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Aliases for LRTM1 Gene

Aliases for LRTM1 Gene

  • Leucine Rich Repeats And Transmembrane Domains 1 2 3 5
  • Leucine-Rich Repeat And Transmembrane Domain-Containing Protein 1 3
  • HT017 3

External Ids for LRTM1 Gene

Summaries for LRTM1 Gene

GeneCards Summary for LRTM1 Gene

LRTM1 (Leucine Rich Repeats And Transmembrane Domains 1) is a Protein Coding gene. Diseases associated with LRTM1 include Diaphragmatic Hernia, Congenital. An important paralog of this gene is LRTM2.

Additional gene information for LRTM1 Gene

No data available for Entrez Gene Summary , CIViC summary , UniProtKB/Swiss-Prot , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for LRTM1 Gene

Genomics for LRTM1 Gene

GeneHancer (GH) Regulatory Elements for LRTM1 Gene

Promoters and enhancers for LRTM1 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH03I054964 Promoter/Enhancer 1.5 EPDnew Ensembl ENCODE dbSUPER 550.8 0.0 -49 5.8 FOXA2 EBF1 ZIC2 ZNF7 PRDM6 JUND POLR2A FOS EZH2 LRTM1 ENSG00000239991 CACNA2D3
GH03I054928 Promoter 0.5 EPDnew 550.3 +39.0 39009 0.1 LRTM1 CACNA2D3-AS1 CACNA2D3
GH03I054888 Enhancer 1.3 Ensembl ENCODE dbSUPER 9.9 +75.5 75538 6.4 NFIB KLF17 SIN3A BATF RAD21 ZBTB40 GLIS2 SMARCC2 FOS DEK LRTM1 GC03M054892 CACNA2D3-AS1 GC03M054844 CACNA2D3
GH03I055167 Enhancer 1.1 FANTOM5 ENCODE dbSUPER 10.2 -202.2 -202174 4.5 MXI1 JUN MAX BRCA1 RFX5 POLR2A NFYB FOS NFE2L2 CHD2 LRTM1 WNT5A WNT5A-AS1 ENSG00000239991
GH03I054881 Enhancer 0.9 Ensembl ENCODE dbSUPER 10.4 +84.7 84653 1.6 SP1 JUND GLIS1 FOSL2 FOS LRTM1 GC03M054892 CACNA2D3-AS1 GC03M054844 CACNA2D3
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around LRTM1 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the LRTM1 gene promoter:

Genomic Locations for LRTM1 Gene

Genomic Locations for LRTM1 Gene
chr3:54,918,237-54,967,088
(GRCh38/hg38)
Size:
48,852 bases
Orientation:
Minus strand
chr3:54,952,264-55,001,115
(GRCh37/hg19)

Genomic View for LRTM1 Gene

Genes around LRTM1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
LRTM1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for LRTM1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for LRTM1 Gene

Proteins for LRTM1 Gene

  • Protein details for LRTM1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9HBL6-LRTM1_HUMAN
    Recommended name:
    Leucine-rich repeat and transmembrane domain-containing protein 1
    Protein Accession:
    Q9HBL6
    Secondary Accessions:
    • Q8IUU2

    Protein attributes for LRTM1 Gene

    Size:
    345 amino acids
    Molecular mass:
    38171 Da
    Quaternary structure:
    No Data Available

    Alternative splice isoforms for LRTM1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for LRTM1 Gene

Post-translational modifications for LRTM1 Gene

  • Glycosylation at isoforms=2104 and posLast=147147

Other Protein References for LRTM1 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for LRTM1 Gene

Domains & Families for LRTM1 Gene

Gene Families for LRTM1 Gene

Human Protein Atlas (HPA):
  • Predicted membrane proteins

Suggested Antigen Peptide Sequences for LRTM1 Gene

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with LRTM1: view

No data available for UniProtKB/Swiss-Prot for LRTM1 Gene

Function for LRTM1 Gene

Phenotypes From GWAS Catalog for LRTM1 Gene

Gene Ontology (GO) - Molecular Function for LRTM1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004860 protein kinase inhibitor activity IBA --
genes like me logo Genes that share ontologies with LRTM1: view
genes like me logo Genes that share phenotypes with LRTM1: view

Clone Products

No data available for Molecular function , Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for LRTM1 Gene

Localization for LRTM1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for LRTM1 Gene

Membrane; Single-pass type I membrane protein.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for LRTM1 gene
Compartment Confidence
plasma membrane 3
extracellular 2

Gene Ontology (GO) - Cellular Components for LRTM1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IBA --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with LRTM1: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for LRTM1 Gene

Pathways & Interactions for LRTM1 Gene

SuperPathways for LRTM1 Gene

No Data Available

Gene Ontology (GO) - Biological Process for LRTM1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006469 negative regulation of protein kinase activity IBA --
GO:0019221 cytokine-mediated signaling pathway IBA --
GO:0046426 negative regulation of JAK-STAT cascade IBA --
GO:0051965 positive regulation of synapse assembly IEA --
genes like me logo Genes that share ontologies with LRTM1: view

No data available for Pathways by source and SIGNOR curated interactions for LRTM1 Gene

Drugs & Compounds for LRTM1 Gene

No Compound Related Data Available

Transcripts for LRTM1 Gene

mRNA/cDNA for LRTM1 Gene

Unigene Clusters for LRTM1 Gene

Leucine-rich repeats and transmembrane domains 1:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for LRTM1 Gene

No ASD Table

Relevant External Links for LRTM1 Gene

GeneLoc Exon Structure for
LRTM1
ECgene alternative splicing isoforms for
LRTM1

Expression for LRTM1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for LRTM1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for LRTM1 Gene

This gene is overexpressed in Spleen (x40.1).

