Letm1 (leucine zipper and EF-hand containing transmembrane protein 1) - Rat Genome Database

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Gene: Letm1 (leucine zipper and EF-hand containing transmembrane protein 1) Rattus norvegicus
Analyze
Symbol: Letm1
Name: leucine zipper and EF-hand containing transmembrane protein 1
RGD ID: 1359678
Description: Predicted to enable calcium:proton antiporter activity. Predicted to be involved in several processes, including cristae formation; negative regulation of mitochondrial calcium ion concentration; and protein complex oligomerization. Predicted to be located in mitochondrial inner membrane. Orthologous to human LETM1 (leucine zipper and EF-hand containing transmembrane protein 1); INTERACTS WITH amphetamine; bisphenol A; buspirone.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: LETM1 and EF-hand domain-containing protein 1, mitochondrial; leucine zipper-EF-hand containing transmembrane protein 1; leucine zipper-EF-hand-containing transmembrane protein 1; MGC94466
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
mRatBN7.21476,942,647 - 76,982,220 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1476,942,729 - 76,984,904 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1481,395,109 - 81,434,584 (+)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.01482,635,714 - 82,675,193 (+)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.01479,081,018 - 79,120,498 (+)NCBIRnor_WKY
Rnor_6.01482,227,790 - 82,267,298 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1482,227,708 - 82,267,350 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01482,917,692 - 82,959,167 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41482,637,839 - 82,677,419 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11482,640,229 - 82,679,808 (+)NCBI
Celera1475,866,265 - 75,905,572 (+)NCBICelera
Cytogenetic Map14q21NCBI
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. LETM1, a novel gene encoding a putative EF-hand Ca(2+)-binding protein, flanks the Wolf-Hirschhorn syndrome (WHS) critical region and is deleted in most WHS patients. Endele S, etal., Genomics 1999 Sep 1;60(2):218-25.
2. 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.
3. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
4. Integrated analysis of protein composition, tissue diversity, and gene regulation in mouse mitochondria. Mootha VK, etal., Cell 2003 Nov 26;115(5):629-40.
5. GOA pipeline RGD automated data pipeline
6. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
7. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
Additional References at PubMed
PMID:12865426   PMID:15489334   PMID:18614015   PMID:18628306   PMID:19797662   PMID:23645710   PMID:25077561   PMID:26316108   PMID:26975899   PMID:27669901   PMID:29476059  


