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LETMD1 LETM1 domain containing 1 [ Homo sapiens (human) ]

Gene ID: 25875, updated on 21-Dec-2019

Summary

Official Symbol
LETMD1provided by HGNC
Official Full Name
LETM1 domain containing 1provided by HGNC
Primary source
HGNC:HGNC:24241
See related
Ensembl:ENSG00000050426
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
HCCR; HCCR1; HCCR2; HCCR-1; HCCR-2; HCRR-2; SLC55A3; 1110019O13Rik
Summary
This gene encodes a mitochondrial outer membrane protein. It has a potential role in tumorigenesis, which may result from negative regulation of the p53 tumor suppressor gene. Alternatively spliced transcript variants have been noted for this gene. [provided by RefSeq, Aug 2011]
Expression
Ubiquitous expression in thyroid (RPKM 15.5), fat (RPKM 12.3) and 25 other tissues See more
Orthologs

Genomic context

See LETMD1 in Genome Data Viewer
Location:
12q13.12
Exon count:
11
Annotation release Status Assembly Chr Location
109.20191205 current GRCh38.p13 (GCF_000001405.39) 12 NC_000012.12 (51048220..51068958)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (51442082..51454207)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene solute carrier family 11 member 2 Neighboring gene RNA, U6 small nuclear 87, pseudogene Neighboring gene RNA, U6 small nuclear 1273, pseudogene Neighboring gene cysteine and serine rich nuclear protein 2 Neighboring gene transcription factor CP2 Neighboring gene ribosomal protein L35a pseudogene 29 Neighboring gene prohibitin pseudogene 19

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

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • DKFZp586A011

Gene Ontology Provided by GOA

Function Evidence Code Pubs
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
ribosome binding IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
integral component of membrane IEA
Inferred from Electronic Annotation
more info
 
mitochondrial outer membrane IEA
Inferred from Electronic Annotation
more info
 
mitochondrion IDA
Inferred from Direct Assay
more info
 
nucleolus IDA
Inferred from Direct Assay
more info
 
nucleoplasm IDA
Inferred from Direct Assay
more info
 

General protein information

Preferred Names
LETM1 domain-containing protein 1
Names
cervical cancer 1 proto-oncogene protein p40
cervical cancer proto-oncogene 2 protein
epididymis secretory sperm binding protein
human cervical cancer oncogene
regulator of TP53

NCBI Reference Sequences (RefSeq)

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.

Genomic

  1. NG_029858.2 RefSeqGene

    Range
    5080..17205
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001243689.2NP_001230618.1  LETM1 domain-containing protein 1 isoform b

    See identical proteins and their annotated locations for NP_001230618.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) uses an alternate in-frame donor splice site at an internal exon in the 5' coding region compared to variant 1. This results in a longer isoform (b, also known as 3) containing a 13 aa protein segment not found in isoform 1.
    Source sequence(s)
    AC087884
    Consensus CDS
    CCDS58231.1
    UniProtKB/Swiss-Prot
    Q6P1Q0
    Related
    ENSP00000389903.2, ENST00000418425.6
    Conserved Domains (1) summary
    pfam07766
    Location:80351
    LETM1; LETM1-like protein
  2. NM_001300765.2NP_001287694.1  LETM1 domain-containing protein 1 isoform c

    See identical proteins and their annotated locations for NP_001287694.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (7) lacks three alternate in-frame exons in the central coding region, compared to variant 1. The encoded isoform (c, also known as 7) is shorter than isoform 1.
    Source sequence(s)
    AC087884
    Consensus CDS
    CCDS73469.1
    UniProtKB/TrEMBL
    F8W1Z2
    Related
    ENSP00000447419.1, ENST00000547008.5
    Conserved Domains (1) summary
    pfam07766
    Location:79221
    LETM1; LETM1-like protein
  3. NM_001351312.2NP_001338241.1  LETM1 domain-containing protein 1 isoform d

