Lum (lumican) - Rat Genome Database

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Advanced Search (OLGA)
Gene: Lum (lumican) Rattus norvegicus
Analyze
Symbol: Lum
Name: lumican
RGD ID: 620984
Description: Predicted to enable collagen binding activity. Involved in cartilage development; response to Aroclor 1254; and response to growth factor. Predicted to be located in extracellular matrix. Predicted to be part of fibrillar collagen trimer. Predicted to be active in extracellular space. Biomarker of ureteral obstruction. Human ortholog(s) of this gene implicated in carotid artery disease; coronary artery disease; and pancreatic cancer. Orthologous to human LUM (lumican); INTERACTS WITH 1-naphthyl isothiocyanate; 17alpha-ethynylestradiol; 2,3,7,8-tetrachlorodibenzodioxine.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: keratan sulfate proteoglycan lumican; KSPG lumican
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8734,245,323 - 34,252,510 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl734,245,360 - 34,252,508 (+)EnsemblGRCr8
mRatBN7.2732,358,990 - 32,365,794 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl732,358,614 - 32,365,793 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx734,326,157 - 34,332,958 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0736,514,385 - 36,521,189 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0736,248,713 - 36,255,514 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0738,820,058 - 38,826,862 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl738,819,771 - 38,826,862 (+)Ensemblrn6Rnor6.0
Rnor_5.0738,861,407 - 38,868,211 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4735,083,480 - 35,090,284 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera729,396,589 - 29,403,393 (+)NCBICelera
RGSC_v3.1735,103,750 - 35,110,554 (+)NCBI
Cytogenetic Map7q13NCBI
JBrowse:




Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
1,2-dimethylhydrazine  (ISO)
1-naphthyl isothiocyanate  (EXP)
17alpha-ethynylestradiol  (EXP,ISO)
17beta-estradiol  (ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,4,6-tribromophenol  (ISO)
2,4,6-trinitrobenzenesulfonic acid  (ISO)
2-butoxyethanol  (ISO)
3,3',5,5'-tetrabromobisphenol A  (ISO)
3,7-dihydropurine-6-thione  (EXP)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
3-methylcholanthrene  (ISO)
3-Nitrobenzanthrone  (ISO)
4,4'-diaminodiphenylmethane  (EXP)
4,4'-sulfonyldiphenol  (ISO)
4-hydroxyphenyl retinamide  (ISO)
6-propyl-2-thiouracil  (EXP)
8-Br-cAMP  (ISO)
aflatoxin B1  (EXP,ISO)
all-trans-retinoic acid  (EXP,ISO)
alpha-Zearalanol  (EXP)
ammonium chloride  (EXP)
amphetamine  (EXP)
antimycin A  (ISO)
arotinoid acid  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
atrazine  (ISO)
benzo[a]pyrene  (EXP,ISO)
benzo[b]fluoranthene  (ISO)
bexarotene  (EXP)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
butanal  (ISO)
Butylbenzyl phthalate  (ISO)
cadmium atom  (ISO)
cadmium dichloride  (EXP,ISO)
calcitriol  (ISO)
cantharidin  (ISO)
captan  (ISO)
carbon nanotube  (ISO)
CHIR 99021  (ISO)
choline  (ISO)
chromium(6+)  (ISO)
chrysene  (ISO)
cisplatin  (ISO)
copper atom  (EXP,ISO)
copper(0)  (EXP,ISO)
corosolic acid  (ISO)
cortisol  (ISO)
Cuprizon  (EXP)
cyclosporin A  (ISO)
cytarabine  (ISO)
DDT  (EXP)
decabromodiphenyl ether  (ISO)
dexamethasone  (EXP,ISO)
diazinon  (EXP)
dibutyl phthalate  (ISO)
diethyl maleate  (EXP)
diisononyl phthalate  (ISO)
dimethylarsinic acid  (EXP)
dioxygen  (EXP)
diquat  (ISO)
diuron  (EXP)
dorsomorphin  (ISO)
doxorubicin  (ISO)
endosulfan  (EXP)
epoxiconazole  (ISO)
ethanol  (ISO)
folic acid  (ISO)
furan  (EXP)
glycidol  (EXP)
indometacin  (ISO)
inulin  (ISO)
L-ascorbic acid  (ISO)
L-ascorbic acid 2-phosphate  (ISO)
L-methionine  (ISO)
lead diacetate  (EXP)
lead nitrate  (ISO)
lipopolysaccharide  (ISO)
losartan  (EXP)
manganese atom  (ISO)
manganese(0)  (ISO)
manganese(II) chloride  (ISO)
mercaptopurine  (EXP)
mercury atom  (ISO)
mercury(0)  (ISO)
methamphetamine  (ISO)
methotrexate  (ISO)
methylmercury chloride  (ISO)
mifepristone  (ISO)
N-ethyl-N-nitrosourea  (EXP)
N-methyl-4-phenylpyridinium  (ISO)
N-nitrosodiethylamine  (ISO)
N-nitrosodimethylamine  (EXP)
okadaic acid  (ISO)
oxaliplatin  (EXP)
paclitaxel  (ISO)
paracetamol  (ISO)
pentachlorophenol  (ISO)
pentanal  (ISO)
perfluorononanoic acid  (ISO)
perfluorooctane-1-sulfonic acid  (EXP,ISO)
perfluorooctanoic acid  (EXP)
phenformin  (EXP)
phenobarbital  (ISO)
phenylmercury acetate  (ISO)
PhIP  (EXP)
phorbol 13-acetate 12-myristate  (ISO)
picoxystrobin  (ISO)
pirinixic acid  (EXP)
potassium dichromate  (ISO)
procymidone  (EXP)
progesterone  (ISO)
propanal  (ISO)
purine-6-thiol  (EXP)
raloxifene  (ISO)
resveratrol  (ISO)
rotenone  (EXP,ISO)
S-(1,2-dichlorovinyl)-L-cysteine  (ISO)
SB 431542  (ISO)
silicon dioxide  (EXP,ISO)
sodium arsenite  (ISO)
sodium fluoride  (EXP)
sulforaphane  (ISO)
tamoxifen  (ISO)
tebufenpyrad  (ISO)
testosterone  (EXP)
testosterone enanthate  (ISO)
tetrachloroethene  (ISO)
tetrachloromethane  (ISO)
tetraphene  (ISO)
thapsigargin  (ISO)
titanium dioxide  (ISO)
toluene  (EXP)
topotecan  (EXP,ISO)
trichloroethene  (ISO)
triclosan  (ISO)
trimellitic anhydride  (ISO)
troglitazone  (ISO)
tunicamycin  (ISO)
valproic acid  (ISO)
vinclozolin  (EXP)
vincristine  (ISO)
XAV939  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function
collagen binding  (IBA,IEA,ISO)
protein binding  (ISO)

