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    LETM2 leucine zipper and EF-hand containing transmembrane protein 2 [ Homo sapiens (human) ]

    Gene ID: 137994, updated on 11-Apr-2024

    Summary

    Official Symbol
    LETM2provided by HGNC
    Official Full Name
    leucine zipper and EF-hand containing transmembrane protein 2provided by HGNC
    Primary source
    HGNC:HGNC:14648
    See related
    Ensembl:ENSG00000165046 MIM:620380; AllianceGenome:HGNC:14648
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    SLC55A2
    Summary
    Predicted to enable ribosome binding activity. Predicted to be involved in cellular metal ion homeostasis. Predicted to be located in mitochondrial inner membrane. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Broad expression in testis (RPKM 3.0), brain (RPKM 0.6) and 14 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See LETM2 in Genome Data Viewer
    Location:
    8p11.23
    Exon count:
    16
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 8 NC_000008.11 (38382431..38409527)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 8 NC_060932.1 (38659474..38686498)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 8 NC_000008.10 (38243994..38267045)

    Chromosome 8 - NC_000008.11Genomic Context describing neighboring genes Neighboring gene DDHD domain containing 2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19119 Neighboring gene phospholipid phosphatase 5 Neighboring gene nuclear receptor binding SET domain protein 3 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19120 Neighboring gene NUP98-NSD3 recombination region Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27247 Neighboring gene OCT4 hESC enhancer GRCh37_chr8:38235530-38236031 Neighboring gene OCT4 hESC enhancer GRCh37_chr8:38238312-38238846 Neighboring gene H3K27ac hESC enhancer GRCh37_chr8:38239137-38239927 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19122 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19123 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:38242638-38243268 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr8:38243269-38243898 Neighboring gene OCT4 hESC enhancer GRCh37_chr8:38244052-38244553 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19125 Neighboring gene OCT4 hESC enhancer GRCh37_chr8:38247000-38247501 Neighboring gene OCT4 hESC enhancer GRCh37_chr8:38248280-38248781 Neighboring gene OCT4 hESC enhancer GRCh37_chr8:38257600-38258101 Neighboring gene uncharacterized LOC102723716 Neighboring gene OCT4-H3K4me1 hESC enhancer GRCh37_chr8:38261681-38262180 Neighboring gene OCT4 hESC enhancer GRCh37_chr8:38262831-38263332 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19126 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:38269931-38270603 Neighboring gene OCT4-H3K4me1 hESC enhancer GRCh37_chr8:38270604-38271277 Neighboring gene OCT4-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:38272896-38273666 Neighboring gene OCT4-H3K27ac hESC enhancer GRCh37_chr8:38274107-38274772 Neighboring gene OCT4 hESC enhancer GRCh37_chr8:38275681-38276444 Neighboring gene OCT4 hESC enhancer GRCh37_chr8:38277305-38277806 Neighboring gene OCT4-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:38277908-38278453 Neighboring gene OCT4-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:38278454-38278998 Neighboring gene OCT4-H3K4me1 hESC enhancer GRCh37_chr8:38278999-38279544 Neighboring gene OCT4-H3K4me1 hESC enhancer GRCh37_chr8:38279545-38280088 Neighboring gene OCT4-H3K27ac hESC enhancer GRCh37_chr8:38280202-38280702 Neighboring gene OCT4-H3K27ac hESC enhancer GRCh37_chr8:38280703-38281203 Neighboring gene OCT4-H3K4me1 hESC enhancer GRCh37_chr8:38282951-38283642 Neighboring gene OCT4-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:38285189-38286186 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:38287183-38288180 Neighboring gene OCT4-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:38289284-38289961 Neighboring gene OCT4-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:38289962-38290638 Neighboring gene OCT4-H3K27ac hESC enhancer GRCh37_chr8:38292133-38292640 Neighboring gene OCT4-H3K27ac hESC enhancer GRCh37_chr8:38292641-38293146 Neighboring gene OCT4-H3K27ac hESC enhancer GRCh37_chr8:38293147-38293653 Neighboring gene OCT4 hESC enhancer GRCh37_chr8:38294553-38295054 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:38296366-38297156 Neighboring gene fibroblast growth factor receptor 1 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:38297948-38298737 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:38298738-38299528 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:38299529-38300319 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:38300320-38301110 Neighboring gene H3K27ac hESC enhancer GRCh37_chr8:38301111-38301900 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:38303357-38303904 Neighboring gene OCT4-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:38303905-38304451 Neighboring gene ribosomal protein S20 pseudogene 22 Neighboring gene OCT4-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:38308051-38308774 Neighboring gene OCT4-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:38308775-38309498 Neighboring gene OCT4-H3K4me1 hESC enhancer GRCh37_chr8:38310223-38310946 Neighboring gene OCT4-H3K4me1 hESC enhancer GRCh37_chr8:38312456-38313158 Neighboring gene OCT4 hESC enhancer GRCh37_chr8:38314169-38314670 Neighboring gene OCT4 hESC enhancer GRCh37_chr8:38315184-38316172 Neighboring gene OCT4 hESC enhancer GRCh37_chr8:38322798-38323299 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19127 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27250 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19128 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19129 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:38325893-38326879 Neighboring gene OCT4-H3K4me1 hESC enhancer GRCh37_chr8:38329497-38330290 Neighboring gene OCT4-H3K4me1 hESC enhancer GRCh37_chr8:38330291-38331084 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:38331715-38332697 Neighboring gene OCT4 hESC enhancer GRCh37_chr8:38335294-38335795 Neighboring gene OCT4 hESC enhancer GRCh37_chr8:38337885-38338386 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:38342043-38342691 Neighboring gene OCT4-H3K4me1 hESC enhancer GRCh37_chr8:38342692-38343339 Neighboring gene OCT4 hESC enhancer GRCh37_chr8:38343723-38344224 Neighboring gene OCT4 hESC enhancer GRCh37_chr8:38345990-38346491 Neighboring gene OCT4 hESC enhancer GRCh37_chr8:38347499-38348000 Neighboring gene OCT4 hESC enhancer GRCh37_chr8:38348154-38348655 Neighboring gene Sharpr-MPRA regulatory region 7766 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:38353597-38354164 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:38354165-38354733 Neighboring gene OCT4-H3K4me1 hESC enhancer GRCh37_chr8:38359246-38360101 Neighboring gene OCT4-H3K4me1 hESC enhancer GRCh37_chr8:38360102-38360956 Neighboring gene OCT4-H3K4me1 hESC enhancer GRCh37_chr8:38360976-38361766 Neighboring gene OCT4-H3K4me1 hESC enhancer GRCh37_chr8:38361767-38362556 Neighboring gene OCT4-H3K27ac hESC enhancer GRCh37_chr8:38368263-38369061 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr8:38369732-38370310 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr8:38370311-38370888 Neighboring gene OCT4 hESC enhancer GRCh37_chr8:38376955-38377456 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:38379090-38380048 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr8:38385147-38386346 Neighboring gene long intergenic non-protein coding RNA 3042