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2), as well as variant 12, encodes isoform d.
    Source sequence(s)
    AC087884
    Consensus CDS
    CCDS44883.1
    Related
    ENSP00000450163.1, ENST00000550929.5
    Conserved Domains (1) summary
    pfam07766
    Location:23289
    LETM1; LETM1-like protein
  4. NM_001351313.2NP_001338242.1  LETM1 domain-containing protein 1 isoform e

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4), as well as variants 25-27, encodes isoform e.
    Source sequence(s)
    AC087884
    Conserved Domains (1) summary
    pfam07766
    Location:1188
    LETM1; LETM1-like protein
  5. NM_001351315.2NP_001338244.1  LETM1 domain-containing protein 1 isoform f

    Status: REVIEWED

    Source sequence(s)
    AC087884
    Conserved Domains (1) summary
    pfam07766
    Location:86352
    LETM1; LETM1-like protein
  6. NM_001351316.2NP_001338245.1  LETM1 domain-containing protein 1 isoform g

    Status: REVIEWED

    Source sequence(s)
    AC087884
    Conserved Domains (1) summary
    pfam07766
    Location:86312
    LETM1; LETM1-like protein
  7. NM_001351317.2NP_001338246.1  LETM1 domain-containing protein 1 isoform h

    Status: REVIEWED

    Source sequence(s)
    AC087884
    Conserved Domains (1) summary
    pfam07766
    Location:79305
    LETM1; LETM1-like protein
  8. NM_001351319.2NP_001338248.1  LETM1 domain-containing protein 1 isoform d

    Status: REVIEWED

    Description
    Transcript Variant: This variant (12), as well as variant 2, encodes isoform d.
    Source sequence(s)
    AC087884
    Consensus CDS
    CCDS44883.1
    Conserved Domains (1) summary
    pfam07766
    Location:23289
    LETM1; LETM1-like protein
  9. NM_001351320.2NP_001338249.1  LETM1 domain-containing protein 1 isoform k

    Status: REVIEWED

    Source sequence(s)
    AC087884
    Conserved Domains (1) summary
    pfam07766
    Location:23249
    LETM1; LETM1-like protein
  10. NM_001351321.2NP_001338250.1  LETM1 domain-containing protein 1 isoform l

    Status: REVIEWED

    Source sequence(s)
    AC087884
    Conserved Domains (1) summary
    pfam07766
    Location:79255
    LETM1; LETM1-like protein
  11. NM_001351322.2NP_001338251.1  LETM1 domain-containing protein 1 isoform m

    Status: REVIEWED

    Source sequence(s)
    AC087884
    Conserved Domains (1) summary
    pfam07766
    Location:1251
    LETM1; LETM1-like protein
  12. NM_001351323.2NP_001338252.1  LETM1 domain-containing protein 1 isoform m

    Status: REVIEWED

    Source sequence(s)
    AC087884
    Conserved Domains (1) summary
    pfam07766
    Location:1251
    LETM1; LETM1-like protein
  13. NM_001351324.2NP_001338253.1  LETM1 domain-containing protein 1 isoform m

    Status: REVIEWED

    Source sequence(s)
    AC087884
    Conserved Domains (1) summary
    pfam07766
    Location:1251
    LETM1; LETM1-like protein
  14. NM_001351325.2NP_001338254.1  LETM1 domain-containing protein 1 isoform n

    Status: REVIEWED

    Source sequence(s)
    AC087884
    Conserved Domains (1) summary
    pfam07766
    Location:116244
    LETM1; LETM1-like protein
  15. NM_001351326.2NP_001338255.1  LETM1 domain-containing protein 1 isoform o

    Status: REVIEWED

    Source sequence(s)
    AC087884
    Conserved Domains (1) summary
    pfam07766
    Location:37239
    LETM1; LETM1-like protein
  16. NM_001351327.2NP_001338256.1  LETM1 domain-containing protein 1 isoform o

    Status: REVIEWED

    Source sequence(s)
    AC087884
    Conserved Domains (1) summary
    pfam07766
    Location:37239
    LETM1; LETM1-like protein
  17. NM_001351328.2NP_001338257.1  LETM1 domain-containing protein 1 isoform p

