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 molecular adaptor activity. Predicted to be involved in mitochondrion organization; regulation of inflammatory response; and regulation of phagocytosis. Predicted to act upstream of or within several processes, including non-canonical NF-kappaB signal transduction; nucleobase-containing compound biosynthetic process; and positive regulation of cold-induced thermogenesis. Predicted to be located in mitochondrial inner membrane. Predicted to be active in mitochondrion and nucleus. Orthologous to human LETMD1 (LETM1 domain containing 1); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 6-propyl-2-thiouracil; amitrole.
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
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr87133,461,920 - 133,476,592 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl7133,462,825 - 133,476,591 (+)EnsemblGRCr8
mRatBN7.27131,584,241 - 131,597,797 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl7131,584,259 - 131,597,796 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx7133,386,530 - 133,396,013 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.07135,612,107 - 135,621,590 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.07135,525,758 - 135,535,244 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.07142,106,364 - 142,119,900 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl7142,106,465 - 142,119,899 (+)Ensemblrn6Rnor6.0
Rnor_5.07139,913,885 - 139,927,371 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.47139,172,373 - 139,181,857 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera7128,061,659 - 128,071,143 (+)NCBICelera
Cytogenetic Map7q36NCBI
JBrowse:




Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
mitochondrial inner membrane  (IEA,ISO)
mitochondrion  (IBA,IEA,ISO)
nucleus  (IEA,ISO)

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
GRCr87133,461,920 - 133,476,592 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl7133,462,825 - 133,476,591 (+)EnsemblGRCr8
mRatBN7.27131,584,241 - 131,597,797 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl7131,584,259 - 131,597,796 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx7133,386,530 - 133,396,013 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.07135,612,107 - 135,621,590 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.07135,525,758 - 135,535,244 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.07142,106,364 - 142,119,900 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl7142,106,465 - 142,119,899 (+)Ensemblrn6Rnor6.0
Rnor_5.07139,913,885 - 139,927,371 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.47139,172,373 - 139,181,857 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
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.p14 Ensembl1251,047,962 - 51,060,426 (+)Ensemblhg38GRCh38
GRCh371251,442,003 - 51,462,741 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361249,728,351 - 49,740,474 (+)NCBIBuild 36Build 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 EnsemblGRCm39
GRCm3815100,462,421 - 100,479,252 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl15100,469,023 - 100,479,164 (+)Ensemblmm10GRCm38
MGSCv3715100,299,465 - 100,309,683 (+)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv3615100,297,128 - 100,307,198 (+)NCBIMGSCv36mm8
Celera15102,621,292 - 102,631,510 (+)NCBICelera
Cytogenetic Map15F1NCBI
cM Map1556.31NCBI
Letmd1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555471,574,265 - 1,582,786 (+)Ensembl
ChiLan1.0NW_0049555471,574,210 - 1,586,432 (+)NCBIChiLan1.0ChiLan1.0
LETMD1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21043,125,558 - 43,138,023 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11243,122,320 - 43,134,785 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01237,685,741 - 37,705,104 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11238,587,366 - 38,609,810 (-)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1238,597,728 - 38,609,810 (-)EnsemblpanPan2panpan1.1
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 (-)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha2742,486,087 - 42,494,364 (+)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.0273,809,305 - 3,817,581 (-)NCBIROS_Cfam_1.0ROS_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_1.0UU_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 Ensembl
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 (+)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
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_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_0046248161,148,634 - 1,170,981 (-)NCBIHetGla 1.0HetGla 1.0hetGla2
Letmd1
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v11262,609,799 - 262,623,539 (-)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Letmd1
39 total Variants
miRNA Target Status (No longer updated)

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 (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1331748Bp215Blood pressure QTL 2154.043arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)7110725024135371468Rat
1354582Stl11Serum triglyceride level QTL 113.42blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)7121393075137014596Rat
634331Pia17Pristane induced arthritis QTL 174.7joint integrity trait (VT:0010548)arthritic paw count (CMO:0001460)7132099939137014596Rat
731176Glom5Glomerulus QTL 52.50.0035kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)798549867137014596Rat
1300112Bp183Blood pressure QTL 1833.51arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)7119280025135560836Rat
61428Scl3Serum cholesterol level QTL 33.2blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)7100548246137014596Rat
61397Bw17Body weight QTL 176.3body mass (VT:0001259)body weight (CMO:0000012)795485047137014596Rat
1331746Kidm9Kidney mass QTL 93.934kidney mass (VT:0002707)right kidney wet weight (CMO:0000082)782111245134948181Rat
1358914Bp266Blood pressure QTL 266arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)7115313999136544683Rat
1331731Bp216Blood pressure QTL 2162.851arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)7104186212135371468Rat
1549899Stresp8Stress response QTL 84.370.0008stress-related behavior trait (VT:0010451)defensive burying duration (CMO:0001961)792362341137014596Rat
1358891Bp265Blood pressure QTL 2652.21arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)771827901136544683Rat

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

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
18 13 82 205 91 90 59 138 59 6 452 262 21 182 105 112 31 34 34

Sequence


Ensembl Acc Id: ENSRNOT00000042786   ⟹   ENSRNOP00000039848
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl7133,462,825 - 133,472,640 (+)Ensembl
mRatBN7.2 Ensembl7131,584,259 - 131,593,846 (+)Ensembl
Rnor_6.0 Ensembl7142,106,465 - 142,115,948 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000088681   ⟹   ENSRNOP00000075497
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl7133,463,176 - 133,476,591 (+)Ensembl
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
GRCr87133,463,157 - 133,472,641 (+)NCBI
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
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr87133,461,920 - 133,476,592 (+)NCBI
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_063264251   ⟹   XP_063120321
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr87133,463,764 - 133,476,592 (+)NCBI
RefSeq Acc Id: XM_063264252   ⟹   XP_063120322
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr87133,461,920 - 133,472,641 (+)NCBI
RefSeq Acc Id: NP_001116253   ⟸   NM_001122781
- UniProtKB: G3V996 (UniProtKB/TrEMBL),   A6KCJ7 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006242416   ⟸   XM_006242354
- Peptide Label: isoform X1
- UniProtKB: B0K026 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000039848   ⟸   ENSRNOT00000042786
Ensembl Acc Id: ENSRNOP00000075497   ⟸   ENSRNOT00000088681
RefSeq Acc Id: XP_063120322   ⟸   XM_063264252
- Peptide Label: isoform X3
RefSeq Acc Id: XP_063120321   ⟸   XM_063264251
- 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 Transcript ENSRNOT00000042786 ENTREZGENE
  ENSRNOT00000042786.6 UniProtKB/TrEMBL
  ENSRNOT00000088681 ENTREZGENE
  ENSRNOT00000088681.3 UniProtKB/TrEMBL
InterPro LETM1/MDM38-like UniProtKB/TrEMBL
  LETM1_RBD UniProtKB/TrEMBL
KEGG Report rno:681352 UniProtKB/TrEMBL
NCBI Gene 681352 ENTREZGENE
PANTHER LETM1 DOMAIN-CONTAINING PROTEIN 1 UniProtKB/TrEMBL
  PTHR14009 UniProtKB/TrEMBL
Pfam LETM1 UniProtKB/TrEMBL
PhenoGen Letmd1 PhenoGen
PROSITE LETM1_RBD UniProtKB/TrEMBL
RatGTEx ENSRNOG00000029855 RatGTEx
UniProt A6KCJ7 ENTREZGENE, UniProtKB/TrEMBL
  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 from RGD:1310591 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