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LRTM1 Gene

protein-coding   GIFtS: 46
GCID: GC03M054928

Leucine-Rich Repeats And Transmembrane Domains 1

  See related diseases
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
Leucine-Rich Repeats And Transmembrane Domains 11 2
Leucine-Rich Repeat And Transmembrane Domain-Containing Protein 12

External Ids:    HGNC: 250231   Entrez Gene: 574082   Ensembl: ENSG000001447717   UniProtKB: Q9HBL63   

Export aliases for LRTM1 gene to outside databases


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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GeneCards Summary for LRTM1 Gene:
LRTM1 (leucine-rich repeats and transmembrane domains 1) is a protein-coding gene. Diseases associated with LRTM1 include congenital diaphragmatic hernia, and hypertrichosis. An important paralog of this gene is SLITRK5.


(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence:
NC_000003.12  NT_022517.19  NC_018914.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the LRTM1 gene promoter:
         USF1   NF-YA   MyoD   NF-YB   CBF-A   CBF-B   USF-1   CP1A   NF-Y   CBF(2)   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidLRTM1 promoter sequence
   Search Chromatin IP Primers for LRTM1

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat LRTM1


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 3p14.3   Ensembl cytogenetic band:  3p14.3   HGNC cytogenetic band: 3p14.3

LRTM1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
LRTM1 gene location

GeneLoc information about chromosome 3         GeneLoc Exon Structure

GeneLoc location for GC03M054928:  view genomic region     (about GC identifiers)

Start:
54,952,264 bp from pter      End:
55,001,115 bp from pter
Size:
48,852 bases      Orientation:
minus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
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UniProtKB/Swiss-Prot: LRTM1_HUMAN, Q9HBL6 (See protein sequence)
Recommended Name: Leucine-rich repeat and transmembrane domain-containing protein 1 precursor  
Size: 345 amino acids; 38171 Da
Secondary accessions: Q8IUU2
Alternative splicing: 2 isoforms:  Q9HBL6-1   Q9HBL6-2   

Explore the universe of human proteins at neXtProt for LRTM1: NX_Q9HBL6

Explore proteomics data for LRTM1 at MOPED

Post-translational modifications: 

  • Glycosylation2 at Asn104, Asn147

  • See LRTM1 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_065729.1  
    ENSEMBL proteins: 
     ENSP00000273286   ENSP00000419772  

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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    4 InterPro protein domains:
     IPR000483 Cys-rich_flank_reg_C
     IPR001611 Leu-rich_rpt
     IPR003591 Leu-rich_rpt_typical-subtyp
     IPR000372 LRR-contain_N

    Graphical View of Domain Structure for InterPro Entry Q9HBL6

    ProtoNet protein and cluster: Q9HBL6

    2 Blocks protein domains:
    IPB000483 Cysteine-rich flanking region
    IPB001611 Leucine-rich repeat signature


    UniProtKB/Swiss-Prot: LRTM1_HUMAN, Q9HBL6
    Similarity: Contains 5 LRR (leucine-rich) repeats
    Similarity: Contains 1 LRRCT domain
    Similarity: Contains 1 LRRNT domain


    LRTM1 for domains           About GeneDecksing


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
    transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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         Gene Ontology (GO): 1 molecular function term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005515protein binding ----
         
    LRTM1 for ontologies           About GeneDecksing


    Animal Models:
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    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Subcellular locations from UniProtKB/Swiss-Prot
    LRTM1_HUMAN, Q9HBL6: Membrane; Single-pass type I membrane protein (Potential)
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    plasma membrane3
    extracellular2
    cytosol1
    nucleus1

    Gene Ontology (GO): 1 cellular component term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0016021integral component of membrane IEA--

    LRTM1 for ontologies           About GeneDecksing


    (SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for LRTM1
    Interactions:

        Search GeneGlobe Interaction Network for LRTM1

    STRING Interaction Network Preview (showing 2 interactants - click image to see more details)

    2 Interacting proteins for LRTM1 (ENSP000002732864) via UniProtKB, MINT, STRING, and/or I2D
    InteractantInteraction Details
    GeneCardExternal ID(s)
    CAB39ENSP000002584184STRING: ENSP00000258418
    CAB39LENSP000002616694STRING: ENSP00000261669
    About this table

    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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    Browse Small Molecules at EMD Millipore
       Browse drugs & compounds from Enzo Life Sciences
      Browse compounds at ApexBio 

    Browse Tocris compounds for LRTM1



    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    Conferences by KenesGroup, exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, and/or QIAGEN )
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    REFSEQ mRNAs for LRTM1 gene: 
    NM_020678.2  

    Unigene Cluster for LRTM1:

    Leucine-rich repeats and transmembrane domains 1
    Hs.591668  [show with all ESTs]
    Unigene Representative Sequence: BC040732
    2 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000273286(uc003dhl.3) ENST00000493075
    miRNA
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      QuantiTect SYBR Green Assays in human, mouse, rat LRTM1
      QuantiFast Probe-based Assays in human, mouse, rat LRTM1

    Additional mRNA sequence: 

    AF225421.1 BC040732.1 BC074741.2 

    4 DOTS entries:

    DT.100748493  DT.116604  DT.100748494  DT.95366896 

    Selected AceView cDNA sequences (see all 78):

    AW959797 AA298309 AA298389 AA298298 AA716035 AA702392 BC074741 AA298327 
    AA298378 AA298332 AA298395 BM703580 AI761918 AI193267 AA298331 AA758427 
    AI802922 AA298392 BM706979 BX119799 BC040732 AA298357 BU736480 H53445 

    GeneLoc Exon Structure


    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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    LRTM1 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: GGGGACCCTT
    LRTM1 Expression
    About this image


    LRTM1 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 2) fully expand
     
     Eye (Sensory Organs)    fully expand to see all 2 entries
             Mature Rod Bipolar Cells Inner Nuclear Layer
     
     Neurons
             Mature Rod Bipolar Cells Inner Nuclear Layer
    LRTM1 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    LRTM1 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.591668
        Custom PCR Arrays for LRTM1
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for LRTM1

    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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    This gene was present in the common ancestor of animals.