References

References - curated
# Reference Title Reference Citation
1. Immunolocalization of Proteoglycans in Meckel's Cartilage of the Rat. Ababneh KT and Al-Khateeb TH, Open Dent J. 2009 Aug 22;3:177-83.
2. Expression and localization of lumican in the ischemic and reperfused rat heart. Baba H, etal., Jpn Circ J. 2001 May;65(5):445-50.
3. Assessment of gene expression profiles in peripheral occlusive arterial disease. Bubenek S, etal., Can J Cardiol. 2012 Nov-Dec;28(6):712-20. doi: 10.1016/j.cjca.2012.03.013. Epub 2012 Jun 19.
4. Association of breast cancer susceptibility variants with risk of pancreatic cancer. Couch FJ, etal., Cancer Epidemiol Biomarkers Prev. 2009 Nov;18(11):3044-8. Epub 2009 Oct 20.
5. 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.
6. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
7. Role of lumican in cancer cells and adjacent stromal tissues in human pancreatic cancer. Ishiwata T, etal., Oncol Rep. 2007 Sep;18(3):537-43.
8. Differential expression of keratan sulphate proteoglycans fibromodulin, lumican and aggrecan in normal and fibrotic rat liver. Krull NB and Gressner AM, FEBS Lett. 1992 Nov 2;312(1):47-52.
9. Gene expression profiles in varicose veins using complementary DNA microarray. Lee S, etal., Dermatol Surg. 2005 Apr;31(4):391-5.
10. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
11. Transient and ectopic expression of lumican by acinar cells in L-arginine-induced acute pancreatitis. Naito Z, etal., Exp Mol Pathol 2003 Feb;74(1):33-9.
12. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
13. Expression of lumican in thickened intima and smooth muscle cells in human coronary atherosclerosis. Onda M, etal., Exp Mol Pathol. 2002 Apr;72(2):142-9.
14. GOA pipeline RGD automated data pipeline
15. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
16. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
17. Comprehensive gene review and curation RGD comprehensive gene curation
18. Gene expression profiles following exposure to a developmental neurotoxicant, Aroclor 1254: pathway analysis for possible mode(s) of action. Royland JE and Kodavanti PR, Toxicol Appl Pharmacol. 2008 Sep 1;231(2):179-96. Epub 2008 May 6.
19. Altered expression of immune modulator and structural genes in neonatal unilateral ureteral obstruction. Silverstein DM, etal., Kidney Int. 2003 Jul;64(1):25-35.
20. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
21. Analysis of intimal proteoglycans in atherosclerosis-prone and atherosclerosis-resistant human arteries by mass spectrometry. Talusan P, etal., Mol Cell Proteomics. 2005 Sep;4(9):1350-7. Epub 2005 Jun 21.
22. Involvement of acidic fibroblast growth factor in spinal cord injury repair processes revealed by a proteomics approach. Tsai MC, etal., Mol Cell Proteomics. 2008 Sep;7(9):1668-87. Epub 2008 May 14.
Additional References at PubMed
PMID:10734230   PMID:10892350   PMID:12128073   PMID:15489334   PMID:15849191   PMID:20551380   PMID:21931815   PMID:23376485   PMID:23533145   PMID:24006456   PMID:26316108   PMID:27068509  
PMID:27559042   PMID:32235499  


