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LRTOMT leucine rich transmembrane and O-methyltransferase domain containing [ Homo sapiens (human) ]

Gene ID: 220074, updated on 13-Feb-2019

Summary

Official Symbol
LRTOMTprovided by HGNC
Official Full Name
leucine rich transmembrane and O-methyltransferase domain containingprovided by HGNC
Primary source
HGNC:HGNC:25033
See related
Ensembl:ENSG00000184154 MIM:612414
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
DFNB63; LRRC51; CFAP111
Summary
This gene has evolved in primates as a fusion of two ancestral neighboring genes, Lrrc51 and Tomt, which exist as two independent genes in rodents. The fusion gene contains some shared exons, but encodes structurally unrelated proteins, LRTOMT1 and LRTOMT2. Those variants that utilize the more centromere-proximal 3' terminal exon (short transcript form) encode LRTOMT1, while those variants that use a more centromere-distal 3' terminal exon (long transcript form) encode the LRTOMT2 protein. There is a small region within one of the exons of this gene that contains overlapping alternate reading frames for both LRTOMT1 and LRTOMT2. LRTOMT1 shares similarity with the protein encoded by mouse Lrrc51, while LRTOMT2 shares similarity with the protein encoded by mouse Tomt. Alternative splicing results in multiple transcript variants, encoding different isoforms of both LRTOMT1 and LRTOMT2. The LRTOMT1 protein is a leucine-rich repeat-containing protein, while the LRTOMT2 protein is a catechol-O-methyltransferase that catalyzes the transfer of a methyl group from S-adenosyl-L-methionine to a hydroxyl group of catechols and is essential for auditory and vestibular function. Mutations in this gene have been associated with nonsyndromic deafness. [provided by RefSeq, Nov 2017]
Expression
Broad expression in testis (RPKM 6.2), thyroid (RPKM 2.2) and 25 other tissues See more
Orthologs

Genomic context

See LRTOMT in Genome Data Viewer
Location:
11q13.4
Exon count:
14
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 11 NC_000011.10 (72080331..72110782)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (71791377..71821828)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC100128494 Neighboring gene nuclear mitotic apparatus protein 1 Neighboring gene microRNA 3165 Neighboring gene late endosomal/lysosomal adaptor, MAPK and MTOR activator 1 Neighboring gene anaphase promoting complex subunit 15 Neighboring gene ribulose-5-phosphate-3-epimerase pseudogene 6 Neighboring gene folate receptor 3

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 FunctionsWhat's a GeneRIF?

Pathways from BioSystems

  • noradrenaline and adrenaline degradation, organism-specific biosystem (from BIOCYC)
    noradrenaline and adrenaline degradation, organism-specific biosystemGeneral Background The catecholamines : DOPAMINE, : NOREPINEPHRINE (norepinephrine), and : L-EPINEPHRINE (epinephrine) function as neurotransmitters and hormones. They have important physiological ...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ52451

Gene Ontology Provided by GOA

Function Evidence Code Pubs
L-dopa O-methyltransferase activity IEA
Inferred from Electronic Annotation
more info
 
catechol O-methyltransferase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
catechol O-methyltransferase activity ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
catechol O-methyltransferase activity TAS
Traceable Author Statement
more info
 
orcinol O-methyltransferase activity IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
auditory receptor cell development ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
catecholamine catabolic process IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
catecholamine catabolic process ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
developmental process IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
dopamine metabolic process IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
methylation IEA
Inferred from Electronic Annotation
more info
 
neurotransmitter catabolic process IEA
Inferred from Electronic Annotation
more info
 
sensory perception of sound ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
Component Evidence Code Pubs
cellular_component ND
No biological Data available
more info
 
endoplasmic reticulum IEA
Inferred from Electronic Annotation
more info
 
integral component of membrane IEA
Inferred from Electronic Annotation
more info
 
plasma membrane TAS
Traceable Author Statement
more info
 

General protein information

Preferred Names
transmembrane O-methyltransferase; leucine-rich repeat-containing protein 51
Names
leucine rich transmembrane and 0-methyltransferase domain containing
NP_001138779.1
NP_001138780.1
NP_001138781.1
NP_001138782.1
NP_001192067.1
NP_001258400.1
NP_001305732.1
NP_660352.1
XP_006718536.1
XP_006718537.1
XP_011543149.1
XP_011543150.1
XP_024304169.1

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_021423.1 RefSeqGene

    Range
    4996..35447
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001145307.4NP_001138779.1  leucine-rich repeat-containing protein 51 isoform LRTOMT1b

