Lce1m (late cornified envelope 1M) - Rat Genome Database

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Gene: Lce1m (late cornified envelope 1M) Mus musculus
Analyze
Symbol: Lce1m
Name: late cornified envelope 1M
RGD ID: 1614383
MGI Page MGI
Description: ENCODES a protein that exhibits identical protein binding (ortholog); ASSOCIATED WITH gastrointestinal stromal tumor (ortholog); genetic disease (ortholog); immunodeficiency 42 (ortholog); INTERACTS WITH 3,4-methylenedioxymethamphetamine; 4,4'-diaminodiphenylmethane; benzalkonium chloride
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: 1110059L13Rik; AI131654; late cornified envelope 5A; late cornified envelope protein 5A; Lce; Lce5a; MGC129452; MGC129453; small proline rich-like 10; Sp; Sprrl10
RGD Orthologs
Human
Rat
Alliance Genes
More Info more info ...
Latest Assembly: GRCm39 - Mouse Genome Assembly GRCm39
Position:
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39392,925,114 - 92,926,368 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl392,925,117 - 92,926,367 (-)EnsemblGRCm39 Ensembl
GRCm38393,017,807 - 93,019,061 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl393,017,810 - 93,019,060 (-)EnsemblGRCm38mm10GRCm38
MGSCv37392,821,729 - 92,822,982 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36393,103,213 - 93,104,463 (-)NCBIMGSCv36mm8
Celera394,059,933 - 94,061,186 (+)NCBICelera
Cytogenetic Map3F1NCBI
cM Map340.14NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

Phenotype Annotations     Click to see Annotation Detail View

Mammalian Phenotype
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:10349636   PMID:11042159   PMID:11076861   PMID:11217851   PMID:11698679   PMID:12466851   PMID:12477932   PMID:15854049   PMID:16141072   PMID:16141073   PMID:16602821   PMID:17410201  
PMID:19303854   PMID:21267068   PMID:21677750   PMID:21873635   PMID:22201818   PMID:27626380   PMID:30973865  


Genomics

Comparative Map Data
Lce1m
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39392,925,114 - 92,926,368 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl392,925,117 - 92,926,367 (-)EnsemblGRCm39 Ensembl
GRCm38393,017,807 - 93,019,061 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl393,017,810 - 93,019,060 (-)EnsemblGRCm38mm10GRCm38
MGSCv37392,821,729 - 92,822,982 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36393,103,213 - 93,104,463 (-)NCBIMGSCv36mm8
Celera394,059,933 - 94,061,186 (+)NCBICelera
Cytogenetic Map3F1NCBI
cM Map340.14NCBI
LCE5A
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381152,510,803 - 152,512,177 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1152,510,803 - 152,512,177 (+)EnsemblGRCh38hg38GRCh38
GRCh371152,483,279 - 152,484,653 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361150,749,944 - 150,751,277 (+)NCBINCBI36Build 36hg18NCBI36
Build 341149,296,392 - 149,297,725NCBI
Celera1125,594,141 - 125,595,474 (+)NCBICelera
Cytogenetic Map1q21.3NCBI
HuRef1123,856,808 - 123,858,141 (+)NCBIHuRef
CHM1_11153,878,669 - 153,880,002 (+)NCBICHM1_1
T2T-CHM13v2.01151,647,352 - 151,648,726 (+)NCBIT2T-CHM13v2.0
Lce1m
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr82181,333,098 - 181,334,300 (-)NCBIGRCr8
mRatBN7.22178,637,495 - 178,638,697 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl2178,637,495 - 178,638,697 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHRSP_BbbUtx_1.02184,187,027 - 184,188,214 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
Rnor_6.02193,333,799 - 193,336,789 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2193,333,800 - 193,335,002 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02211,534,988 - 211,536,190 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42186,053,050 - 186,054,252 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera2171,622,444 - 171,623,646 (+)NCBICelera
Cytogenetic Map2q34NCBI

