Lsmem1 (leucine-rich single-pass membrane protein 1) - Rat Genome Database

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Gene: Lsmem1 (leucine-rich single-pass membrane protein 1) Rattus norvegicus
Analyze
Symbol: Lsmem1
Name: leucine-rich single-pass membrane protein 1
RGD ID: 1587073
Description: Orthologous to human LSMEM1 (leucine rich single-pass membrane protein 1); INTERACTS WITH 2,3,7,8-Tetrachlorodibenzofuran; alpha-Zearalanol; bisphenol A.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: hypothetical protein LOC680810; LOC680810
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
GRCr8662,978,880 - 62,988,750 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl662,978,885 - 62,988,750 (-)EnsemblGRCr8
mRatBN7.2657,251,720 - 57,261,590 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl657,252,056 - 57,261,653 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx657,530,609 - 57,540,461 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0657,845,554 - 57,855,408 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0657,321,079 - 57,330,933 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0660,114,077 - 60,124,297 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl660,114,103 - 60,124,274 (-)Ensemblrn6Rnor6.0
Rnor_5.0669,701,016 - 69,712,471 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4659,413,670 - 59,419,484 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera656,292,914 - 56,303,197 (-)NCBICelera
Cytogenetic Map6q21NCBI
JBrowse:




Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
cytosol  (IEA,ISO)

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions

Genomics

Comparative Map Data
Lsmem1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8662,978,880 - 62,988,750 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl662,978,885 - 62,988,750 (-)EnsemblGRCr8
mRatBN7.2657,251,720 - 57,261,590 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl657,252,056 - 57,261,653 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx657,530,609 - 57,540,461 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0657,845,554 - 57,855,408 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0657,321,079 - 57,330,933 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0660,114,077 - 60,124,297 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl660,114,103 - 60,124,274 (-)Ensemblrn6Rnor6.0
Rnor_5.0669,701,016 - 69,712,471 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4659,413,670 - 59,419,484 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera656,292,914 - 56,303,197 (-)NCBICelera
Cytogenetic Map6q21NCBI
LSMEM1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh387112,480,304 - 112,491,062 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl7112,480,853 - 112,491,062 (+)Ensemblhg38GRCh38
GRCh377112,120,908 - 112,131,117 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 367111,908,282 - 111,918,178 (+)NCBIBuild 36Build 36hg18NCBI36
Celera7106,932,874 - 106,942,905 (+)NCBICelera
Cytogenetic Map7q31.1NCBI
HuRef7106,488,571 - 106,498,604 (+)NCBIHuRef
CHM1_17112,055,026 - 112,065,050 (+)NCBICHM1_1
T2T-CHM13v2.07113,797,449 - 113,809,353 (+)NCBIT2T-CHM13v2.0
CRA_TCAGchr7v27111,489,413 - 111,499,441 (+)NCBI
Lsmem1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391240,226,385 - 40,249,314 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1240,225,492 - 40,249,489 (-)EnsemblGRCm39 EnsemblGRCm39
GRCm381240,176,386 - 40,199,315 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1240,175,493 - 40,199,490 (-)Ensemblmm10GRCm38
MGSCv371240,902,973 - 40,925,902 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv361240,686,809 - 40,709,738 (-)NCBIMGSCv36mm8
Celera1241,604,963 - 41,627,446 (-)NCBICelera
Cytogenetic Map12B1NCBI
cM Map1218.06NCBI
Lsmem1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495541016,224,294 - 16,235,975 (+)Ensembl
ChiLan1.0NW_00495541016,224,294 - 16,235,975 (+)NCBIChiLan1.0ChiLan1.0
LSMEM1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v26149,304,830 - 149,323,845 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan171,313,521 - 1,334,470 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v07104,441,634 - 104,459,220 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.17117,144,969 - 117,161,709 (+)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl7117,144,969 - 117,161,709 (+)EnsemblpanPan2panpan1.1
LSMEM1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11452,080,931 - 52,092,851 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1452,053,434 - 52,092,365 (+)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha1451,534,973 - 51,546,585 (+)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.01452,127,043 - 52,138,793 (+)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1452,131,690 - 52,138,799 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11452,145,240 - 52,156,834 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01451,825,179 - 51,836,742 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01452,201,269 - 52,212,916 (+)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Lsmem1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440511871,817,075 - 71,827,468 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936795561,341 - 567,026 (-)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_004936795561,322 - 567,154 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
LSMEM1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1833,184,171 - 33,190,831 (-)EnsemblsusScr11Sscrofa11.1
Sscrofa11.11833,184,167 - 33,190,910 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21835,901,616 - 35,907,161 (-)NCBISscrofa10.2Sscrofa10.2susScr3
LSMEM1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12181,296,507 - 81,307,362 (+)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366604222,508,116 - 22,516,891 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Lsmem1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462473917,427,457 - 17,440,088 (-)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_00462473917,427,239 - 17,441,391 (-)NCBIHetGla 1.0HetGla 1.0hetGla2
Lsmem1
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v1753,412,362 - 53,417,851 (-)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Lsmem1
38 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:95
Count of miRNA genes:85
Interacting mature miRNAs:86
Transcripts:ENSRNOT00000059823
Prediction methods:Microtar, Miranda, Rnahybrid
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
9590290Uminl2Urine mineral level QTL 23.960.001urine mineral amount (VT:0015086)urine electrolyte level (CMO:0000593)64451097489510974Rat
634318Bw118Body weight QTL 1183.55abdominal fat pad mass (VT:1000711)abdominal fat pad weight (CMO:0000088)63902865963457441Rat
4889933Bss88Bone structure and strength QTL 883.8tibia size trait (VT:0100001)tibia total bone volume (CMO:0001724)65368492198684921Rat
634307Bp141Blood pressure QTL 1414arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)64095756485957564Rat
10401812Kidm54Kidney mass QTL 54kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)62009763565097635Rat
1331743Uae28Urinary albumin excretion QTL 284.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)64515378690153786Rat
8552910Pigfal5Plasma insulin-like growth factor 1 level QTL 54.3blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)62265388967653889Rat
5684992Bmd83Bone mineral density QTL 824.8tibia mineral mass (VT:1000283)bone mineral content (CMO:0001554)65368492198684921Rat
10401800Kidm49Kidney mass QTL 49kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)62009763565097635Rat
1331779Rf38Renal function QTL 382.876kidney blood vessel physiology trait (VT:0100012)absolute change in renal vascular resistance (CMO:0001900)63118500276185002Rat
737827Hcar11Hepatocarcinoma resistance QTL 114.4liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)646050607116278722Rat
724513Uae14Urinary albumin excretion QTL 146.5urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)64604735391047353Rat
2293839Kiddil2Kidney dilation QTL 24.8kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)62661831486868070Rat
1576309Emca7Estrogen-induced mammary cancer QTL 74mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)620859430113082285Rat
9590140Scort4Serum corticosterone level QTL 414.490.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)64451097489510974Rat
2301964Bp323Blood pressure QTL 3234.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)6186868070Rat
9590306Scort18Serum corticosterone level QTL 182.880.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)64451097489510974Rat
1578665Bss16Bone structure and strength QTL 164.4femur morphology trait (VT:0000559)bone trabecular cross-sectional area (CMO:0002311)63332884178328841Rat
2293841Kiddil4Kidney dilation QTL 44.4kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)62661831486868070Rat
1641898Colcr4Colorectal carcinoma resistance QTL43.710.0007intestine integrity trait (VT:0010554)well differentiated malignant colorectal tumor surface area measurement (CMO:0002077)63093763275937632Rat
1578668Bmd14Bone mineral density QTL 143.8femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)63332884178328841Rat
6893340Cm77Cardiac mass QTL 770.260.57heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)63902865986867923Rat
5684963Bss99Bone structure and strength QTL 993.1tibia area (VT:1000281)tibia area measurement (CMO:0001382)65368492198684921Rat
70199Coreg1Compensatory renal growth QTL 111.8kidney mass (VT:0002707)compensatory renal growth score (CMO:0001894)61459947363457687Rat
1300143Rf14Renal function QTL 142.92renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)64016318385163183Rat
1354664Slep2Serum leptin concentration QTL 24.49blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)62228825767288257Rat