    Genomic regions, transcripts, and products

    Expression

    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • FLJ25409

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables ribosome binding IEA
    Inferred from Electronic Annotation
    more info
     
    Process Evidence Code Pubs
    involved_in intracellular monoatomic cation homeostasis IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    Component Evidence Code Pubs
    located_in mitochondrial inner membrane IEA
    Inferred from Electronic Annotation
    more info
     

    General protein information

    Preferred Names
    LETM1 domain-containing protein LETM2, mitochondrial
    Names
    LETM1 and EF-hand domain-containing protein 2
    leucine zipper-EF-hand containing transmembrane protein 1-like protein
    leucine zipper-EF-hand containing transmembrane protein 2

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_001199659.3NP_001186588.1  LETM1 domain-containing protein LETM2, mitochondrial isoform 1

      See identical proteins and their annotated locations for NP_001186588.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes isoform (1).
      Source sequence(s)
      AC087623, AY173945, BC069830
      Consensus CDS
      CCDS56534.1
      UniProtKB/TrEMBL
      B4DY93
      Related
      ENSP00000428765.2, ENST00000523983.6
      Conserved Domains (1) summary
      pfam07766
      Location:77331
      LETM1; LETM1-like protein
    2. NM_001199660.3NP_001186589.1  LETM1 domain-containing protein LETM2, mitochondrial isoform 3

      See identical proteins and their annotated locations for NP_001186589.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR and coding sequence compared to variant 1. The resulting isoform (3) is shorter at the N-terminus compared to isoform 1. Variants 3 and 4 enocode the same isoform (3).
      Source sequence(s)
      AC087623, BC024250, BC069830
      Conserved Domains (1) summary
      pfam07766
      Location:1182
      LETM1; LETM1-like protein
    3. NM_001286787.2NP_001273716.1  LETM1 domain-containing protein LETM2, mitochondrial isoform 3