    Status: REVIEWED

    Source sequence(s)
    AC087884
    Conserved Domains (1) summary
    pfam07766
    Location:86228
    LETM1; LETM1-like protein
  18. NM_001351330.2NP_001338259.1  LETM1 domain-containing protein 1 isoform t

    Status: REVIEWED

    Source sequence(s)
    AC087884
    Consensus CDS
    CCDS86301.1
    Related
    ENSP00000450333.1, ENST00000552739.5
    Conserved Domains (1) summary
    pfam07766
    Location:42228
    LETM1; LETM1-like protein
  19. NM_001351332.2NP_001338261.1  LETM1 domain-containing protein 1 isoform u

    Status: REVIEWED

    Source sequence(s)
    AC087884
    Conserved Domains (1) summary
    pfam07766
    Location:93228
    LETM1; LETM1-like protein
  20. NM_001351333.2NP_001338262.1  LETM1 domain-containing protein 1 isoform q

    Status: REVIEWED

    Source sequence(s)
    AC087884
    Conserved Domains (1) summary
    pfam07766
    Location:79181
    LETM1; LETM1-like protein
  21. NM_001351334.2NP_001338263.1  LETM1 domain-containing protein 1 isoform e

    Status: REVIEWED

    Description
    Transcript Variant: This variant (25), as well as variants 4, 26, and 27, encodes isoform e (also called isoform r).
    Source sequence(s)
    AC087884
    Conserved Domains (1) summary
    pfam07766
    Location:1188
    LETM1; LETM1-like protein
  22. NM_001351335.2NP_001338264.1  LETM1 domain-containing protein 1 isoform e

    Status: REVIEWED

    Description
    Transcript Variant: This variant (26), as well as variants 4, 25, and 27, encodes isoform e (also called isoform r).
    Source sequence(s)
    AC087884
    Conserved Domains (1) summary
    pfam07766
    Location:1188
    LETM1; LETM1-like protein
  23. NM_001351336.2NP_001338265.1  LETM1 domain-containing protein 1 isoform e

    Status: REVIEWED

    Description
    Transcript Variant: This variant (27), as well as variants 4, 25, and 26, encodes isoform e (also called isoform r).
    Source sequence(s)
    AC087884
    Conserved Domains (1) summary
    pfam07766
    Location:1188
    LETM1; LETM1-like protein
  24. NM_001351337.2NP_001338266.1  LETM1 domain-containing protein 1 isoform s

    Status: REVIEWED

    Source sequence(s)
    AC087884, KF455649
    Conserved Domains (1) summary
    pfam07766
    Location:79181
    LETM1; LETM1-like protein
  25. NM_015416.5NP_056231.3  LETM1 domain-containing protein 1 isoform a

    See identical proteins and their annotated locations for NP_056231.3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the predominant protein-coding transcript, and encodes isoform a (also known as HCCR-1 or 1).
    Source sequence(s)
    AC087884
    Consensus CDS
    CCDS8806.1
    UniProtKB/Swiss-Prot
    Q6P1Q0
    Related
    ENSP00000262055.4, ENST00000262055.9
    Conserved Domains (1) summary
    pfam07766
    Location:79345
    LETM1; LETM1-like protein

RNA

  1. NR_045019.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) lacks two consecutive exons compared to variant 1. It is represented as non-coding due to the presence of an upstream ORF that is predicted to interfere with the translation of the longest ORF; translation of the upstream ORF renders this transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AC087884
    Related
    ENST00000547318.5
  2. NR_045020.3 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC087884, KF455649
  3. NR_147098.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC087884, BU688852
  4. NR_147099.2 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC087884
  5. NR_147100.2 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC087884
  6. NR_147101.2 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC087884
  7. NR_147102.2 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC087884
  8. NR_147103.2 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC087884
  9. NR_147104.2 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC087884
  10. NR_147105.2 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC087884
  11. NR_147106.2 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC087884
  12. NR_147107.2 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC087884
  13. NR_147108.2 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC087884
  14. NR_147109.2 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC087884
  15. NR_147110.2 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC087884
  16. NR_147111.2 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC087884
  17. NR_147112.2 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC087884
    Related
    ENST00000550100.5
  18. NR_147113.2 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC087884
    Related
    ENST00000547555.5
  19. NR_147114.2 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC087884
  20. NR_147115.2 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC087884
    Related
    ENST00000380135.7
  21. NR_147116.2 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC087884
  22. NR_147117.2 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC087884
  23. NR_147118.2 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC087884
  24. NR_147119.2 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC087884
  25. NR_147120.2 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC087884