Genomics

Comparative Map Data
Lum
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8734,245,323 - 34,252,510 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl734,245,360 - 34,252,508 (+)EnsemblGRCr8
mRatBN7.2732,358,990 - 32,365,794 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl732,358,614 - 32,365,793 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx734,326,157 - 34,332,958 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0736,514,385 - 36,521,189 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0736,248,713 - 36,255,514 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0738,820,058 - 38,826,862 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl738,819,771 - 38,826,862 (+)Ensemblrn6Rnor6.0
Rnor_5.0738,861,407 - 38,868,211 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4735,083,480 - 35,090,284 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera729,396,589 - 29,403,393 (+)NCBICelera
RGSC_v3.1735,103,750 - 35,110,554 (+)NCBI
Cytogenetic Map7q13NCBI
LUM
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381291,102,629 - 91,111,494 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1291,102,629 - 91,111,512 (-)Ensemblhg38GRCh38
GRCh371291,496,406 - 91,505,271 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361290,021,363 - 90,029,673 (-)NCBIBuild 36Build 36hg18NCBI36
Build 341289,999,795 - 90,007,762NCBI
Celera1291,168,384 - 91,176,693 (-)NCBICelera
Cytogenetic Map12q21.33NCBI
HuRef1288,565,018 - 88,573,311 (-)NCBIHuRef
CHM1_11291,462,214 - 91,470,560 (-)NCBICHM1_1
T2T-CHM13v2.01291,080,108 - 91,088,974 (-)NCBIT2T-CHM13v2.0
Lum
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391097,401,363 - 97,408,565 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1097,400,990 - 97,408,565 (+)EnsemblGRCm39 EnsemblGRCm39
GRCm381097,565,501 - 97,572,703 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1097,565,128 - 97,572,703 (+)Ensemblmm10GRCm38
MGSCv371097,028,135 - 97,035,337 (+)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv361096,995,518 - 97,002,392 (+)NCBIMGSCv36mm8
Celera1099,536,481 - 99,543,683 (+)NCBICelera
Cytogenetic Map10C3NCBI
cM Map1050.32NCBI
Lum
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540528,298,988 - 28,308,054 (-)Ensembl
ChiLan1.0NW_00495540528,299,966 - 28,307,982 (-)NCBIChiLan1.0ChiLan1.0
LUM
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21099,136,692 - 99,144,880 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11299,133,086 - 99,141,066 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01288,636,825 - 88,644,665 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11291,952,277 - 91,960,388 (-)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1291,952,277 - 91,960,388 (-)EnsemblpanPan2panpan1.1
LUM
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11531,792,872 - 31,800,444 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1531,793,233 - 31,800,912 (-)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha1532,247,441 - 32,254,994 (-)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.01532,449,009 - 32,456,782 (-)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1532,449,009 - 32,456,645 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11531,741,534 - 31,749,085 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01531,805,190 - 31,812,738 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01532,098,606 - 32,106,158 (-)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Lum
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494528,380,086 - 28,387,678 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365077,846,681 - 7,855,455 (-)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_0049365077,847,761 - 7,855,311 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
LUM
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl591,748,885 - 91,757,598 (+)EnsemblsusScr11Sscrofa11.1
Sscrofa11.1591,748,871 - 91,756,381 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2596,175,872 - 96,183,382 (+)NCBISscrofa10.2Sscrofa10.2susScr3
LUM
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11186,510,824 - 86,519,008 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1186,509,722 - 86,519,010 (-)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_023666037158,664,710 - 158,672,984 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Lum
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462475015,553,383 - 15,559,408 (+)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_00462475015,553,400 - 15,560,746 (+)NCBIHetGla 1.0HetGla 1.0hetGla2