Protein differential expression in normal tissues from HIPED for LRTM1 Gene

This gene is overexpressed in Plasma (55.9) and Heart (13.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for LRTM1 Gene



Protein tissue co-expression partners for LRTM1 Gene

NURSA nuclear receptor signaling pathways regulating expression of LRTM1 Gene:

LRTM1

SOURCE GeneReport for Unigene cluster for LRTM1 Gene:

Hs.591668

Evidence on tissue expression from TISSUES for LRTM1 Gene

  • Nervous system(4.5)
  • Pancreas(4.1)
genes like me logo Genes that share expression patterns with LRTM1: view

No data available for mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for LRTM1 Gene

Orthologs for LRTM1 Gene

This gene was present in the common ancestor of animals.

Orthologs for LRTM1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia LRTM1 33 34
  • 96.81 (n)
cow
(Bos Taurus)
Mammalia LRTM1 33 34
  • 82.56 (n)
dog
(Canis familiaris)
Mammalia LRTM1 34
  • 80 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia LOC102547963 33
  • 73.55 (n)
mouse
(Mus musculus)
Mammalia Lrtm1 33 16 34
  • 72.48 (n)
oppossum
(Monodelphis domestica)
Mammalia LRTM1 34
  • 62 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia LRTM1 34
  • 57 (a)
OneToOne
chicken
(Gallus gallus)
Aves LRTM1 34
  • 51 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia LRTM1 34
  • 42 (a)
OneToOne
zebrafish
(Danio rerio)
Actinopterygii LOC101883439 33
  • 54.09 (n)
LRTM1 34
  • 42 (a)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta kek4 34
  • 11 (a)
ManyToMany
kek2 34
  • 9 (a)
ManyToMany
kek1 34
  • 8 (a)
ManyToMany
kek3 34
  • 8 (a)
ManyToMany
kek5 34
  • 8 (a)
ManyToMany
kek6 34
  • 8 (a)
ManyToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 22 (a)
ManyToMany
CSA.1672 34
  • 19 (a)
ManyToMany
-- 34
  • 13 (a)
ManyToMany
Species where no ortholog for LRTM1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for LRTM1 Gene

ENSEMBL:
Gene Tree for LRTM1 (if available)
TreeFam:
Gene Tree for LRTM1 (if available)

Paralogs for LRTM1 Gene

Paralogs for LRTM1 Gene

(1) SIMAP similar genes for LRTM1 Gene using alignment to 1 proteins:

genes like me logo Genes that share paralogs with LRTM1: view

Variants for LRTM1 Gene

Sequence variations from dbSNP and Humsavar for LRTM1 Gene

SNP ID Clin Chr 03 pos Variation AA Info Type
rs1000028458 -- 54,932,504(-) A/T genic_upstream_transcript_variant, intron_variant
rs1000066392 -- 54,965,680(-) G/A genic_upstream_transcript_variant, intron_variant
rs1000080299 -- 54,932,659(-) T/G genic_upstream_transcript_variant, intron_variant
rs1000183555 -- 54,964,551(-) C/T genic_upstream_transcript_variant, intron_variant
rs1000187815 -- 54,936,929(-) G/A/C/T genic_upstream_transcript_variant, intron_variant

Structural Variations from Database of Genomic Variants (DGV) for LRTM1 Gene

Variant ID Type Subtype PubMed ID
nsv517851 CNV gain 19592680
esv3561910 CNV deletion 23714750

Variation tolerance for LRTM1 Gene

Residual Variation Intolerance Score: 72.3% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.08; 50.76% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for LRTM1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
LRTM1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for LRTM1 Gene

Disorders for LRTM1 Gene

MalaCards: The human disease database

(1) MalaCards diseases for LRTM1 Gene - From: DISEASES

Disorder Aliases PubMed IDs
diaphragmatic hernia, congenital
  • dih
- elite association - COSMIC cancer census association via MalaCards
Search LRTM1 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for LRTM1

genes like me logo Genes that share disorders with LRTM1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for LRTM1 Gene

Publications for LRTM1 Gene

  1. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 58
  2. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PMID: 12477932) Strausberg RL … Mammalian Gene Collection Program Team (Proceedings of the National Academy of Sciences of the United States of America 2002) 2 3 58
  3. Gene expression profiling in the human hypothalamus-pituitary-adrenal axis and full-length cDNA cloning. (PMID: 10931946) Hu RM … Chen JL (Proceedings of the National Academy of Sciences of the United States of America 2000) 3 4 58
  4. The BioPlex Network: A Systematic Exploration of the Human Interactome. (PMID: 26186194) Huttlin EL … Gygi SP (Cell 2015) 3 58
  5. Fraction of exhaled nitric oxide values in childhood are associated with 17q11.2-q12 and 17q12-q21 variants. (PMID: 24315451) van der Valk RJ … EArly Genetics & Lifecourse Epidemiology (EAGLE) Consortium (The Journal of allergy and clinical immunology 2014) 3 58

Products for LRTM1 Gene

Sources for LRTM1 Gene

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