipoprotein triglyceride level (CMO:0002685)35860129171157804Rat
1358888Bp264Blood pressure QTL 2644.43arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)35675975141509147Rat
4889975Bmd81Bone mineral density QTL 814.3tibia mineral mass (VT:1000283)total volumetric bone mineral density (CMO:0001728)35911940270710963Rat
1300178Hrtrt4Heart rate QTL 43.74heart pumping trait (VT:2000009)heart rate (CMO:0000002)351490129111359995Rat
634317Bw117Body weight QTL 1173.58abdominal fat pad mass (VT:1000711)abdominal fat pad weight to body weight ratio (CMO:0000095)35986366373704481Rat
1331795Rf30Renal function QTL 303.708urine potassium amount (VT:0010539)urine potassium level (CMO:0000128)35986366387321459Rat
70216Cm14Cardiac mass QTL 142.1heart mass (VT:0007028)heart wet weight (CMO:0000069)351581665184004958Rat
1354589Bw31Body weight QTL 313.3body mass (VT:0001259)body weight (CMO:0000012)35365182698651826Rat
2303593Gluco46Glucose level QTL 463blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)34887661993876619Rat
1354590Despr11Despair related QTL 110.000031locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)34887661993876619Rat
2313079Bss73Bone structure and strength QTL 731.5tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)34790417270710963Rat
1331777Bw24Body weight QTL 243.503body mass (VT:0001259)body weight (CMO:0000012)35986366387321459Rat
631647Bp122Blood pressure QTL 1226.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)35109256196092561Rat
2313076Bss74Bone structure and strength QTL 7420.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)34790417270710963Rat
1300169Bp177Blood pressure QTL 1772.96arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)33642511681425116Rat
10450813Scl74Serum cholesterol level QTL 745.80.001blood LDL cholesterol amount (VT:0000181)blood low density lipoprotein cholesterol level (CMO:0000053)35860129171157804Rat
2302276Bw82Body weight QTL 824.32body mass (VT:0001259)body weight (CMO:0000012)35986366383358329Rat
738019Anxrr10Anxiety related response QTL 103.9exploratory behavior trait (VT:0010471)number of entries into a discrete space in an experimental apparatus (CMO:0000960)358925062103925062Rat
9590136Scort3Serum corticosterone level QTL 323.370.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)34865774493657744Rat
61419Cia11Collagen induced arthritis QTL 115.6joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)35076614595766145Rat
1558650Cm48Cardiac mass QTL 4840.0001heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)35076614595766145Rat
1354597Kidm13Kidney mass QTL 132.9kidney mass (VT:0002707)right kidney wet weight (CMO:0000082)342158111124558371Rat
2325840Bp345Blood pressure QTL 3450.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)33870893183708931Rat
8552950Pigfal12Plasma insulin-like growth factor 1 level QTL 127.3blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)34865774493657744Rat
631676Cm8Cardiac mass QTL 87.030.0001aorta mass (VT:0002845)aorta weight (CMO:0000076)33736373482363734Rat
8694386Bw159Body weight QTL 1594.520.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)34865774493657744Rat
1354604Bw36Body weight QTL 362.9body mass (VT:0001259)body weight (CMO:0000012)342158111124558371Rat
2313049Bss72Bone structure and strength QTL 722.60.0001tibia area (VT:1000281)tibia midshaft cross-sectional area (CMO:0001717)34790417270710963Rat

Markers in Region
D3Rat123  
Rat AssemblyChrPosition (strand)SourceJBrowse
GRCr8365,213,796 - 65,214,023 (+)Marker Load Pipeline
mRatBN7.2344,805,104 - 44,805,331 (+)MAPPERmRatBN7.2
Rnor_6.0346,410,151 - 46,410,377NCBIRnor6.0
Rnor_5.0351,518,275 - 51,518,501UniSTSRnor5.0
RGSC_v3.4342,040,765 - 42,040,991UniSTSRGSC3.4
RGSC_v3.4342,040,764 - 42,040,991RGDRGSC3.4
Celera342,846,752 - 42,846,978UniSTS
RGSC_v3.1341,937,136 - 41,937,363RGD
SHRSP x BN Map332.8199UniSTS
SHRSP x BN Map332.8199RGD
Cytogenetic Map3q21UniSTS


