Letmd1 (LETM1 domain containing 1) - Rat Genome Database

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Gene: Letmd1 (LETM1 domain containing 1) Rattus norvegicus
Analyze
Symbol: Letmd1
Name: LETM1 domain containing 1
RGD ID: 1596738
Description: Predicted to enable ribosome binding activity. Predicted to be involved in mitochondrion organization; regulation of inflammatory response; and regulation of phagocytosis. Predicted to be located in mitochondrion; nucleolus; and nucleoplasm. Orthologous to human LETMD1 (LETM1 domain containing 1); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; bisphenol A; fenvalerate.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LETM1 domain-containing protein 1; LOC363003; LOC681352; MGC188743; RGD1310591; similar to cervical cancer receptor; similar to LETM1 domain containing 1 isoform 4
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
mRatBN7.27131,584,241 - 131,597,797 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl7131,584,259 - 131,597,796 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx7133,386,530 - 133,396,013 (+)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.07135,612,107 - 135,621,590 (+)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.07135,525,758 - 135,535,244 (+)NCBIRnor_WKY
Rnor_6.07142,106,364 - 142,119,900 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl7142,106,465 - 142,119,899 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.07139,913,885 - 139,927,371 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.47139,172,373 - 139,181,857 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera7128,061,659 - 128,071,143 (+)NCBICelera
Cytogenetic Map7q36NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

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. Oncoprotein HCCR-1 expression in breast cancer is well correlated with known breast cancer prognostic factors including the HER2 overexpression, p53 mutation, and ER/PR status. Ha SA, etal., BMC Cancer. 2009 Feb 11;9:51.
3. Identification and differential expression of novel human cervical cancer oncogene HCCR-2 in human cancers and its involvement in p53 stabilization. Ko J, etal., Oncogene. 2003 Jul 24;22(30):4679-89.
4. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
5. Comprehensive gene review and curation RGD comprehensive gene curation
Additional References at PubMed
PMID:8889548   PMID:12477932   PMID:15632090   PMID:18614015  