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
7 12 63 59 45 47 18 32 18 6 223 124 11 40 66 75 29 3 3

Sequence


Ensembl Acc Id: ENSRNOT00000059823   ⟹   ENSRNOP00000056569
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl662,978,885 - 62,988,750 (-)Ensembl
mRatBN7.2 Ensembl657,252,056 - 57,261,653 (-)Ensembl
Rnor_6.0 Ensembl660,114,103 - 60,124,274 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000104603   ⟹   ENSRNOP00000094415
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl657,252,056 - 57,260,764 (-)Ensembl
RefSeq Acc Id: NM_001398683   ⟹   NP_001385612
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8662,978,880 - 62,988,750 (-)NCBI
mRatBN7.2657,251,720 - 57,261,590 (-)NCBI
Protein Sequences
Protein RefSeqs NP_001385612 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDM03337 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000056569
  ENSRNOP00000056569.2
Ensembl Acc Id: ENSRNOP00000056569   ⟸   ENSRNOT00000059823
Ensembl Acc Id: ENSRNOP00000094415   ⟸   ENSRNOT00000104603
RefSeq Acc Id: NP_001385612   ⟸   NM_001398683
- UniProtKB: D3ZU79 (UniProtKB/TrEMBL),   A6HBD2 (UniProtKB/TrEMBL)

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZU79-F1-model_v2 AlphaFold D3ZU79 1-128 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:1587073 AgrOrtholog
BioCyc Gene G2FUF-37744 BioCyc
Ensembl Genes ENSRNOG00000039110 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000059823 ENTREZGENE
  ENSRNOT00000059823.4 UniProtKB/TrEMBL
InterPro DUF4577 UniProtKB/TrEMBL
NCBI Gene 680810 ENTREZGENE
PANTHER LEUCINE-RICH SINGLE-PASS MEMBRANE PROTEIN 1 UniProtKB/TrEMBL
  PTHR36475 UniProtKB/TrEMBL
Pfam DUF4577 UniProtKB/TrEMBL
PhenoGen Lsmem1 PhenoGen
RatGTEx ENSRNOG00000039110 RatGTEx
UniProt A6HBD2 ENTREZGENE, UniProtKB/TrEMBL
  D3ZU79 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2013-03-20 Lsmem1  leucine-rich single-pass membrane protein 1  LOC680810  hypothetical protein LOC680810  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-01-09 LOC680810  hypothetical protein LOC680810  LOC687236  hypothetical protein LOC687236  Data merged from RGD:1587742 1643240 APPROVED
2006-11-19 LOC680810  hypothetical protein LOC680810      Symbol and Name status set to provisional 70820 PROVISIONAL
2006-11-19 LOC687236  hypothetical protein LOC687236      Symbol and Name status set to provisional 70820 PROVISIONAL