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 10 67 165 91 90 59 92 59 6 352 190 11 144 79 92 31 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000010683   ⟹   ENSRNOP00000010683
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl365,173,395 - 65,260,878 (-)Ensembl
mRatBN7.2 Ensembl344,765,122 - 44,852,374 (-)Ensembl
Rnor_6.0 Ensembl346,365,165 - 46,457,201 (-)Ensembl
RefSeq Acc Id: NM_001427146   ⟹   NP_001414075
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8365,173,395 - 65,260,878 (-)NCBI
Protein Sequences
Protein RefSeqs NP_001414075 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDM00379 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000010683
  ENSRNOP00000010683.6
Ensembl Acc Id: ENSRNOP00000010683   ⟸   ENSRNOT00000010683
RefSeq Acc Id: NP_001414075   ⟸   NM_001427146
- Peptide Label: precursor
- UniProtKB: D3ZQK8 (UniProtKB/TrEMBL)
Protein Domains
C-type lectin   Fibronectin type-II

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZQK8-F1-model_v2 AlphaFold D3ZQK8 1-1741 view protein structure

Transcriptome

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

Promoters
RGD ID:13692095
Promoter ID:EPDNEW_R2616
Type:multiple initiation site
Name:Ly75_1
Description:lymphocyte antigen 75
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_6.0346,457,160 - 46,457,220EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1565962 AgrOrtholog
BioCyc Gene G2FUF-49619 BioCyc
Ensembl Genes ENSRNOG00000007012 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000010683 ENTREZGENE
  ENSRNOT00000010683.9 UniProtKB/TrEMBL
Gene3D-CATH 2.10.10.10 UniProtKB/TrEMBL
  2.80.10.50 UniProtKB/TrEMBL
  3.10.100.10 UniProtKB/TrEMBL
InterPro C-type_lectin UniProtKB/TrEMBL
  C-type_lectin-like UniProtKB/TrEMBL
  C-type_lectin/snaclec_domain UniProtKB/TrEMBL
  C-type_lectin_CS UniProtKB/TrEMBL
  C-type_lectin_fold UniProtKB/TrEMBL
  FN_type2_col-bd UniProtKB/TrEMBL
  FN_type2_sf UniProtKB/TrEMBL
  Kringle-like UniProtKB/TrEMBL
  Ricin_B-like_lectins UniProtKB/TrEMBL
  Ricin_B_lectin UniProtKB/TrEMBL
NCBI Gene 499800 ENTREZGENE
PANTHER MANNOSE, PHOSPHOLIPASE, LECTIN RECEPTOR RELATED UniProtKB/TrEMBL
Pfam CysR_MRC2_N UniProtKB/TrEMBL
  fn2 UniProtKB/TrEMBL
  Lectin_C UniProtKB/TrEMBL
PhenoGen Ly75 PhenoGen
PROSITE C_TYPE_LECTIN_1 UniProtKB/TrEMBL
  C_TYPE_LECTIN_2 UniProtKB/TrEMBL
  FN2_1 UniProtKB/TrEMBL
  FN2_2 UniProtKB/TrEMBL
  RICIN_B_LECTIN UniProtKB/TrEMBL
RatGTEx ENSRNOG00000007012 RatGTEx
SMART CLECT UniProtKB/TrEMBL
  FN2 UniProtKB/TrEMBL
  RICIN UniProtKB/TrEMBL
Superfamily-SCOP C-type_lectin_fold UniProtKB/TrEMBL
  Kringle-like UniProtKB/TrEMBL
  RicinB_like UniProtKB/TrEMBL
UniProt D3ZQK8 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-03-06 Ly75  lymphocyte antigen 75  RGD1565962_predicted  similar to DEC-205 (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-07 RGD1565962_predicted  similar to DEC-205 (predicted)  LOC499800  similar to DEC-205  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC499800  similar to DEC-205      Symbol and Name status set to provisional 70820 PROVISIONAL