Variants

.
Variants in Lce1m
56 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:81
Count of miRNA genes:73
Interacting mature miRNAs:76
Transcripts:ENSMUST00000029520
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 (GRCm39)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
26884378Skwq6_mskull length QTL 6, 10 week (mouse)351907421102307316Mouse
1302052Etohcta4_methanol conditioned taste aversion 4 (mouse)Not determined391000105125008748Mouse
11049572Lmr11c_mleishmaniasis resistance 11c (mouse)372139967106140094Mouse
1357583Sle18_msystematic lupus erythematosus susceptibility 18 (mouse)Not determined387208904125316236Mouse
1300595Tmevd2_mTheiler's murine encephalomyelitis virus induced demyelinating disease susceptibility 2 (mouse)Not determined375463302109463549Mouse
12738440Twq3_mtestis weight QTL 3 (mouse)387228015121228015Mouse
26884380Skwq1_mskull length QTL 1, 5 week (mouse)343954435101607316Mouse
1301904Iba2_minduction of brown adipocytes 2 (mouse)Not determined382147043116147184Mouse
11041900Lmr11a_mleishmaniasis resistance 11a (mouse)383463991117464137Mouse
11039511Ltpr3c_mLeishmania tropica response 3c (mouse)383463991117464137Mouse
1301398Rapop3_mradiation-induced apoptosis 3 (mouse)Not determined390511217100464137Mouse
11039509Ltpr3e_mLeishmania tropica response 3e (mouse)383463991117464137Mouse
4142178Ctrq2_mC. trachomatis resistance QTL 2 (mouse)Not determined389139967137453008Mouse
11039507Ltpr3g_mLeishmania tropica response 3g (mouse)383463991117464137Mouse
4142099Cq3_mcholesterol QTL 3 (mouse)Not determined384888918118889067Mouse
1301349Pgia26_mproteoglycan induced arthritis 26 (mouse)Not determined392251533126251650Mouse
4142399Aec1_mautoimmune exocrinopathy 1 (mouse)Not determined7586174102690034Mouse
26884427Cvht4_mcranial vault height 4, 10 week (mouse)316054164109707316Mouse
25314313Syncl1_msynaptonemal complex length 1 (mouse)367907333128393649Mouse
10766455Sle22_msystematic lupus erythematosus susceptibility 22 (mouse)390376936124377072Mouse
13207570Tcq12_mtotal cholesterol QTL 12 (mouse)316504164130163649Mouse
13208566Bmiq5_mbody mass index QTL 5 (mouse)340954435115793649Mouse
1301947Pcfm3_mperiosteal circumference and femur length 3 (mouse)Not determined381084652115084797Mouse
14746984Manh54_mmandible shape 54 (mouse)385289152119289152Mouse
11251721Ewc3_methanol withdrawal and consumption 3 (mouse)369568554103568554Mouse
26884382Bzwq1_mbi-zygomatic width QTL 1, 5 week (mouse)352207421137205761Mouse
11039519Ltpr3_mLeishmania tropica response 3 (mouse)356704102100464137Mouse
4141294Bmd24_mbone mineral density 24 (mouse)Not determined36174006195740241Mouse
11039512Ltpr3b_mLeishmania tropica response 3b (mouse)383463991117464137Mouse
1301392Eae3_msusceptibility to experimental allergic encephalomyelitis 3 (mouse)Not determined379548730113548837Mouse
11039510Ltpr3d_mLeishmania tropica response 3d (mouse)383463991117464137Mouse
1301422Sle11_msystematic lupus erythematosus susceptibility 11 (mouse)Not determined370208904104209042Mouse
1300982Lmr11_mleishmaniasis resistance 11 (mouse)Not determined372139967106140094Mouse
1301272Cfsw1_mcystic fibrosis survival to weaning 1 (mouse)Not determined383882912117883044Mouse
14747001Mancz4_mmandible centroid size 4 (mouse)390378017124378017Mouse
26884436Zlq3_mzygomatic length QTL 3, 10 week (mouse)33265060142405761Mouse
26884422Cvht7_mcranial vault height 7, 16 week (mouse)328954149118893649Mouse
1302056Orgwq4_morgan weight QTL 4 (mouse)Not determined330067588147304689Mouse
1301705Sles3_msystemic lupus erythmatosus suppressor 3 (mouse)Not determined337174862143353183Mouse
1301971Cia5_mcollagen induced arthritis QTL 5 (mouse)Not determined366046658100046795Mouse
1301791Char4_mP. chabaudi malaria resistance QTL 4 (mouse)Not determined369625509100655290Mouse
11039508Ltpr3f_mLeishmania tropica response 3f (mouse)383463991117464137Mouse