Lum
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v11176,763,272 - 176,770,338 (+)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Lum
76 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:52
Count of miRNA genes:46
Interacting mature miRNAs:47
Transcripts:ENSRNOT00000006109
Prediction methods:Miranda
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
1354644Spl4Serum phospholipid level QTL 44.9blood phospholipid amount (VT:0006084)blood phospholipid level (CMO:0001169)72154197751639954Rat
7411569Bw137Body weight QTL 1370.001body mass (VT:0001259)body weight gain (CMO:0000420)72380760668807606Rat
9590102Sffal5Serum free fatty acids level QTL 58.620.001blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)7721609752216097Rat
1578652Bmd15Bone mineral density QTL 155.2femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)71051708662346019Rat
631503Bp102Blood pressure QTL 1021.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)7170952746709527Rat
1549840Bss5Bone structure and strength QTL 59.8femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)72663805771638057Rat
1300127Srn1Serum renin concentration QTL 13.87blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)72417947886817926Rat
1358361Sradr5Stress Responsive Adrenal Weight QTL 55.55adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)731770293110435881Rat
2298547Neuinf5Neuroinflammation QTL 53.7nervous system integrity trait (VT:0010566)spinal cord Cd74 protein level (CMO:0002131)71011291660150541Rat
10059592Kidm45Kidney mass QTL 453.950.025kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)7946087754460877Rat
1354637Scl30Serum cholesterol level QTL 303.7blood cholesterol amount (VT:0000180)blood total cholesterol level (CMO:0000051)72154197751639954Rat
10755453Coatc12Coat color QTL 120coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)73299870277998702Rat
724560Plsm3Polydactyly-luxate syndrome (PLS) morphotypes QTL 30.0003tibia length (VT:0004357)tibia length (CMO:0000450)7134650782Rat
1354639Spl5Serum phospholipid level QTL 53.9blood LDL phospholipid amount (VT:0010505)blood low density lipoprotein phospholipid level (CMO:0001568)72154197735707405Rat
61410Bw19Body weight QTL 196.20.001body mass (VT:0001259)body weight (CMO:0000012)7166965846669658Rat
1643004Pain2Pain QTL 21mechanical nociception trait (VT:0002734)self mutilation severity score (CMO:0002145)71011291699900612Rat
1300149Cm6Cardiac mass QTL 64.09heart mass (VT:0007028)heart left ventricle weight to body weight ratio (CMO:0000530)71104117804Rat
634336Anxrr17Anxiety related response QTL 173.66locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)71509236116977875Rat
1582260Bw72Body weight QTL 723.20.0043body mass (VT:0001259)body weight (CMO:0000012)7139960528Rat
1582261Bw69Body weight QTL 693.20.0048body mass (VT:0001259)body weight (CMO:0000012)7139960528Rat
1582262Bw75Body weight QTL 7530.0038body mass (VT:0001259)body weight (CMO:0000012)7139960528Rat
70190Mcs6Mammary carcinoma susceptibility QTL 62.29mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)72862457565788017Rat
1300132Bp182Blood pressure QTL 1823.49arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)72154197786817926Rat
1300138Hrtrt9Heart rate QTL 94.72heart pumping trait (VT:2000009)heart rate (CMO:0000002)71049882055498820Rat
61369Mcs2Mammary carcinoma susceptibility QTL 23.38mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)72092049437412865Rat
738033Anxrr6Anxiety related response QTL 64.1exploratory behavior trait (VT:0010471)percentage of entries into a discrete space in an experimental apparatus (CMO:0000961)71746044762460447Rat
70207Niddm31Non-insulin dependent diabetes mellitus QTL 313.9blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)72005723265057232Rat
61439Cia8Collagen induced arthritis QTL 85.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)72718291472182914Rat

Markers in Region
RH128143  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2732,365,322 - 32,365,523 (+)MAPPERmRatBN7.2
Rnor_6.0738,826,391 - 38,826,591NCBIRnor6.0
Rnor_5.0738,867,740 - 38,867,940UniSTSRnor5.0
RGSC_v3.4735,089,813 - 35,090,013UniSTSRGSC3.4
Celera729,402,922 - 29,403,122UniSTS
RH 3.4 Map7255.6UniSTS
Cytogenetic Map7q13UniSTS


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 67 149 91 90 59 28 59 6 262 128 11 128 51 92 31 8 8

