Human Gene LETM1 (ENST00000302787.3_7) from GENCODE V47lift37
  Description: leucine zipper and EF-hand containing transmembrane protein 1 (from RefSeq NM_012318.3)
Gencode Transcript: ENST00000302787.3_7
Gencode Gene: ENSG00000168924.15_9
Transcript (Including UTRs)
   Position: hg19 chr4:1,813,206-1,857,883 Size: 44,678 Total Exon Count: 14 Strand: -
Coding Region
   Position: hg19 chr4:1,816,151-1,857,677 Size: 41,527 Coding Exon Count: 14 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr4:1,813,206-1,857,883)mRNA (may differ from genome)Protein (739 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsHGNC
MalacardsMGIOMIMPubMedReactomeUniProtKB
WikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: LETM1_HUMAN
DESCRIPTION: RecName: Full=LETM1 and EF-hand domain-containing protein 1, mitochondrial; AltName: Full=Leucine zipper-EF-hand-containing transmembrane protein 1; Flags: Precursor;
FUNCTION: Crucial for the maintenance of mitochondrial tubular networks and for the assembly of the supercomplexes of the respiratory chain. Required for the maintenance of the tubular shape and cristae organization.
SUBUNIT: Can form 2 complexes: a major (300kDa) and a minor complex (500-600 kDa). Interacts with BCS1L.
SUBCELLULAR LOCATION: Mitochondrion inner membrane; Single-pass membrane protein.
SIMILARITY: Contains 1 EF-hand domain.
SIMILARITY: Contains 1 LETM1 domain.
SEQUENCE CAUTION: Sequence=CAB63769.2; Type=Erroneous translation; Note=Incomplete prediction of CDS at the C-terminus;

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: LETM1
Diseases sorted by gene-association score: wolf-hirschhorn syndrome (22), chromosomal deletion syndrome (8), chromosomal disease (1)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene
  • C009618 O,O-diethyl O-3,5,6-trichloro-2-pyridyl phosphate
  • C111118 2',3,3',4',5-pentachloro-4-hydroxybiphenyl
  • C532162 2-(1H-indazol-4-yl)-6-(4-methanesulfonylpiperazin-1-ylmethyl)-4-morpholin-4-ylthieno(3,2-d)pyrimidine
  • D001564 Benzo(a)pyrene
  • D016572 Cyclosporine
  • D004958 Estradiol
  • D004997 Ethinyl Estradiol
  • D006861 Hydrogen Peroxide
  • D013629 Tamoxifen
  • D013749 Tetrachlorodibenzodioxin
          more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 19.30 RPKM in Colon - Transverse
Total median expression: 455.93 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -110.10206-0.534 Picture PostScript Text
3' UTR -1118.402945-0.380 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR011992 - EF-hand-like_dom
IPR018247 - EF_Hand_1_Ca_BS
IPR018249 - EF_HAND_2
IPR011685 - LETM1

Pfam Domains:
PF07766 - LETM1-like protein
PF13833 - EF-hand domain pair

SCOP Domains:
63446 - Type I dockerin domain
68906 - SAP domain
47473 - EF-hand
58100 - Bacterial hemolysins

ModBase Predicted Comparative 3D Structure on O95202
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologGenome BrowserGenome Browser
Gene DetailsGene Details Gene DetailsGene DetailsGene Details
Gene SorterGene Sorter Gene SorterGene SorterGene Sorter
 RGDEnsembl WormBaseSGD
    Protein SequenceProtein Sequence
    AlignmentAlignment

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005509 calcium ion binding
GO:0005515 protein binding
GO:0015297 antiporter activity
GO:0015369 calcium:proton antiporter activity
GO:0043022 ribosome binding
GO:0046872 metal ion binding

Biological Process:
GO:0006811 ion transport
GO:0006816 calcium ion transport
GO:0006851 mitochondrial calcium ion transport
GO:0006875 cellular metal ion homeostasis
GO:0034214 protein hexamerization
GO:0042407 cristae formation
GO:0051260 protein homooligomerization
GO:0051560 mitochondrial calcium ion homeostasis
GO:0099093 mitochondrial calcium release

Cellular Component:
GO:0005739 mitochondrion
GO:0005743 mitochondrial inner membrane
GO:0016020 membrane
GO:0016021 integral component of membrane


