Lemd2 (LEM domain nuclear envelope protein 2) - Rat Genome Database

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Gene: Lemd2 (LEM domain nuclear envelope protein 2) Rattus norvegicus
Analyze
Symbol: Lemd2
Name: LEM domain nuclear envelope protein 2
RGD ID: 1305341
Description: Predicted to enable chromatin DNA binding activity. Predicted to be involved in several processes, including heart formation; negative regulation of signal transduction; and protein localization to chromatin. Predicted to act upstream of or within negative regulation of MAPK cascade and skeletal muscle cell differentiation. Predicted to be located in nuclear inner membrane. Predicted to be part of chromatin. Predicted to colocalize with endoplasmic reticulum and nuclear envelope. Human ortholog(s) of this gene implicated in cataract 46 juvenile-onset. Orthologous to human LEMD2 (LEM domain nuclear envelope protein 2); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 3H-1,2-dithiole-3-thione; benzo[a]pyrene.
Type: protein-coding (Ensembl: lncRNA)
RefSeq Status: VALIDATED
Previously known as: LEM domain containing 2; LEM domain-containing protein 2; LEM domain-containing protein 2-like; LOC108348120; LOC361807; MGC112806
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8205,284,275 - 5,298,281 (-)NCBIGRCr8
mRatBN7.2205,282,397 - 5,296,621 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl205,282,397 - 5,296,626 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx205,993,689 - 6,007,584 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0205,355,436 - 5,369,329 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0205,836,295 - 5,850,161 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0205,779,742 - 5,786,213 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl206,545,083 - 6,556,350 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0208,789,656 - 8,800,115 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4205,425,689 - 5,436,856 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1205,426,758 - 5,496,911 (-)NCBI
Celera206,846,384 - 6,857,575 (-)NCBICelera
Cytogenetic Map20p12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

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:12477932   PMID:16339967   PMID:17097643   PMID:19720741   PMID:19946888   PMID:25790465   PMID:28242692  