Genomics

Comparative Map Data
Letm1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21476,942,647 - 76,982,220 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1476,942,729 - 76,984,904 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1481,395,109 - 81,434,584 (+)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.01482,635,714 - 82,675,193 (+)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.01479,081,018 - 79,120,498 (+)NCBIRnor_WKY
Rnor_6.01482,227,790 - 82,267,298 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1482,227,708 - 82,267,350 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01482,917,692 - 82,959,167 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41482,637,839 - 82,677,419 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11482,640,229 - 82,679,808 (+)NCBI
Celera1475,866,265 - 75,905,572 (+)NCBICelera
Cytogenetic Map14q21NCBI
LETM1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh3841,811,479 - 1,856,156 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl41,811,479 - 1,856,156 (-)EnsemblGRCh38hg38GRCh38
GRCh3741,813,206 - 1,857,883 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 3641,784,558 - 1,827,772 (-)NCBINCBI36Build 36hg18NCBI36
Build 3441,781,990 - 1,825,205NCBI
Celera41,725,718 - 1,769,826 (-)NCBICelera
Cytogenetic Map4p16.3NCBI
HuRef41,756,076 - 1,799,634 (-)NCBIHuRef
CHM1_141,811,156 - 1,856,557 (-)NCBICHM1_1
T2T-CHM13v2.041,809,954 - 1,854,630 (-)NCBIT2T-CHM13v2.0
Letm1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39533,897,017 - 33,940,061 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl533,897,017 - 33,940,161 (-)EnsemblGRCm39 Ensembl
GRCm38533,739,673 - 33,782,717 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl533,739,673 - 33,782,817 (-)EnsemblGRCm38mm10GRCm38
MGSCv37534,084,001 - 34,125,353 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36534,058,209 - 34,099,561 (-)NCBIMGSCv36mm8
Celera531,217,468 - 31,258,804 (-)NCBICelera
Cytogenetic Map5B2NCBI
Letm1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555141,042,307 - 1,069,114 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049555141,040,103 - 1,069,297 (-)NCBIChiLan1.0ChiLan1.0
LETM1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.141,862,788 - 1,897,029 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl41,862,788 - 1,900,901 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v041,953,033 - 1,994,958 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
LETM1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1362,268,027 - 62,304,767 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl362,267,708 - 62,302,136 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha364,785,792 - 64,822,554 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0362,743,457 - 62,780,252 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl362,743,480 - 62,778,969 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1362,237,035 - 62,273,781 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0362,440,602 - 62,477,319 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0362,799,711 - 62,836,516 (+)NCBIUU_Cfam_GSD_1.0
Letm1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440528567,848,412 - 67,887,970 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493647721,550,013 - 21,587,007 (+)EnsemblSpeTri2.0
SpeTri2.0NW_00493647721,550,104 - 21,589,662 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
LETM1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl8898,181 - 926,593 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.18898,178 - 926,500 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.28349,636 - 376,777 (-)NCBISscrofa10.2Sscrofa10.2susScr3
LETM1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12746,912,882 - 46,954,295 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2746,912,819 - 46,956,164 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_0236660513,289,082 - 3,330,719 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Letm1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462475525,604,454 - 25,631,716 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462475525,604,636 - 25,631,974 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Letm1
243 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:174
Count of miRNA genes:146
Interacting mature miRNAs:159
Transcripts:ENSRNOT00000022540
Prediction methods:Microtar, 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
631839Niddm37Non-insulin dependent diabetes mellitus QTL 373.37blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)141103062295876975Rat
70187Pancm5Pancreatic morphology QTL 516.7pancreas mass (VT:0010144)pancreas weight to body weight ratio (CMO:0000630)143032009280829842Rat
2313048Bss84Bone structure and strength QTL 843.10.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)143766971982669719Rat
2313084Bss83Bone structure and strength QTL 832.90.0001tibia size trait (VT:0100001)tibia midshaft endosteal cross-sectional area (CMO:0001716)143766971982669719Rat
2313089Bss81Bone structure and strength QTL 813.40.0001body length (VT:0001256)body length, nose to rump (CMO:0000079)143766971982669719Rat
2313100Bss82Bone structure and strength QTL 8230.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)143766971982669719Rat
738037Hcas6Hepatocarcinoma susceptibility QTL 62.93liver integrity trait (VT:0010547)liver nonremodeling tumorous lesion volume to total liver volume ratio (CMO:0001464)143905723783368335Rat
631523Pia13Pristane induced arthritis QTL 133.3joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)144079346098037301Rat
1300136Rf22Renal function QTL 223.9renal blood flow trait (VT:2000006)absolute change in renal vascular resistance (CMO:0001900)144226252995023211Rat
1549834Scl45Serum cholesterol level QTL 455.8blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)145002321195023211Rat
2300197Scl59Serum cholesterol level QTL 59blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)1455147478100147478Rat
9590294Uminl4Urine mineral level QTL 45.660.001urine mineral amount (VT:0015086)urine electrolyte level (CMO:0000593)1455624247100624247Rat
9589034Epfw11Epididymal fat weight QTL 1160.001epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)1455624247100624247Rat
2317879Alcrsp27Alcohol response QTL 273.30.63response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)1456631369101631369Rat
634328Hc5Hypercalciuria QTL 52.3urine calcium amount (VT:0002985)urine calcium excretion rate (CMO:0000763)1458184885103184885Rat
70153Bp59Blood pressure QTL 593.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)146875779683368335Rat
1582259Gluco23Glucose level QTL 233.10.0008blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)1470053989104886043Rat
1641900Alcrsp11Alcohol response QTL 11alcohol metabolism trait (VT:0015089)blood ethanol level (CMO:0000535)1470053989104886043Rat
1582197Gluco27Glucose level QTL 273.40.0006blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)147341532392554092Rat
1582209Gluco20Glucose level QTL 203.80.0005blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)147341532392554092Rat
1582236Gluco22Glucose level QTL 223.30.0164blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)147341532392554092Rat
1582255Gluco29Glucose level QTL 293.10.0025blood glucose amount (VT:0000188)absolute change in blood glucose level area under curve (CMO:0002034)147341532392554092Rat
1582250Gluco26Glucose level QTL 263.30.0009blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)147341532395876975Rat


