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

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Gene: Lce1m (late cornified envelope 1M) Rattus norvegicus
Analyze
Symbol: Lce1m
Name: late cornified envelope 1M
RGD ID: 1588875
Description: Predicted to enable identical protein binding activity. Predicted to be involved in keratinization. Orthologous to human LCE5A (late cornified envelope 5A); INTERACTS WITH 6-propyl-2-thiouracil; endosulfan; 2-hydroxypropanoic acid (ortholog).
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: hypothetical protein LOC688413; LOC688413
RGD Orthologs
Human
Mouse
Green Monkey
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr82181,333,098 - 181,334,300 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl2181,333,098 - 181,334,300 (-)EnsemblGRCr8
mRatBN7.22178,637,495 - 178,638,697 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl2178,637,495 - 178,638,697 (-)EnsemblmRatBN7.2
UTH_Rnor_SHRSP_BbbUtx_1.02184,187,027 - 184,188,214 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
Rnor_6.02193,333,799 - 193,336,789 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2193,333,800 - 193,335,002 (-)Ensemblrn6Rnor6.0
Rnor_5.02211,534,988 - 211,536,190 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.42186,053,050 - 186,054,252 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera2171,622,444 - 171,623,646 (+)NCBICelera
Cytogenetic Map2q34NCBI
JBrowse:




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

Biological Process

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

Genomics

Comparative Map Data
Lce1m
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr82181,333,098 - 181,334,300 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl2181,333,098 - 181,334,300 (-)EnsemblGRCr8
mRatBN7.22178,637,495 - 178,638,697 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl2178,637,495 - 178,638,697 (-)EnsemblmRatBN7.2
UTH_Rnor_SHRSP_BbbUtx_1.02184,187,027 - 184,188,214 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
Rnor_6.02193,333,799 - 193,336,789 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2193,333,800 - 193,335,002 (-)Ensemblrn6Rnor6.0
Rnor_5.02211,534,988 - 211,536,190 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.42186,053,050 - 186,054,252 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera2171,622,444 - 171,623,646 (+)NCBICelera
Cytogenetic Map2q34NCBI
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 (+)Ensemblhg38GRCh38
GRCh371152,483,279 - 152,484,653 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361150,749,944 - 150,751,277 (+)NCBIBuild 36Build 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
(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 EnsemblGRCm39
GRCm38393,017,807 - 93,019,061 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl393,017,810 - 93,019,060 (-)Ensemblmm10GRCm38
MGSCv37392,821,729 - 92,822,982 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv36393,103,213 - 93,104,463 (-)NCBIMGSCv36mm8
Celera394,059,933 - 94,061,186 (+)NCBICelera
Cytogenetic Map3F1NCBI
cM Map340.14NCBI
LCE5A
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12011,188,929 - 11,191,668 (-)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366603810,673,926 - 10,675,485 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0