Markers in Region
AI131654  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm38393,017,917 - 93,018,061UniSTSGRCm38
MGSCv37392,821,839 - 92,821,983UniSTSGRCm37
Celera394,060,932 - 94,061,076UniSTS
Cytogenetic Map3F2UniSTS
Whitehead/MRC_RH31039.42UniSTS
UniSTS:487878  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm38393,017,925 - 93,019,062UniSTSGRCm38
MGSCv37392,821,847 - 92,822,984UniSTSGRCm37
Celera394,059,931 - 94,061,068UniSTS
Cytogenetic Map3F2UniSTS


Expression


Sequence


Reference Sequences
RefSeq Acc Id: ENSMUST00000029520   ⟹   ENSMUSP00000029520
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl392,925,117 - 92,926,367 (-)Ensembl
GRCm38.p6 Ensembl393,017,810 - 93,019,060 (-)Ensembl
RefSeq Acc Id: ENSMUST00000193944   ⟹   ENSMUSP00000141488
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl392,925,814 - 92,926,366 (-)Ensembl
GRCm38.p6 Ensembl393,018,507 - 93,019,059 (-)Ensembl
RefSeq Acc Id: NM_001355725   ⟹   NP_001342654
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39392,925,114 - 92,926,368 (-)NCBI
GRCm38393,017,807 - 93,019,061 (-)NCBI
Sequence:
RefSeq Acc Id: NM_025420   ⟹   NP_079696
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39392,925,114 - 92,926,368 (-)NCBI
GRCm38393,017,807 - 93,019,061 (-)NCBI
MGSCv37392,821,729 - 92,822,982 (-)RGD
Celera394,059,933 - 94,061,186 (+)RGD
cM Map3 ENTREZGENE
Sequence:
Reference Protein Sequences
RefSeq Acc Id: NP_079696   ⟸   NM_025420
- UniProtKB: Q9CR91 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: NP_001342654   ⟸   NM_001355725
- UniProtKB: Q9CR91 (UniProtKB/TrEMBL)
RefSeq Acc Id: ENSMUSP00000029520   ⟸   ENSMUST00000029520
RefSeq Acc Id: ENSMUSP00000141488   ⟸   ENSMUST00000193944

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q9CR91-F1-model_v2 AlphaFold Q9CR91 1-182 view protein structure

Promoters
RGD ID:6881462
Promoter ID:EPDNEW_M4182
Type:single initiation site
Name:Lce1m_1
Description:Mus musculus late cornified envelope 1M , transcript variant1, mRNA.
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38393,019,059 - 93,019,119EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene MGI:1913453 AgrOrtholog
Ensembl Genes ENSMUSG00000027912 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSMUST00000029520 ENTREZGENE
  ENSMUST00000029520.9 UniProtKB/TrEMBL
  ENSMUST00000193944.2 UniProtKB/TrEMBL
InterPro LCE UniProtKB/TrEMBL
MGD MGI:1913453 ENTREZGENE
NCBI Gene 66203 ENTREZGENE
Pfam LCE UniProtKB/TrEMBL
PhenoGen Lce1m PhenoGen
UniProt A0A0A6YWC3_MOUSE UniProtKB/TrEMBL
  Q9CR91 ENTREZGENE, UniProtKB/TrEMBL