      See identical proteins and their annotated locations for NP_001273716.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) uses two alternate splice sites in the 5' UTR which results in the use of a downstream start codon compared to variant 1. The encoded isoform (3) has a shorter N-terminus compared to isoform 1. Variants 3 and 4 enocode the same isoform (3).
      Source sequence(s)
      AC087623, BC069830
      Conserved Domains (1) summary
      pfam07766
      Location:1182
      LETM1; LETM1-like protein
    4. NM_001286819.2NP_001273748.1  LETM1 domain-containing protein LETM2, mitochondrial isoform 4

      See identical proteins and their annotated locations for NP_001273748.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (5) uses two alternate splice sites in the coding region which results in the use of an upstream AUG, compared to variant 1. The encoded isoform (4) has a longer N-terminus compared to isoform 1.
      Source sequence(s)
      AC087623
      Consensus CDS
      CCDS69466.1
      UniProtKB/Swiss-Prot
      A6NMG3, Q2VYF4, Q8NCR2, Q96LL1
      UniProtKB/TrEMBL
      B4DY93
      Related
      ENSP00000369291.4, ENST00000379957.9
      Conserved Domains (1) summary
      pfam07766
      Location:124378
      LETM1; LETM1-like protein
    5. NM_001286821.2NP_001273750.1  LETM1 domain-containing protein LETM2, mitochondrial isoform 5

      See identical proteins and their annotated locations for NP_001273750.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (6) differs in both UTR's and the coding region and uses an alternate start codon, compared to variant 1. This results in an isoform (5) that is shorter and has distinct N- and C-termini, compared to isoform 1.
      Source sequence(s)
      AC087623, AK289944, AL832241
      Consensus CDS
      CCDS75731.1
      UniProtKB/TrEMBL
      A8K1M9, E5RIY3, E5RK40
      Related
      ENSP00000429269.2, ENST00000519476.6
      Conserved Domains (1) summary
      pfam07766
      Location:124167
      LETM1; LETM1-like protein
    6. NM_001330515.2NP_001317444.1  LETM1 domain-containing protein LETM2, mitochondrial isoform 6

      Status: VALIDATED

      Source sequence(s)
      AC087623, BC069830, BJ989830, CB242043, CV024670
      Consensus CDS
      CCDS83282.1
      UniProtKB/TrEMBL
      B4DY93, E9PMA4
      Related
      ENSP00000431211.1, ENST00000524874.5
    7. NM_001363204.1NP_001350133.1  LETM1 domain-containing protein LETM2, mitochondrial isoform 7 precursor

      Status: VALIDATED

      Source sequence(s)
      AC087623, BC069830
      Conserved Domains (1) summary
      pfam07766
      Location:2204
      LETM1; LETM1-like protein
    8. NM_001363205.1NP_001350134.1  LETM1 domain-containing protein LETM2, mitochondrial isoform 3

      Status: VALIDATED

      Source sequence(s)
      AC087623, BC069830, BP198673
      Conserved Domains (1) summary
      pfam07766
      Location:1182
      LETM1; LETM1-like protein
    9. NM_144652.4NP_653253.1  LETM1 domain-containing protein LETM2, mitochondrial isoform 2

      See identical proteins and their annotated locations for NP_653253.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks an alternate in-frame exon compared to variant 1. The resulting isoform (2) has the same N- and C-termini but is shorter compared to isoform 1.
      Source sequence(s)
      AC087623, AK058138, BC069830
      Consensus CDS
      CCDS6106.1
      UniProtKB/TrEMBL
      B4DY93
      Related
      ENSP00000297720.5, ENST00000297720.9
      Conserved Domains (1) summary
      pfam07766
      Location:77283
      LETM1; LETM1-like protein

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000008.11 Reference GRCh38.p14 Primary Assembly

      Range
      38382431..38409527
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017013056.2XP_016868545.1  LETM1 domain-containing protein LETM2, mitochondrial isoform X1

      UniProtKB/Swiss-Prot
      A6NMG3, Q2VYF4, Q8NCR2, Q96LL1
      UniProtKB/TrEMBL
      B4DY93
      Conserved Domains (1) summary
      pfam07766
      Location:124378
      LETM1; LETM1-like protein
    2. XM_017013053.2XP_016868542.1  LETM1 domain-containing protein LETM2, mitochondrial isoform X1

      UniProtKB/Swiss-Prot
      A6NMG3, Q2VYF4, Q8NCR2, Q96LL1
      UniProtKB/TrEMBL
      B4DY93
      Conserved Domains (1) summary
      pfam07766
      Location:124378
      LETM1; LETM1-like protein
    3. XM_047421383.1XP_047277339.1  LETM1 domain-containing protein LETM2, mitochondrial isoform X2