Sequence


Ensembl Acc Id: ENSRNOT00000006109   ⟹   ENSRNOP00000006109
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl734,245,360 - 34,252,508 (+)Ensembl
mRatBN7.2 Ensembl732,358,990 - 32,365,793 (+)Ensembl
Rnor_6.0 Ensembl738,819,771 - 38,826,862 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000111145   ⟹   ENSRNOP00000093264
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl732,358,614 - 32,365,793 (+)Ensembl
RefSeq Acc Id: NM_031050   ⟹   NP_112312
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8734,245,706 - 34,252,510 (+)NCBI
mRatBN7.2732,358,990 - 32,365,794 (+)NCBI
Rnor_6.0738,820,058 - 38,826,862 (+)NCBI
Rnor_5.0738,861,407 - 38,868,211 (+)NCBI
RGSC_v3.4735,083,480 - 35,090,284 (+)RGD
Celera729,396,589 - 29,403,393 (+)RGD
Sequence:
RefSeq Acc Id: XM_063264298   ⟹   XP_063120368
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8734,245,323 - 34,252,510 (+)NCBI
Protein Sequences
Protein RefSeqs NP_112312 (Get FASTA)   NCBI Sequence Viewer  
  XP_063120368 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAH61878 (Get FASTA)   NCBI Sequence Viewer  
  CAA58858 (Get FASTA)   NCBI Sequence Viewer  
  EDM16832 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000006109
  ENSRNOP00000006109.2
GenBank Protein P51886 (Get FASTA)   NCBI Sequence Viewer  
RefSeq Acc Id: NP_112312   ⟸   NM_031050
- Peptide Label: precursor
- UniProtKB: P51886 (UniProtKB/Swiss-Prot),   A6IG66 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000006109   ⟸   ENSRNOT00000006109
Ensembl Acc Id: ENSRNOP00000093264   ⟸   ENSRNOT00000111145
RefSeq Acc Id: XP_063120368   ⟸   XM_063264298
- Peptide Label: isoform X1
- UniProtKB: A0A8I6AIN1 (UniProtKB/TrEMBL)
Protein Domains
LRRNT

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-P51886-F1-model_v2 AlphaFold P51886 1-338 view protein structure

Transcriptome

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

Promoters
RGD ID:13695163
Promoter ID:EPDNEW_R5687
Type:multiple initiation site
Name:Lum_2
Description:lumican
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_R5688  
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0738,819,741 - 38,819,801EPDNEW
RGD ID:13695164
Promoter ID:EPDNEW_R5688
Type:initiation region
Name:Lum_1
Description:lumican
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_R5687  
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0738,820,044 - 38,820,104EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:620984 AgrOrtholog
BioCyc Gene G2FUF-34284 BioCyc
Ensembl Genes ENSRNOG00000004610 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000006109 ENTREZGENE
  ENSRNOT00000006109.5 UniProtKB/Swiss-Prot
Gene3D-CATH 3.80.10.10 UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:5599252 IMAGE-MGC_LOAD
InterPro Leu-rich_rpt UniProtKB/Swiss-Prot
  Leu-rich_rpt_typical-subtyp UniProtKB/Swiss-Prot
  LRR_dom_sf UniProtKB/Swiss-Prot
  LRRNT UniProtKB/Swiss-Prot
  SLRP UniProtKB/Swiss-Prot
KEGG Report rno:81682 UniProtKB/Swiss-Prot
MGC_CLONE MGC:72416 IMAGE-MGC_LOAD
NCBI Gene 81682 ENTREZGENE
PANTHER AGAP008170-PA UniProtKB/Swiss-Prot
  PTHR45712:SF6 UniProtKB/Swiss-Prot
Pfam LRR_1 UniProtKB/Swiss-Prot
  LRR_8 UniProtKB/Swiss-Prot
  LRRNT UniProtKB/Swiss-Prot
PhenoGen Lum PhenoGen
PRINTS LEURICHRPT UniProtKB/Swiss-Prot
PROSITE LRR UniProtKB/Swiss-Prot
RatGTEx ENSRNOG00000004610 RatGTEx
SMART LRR_BAC UniProtKB/Swiss-Prot
  LRR_SD22 UniProtKB/Swiss-Prot
  LRR_TYP UniProtKB/Swiss-Prot
  LRRNT UniProtKB/Swiss-Prot
Superfamily-SCOP L domain-like UniProtKB/Swiss-Prot
UniProt A0A8I6AIN1 ENTREZGENE
  A6IG66 ENTREZGENE, UniProtKB/TrEMBL
  LUM_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2004-09-10 Lum  lumican      Symbol and Name status set to approved 1299863 APPROVED
2002-08-07 Lum  lumican      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_expression expressed in ductal and centroacinar cells in the normal pancreas 724427