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

    Gene ID: 57408, updated on 2-Nov-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 located in membrane. [provided by Alliance of Genome Resources, Nov 2024]
    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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    See LRTM1 in Genome Data Viewer
    Location:
    3p14.3
    Exon count:
    4
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (54918231..54967102, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (54952027..55000901, complement)
    RS_2024_09 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 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
    		  
    Component Evidence Code Pubs
    located_in membrane IEA
    Inferred from Electronic Annotation
    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_2024_08

    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

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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