Genomics

Comparative Map Data
Lemd2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8205,284,275 - 5,298,281 (-)NCBIGRCr8
mRatBN7.2205,282,397 - 5,296,621 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl205,282,397 - 5,296,626 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx205,993,689 - 6,007,584 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0205,355,436 - 5,369,329 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0205,836,295 - 5,850,161 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0205,779,742 - 5,786,213 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl206,545,083 - 6,556,350 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0208,789,656 - 8,800,115 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4205,425,689 - 5,436,856 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1205,426,758 - 5,496,911 (-)NCBI
Celera206,846,384 - 6,857,575 (-)NCBICelera
Cytogenetic Map20p12NCBI
LEMD2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38633,771,213 - 33,789,130 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl633,771,202 - 33,789,130 (-)EnsemblGRCh38hg38GRCh38
GRCh37633,738,990 - 33,756,907 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36633,846,968 - 33,864,874 (-)NCBINCBI36Build 36hg18NCBI36
Celera635,293,376 - 35,311,312 (-)NCBICelera
Cytogenetic Map6p21.31NCBI
HuRef633,480,936 - 33,498,853 (-)NCBIHuRef
CHM1_1633,741,239 - 33,759,156 (-)NCBICHM1_1
T2T-CHM13v2.0633,592,393 - 33,610,310 (-)NCBIT2T-CHM13v2.0
Lemd2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391727,408,574 - 27,426,228 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1727,408,574 - 27,423,443 (-)EnsemblGRCm39 Ensembl
GRCm381727,189,600 - 27,205,470 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1727,189,600 - 27,204,469 (-)EnsemblGRCm38mm10GRCm38
MGSCv371727,326,545 - 27,341,383 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361726,917,346 - 26,931,337 (-)NCBIMGSCv36mm8
Celera1727,725,463 - 27,740,360 (-)NCBICelera
Cytogenetic Map17A3.3NCBI
cM Map1713.82NCBI
Lemd2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554372,163,878 - 2,176,665 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554372,163,977 - 2,178,783 (-)NCBIChiLan1.0ChiLan1.0
LEMD2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2548,250,279 - 48,274,131 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1644,117,224 - 44,136,002 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0633,344,372 - 33,363,143 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1634,452,332 - 34,469,795 (-)NCBIpanpan1.1PanPan1.1panPan2
LEMD2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1123,114,175 - 3,131,779 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl123,115,460 - 3,131,919 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha123,130,070 - 3,147,660 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0123,446,589 - 3,464,216 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl123,447,058 - 3,464,190 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1123,112,813 - 3,130,403 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0123,194,850 - 3,212,427 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0123,292,189 - 3,309,758 (-)NCBIUU_Cfam_GSD_1.0
Lemd2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494638,771,969 - 38,789,333 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493647625,170,973 - 25,186,965 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_00493647625,170,954 - 25,188,298 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
LEMD2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl729,980,401 - 29,997,115 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1729,980,394 - 29,997,077 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2734,640,183 - 34,656,850 (-)NCBISscrofa10.2Sscrofa10.2susScr3
LEMD2
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11738,291,100 - 38,309,134 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1738,291,217 - 38,307,745 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604433,664,152 - 33,682,118 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Lemd2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462475423,158,985 - 23,173,885 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462475423,159,234 - 23,173,452 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Lemd2
65 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:146
Count of miRNA genes:114
Interacting mature miRNAs:133
Transcripts:ENSRNOT00000035819
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 (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1354642Despr15Despair related QTL 150.0027locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)20124159021Rat
1600382Edcs3Endometrial carcinoma susceptibility QTL33.50.003uterus morphology trait (VT:0001120)percentage of study population developing endometrioid carcinoma during a period of time (CMO:0001759)20125159026Rat
2317851Alcrsp22Alcohol response QTL 223.20.05response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)20127339237Rat
1641893Alcrsp7Alcohol response QTL 7response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)20127339237Rat
8694189Bw153Body weight QTL 1533.130.001body mass (VT:0001259)body weight gain (CMO:0000420)20129191651Rat
9590275Scort15Serum corticosterone level QTL 153.480.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20129191651Rat
7411650Foco23Food consumption QTL 2320.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20129191651Rat
9590109Sffal8Serum free fatty acids level QTL 85.320.01blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)20129191651Rat
9589155Insul32Insulin level QTL 326.380.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)20129191651Rat
6893685Bw111Body weight QTL 1112.70.004body mass (VT:0001259)body weight (CMO:0000012)20132578807Rat
7411668Foco32Food consumption QTL 3280.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20136600972Rat
9590252Scort12Serum corticosterone level QTL 1220.460.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20136600972Rat
2305926Iddm37Insulin dependent diabetes mellitus QTL 376blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)20152784246527842Rat
2306850Pia40Pristane induced arthritis QTL 400.0001joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)2015279595304575Rat
1641915Colcr9Colorectal carcinoma resistance QTL 92.970.0024intestine integrity trait (VT:0010554)benign colorectal tumor number (CMO:0001795)20153065546530655Rat
1598816Memor12Memory QTL 122.4exploratory behavior trait (VT:0010471)average horizontal distance between subject and target during voluntary locomotion in an experimental apparatus (CMO:0002674)20260683647606836Rat
2317057Aia27Adjuvant induced arthritis QTL 272.83joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)20289259726381954Rat
1300152Bp195Blood pressure QTL 1953.46arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2036216499243559Rat
1331772Cdexp2CD45RC expression in CD8 T cells QTL 25.7CD8-positive T cell quantity (VT:0008077)blood CD45RC(high) CD8 T cell count to CD45RC(low) CD8 T cell count ratio (CMO:0001990)20362164910078919Rat
61432Cia1Collagen induced arthritis QTL 1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)20362165614101050Rat
61474Eae1Experimental allergic encephalomyelitis QTL 13nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis severity score (CMO:0001419)2046066076691706Rat
4889857Pur27Proteinuria QTL 2712.20.001urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)20460660717617956Rat
1558640Prcs2Prostate cancer susceptibility QTL 23.3prostate integrity trait (VT:0010571)percentage of study population developing ventral prostate tumorous lesions during a period of time (CMO:0000943)20460660717617956Rat

Markers in Region
RH139300  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2205,282,578 - 5,282,738 (+)MAPPERmRatBN7.2
Rnor_6.0206,545,107 - 6,545,266NCBIRnor6.0
Rnor_6.0205,779,766 - 5,779,925NCBIRnor6.0
Rnor_5.0208,789,680 - 8,789,839UniSTSRnor5.0
RGSC_v3.4205,425,713 - 5,425,872UniSTSRGSC3.4
Celera206,846,408 - 6,846,567UniSTS
RH 3.4 Map2057.14UniSTS
Cytogenetic Map20p12UniSTS