-  Descriptions from all associated GenBank mRNAs
  AF061025 - Homo sapiens leucine zipper-EF-hand containing transmembrane protein 1 (LETM1) mRNA, complete cds.
BC021208 - Homo sapiens leucine zipper-EF-hand containing transmembrane protein 1, mRNA (cDNA clone MGC:12631 IMAGE:4126510), complete cds.
BC014500 - Homo sapiens leucine zipper-EF-hand containing transmembrane protein 1, mRNA (cDNA clone MGC:23613 IMAGE:4860194), complete cds.
DQ893606 - Synthetic construct clone IMAGE:100006236; FLH181781.01X; RZPDo839H01136D leucine zipper-EF-hand containing transmembrane protein 1 (LETM1) gene, encodes complete protein.
AL133650 - Homo sapiens mRNA; cDNA DKFZp434C229 (from clone DKFZp434C229).
BX537709 - Homo sapiens mRNA; cDNA DKFZp686C1849 (from clone DKFZp686C1849).
JD535845 - Sequence 516869 from Patent EP1572962.
JD404082 - Sequence 385106 from Patent EP1572962.
JD046632 - Sequence 27656 from Patent EP1572962.
JD328360 - Sequence 309384 from Patent EP1572962.
JD248076 - Sequence 229100 from Patent EP1572962.
JD452526 - Sequence 433550 from Patent EP1572962.
JD117975 - Sequence 98999 from Patent EP1572962.
JD073609 - Sequence 54633 from Patent EP1572962.
JD455485 - Sequence 436509 from Patent EP1572962.
JD186958 - Sequence 167982 from Patent EP1572962.
JD402647 - Sequence 383671 from Patent EP1572962.
JD317286 - Sequence 298310 from Patent EP1572962.
JD088231 - Sequence 69255 from Patent EP1572962.
JD287547 - Sequence 268571 from Patent EP1572962.
JD100829 - Sequence 81853 from Patent EP1572962.
JD386524 - Sequence 367548 from Patent EP1572962.
JD274618 - Sequence 255642 from Patent EP1572962.
JD180854 - Sequence 161878 from Patent EP1572962.
JD526566 - Sequence 507590 from Patent EP1572962.
JD195097 - Sequence 176121 from Patent EP1572962.
JD460358 - Sequence 441382 from Patent EP1572962.
JD456645 - Sequence 437669 from Patent EP1572962.
JD368648 - Sequence 349672 from Patent EP1572962.
JD050471 - Sequence 31495 from Patent EP1572962.
JD080148 - Sequence 61172 from Patent EP1572962.
JD116603 - Sequence 97627 from Patent EP1572962.
JD282878 - Sequence 263902 from Patent EP1572962.
JD176345 - Sequence 157369 from Patent EP1572962.
JD563030 - Sequence 544054 from Patent EP1572962.
JD283247 - Sequence 264271 from Patent EP1572962.
JD477478 - Sequence 458502 from Patent EP1572962.
JD159506 - Sequence 140530 from Patent EP1572962.
JD495009 - Sequence 476033 from Patent EP1572962.
JD340441 - Sequence 321465 from Patent EP1572962.
DQ597033 - Homo sapiens piRNA piR-35099, complete sequence.
AK293572 - Homo sapiens cDNA FLJ60432 complete cds, highly similar to Leucine zipper-EF-hand-containing transmembrane protein 1.
AK310563 - Homo sapiens cDNA, FLJ17605.
JD204519 - Sequence 185543 from Patent EP1572962.
JD440585 - Sequence 421609 from Patent EP1572962.
JD408457 - Sequence 389481 from Patent EP1572962.
JD487794 - Sequence 468818 from Patent EP1572962.
JD406147 - Sequence 387171 from Patent EP1572962.
JD276379 - Sequence 257403 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein O95202 (Reactome details) participates in the following event(s):

R-HSA-8949687 LETM1 exchanges protons (mitochondrial intermembrane space) for calcium (mitochondrial matrix)
R-HSA-8949215 Mitochondrial calcium ion transport
R-HSA-382551 Transport of small molecules

-  Other Names for This Gene
  Alternate Gene Symbols: B4DED2, ENST00000302787.1, ENST00000302787.2, LETM1 , LETM1_HUMAN, NM_012318, O95202, Q9UF65, uc317ncs.1, uc317ncs.2
UCSC ID: ENST00000302787.3_7
RefSeq Accession: NM_012318.3
Protein: O95202 (aka LETM1_HUMAN)

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.