    See identical proteins and their annotated locations for NP_001138779.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2, also known as B) represents the short transcript form. It lacks a segment in the 3' exon, compared to variant 1. The resulting isoform (LRTOMT1b) is a LRR-containing protein, but has a shorter and distinct C-terminus, compared to isoform LRTOMT1a. This protein is supported by Western blot as reported in PMID:18953341.
    Source sequence(s)
    BC012855, DA151871
    Consensus CDS
    CCDS44667.1
    UniProtKB/Swiss-Prot
    Q96E66
    Related
    ENSP00000438522.1, ENST00000541614.5
    Conserved Domains (2) summary
    sd00033
    Location:5280
    LRR_RI; leucine-rich repeat [structural motif]
    pfam14580
    Location:89146
    LRR_9; Leucine-rich repeat
  2. NM_001145308.4NP_001138780.1  transmembrane O-methyltransferase isoform LRTOMT2a

    See identical proteins and their annotated locations for NP_001138780.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) represents the long transcript form. It has multiple differences from variant 1. This variant lacks the upstream open reading frame as seen in the other variants of the long transcript form. The encoded isoform (LRTOMT2a) is a transmembrane catechol-O-methyltransferase. This protein is supported by Western blot as reported in PMID:18953341. Variants 4 and 5 encode the same isoform LRTOMT2a.
    Source sequence(s)
    AK302772, BX115135, DA151871, EU627069
    Consensus CDS
    CCDS44668.1
    UniProtKB/Swiss-Prot
    Q8WZ04
    Related
    ENSP00000305742.7, ENST00000307198.11
    Conserved Domains (1) summary
    cl17173
    Location:88249
    AdoMet_MTases; S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). ...
  3. NM_001145309.3NP_001138781.1  transmembrane O-methyltransferase isoform LRTOMT2a

    See identical proteins and their annotated locations for NP_001138781.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5, also known as D') represents the long transcript form. It lacks the 3' terminal exon and includes several alternate exons, compared to variant 1. This variant encodes isoform LRTOMT2a, which is a transmembrane catechol-O-methyltransferase and is supported by Western blot as reported in PMID: 18953341. Variants 4 and 5 encode the same isoform LRTOMT2a.
    Source sequence(s)
    BX115135, DA151871, EU627069
    UniProtKB/Swiss-Prot
    Q8WZ04
    Conserved Domains (1) summary
    cl17173
    Location:88249
    AdoMet_MTases; S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). ...
  4. NM_001145310.3NP_001138782.1  transmembrane O-methyltransferase isoform LRTOMT2b

    See identical proteins and their annotated locations for NP_001138782.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (6, also known as E') represents the long transcript form. It lacks the 3' terminal exon and includes several alternate exons, compared to variant 1. This variant encodes isoform LRTOMT2b, which lacks an internal segment including the transmembrane region, compared to isoform LRTOMT2a. Isoform LRTOMT2b is a catechol-O-methyltransferase, which is supported by Western blot as reported in PMID: 18953341.
    Source sequence(s)
    DA151871, EU627070
    UniProtKB/Swiss-Prot
    Q8WZ04
    Conserved Domains (1) summary
    cl17173
    Location:48209
    AdoMet_MTases; S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). ...
  5. NM_001205138.3NP_001192067.1  leucine-rich repeat-containing protein 51 isoform LRTOMT1c

    See identical proteins and their annotated locations for NP_001192067.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (7) represents the short transcript form. It lacks the exon containing the expected translation start codon, compared to variant 1. This difference results in an upstream translation start codon and the encoded isoform (LRTOMT1c) is a LRR-containing protein, but has a shorter and distinct N-terminus, compared to isoform LRTOMT1a.
    Source sequence(s)
    BC012855, DA151871
    Consensus CDS
    CCDS55778.1
    UniProtKB/Swiss-Prot
    Q96E66
    Related
    ENSP00000441249.1, ENST00000423494.6
    Conserved Domains (2) summary
    sd00033
    Location:3462
    LRR_RI; leucine-rich repeat [structural motif]
    pfam13855
    Location:62121
    LRR_8; Leucine rich repeat
  6. NM_001271471.2NP_001258400.1  leucine-rich repeat-containing protein 51 isoform LRTOMT1d

    See identical proteins and their annotated locations for NP_001258400.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (8, also known as C) represents the short transcript form. It lacks a splice junction in the 3' region, which results in a longer transcript and immediate translation termination, compared to variant 1. The encoded isoform (LRTOMT1d) is a LRR-containing protein, but is truncated at the C-terminus, compared to isoform LRTOMT1a. This protein is supported by Western blot as reported in PMID:18953341.
    Source sequence(s)
    AP000812, DA151871, EU627068
    Consensus CDS
    CCDS59227.1
    UniProtKB/Swiss-Prot
    Q96E66
    Related
    ENSP00000440693.1, ENST00000324866.11
    Conserved Domains (2) summary
    sd00033
    Location:5280
    LRR_RI; leucine-rich repeat [structural motif]
    pfam14580
    Location:89146
    LRR_9; Leucine-rich repeat
  7. NM_001318803.1NP_001305732.1  transmembrane O-methyltransferase isoform LRTOMT1a