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 3 43 57 41 19 41 8 11 74 35 41 11 8
Low
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000022540   ⟹   ENSRNOP00000022540
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1476,942,729 - 76,984,904 (+)Ensembl
Rnor_6.0 Ensembl1482,227,708 - 82,267,350 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000099794   ⟹   ENSRNOP00000078896
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1476,953,149 - 76,984,904 (+)Ensembl
RefSeq Acc Id: NM_001005884   ⟹   NP_001005884
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21476,942,709 - 76,982,220 (+)NCBI
Rnor_6.01482,227,790 - 82,267,298 (+)NCBI
Rnor_5.01482,917,692 - 82,959,167 (+)NCBI
RGSC_v3.41482,637,839 - 82,677,419 (+)RGD
Celera1475,866,265 - 75,905,572 (+)RGD
Sequence:
RefSeq Acc Id: XM_039091978   ⟹   XP_038947906
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21476,942,647 - 76,976,997 (+)NCBI
Protein Sequences
Protein RefSeqs NP_001005884 (Get FASTA)   NCBI Sequence Viewer  
  XP_038947906 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAH83642 (Get FASTA)   NCBI Sequence Viewer  
  EDM00114 (Get FASTA)   NCBI Sequence Viewer  
  Q5XIN6 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001005884   ⟸   NM_001005884
- Peptide Label: precursor
- UniProtKB: Q5XIN6 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000022540   ⟸   ENSRNOT00000022540
RefSeq Acc Id: XP_038947906   ⟸   XM_039091978
- Peptide Label: isoform X1
RefSeq Acc Id: ENSRNOP00000078896   ⟸   ENSRNOT00000099794
Protein Domains
EF-hand   Letm1 RBD

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q5XIN6-F1-model_v2 AlphaFold Q5XIN6 1-739 view protein structure

Transcriptome

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

Promoters
RGD ID:13699408
Promoter ID:EPDNEW_R9932
Type:multiple initiation site
Name:Letm1_1
Description:leucine zipper and EF-hand containing transmembrane protein 1
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_6.01482,227,824 - 82,227,884EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1359678 AgrOrtholog
BioCyc Gene G2FUF-15269 BioCyc
Ensembl Genes ENSRNOG00000016427 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000022540 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOP00000078896.1 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000022540 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOT00000099794.1 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7134917 IMAGE-MGC_LOAD
InterPro EF-hand-dom_pair UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  EF_Hand_1_Ca_BS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  LETM1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  LETM1/MDM38-like UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  LETM1_RBD UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:305457 UniProtKB/Swiss-Prot
MGC_CLONE MGC:94466 IMAGE-MGC_LOAD
NCBI Gene 305457 ENTREZGENE
PANTHER PTHR14009 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam LETM1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Letm1 PhenoGen
PROSITE EF_HAND_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  LETM1_RBD UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF47473 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A8I5ZLQ4_RAT UniProtKB/TrEMBL
  LETM1_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-03-08 Letm1  leucine zipper and EF-hand containing transmembrane protein 1  Letm1  leucine zipper-EF-hand containing transmembrane protein 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-30 Letm1  leucine zipper-EF-hand containing transmembrane protein 1      Symbol and Name status set to approved 1299863 APPROVED
2005-07-29 Letm1  leucine zipper-EF-hand containing transmembrane protein 1      Symbol and Name status set to provisional 70820 PROVISIONAL