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; 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
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
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
JBrowse: View Region in Genome Browser (JBrowse)
Model


Object Symbol
Species
Term
Qualifier
Evidence
With
Reference
Notes
Source
Original Reference(s)
Lce1mRatgastrointestinal stromal tumor  ISOLCE5A (Homo sapiens)8554872ClinVar Annotator: match by term: Gastrointestinal stromal tumorClinVarPMID:28492532
Lce1mRatimmunodeficiency 42  ISOLCE5A (Homo sapiens)8554872ClinVar Annotator: match by term: Autosomal recessive mendelian susceptibility to mycobacterial diseases due to complete RORgamma receptor deficiencyClinVarPMID:28492532
Lce1mRatMHC class II deficiency  ISOLCE5A (Homo sapiens)8554872ClinVar Annotator: match by term: MHC class II deficiencyClinVarPMID:28492532
Lce1mRatparathyroid carcinoma  ISOLCE5A (Homo sapiens)8554872ClinVar Annotator: match by term: Parathyroid carcinomaClinVarPMID:28492532
Lce1mRatsevere congenital neutropenia 3  ISOLCE5A (Homo sapiens)8554872ClinVar Annotator: match by term: Kostmann syndromeClinVarPMID:28492532
Lce1mRatsevere congenital neutropenia 5  ISOLCE5A (Homo sapiens)8554872ClinVar Annotator: match by term: Congenital neutropenia-myelofibrosis-nephromegaly syndromeClinVarPMID:28492532

1 to 14 of 14 rows

  
Object Symbol
Species
Term
Qualifier
Evidence
With
Reference
Notes
Source
Original Reference(s)
Lce1mRat2-hydroxypropanoic acid decreases expressionISOLCE5A (Homo sapiens)6480464Lactic Acid results in decreased expression of LCE5A mRNACTDPMID:30851411
Lce1mRat3,4-methylenedioxymethamphetamine decreases expressionISOLce1m (Mus musculus)6480464N-Methyl-3 and 4-methylenedioxyamphetamine results in decreased expression of LCE1M mRNACTDPMID:20188158
Lce1mRat4,4'-diaminodiphenylmethane increases expressionISOLce1m (Mus musculus)64804644 and 4'-diaminodiphenylmethane results in increased expression of LCE1M mRNACTDPMID:18648102
Lce1mRat6-propyl-2-thiouracil decreases expressionEXP 6480464Propylthiouracil results in decreased expression of LCE1M mRNACTDPMID:24780913
Lce1mRataflatoxin B1 decreases expressionISOLCE5A (Homo sapiens)6480464Aflatoxin B1 results in decreased expression of LCE5A mRNACTDPMID:22100608
Lce1mRatbenzalkonium chloride decreases expressionISOLce1m (Mus musculus)6480464Benzalkonium Compounds results in decreased expression of LCE1M mRNACTDPMID:30171875
Lce1mRatbenzo[a]pyrene increases methylationISOLCE5A (Homo sapiens)6480464Benzo(a)pyrene results in increased methylation of LCE5A 3' UTR more ...CTDPMID:27901495
Lce1mRatcadmium dichloride multiple interactionsISOLce1m (Mus musculus)6480464MT3 affects the reaction [Cadmium Chloride affects the expression of LCE1M mRNA]CTDPMID:20371981
Lce1mRatendosulfan decreases expressionEXP 6480464Endosulfan results in decreased expression of LCE1M mRNACTDPMID:29391264
Lce1mRatparacetamol affects expressionISOLce1m (Mus musculus)6480464Acetaminophen affects the expression of LCE1M mRNACTDPMID:17562736
Lce1mRatpotassium dichromate decreases expressionISOLce1m (Mus musculus)6480464Potassium Dichromate results in decreased expression of LCE1M mRNACTDPMID:23608068
Lce1mRatrac-lactic acid decreases expressionISOLCE5A (Homo sapiens)6480464Lactic Acid results in decreased expression of LCE5A mRNACTDPMID:30851411
Lce1mRatresveratrol multiple interactionsISOLCE5A (Homo sapiens)6480464[Plant Extracts co-treated with Resveratrol] results in decreased expression of LCE5A mRNACTDPMID:23557933
Lce1mRattriptonide increases expressionISOLce1m (Mus musculus)6480464triptonide results in increased expression of LCE1M mRNACTDPMID:33045310

1 to 14 of 14 rows

Biological Process

  
Object Symbol
Species
Term
Qualifier
Evidence
With
Reference
Notes
Source
Original Reference(s)
Lce1mRatkeratinization involved_inIEAUniProtKB-KW:KW-04171600115GO_REF:0000043UniProtGO_REF:0000043

Molecular Function

  


#
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


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
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
(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

.

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Variants in Lce1m
10 total Variants

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.


1 to 10 of 65 rows
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD ID
Symbol
Name
LOD
P Value
Trait
Sub Trait
Chr
Start
Stop
Species
1578648Bss11Bone structure and strength QTL 114.7femur morphology trait (VT:0000559)femoral neck cortical cross-sectional area (CMO:0001702)2114837527211674221Rat
1358356Srcrt1Stress Responsive Cort QTL13.66blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)2161699179222436696Rat
1331734Bp204Blood pressure QTL 2043.61192arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2168358098223265385Rat
1298074Bp164Blood pressure QTL 1640.003arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)242804607202447032Rat
1354648Bp239Blood pressure QTL 2390.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)266118463226797303Rat
1354649Kidm17Kidney mass QTL 172.9kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)281754530227146641Rat
10755499Bp389Blood pressure QTL 3892.61arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)218960362228801039Rat
1298076Bp166Blood pressure QTL 1660.0009arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2136445150202447032Rat
152025245Scl81Serum cholesterol level QTL 813.49blood cholesterol amount (VT:0000180)2122609194206936711Rat
70162Bp63Blood pressure QTL 635.64arterial blood pressure trait (VT:2000000)blood pressure measurement (CMO:0000003)2169745596214745596Rat

1 to 10 of 65 rows



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
6 2 6 24 26 28 6 10 6 6 42 28 12 28 22



Ensembl Acc Id: ENSRNOT00000012691   ⟹   ENSRNOP00000012692
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
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 RefSeqs NP_001102970 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL87864 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000012692.2
RefSeq Acc Id: NP_001102970   ⟸   NM_001109500
- UniProtKB: D3ZG26 (UniProtKB/TrEMBL),   A6KMN4 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000012692   ⟸   ENSRNOT00000012691

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


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

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


1 to 11 of 11 rows
Database
Acc Id
Source(s)
BioCyc Gene G2FUF-52249 BioCyc
Ensembl Genes ENSRNOG00000009581 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000012691.4 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
1 to 11 of 11 rows


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