Variants

.
Variants in Lce1m
20 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:33
Count of miRNA genes:30
Interacting mature miRNAs:33
Transcripts:ENSRNOT00000012691
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 (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1358356Srcrt1Stress Responsive Cort QTL13.66blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)2163997722225110681Rat
1578648Bss11Bone structure and strength QTL 114.7femur morphology trait (VT:0000559)femoral neck cortical cross-sectional area (CMO:0001702)2169358774214358774Rat
1331734Bp204Blood pressure QTL 2043.61192arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2170656145239614549Rat
631566Bp90Blood pressure QTL 900.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2149957381221199885Rat
1298074Bp164Blood pressure QTL 1640.003arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)244537979205135428Rat
1354648Bp239Blood pressure QTL 2390.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)267845370229470703Rat
1354649Kidm17Kidney mass QTL 172.9kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)283465462229820014Rat
10755499Bp389Blood pressure QTL 3892.61arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)220695736231474293Rat
1298076Bp166Blood pressure QTL 1660.0009arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2138595962205135428Rat
1581576Pur7Proteinuria QTL 70.0001urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)280396178220931218Rat
152025245Scl81Serum cholesterol level QTL 813.49blood cholesterol amount (VT:0000180)2124537199209621565Rat
1581578Cm49Cardiac mass QTL 494.90.01heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)2145807215220931416Rat
631198Cm22Cardiac mass QTL 224.30.0008heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)278269809208420281Rat
1554319Bmd2Bone mineral density QTL 213.40.0001lumbar vertebra area (VT:0010570)lumbar vertebra cross-sectional area (CMO:0001689)2122597372215234002Rat
12879836Kidm61Kidney mass QTL 610.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)2154723085199723085Rat
1581569Uae32Urinary albumin excretion QTL 320.0001urine protein amount (VT:0005160)urine albumin excretion rate (CMO:0000757)280396178220931218Rat
10043136Iddm54Insulin dependent diabetes mellitus QTL 543.40.0001blood glucose amount (VT:0000188)age at onset/diagnosis of type 1 diabetes mellitus (CMO:0001140)2145807215190807215Rat
12879837Am2Aortic mass QTL 20.001aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)2154723085199723085Rat
10043139Iddm55Insulin dependent diabetes mellitus QTL 553.10.0001blood glucose amount (VT:0000188)age at onset/diagnosis of type 1 diabetes mellitus (CMO:0001140)2150313808195313808Rat
12879838Cm86Cardiac mass QTL 860.002heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)2154723085199723085Rat
1302793Bw16Body weight QTL 1650.0001body mass (VT:0001259)body weight (CMO:0000012)2159440891205135267Rat
12879839Cm85Cardiac mass QTL 850.001heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)2154723085199723085Rat
1549833Bp257Blood pressure QTL 2570.003arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2170652929215652929Rat
1358900Bw48Body weight QTL 484.88body mass (VT:0001259)body weight (CMO:0000012)2159440891220931218Rat
4889834Pur24Proteinuria QTL 245.80.014urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)2171994826205135428Rat
1359030Bp277Blood pressure QTL 277arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)2143565208188565208Rat
1331760Bp206Blood pressure QTL 2063.62454arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)24265106205135428Rat
12879840Bw179Body weight QTL 1790.005body mass (VT:0001259)body weight (CMO:0000012)2154723085199723085Rat
1581502Esta3Estrogen-induced thymic atrophy QTL 3thymus mass (VT:0004954)thymus wet weight (CMO:0000855)2139067258192287892Rat
1359032Hrtrt18Heart rate QTL 18heart pumping trait (VT:2000009)heart rate (CMO:0000002)2159440760195313808Rat
2301966Bp322Blood pressure QTL 3223.58arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2144882354205135428Rat
1298080Bp163Blood pressure QTL 1630.02arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)267845182205135428Rat
1357991Ael2Aortic elastin QTL 24.20.000071aorta elastin amount (VT:0003905)aortic elastin2169227906214227906Rat
8662832Vetf7Vascular elastic tissue fragility QTL 73.5aorta elastin amount (VT:0003905)aorta wall extracellular elastin dry weight to aorta wall dry weight ratio (CMO:0002002)283400752223709938Rat
1298085Bp165Blood pressure QTL 1650.0006arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)244537979205135428Rat
1578671Bmd10Bone mineral density QTL 105.4femur mineral mass (VT:0010011)compact volumetric bone mineral density (CMO:0001730)2175931416220931416Rat
1359022Ppulsi1Prepulse inhibition QTL 13.63prepulse inhibition trait (VT:0003088)acoustic startle response measurement (CMO:0001519)2139067258184067258Rat
1641891Alcrsp17Alcohol response QTL 17response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)2151869660251712708Rat
724534Uae6Urinary albumin excretion QTL 610urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)280396034220931416Rat
61374Edpm2Estrogen-dependent pituitary mass QTL 24.420.86pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)278269809205135428Rat
8662843Vetf9Vascular elastic tissue fragility QTL 92.05thoracic aorta molecular composition trait (VT:0010568)aorta wall extracellular elastin dry weight to aorta wall extracellular collagen weight ratio (CMO:0002003)2159440760228950743Rat
1331794Bp202Blood pressure QTL 2023.66819arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2143344967251712708Rat
71113Cari2Carrageenan-induced inflammation QTL 22.70.009hypodermis integrity trait (VT:0010550)inflammatory exudate volume (CMO:0001429)2143746578205135428Rat
1331805Cm29Cardiac mass QTL 293.50746heart mass (VT:0007028)heart wet weight (CMO:0000069)2143344967251712708Rat
634308Sach6Saccharin preference QTL 64.9taste sensitivity trait (VT:0001986)saccharin intake volume to total fluid intake volume ratio (CMO:0001601)2114384617215381366Rat
1598805Memor8Memory QTL 83exploratory behavior trait (VT:0010471)average horizontal distance between subject and target during voluntary locomotion in an experimental apparatus (CMO:0002674)2150096616195096616Rat
1358917Cm42Cardiac mass QTL 422.82heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)227148328206613235Rat
724568Uae13Urinary albumin excretion QTL 134.4urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)2145306936212705578Rat
1358913Cm41Cardiac mass QTL 412.73heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)227148328206613235Rat
1300165Rf9Renal function QTL 93.28kidney glomerulus integrity trait (VT:0010546)index of glomerular damage (CMO:0001135)2113746222205135428Rat
61401Niddm2Non-insulin dependent diabetes mellitus QTL 24.54blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)2147287892192287892Rat
631507Bp105Blood pressure QTL 1050.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2114384617215381366Rat
1641925Alcrsp2Alcohol response QTL 2response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)2151869660223841096Rat
1354609Niddm62Non-insulin dependent diabetes mellitus QTL 624.720.000006insulin secretion trait (VT:0003564)plasma insulin level (CMO:0000342)2117415288205135428Rat
1598833Bp295Blood pressure QTL 2953.5arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2150096616195096616Rat
1354622Kidm16Kidney mass QTL 163kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)283465462225110681Rat
631266Bp132Blood pressure QTL 1320.0005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)247856345205135428Rat
631522Bp74Blood pressure QTL 740.05arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2175008837220008837Rat
7488927Bp365Blood pressure QTL 3650.008arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2165453811210453811Rat
7488925Bp364Blood pressure QTL 3640.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2163253030208253030Rat
2293843Kiddil6Kidney dilation QTL 63.1kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)244537979184731399Rat
2306901Bp337Blood pressure QTL 3370.01arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2166372086229820014Rat
1354605Rf48Renal function QTL 482.9blood creatinine amount (VT:0005328)plasma creatinine level (CMO:0000537)276328396209350714Rat