Genomics

Comparative Map Data
Letmd1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.27131,584,241 - 131,597,797 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl7131,584,259 - 131,597,796 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx7133,386,530 - 133,396,013 (+)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.07135,612,107 - 135,621,590 (+)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.07135,525,758 - 135,535,244 (+)NCBIRnor_WKY
Rnor_6.07142,106,364 - 142,119,900 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl7142,106,465 - 142,119,899 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.07139,913,885 - 139,927,371 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.47139,172,373 - 139,181,857 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera7128,061,659 - 128,071,143 (+)NCBICelera
Cytogenetic Map7q36NCBI
LETMD1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381251,048,220 - 51,068,958 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl1251,047,962 - 51,060,424 (+)EnsemblGRCh38hg38GRCh38
GRCh371251,442,003 - 51,462,741 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361249,728,351 - 49,740,474 (+)NCBINCBI36Build 36hg18NCBI36
Build 341249,728,398 - 49,740,468NCBI
Celera1250,244,071 - 50,256,194 (+)NCBICelera
Cytogenetic Map12q13.12NCBI
HuRef1248,474,666 - 48,486,493 (+)NCBIHuRef
CHM1_11251,408,361 - 51,420,485 (+)NCBICHM1_1
T2T-CHM13v2.01251,011,103 - 51,031,877 (+)NCBIT2T-CHM13v2.0
Letmd1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3915100,360,302 - 100,377,133 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl15100,366,904 - 100,377,045 (+)EnsemblGRCm39 Ensembl
GRCm3815100,462,421 - 100,479,252 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl15100,469,023 - 100,479,164 (+)EnsemblGRCm38mm10GRCm38
MGSCv3715100,299,465 - 100,309,683 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv3615100,297,128 - 100,307,198 (+)NCBIMGSCv36mm8
Celera15102,621,292 - 102,631,510 (+)NCBICelera
Cytogenetic Map15F1NCBI
Letmd1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555471,574,265 - 1,582,786 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049555471,574,210 - 1,586,432 (+)NCBIChiLan1.0ChiLan1.0
LETMD1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11238,587,366 - 38,609,810 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1238,597,728 - 38,609,810 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01237,685,741 - 37,705,104 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
LETMD1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1273,761,880 - 3,770,158 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl273,761,203 - 3,770,103 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2742,486,087 - 42,494,364 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0273,809,305 - 3,817,581 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl273,809,309 - 3,817,542 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1273,776,041 - 3,784,312 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0273,763,396 - 3,771,684 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02742,882,837 - 42,891,111 (+)NCBIUU_Cfam_GSD_1.0
Letmd1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494564,468,798 - 64,480,237 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365128,684,587 - 8,694,074 (+)EnsemblSpeTri2.0
SpeTri2.0NW_0049365128,684,597 - 8,694,074 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
LETMD1
(Sus scrofa - pig)
No map positions available.
LETMD1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11147,258,097 - 47,270,474 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1147,258,084 - 47,270,756 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_023666037198,830,226 - 198,842,605 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Letmd1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248161,158,662 - 1,170,988 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248161,148,634 - 1,170,981 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Letmd1
46 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:558
Count of miRNA genes:257
Interacting mature miRNAs:318
Transcripts:ENSRNOT00000042786
Prediction methods:Microtar, Miranda, 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
1300179Kidm5Kidney mass QTL 53.51kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)743747012135012528Rat
70173Niddm19Non-insulin dependent diabetes mellitus QTL 194.330.00005blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)764002457135012528Rat
1358891Bp265Blood pressure QTL 2652.21arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)783591953134666232Rat
1358914Bp266Blood pressure QTL 266arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)783591953134666232Rat
1558655Swd4Spike wave discharge measurement QTL 43.680.0002brain electrophysiology trait (VT:0010557)brain spike-and-wave discharge severity grade (CMO:0001988)786983365131983365Rat
1549899Stresp8Stress response QTL 84.370.0008stress-related behavior trait (VT:0010451)defensive burying duration (CMO:0001961)790482196135012528Rat
2299163Iddm34Insulin dependent diabetes mellitus QTL 342.71blood glucose amount (VT:0000188)age at onset/diagnosis of type 1 diabetes mellitus (CMO:0001140)791281130135012528Rat
731176Glom5Glomerulus QTL 52.50.0035kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)796670164135012528Rat
1331731Bp216Blood pressure QTL 2162.851arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)7102297359133492884Rat
731174Uae23Urinary albumin excretion QTL 232.40.0042urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)7104603555135012528Rat
2306821Bp335Blood pressure QTL 3350.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)7106571501135012528Rat
631663Bw6Body weight QTL 63.4body mass (VT:0001259)body weight (CMO:0000012)7111075573134976056Rat
1300112Bp183Blood pressure QTL 1833.51arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)7111182207135012528Rat
1331748Bp215Blood pressure QTL 2154.043arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)7112308254133492884Rat
1357339Stl14Serum triglyceride level QTL 143.450.0001blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)7112729683133492707Rat
1354582Stl11Serum triglyceride level QTL 113.42blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)7119513385135012528Rat

Markers in Region
AW530447  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.27131,597,532 - 131,597,712 (+)MAPPERmRatBN7.2
Rnor_6.07142,119,636 - 142,119,815NCBIRnor6.0
Rnor_5.07139,927,107 - 139,927,286UniSTSRnor5.0
RGSC_v3.47139,185,544 - 139,185,723UniSTSRGSC3.4
Celera7128,074,830 - 128,075,009UniSTS
RH 3.4 Map71075.2UniSTS
Cytogenetic Map7q36UniSTS
RH140998  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.27131,593,558 - 131,593,745 (+)MAPPERmRatBN7.2
Rnor_6.07142,115,662 - 142,115,848NCBIRnor6.0
Rnor_5.07139,923,133 - 139,923,319UniSTSRnor5.0
RGSC_v3.47139,181,570 - 139,181,756UniSTSRGSC3.4
Celera7128,070,856 - 128,071,042UniSTS
RH 3.4 Map71075.2UniSTS
Cytogenetic Map7q36UniSTS