    4. XM_011544408.3XP_011542710.1  LETM1 domain-containing protein LETM2, mitochondrial isoform X3

      UniProtKB/TrEMBL
      B4DY93
      Conserved Domains (1) summary
      pfam07766
      Location:124378
      LETM1; LETM1-like protein
    5. XM_017013051.2XP_016868540.1  LETM1 domain-containing protein LETM2, mitochondrial isoform X1

      UniProtKB/Swiss-Prot
      A6NMG3, Q2VYF4, Q8NCR2, Q96LL1
      UniProtKB/TrEMBL
      B4DY93
      Conserved Domains (1) summary
      pfam07766
      Location:124378
      LETM1; LETM1-like protein
    6. XM_017013055.2XP_016868544.1  LETM1 domain-containing protein LETM2, mitochondrial isoform X1

      UniProtKB/Swiss-Prot
      A6NMG3, Q2VYF4, Q8NCR2, Q96LL1
      UniProtKB/TrEMBL
      B4DY93
      Conserved Domains (1) summary
      pfam07766
      Location:124378
      LETM1; LETM1-like protein
    7. XM_017013052.2XP_016868541.1  LETM1 domain-containing protein LETM2, mitochondrial isoform X1

      UniProtKB/Swiss-Prot
      A6NMG3, Q2VYF4, Q8NCR2, Q96LL1
      UniProtKB/TrEMBL
      B4DY93
      Conserved Domains (1) summary
      pfam07766
      Location:124378
      LETM1; LETM1-like protein
    8. XM_017013054.2XP_016868543.1  LETM1 domain-containing protein LETM2, mitochondrial isoform X1

      UniProtKB/Swiss-Prot
      A6NMG3, Q2VYF4, Q8NCR2, Q96LL1
      UniProtKB/TrEMBL
      B4DY93
      Conserved Domains (1) summary
      pfam07766
      Location:124378
      LETM1; LETM1-like protein
    9. XM_011544410.3XP_011542712.1  LETM1 domain-containing protein LETM2, mitochondrial isoform X4

      See identical proteins and their annotated locations for XP_011542712.1

      UniProtKB/Swiss-Prot
      Q2VYF4
      Related
      ENSP00000434867.1, ENST00000527710.5
      Conserved Domains (1) summary
      pfam07766
      Location:2164
      LETM1; LETM1-like protein

    RNA

    1. XR_007060702.1 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060932.1 Alternate T2T-CHM13v2.0

      Range
      38659474..38686498
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054359786.1XP_054215761.1  LETM1 domain-containing protein LETM2, mitochondrial isoform X1

      UniProtKB/Swiss-Prot
      A6NMG3, Q2VYF4, Q8NCR2, Q96LL1
    2. XM_054359781.1XP_054215756.1  LETM1 domain-containing protein LETM2, mitochondrial isoform X1

      UniProtKB/Swiss-Prot
      A6NMG3, Q2VYF4, Q8NCR2, Q96LL1
    3. XM_054359787.1XP_054215762.1  LETM1 domain-containing protein LETM2, mitochondrial isoform X2

    4. XM_054359788.1XP_054215763.1  LETM1 domain-containing protein LETM2, mitochondrial isoform X3

    5. XM_054359785.1XP_054215760.1  LETM1 domain-containing protein LETM2, mitochondrial isoform X1

      UniProtKB/Swiss-Prot
      A6NMG3, Q2VYF4, Q8NCR2, Q96LL1
    6. XM_054359784.1XP_054215759.1  LETM1 domain-containing protein LETM2, mitochondrial isoform X1

      UniProtKB/Swiss-Prot
      A6NMG3, Q2VYF4, Q8NCR2, Q96LL1
    7. XM_054359783.1XP_054215758.1  LETM1 domain-containing protein LETM2, mitochondrial isoform X1

      UniProtKB/Swiss-Prot
      A6NMG3, Q2VYF4, Q8NCR2, Q96LL1
    8. XM_054359782.1XP_054215757.1  LETM1 domain-containing protein LETM2, mitochondrial isoform X1

      UniProtKB/Swiss-Prot
      A6NMG3, Q2VYF4, Q8NCR2, Q96LL1
    9. XM_054359789.1XP_054215764.1  LETM1 domain-containing protein LETM2, mitochondrial isoform X4

    RNA

    1. XR_008487809.1 RNA Sequence