    Status: REVIEWED

    Description
    Transcript Variant: This variant (9, also known as A) differs in the 5' UTR compared to variant 1. It encodes the longest isoform (LRTOMT1a) of the leucine-rich repeat (LRR)-containing protein. This protein is supported by Western blot as reported in PMID:18953341. Variants 1 and 9 both encode the same isoform (LRTOMT1a).
    Source sequence(s)
    BI461207, DA151871, EU627066
    Consensus CDS
    CCDS8208.1
    UniProtKB/Swiss-Prot
    Q96E66
    UniProtKB/TrEMBL
    A0A024R5L6
    Related
    ENSP00000444583.1, ENST00000538478.5
    Conserved Domains (2) summary
    sd00033
    Location:5280
    LRR_RI; leucine-rich repeat [structural motif]
    pfam14580
    Location:89173
    LRR_9; Leucine-rich repeat
  8. NM_145309.5NP_660352.1  leucine-rich repeat-containing protein 51 isoform LRTOMT1a

    See identical proteins and their annotated locations for NP_660352.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1, also known as A) represents the short transcript form. It encodes the longest isoform (LRTOMT1a) of the leucine-rich repeat (LRR)-containing protein. This protein is supported by Western blot as reported in PMID:18953341.
    Source sequence(s)
    BC012855, DA151871
    Consensus CDS
    CCDS8208.1
    UniProtKB/Swiss-Prot
    Q96E66
    UniProtKB/TrEMBL
    A0A024R5L6
    Related
    ENSP00000289488.2, ENST00000289488.7
    Conserved Domains (2) summary
    sd00033
    Location:5280
    LRR_RI; leucine-rich repeat [structural motif]
    pfam14580
    Location:89173
    LRR_9; Leucine-rich repeat

RNA

  1. NR_026886.3 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) represents the short transcript form. It includes an alternate exon in the central region, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AK311690, BC012855, DA151871
  2. NR_134858.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (10) lacks two alternate internal exons compared to variant 1. This variant is represented as non-coding because it lacks a large portion of the coding region, including the translational start codon, found in variant 1.
    Source sequence(s)
    DA004114, DA151871, EU627066
    Related
    ENST00000642510.1

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000011.10 Reference GRCh38.p12 Primary Assembly

    Range
    72080331..72110782
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006718474.4XP_006718537.1  leucine-rich repeat-containing protein 51 isoform X1

    See identical proteins and their annotated locations for XP_006718537.1

    UniProtKB/Swiss-Prot
    Q96E66
    UniProtKB/TrEMBL
    A0A024R5L6
    Related
    ENSP00000438762.2, ENST00000538413.6
    Conserved Domains (2) summary
    sd00033
    Location:5280
    LRR_RI; leucine-rich repeat [structural motif]
    pfam14580
    Location:89173
    LRR_9; Leucine-rich repeat
  2. XM_011544848.3XP_011543150.1  leucine-rich repeat-containing protein 51 isoform X1

    See identical proteins and their annotated locations for XP_011543150.1

    UniProtKB/Swiss-Prot
    Q96E66
    UniProtKB/TrEMBL
    A0A024R5L6
    Related
    ENSP00000494072.1, ENST00000647530.1
    Conserved Domains (2) summary
    sd00033
    Location:5280
    LRR_RI; leucine-rich repeat [structural motif]
    pfam14580
    Location:89173
    LRR_9; Leucine-rich repeat
  3. XM_006718473.4XP_006718536.1  leucine-rich repeat-containing protein 51 isoform X1

    See identical proteins and their annotated locations for XP_006718536.1

    UniProtKB/Swiss-Prot
    Q96E66
    UniProtKB/TrEMBL
    A0A024R5L6
    Related
    ENSP00000494362.1, ENST00000642648.1
    Conserved Domains (2) summary
    sd00033
    Location:5280
    LRR_RI; leucine-rich repeat [structural motif]
    pfam14580
    Location:89173
    LRR_9; Leucine-rich repeat
  4. XM_011544847.3XP_011543149.1  leucine-rich repeat-containing protein 51 isoform X1

    See identical proteins and their annotated locations for XP_011543149.1

    UniProtKB/Swiss-Prot
    Q96E66
    UniProtKB/TrEMBL
    A0A024R5L6
    Conserved Domains (2) summary
    sd00033
    Location:5280
    LRR_RI; leucine-rich repeat [structural motif]
    pfam14580
    Location:89173
    LRR_9; Leucine-rich repeat
  5. XM_024448401.1XP_024304169.1  transmembrane O-methyltransferase isoform X2

    Conserved Domains (1) summary
    COG4122
    Location:190326
    YrrM; Predicted O-methyltransferase YrrM [General function prediction only]

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NR_073187.2: Suppressed sequence

    Description
    NR_073187.2: This RefSeq was permanently suppressed because this transcript has been represented by NM_001145309.3.
  2. NR_073188.2: Suppressed sequence

    Description
    NR_073188.2: This RefSeq was permanently suppressed because this transcript has been represented by NM_001145310.3.
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