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 34 57 41 19 41 1 1 74 35 41 11 1
Low 9 7 10 7
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000042786   ⟹   ENSRNOP00000039848
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl7131,584,259 - 131,593,846 (+)Ensembl
Rnor_6.0 Ensembl7142,106,465 - 142,115,948 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000088681   ⟹   ENSRNOP00000075497
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl7131,584,381 - 131,597,796 (+)Ensembl
Rnor_6.0 Ensembl7142,106,484 - 142,119,899 (+)Ensembl
RefSeq Acc Id: NM_001122781   ⟹   NP_001116253
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27131,584,362 - 131,593,846 (+)NCBI
Rnor_6.07142,106,465 - 142,115,949 (+)NCBI
Rnor_5.07139,913,885 - 139,927,371 (+)NCBI
RGSC_v3.47139,172,373 - 139,181,857 (+)RGD
Celera7128,061,659 - 128,071,143 (+)RGD
Sequence:
RefSeq Acc Id: XM_006242354   ⟹   XP_006242416
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27131,584,241 - 131,597,797 (+)NCBI
Rnor_6.07142,106,364 - 142,119,900 (+)NCBI
Rnor_5.07139,913,885 - 139,927,371 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039079884   ⟹   XP_038935812
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27131,584,385 - 131,597,797 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_001116253   ⟸   NM_001122781
- UniProtKB: B0K026 (UniProtKB/TrEMBL),   G3V996 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006242416   ⟸   XM_006242354
- Peptide Label: isoform X1
- UniProtKB: B0K026 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000039848   ⟸   ENSRNOT00000042786
RefSeq Acc Id: ENSRNOP00000075497   ⟸   ENSRNOT00000088681
RefSeq Acc Id: XP_038935812   ⟸   XM_039079884
- Peptide Label: isoform X2
Protein Domains
Letm1 RBD

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-B0K026-F1-model_v2 AlphaFold B0K026 1-371 view protein structure

Transcriptome

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

Promoters
RGD ID:13695657
Promoter ID:EPDNEW_R6181
Type:multiple initiation site
Name:Letmd1_1
Description:LETM1 domain containing 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_6.07142,106,473 - 142,106,533EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1596738 AgrOrtholog
BioCyc Gene G2FUF-32020 BioCyc
Ensembl Genes ENSRNOG00000029855 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000039848 ENTREZGENE
  ENSRNOP00000039848.3 UniProtKB/TrEMBL
  ENSRNOP00000075497 ENTREZGENE
  ENSRNOP00000075497.1 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000042786 ENTREZGENE
  ENSRNOT00000042786.5 UniProtKB/TrEMBL
  ENSRNOT00000088681 ENTREZGENE
  ENSRNOT00000088681.2 UniProtKB/TrEMBL
InterPro LETM1 UniProtKB/TrEMBL
  LETM1/MDM38-like UniProtKB/TrEMBL
  LETM1_RBD UniProtKB/TrEMBL
KEGG Report rno:681352 UniProtKB/TrEMBL
NCBI Gene 681352 ENTREZGENE
PANTHER PTHR14009 UniProtKB/TrEMBL
Pfam LETM1 UniProtKB/TrEMBL
PhenoGen Letmd1 PhenoGen
PROSITE LETM1_RBD UniProtKB/TrEMBL
UniProt B0K026 ENTREZGENE, UniProtKB/TrEMBL
  G3V996 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2013-05-24 Letmd1  LETM1 domain containing 1  RGD1310591  similar to cervical cancer receptor  Data Merged 1643240 APPROVED
2008-04-30 RGD1310591  similar to cervical cancer receptor   RGD1310591_predicted  similar to cervical cancer receptor (predicted)  'predicted' is removed 2292626 APPROVED
2008-03-05 Letmd1  LETM1 domain containing 1  LOC681352  similar to LETM1 domain containing 1 isoform 4  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-11-20 LOC681352  similar to LETM1 domain containing 1 isoform 4      Symbol and Name status set to provisional 70820 PROVISIONAL
2005-01-20 RGD1310591_predicted  similar to cervical cancer receptor (predicted)  LOC363003_predicted    Symbol and Name status set to approved 1331353 APPROVED
2005-01-12 LOC363003_predicted  similar to cervical cancer receptor (predicted)      Symbol and Name status set to provisional 70820 PROVISIONAL