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LRTM1 leucine rich repeats and transmembrane domains 1 [ Homo sapiens (human) ]

Gene ID: 57408, updated on 11-Apr-2024

Summary

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Official Symbol
LRTM1provided by HGNC
Official Full Name
leucine rich repeats and transmembrane domains 1provided by HGNC
Primary source
HGNC:HGNC:25023
See related
Ensembl:ENSG00000144771 AllianceGenome:HGNC:25023
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
HT017
Summary
Predicted to enable Roundabout binding activity and heparin binding activity. Predicted to be involved in axon guidance and negative chemotaxis. Predicted to act upstream of or within positive regulation of synapse assembly. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Biased expression in spleen (RPKM 2.9), esophagus (RPKM 1.8) and 1 other tissue See more
Orthologs
mouse all
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Genomic context

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Location:
3p14.3
Exon count:
4
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (54918231..54967102, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (54952027..55000901, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (54952258..55001129, complement)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene calcium voltage-gated channel auxiliary subunit alpha2delta 3 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr3:54668358-54668860 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr3:54668861-54669361 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:54673489-54674415 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr3:54743647-54744366 Neighboring gene embryonic stem cell related Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr3:54855004-54855707 Neighboring gene NANOG hESC enhancer GRCh37_chr3:54877384-54877885 Neighboring gene CACNA2D3 antisense RNA 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:54973116-54973616 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:54986884-54987876 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:54987877-54988869 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:54989863-54990854 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:54992683-54993184 Neighboring gene VISTA enhancer hs1436 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr3:55096424-55097039 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:55113410-55113654 Neighboring gene uncharacterized LOC124906243 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:55183044-55183208 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr3:55194201-55195400 Neighboring gene long intergenic non-protein coding RNA 2017 Neighboring gene long intergenic non-protein coding RNA 2030

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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

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Related articles in PubMed

  1. Purification of functional human ES and iPSC-derived midbrain dopaminergic progenitors using LRTM1. Samata B, et al. Nat Commun, 2016 Oct 14. PMID 27739432, Free PMC Article
  2. Fraction of exhaled nitric oxide values in childhood are associated with 17q11.2-q12 and 17q12-q21 variants. van der Valk RJ, et al. J Allergy Clin Immunol, 2014 Jul. PMID 24315451, Free PMC Article
  3. Gene expression profiling in the human hypothalamus-pituitary-adrenal axis and full-length cDNA cloning. Hu RM, et al. Proc Natl Acad Sci U S A, 2000 Aug 15. PMID 10931946, Free PMC Article
  4. Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. Olsen JV, et al. Cell, 2006 Nov 3. PMID 17081983
  5. The BioPlex Network: A Systematic Exploration of the Human Interactome. Huttlin EL, et al. Cell, 2015 Jul 16. PMID 26186194, Free PMC Article

See all (11) citations in PubMed

GeneRIFs: Gene References Into Functions

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
Fraction of exhaled nitric oxide values in childhood are associated with 17q11.2-q12 and 17q12-q21 variants.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables Roundabout binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables heparin binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in axon guidance IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in negative chemotaxis IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
leucine-rich repeat and transmembrane domain-containing protein 1

NCBI Reference Sequences (RefSeq)

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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_001304389.2 → NP_001291318.1  leucine-rich repeat and transmembrane domain-containing protein 1 isoform 2

    See identical proteins and their annotated locations for NP_001291318.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) uses an alternate 5' terminal exon, lacks a portion of the 5' coding region, and initiates translation at a downstream start codon, compared to variant 1. The encoded isoform (2) has a shorter N-terminus, compared to isoform 1.
    Source sequence(s)
    AC092797, AC109584, BC040732
    Consensus CDS
    CCDS77753.1
    UniProtKB/Swiss-Prot
    Q9HBL6
    Related
    ENSP00000419772.1, ENST00000493075.1
    Conserved Domains (2) summary
    sd00031
    Location:24 → 47
    LRR_1; leucine-rich repeat [structural motif]
    pfam13855
    Location:15 → 58
    LRR_8; Leucine rich repeat

  2. NM_020678.4 → NP_065729.1  leucine-rich repeat and transmembrane domain-containing protein 1 isoform 1 precursor

    See identical proteins and their annotated locations for NP_065729.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
    Source sequence(s)
    AC092797, AC109584, AF225421, BM716618
    Consensus CDS
    CCDS2876.1
    UniProtKB/Swiss-Prot
    Q8IUU2, Q9HBL6
    Related
    ENSP00000273286.5, ENST00000273286.6
    Conserved Domains (3) summary
    sd00033
    Location:34 → 51
    LRR_RI; leucine-rich repeat [structural motif]
    pfam12799
    Location:98 → 139
    LRR_4; Leucine Rich repeats (2 copies)
    pfam13855
    Location:50 → 134
    LRR_8; Leucine rich repeat

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_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    54918231..54967102 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    54952027..55000901 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9HBL6.1 GenPept UniProtKB/Swiss-Prot:Q9HBL6

Gene LinkOut

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