    Orthologs for LRTM1 gene from Selected species (see all 12)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Lrtm11 , 5 leucine-rich repeats and transmembrane domains 11, 5 72.48(n)1
    66.86(a)1
      14 (16.80 cM)5
    3194761  NM_176920.41  NP_795894.11 
     290182085 
    chicken
    (Gallus gallus)
    Aves LRTM16
    leucine-rich repeats and transmembrane domains 1
    51(a)
    1 ↔ 1
    12(7650016-7653854)
    lizard
    (Anolis carolinensis)
    Reptilia LRTM16
    leucine-rich repeats and transmembrane domains 1
    42(a)
    1 ↔ 1
    2(161385257-161398024)
    zebrafish
    (Danio rerio)
    Actinopterygii LOC1018834391 leucine-rich repeat and transmembrane domain-containing more 54.09(n)
    46.11(a)
      101883439  XM_005172504.1  XP_005172561.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta kek26
    kek16
    (see all 6)
    kekkon-1
    (see all 6)
    9(a)
    8(a)
    (see all 6)
    many ↔ many
    many ↔ many
    (see all 6)
    2L(11606514-11626124)
    2L(12817000-12822787)


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

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for LRTM1 gene
    SLITRK52  ISLR2  SLIT12  SLIT32  SLITRK62  LRRC382  SLIT22  LRRC262  
    SLITRK12  SLITRK42  LRRC522  LRRC172  SLITRK22  LRTM22  SLITRK32  LRRC552  
    ISLR22  LRRC242  
    1 SIMAP similar gene for LRTM1 using alignment to 1 protein entry:     LRTM1_HUMAN:
    LRTM2

    LRTM1 for paralogs           About GeneDecksing



    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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    8 SNPs for LRTM1    About this table    
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 3 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs355404701,2,4
    ----see VAR_0511452 mis40--------
    rs38066331,2,4
    ----see VAR_0511442 mis40--------
    rs3692759111,2
    ----54960990(+) TTTTT-/TGAGAC 1 -- int10--------
    rs719991481,2
    ----54960566(+) ACACA-/CACA  
            
    CACAC
    1 -- int10--------
    rs588492871,2
    ----54960575(+) CACAC-/ACACAC
            
    TCTGT
    1 -- int10--------
    rs576845601,2
    ----54960571(+) CACAC-/ACAC  
      ACACAC
    TCTGT
    1 -- int10--------
    rs720714931,2
    ----54960542(+) ACACA-/CACACA
            
    CACAC
    1 -- int10--------
    rs3679395611,2
    ----54963855(+) ACATA-/CATA  
            
    ACCAT
    1 -- us2k10--------

    HapMap Linkage Disequilibrium report for LRTM1 (54952264 - 55001115 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 2 variations for LRTM1:    About this table    
    Variant IDTypeSubtypePubMed ID
    nsv517851CNV Gain19592680
    nsv876812CNV Gain21882294

    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing LRTM1
    DNA2.0 Custom Variant and Variant Library Synthesis for LRTM1

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    2 diseases for LRTM1:    
    About MalaCards
    congenital diaphragmatic hernia    hypertrichosis

    2 diseases from the University of Copenhagen DISEASES database for LRTM1:
    Hypertrichosis     Congenital diaphragmatic hernia

    LRTM1 for disorders           About GeneDecksing

    Genetic Association Database (GAD): LRTM1

    Export disorders for LRTM1 gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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    PubMed articles for LRTM1 gene integrated from 10 sources:
    (articles sorted by number of sources associating them with LRTM1)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S.... Malek J. (Genome Res. 2004)
    2. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1, 3 Strausberg R.L....Marra M.A. (Proc. Natl. Acad. Sci. U.S.A. 2002)
    3. Gene expression profiling in the human hypothalamus-pituitary-adrenal axis and full-length cDNA cloning. (PubMed id 10931946)1, 2 Hu R.-M.... Chen J.-L. (Proc. Natl. Acad. Sci. U.S.A. 2000)
    4. Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls. (PubMed id 17554300)4 (Nature 2007)
    5. Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. (PubMed id 17081983)1 Olsen J.V....Mann M. (Cell 2006)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     ANDOR
    Aliases
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 57408 HGNC: 25023 AceView: HT017 Ensembl:ENSG00000144771 euGenes: HUgn57408
    ECgene: LRTM1 H-InvDB: LRTM1

    (According to HUGE)
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      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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    NameDescription
    PharmGKB entry for LRTM1 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for LRTM1 gene:
    Search GeneIP for patents involving LRTM1

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



    (Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Cell lines from GenScript, and ESI BIO, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
    Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
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