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 1 2 14 1
Low 2 43 57 41 17 41 8 11 60 35 41 10 8
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000035819   ⟹   ENSRNOP00000036495
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl205,282,556 - 5,295,660 (-)Ensembl
Rnor_6.0 Ensembl206,545,083 - 6,556,350 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000091051
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl205,282,556 - 5,292,095 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000093645
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl205,286,925 - 5,291,470 (-)Ensembl
Rnor_6.0 Ensembl206,549,269 - 6,553,925 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000093711   ⟹   ENSRNOP00000076316
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl206,547,620 - 6,548,179 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000099806
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl205,282,556 - 5,296,626 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000111549
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl205,282,397 - 5,290,685 (-)Ensembl
RefSeq Acc Id: NM_001039032   ⟹   NP_001034121
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8205,284,275 - 5,298,149 (-)NCBI
mRatBN7.2205,282,397 - 5,296,272 (-)NCBI
Rnor_6.0205,779,742 - 5,786,213 (-)NCBI
Rnor_5.0208,789,656 - 8,800,115 (-)NCBI
RGSC_v3.4205,425,689 - 5,436,856 (-)RGD
Celera206,846,384 - 6,857,575 (-)RGD
Sequence:
RefSeq Acc Id: XM_039098814   ⟹   XP_038954742
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8205,284,275 - 5,298,281 (-)NCBI
mRatBN7.2205,282,397 - 5,296,621 (-)NCBI
Protein Sequences
Protein RefSeqs NP_001034121 (Get FASTA)   NCBI Sequence Viewer  
  XP_038954742 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAH98775 (Get FASTA)   NCBI Sequence Viewer  
Reference Protein Sequences
RefSeq Acc Id: NP_001034121   ⟸   NM_001039032
- Sequence:
RefSeq Acc Id: ENSRNOP00000036495   ⟸   ENSRNOT00000035819
RefSeq Acc Id: ENSRNOP00000076316   ⟸   ENSRNOT00000093711
RefSeq Acc Id: XP_038954742   ⟸   XM_039098814
- Peptide Label: isoform X1
Protein Domains
Man1/Src1-like C-terminal

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q4KM57-F1-model_v2 AlphaFold Q4KM57 1-313 view protein structure

Transcriptome

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


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1305341 AgrOrtholog
BioCyc Gene G2FUF-4488 BioCyc
Ensembl Genes ENSRNOG00000025864 Ensembl, ENTREZGENE
Ensembl Transcript ENSRNOT00000099806 ENTREZGENE
Gene3D-CATH 1.10.10.1180 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7373953 IMAGE-MGC_LOAD
InterPro Inner-Nucl-membr_MAN1 UniProtKB/TrEMBL
  MAN1_winged_helix_dom UniProtKB/TrEMBL
KEGG Report rno:361807 UniProtKB/TrEMBL
MGC_CLONE MGC:112806 IMAGE-MGC_LOAD
NCBI Gene 361807 ENTREZGENE
PANTHER INNER NUCLEAR MEMBRANE PROTEIN MAN1 LEM DOMAIN CONTAINING PROTEIN UniProtKB/TrEMBL
  PTHR13428:SF8 UniProtKB/TrEMBL
Pfam MAN1_C UniProtKB/TrEMBL
PhenoGen Lemd2 PhenoGen
RatGTEx ENSRNOG00000025864 RatGTEx
UniProt Q4KM57_RAT UniProtKB/TrEMBL
UniProt Secondary D3ZED5 UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2021-03-09 Lemd2  LEM domain nuclear envelope protein 2  LOC108348120  LEM domain-containing protein 2-like  Data merged from RGD:11418040 737654 PROVISIONAL
2019-11-11 Lemd2  LEM domain nuclear envelope protein 2  Lemd2  LEM domain containing 2  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2016-08-02 LOC108348120  LEM domain-containing protein 2-like      Symbol and Name status set to provisional 70820 PROVISIONAL
2005-12-06 Lemd2  LEM domain containing 2  Lemd2_predicted  LEM domain containing 2 (predicted)  Symbol and Name updated 1559027 APPROVED
2005-01-12 Lemd2_predicted  LEM domain containing 2 (predicted)      Symbol and Name status set to approved 70820 APPROVED