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20191205

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000012.12 Reference GRCh38.p13 Primary Assembly

    Range
    51048220..51068958
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017019164.1XP_016874653.1  LETM1 domain-containing protein 1 isoform X17

  2. XM_017019161.2XP_016874650.1  LETM1 domain-containing protein 1 isoform X15

  3. XM_017019159.1XP_016874648.1  LETM1 domain-containing protein 1 isoform X13

  4. XM_017019156.1XP_016874645.1  LETM1 domain-containing protein 1 isoform X8

  5. XM_011538163.2XP_011536465.1  LETM1 domain-containing protein 1 isoform X7

    Conserved Domains (1) summary
    pfam07766
    Location:87312
    LETM1; LETM1-like protein
  6. XM_017019151.1XP_016874640.1  LETM1 domain-containing protein 1 isoform X1

  7. XM_017019153.1XP_016874642.1  LETM1 domain-containing protein 1 isoform X3

  8. XM_011538164.2XP_011536466.1  LETM1 domain-containing protein 1 isoform X9

    Conserved Domains (1) summary
    pfam07766
    Location:100295
    LETM1; LETM1-like protein
  9. XM_006719340.1XP_006719403.1  LETM1 domain-containing protein 1 isoform X18

    See identical proteins and their annotated locations for XP_006719403.1

    UniProtKB/Swiss-Prot
    Q6P1Q0
    Conserved Domains (1) summary
    pfam07766
    Location:1188
    LETM1; LETM1-like protein
  10. XM_017019166.1XP_016874655.1  LETM1 domain-containing protein 1 isoform X17

  11. XM_017019162.1XP_016874651.1  LETM1 domain-containing protein 1 isoform X16

  12. XM_017019160.2XP_016874649.1  LETM1 domain-containing protein 1 isoform X14

  13. XM_024448933.1XP_024304701.1  LETM1 domain-containing protein 1 isoform X6

    Conserved Domains (1) summary
    pfam07766
    Location:79305
    LETM1; LETM1-like protein
  14. XM_006719335.1XP_006719398.1  LETM1 domain-containing protein 1 isoform X11

    Related
    ENSP00000449896.1, ENST00000549340.5
    Conserved Domains (1) summary
    pfam07766
    Location:93288
    LETM1; LETM1-like protein
  15. XM_017019152.2XP_016874641.1  LETM1 domain-containing protein 1 isoform X2

  16. XM_017019165.1XP_016874654.1  LETM1 domain-containing protein 1 isoform X17

  17. XM_017019157.1XP_016874646.1  LETM1 domain-containing protein 1 isoform X10

  18. XM_017019154.1XP_016874643.1  LETM1 domain-containing protein 1 isoform X4

  19. XM_017019158.1XP_016874647.1  LETM1 domain-containing protein 1 isoform X12

  20. XM_017019155.2XP_016874644.1  LETM1 domain-containing protein 1 isoform X5

RNA

  1. XR_944516.3 RNA Sequence

  2. XR_002957308.1 RNA Sequence

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_001024668.1: Suppressed sequence

    Description
    NM_001024668.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.
  2. NM_001024669.1: Suppressed sequence

    Description
    NM_001024669.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.
  3. NM_001024670.1: Suppressed sequence

    Description
    NM_001024670.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.
  4. NM_001024671.1: Suppressed sequence

    Description
    NM_001024671.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.
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