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
nervous system
reproductive system
respiratory system
7 2 6 24 26 28 6 10 6 6 43 28 13 29 22

Sequence


Ensembl Acc Id: ENSRNOT00000012691   ⟹   ENSRNOP00000012692
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl2181,333,098 - 181,334,300 (-)Ensembl
mRatBN7.2 Ensembl2178,637,495 - 178,638,697 (-)Ensembl
Rnor_6.0 Ensembl2193,333,800 - 193,335,002 (-)Ensembl
RefSeq Acc Id: NM_001109500   ⟹   NP_001102970
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr82181,333,098 - 181,334,300 (-)NCBI
mRatBN7.22178,637,495 - 178,638,697 (-)NCBI
Rnor_6.02193,333,800 - 193,335,002 (-)NCBI
Rnor_5.02211,534,988 - 211,536,190 (+)NCBI
RGSC_v3.42186,053,050 - 186,054,252 (-)RGD
Celera2171,622,444 - 171,623,646 (+)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001102970 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL87864 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000012692
  ENSRNOP00000012692.2
RefSeq Acc Id: NP_001102970   ⟸   NM_001109500
- UniProtKB: D3ZG26 (UniProtKB/TrEMBL),   A6KMN4 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000012692   ⟸   ENSRNOT00000012691

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZG26-F1-model_v2 AlphaFold D3ZG26 1-169 view protein structure

Transcriptome

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

Promoters
RGD ID:13691517
Promoter ID:EPDNEW_R2042
Type:single initiation site
Name:Lce1m_1
Description:late cornified envelope 1M
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_6.02193,335,001 - 193,335,061EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1588875 AgrOrtholog
BioCyc Gene G2FUF-52249 BioCyc
Ensembl Genes ENSRNOG00000009581 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000012691 ENTREZGENE
  ENSRNOT00000012691.5 UniProtKB/TrEMBL
InterPro LCE UniProtKB/TrEMBL
KEGG Report rno:688413 UniProtKB/TrEMBL
NCBI Gene 688413 ENTREZGENE
Pfam LCE UniProtKB/TrEMBL
PhenoGen Lce1m PhenoGen
RatGTEx ENSRNOG00000009581 RatGTEx
UniProt A6KMN4 ENTREZGENE, UniProtKB/TrEMBL
  D3ZG26 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-04-30 Lce1m  late cornified envelope 1M   Lce1m_predicted  late cornified envelope 1M (predicted)  'predicted' is removed 2292626 APPROVED
2008-01-09 Lce1m_predicted  late cornified envelope 1M (predicted)  LOC679245  hypothetical protein LOC679245  Data merged from RGD:1590713 1643240 APPROVED
2007-04-11 Lce1m_predicted  late cornified envelope 1M (predicted)  LOC688413  hypothetical protein LOC688413  Symbol and Name updated to reflect Human and Mouse nomenclature 1299863 APPROVED
2006-11-20 LOC679245  hypothetical protein LOC679245      Symbol and Name status set to provisional 70820 PROVISIONAL
2006-11-19 LOC688413  hypothetical protein LOC688413      Symbol and Name status set to provisional 70820 PROVISIONAL