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FLRT1 Gene

protein-coding   GIFtS: 52
GCID: GC11P063871

Fibronectin Leucine Rich Transmembrane Protein 1

  See FLRT1-related disease
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
Fibronectin Leucine Rich Transmembrane Protein 11 2
Fibronectin-Like Domain-Containing Leucine-Rich Transmembrane Protein 12 3
SPG682
Leucine-Rich Repeat Transmembrane Protein FLRT12

External Ids:    HGNC: 37601   Entrez Gene: 237692   Ensembl: ENSG000001265007   OMIM: 6048065   UniProtKB: Q9NZU13   

Export aliases for FLRT1 gene to outside databases

Previous GC identifers: GC11M066466 GC11M065550 GC11P064122 GC11P063646 GC11P063627 GC11P060200


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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Entrez Gene summary for FLRT1 Gene:
This gene encodes a member of the fibronectin leucine rich transmembrane protein (FLRT) family. The family members
may function in cell adhesion and/or receptor signalling. Their protein structures resemble small leucine-rich
proteoglycans found in the extracellular matrix. The encoded protein shares sequence similarity with two other
family members, FLRT2 and FLRT3. This gene is expressed in kidney and brain. (provided by RefSeq, Jul 2008)

GeneCards Summary for FLRT1 Gene:
FLRT1 (fibronectin leucine rich transmembrane protein 1) is a protein-coding gene. Diseases associated with FLRT1 include autosomal recessive spastic paraplegia type 68. GO annotations related to this gene include receptor signaling protein activity and protein binding, bridging. An important paralog of this gene is PODN.

UniProtKB/Swiss-Prot: FLRT1_HUMAN, Q9NZU1
Function: May have a function in cell adhesion and/or receptor signaling




(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 at NCBI GenBank:
NC_000011.9  NT_167190.2  NC_018922.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the FLRT1 gene promoter:
         COUP-TF1   Bach1   Egr-1   COUP   HNF-4alpha2   HNF-4alpha1   FOXL1   S8   COUP-TF   FOXO4   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidFLRT1 promoter sequence
   Search Chromatin IP Primers for FLRT1

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat FLRT1


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

Entrez Gene cytogenetic band: 11q13.1   Ensembl cytogenetic band:  11q13.1   HGNC cytogenetic band: 11q13.1

FLRT1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
FLRT1 gene location

GeneLoc information about chromosome 11         GeneLoc Exon Structure

GeneLoc location for GC11P063871:  view genomic region     (about GC identifiers)

Start:
63,870,660 bp from pter      End:
63,886,645 bp from pter
Size:
15,986 bases      Orientation:
plus 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, Cloud-Clone Corp., eBioscience, and/or antibodies-online,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., eBioscience, and/or antibodies-online, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, Cloud-Clone Corp, antibodies-online, and/or others.)
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UniProtKB/Swiss-Prot: FLRT1_HUMAN, Q9NZU1 (See protein sequence)
Recommended Name: Leucine-rich repeat transmembrane protein FLRT1 precursor  
Size: 646 amino acids; 71358 Da
Sequence caution: Sequence=AAF28459.1; Type=Erroneous initiation; Sequence=AAH18370.1; Type=Erroneous initiation;
Sequence=AAQ88675.1; Type=Erroneous initiation; Sequence=BAF82620.1; Type=Erroneous initiation;
Sequence=EAW74194.1; Type=Erroneous initiation;
Secondary accessions: Q8WVA2

Explore the universe of human proteins at neXtProt for FLRT1: NX_Q9NZU1

Explore proteomics data for FLRT1 at MOPED

Post-translational modifications: 

  • N-glycosylated1
  • Glycosylation2 at Asn221, Asn277
  • Modification sites at PhosphoSitePlus

  • See FLRT1 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_037412.2  
    ENSEMBL proteins: 
     ENSP00000246841  

    FLRT1 Human Recombinant Protein Products:

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    Cloud-Clone Corp. Proteins for FLRT1

     
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    antibodies-online proteins for FLRT1 (7 products) 

     
    Search antibodies-online for peptides for FLRT1

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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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    HGNC Gene Families:
    FN3: Fibronectin type III domain containing

    Selected InterPro protein domains (see all 6):
     IPR000483 Cys-rich_flank_reg_C
     IPR001611 Leu-rich_rpt
     IPR003961 Fibronectin_type3
     IPR013783 Ig-like_fold
     IPR003591 Leu-rich_rpt_typical-subtyp

    Graphical View of Domain Structure for InterPro Entry Q9NZU1

    ProtoNet protein and cluster: Q9NZU1

    2 Blocks protein domains:
    IPB000372 Cysteine-rich flanking region
    IPB000483 Cysteine-rich flanking region


    UniProtKB/Swiss-Prot: FLRT1_HUMAN, Q9NZU1
    Similarity: Contains 1 fibronectin type-III domain
    Similarity: Contains 10 LRR (leucine-rich) repeats
    Similarity: Contains 1 LRRCT domain
    Similarity: Contains 1 LRRNT domain


    Find genes that share domains with FLRT1           About GenesLikeMe


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, 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, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: FLRT1_HUMAN, Q9NZU1
    Function: May have a function in cell adhesion and/or receptor signaling

         Genatlas biochemistry entry for FLRT1:
    fibronectin,leucine rich transmembrane protein1,extracellular matrix protein,expressed in kidney and brain

         Gene Ontology (GO): 3 molecular function terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005057receptor signaling protein activity NAS10644439
    GO:0005515protein binding ----
    GO:0030674protein binding, bridging NAS10644439
         
    Find genes that share ontologies with FLRT1           About GenesLikeMe


    Phenotypes:
         1 MGI mutant phenotype (inferred from 1 allele(MGI details for Flrt1):
     no phenotypic analysis 

    Find genes that share phenotypes with FLRT1           About GenesLikeMe

    Animal Models:
         MGI mouse knock-out Flrt1tm1.1Kln for FLRT1

       genOway: Develop your customized and physiologically relevant rodent model for FLRT1

    miRNA
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    hsa-miR-502-5p hsa-miR-196a hsa-miR-544 hsa-miR-196b hsa-miR-654-3p hsa-miR-145 hsa-miR-205* hsa-miR-552
    SwitchGear 3'UTR luciferase reporter plasmidFLRT1 3' UTR sequence
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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
    FLRT1_HUMAN, Q9NZU1: Membrane; Single-pass type I membrane protein (Probable)
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    extracellular5
    plasma membrane5
    peroxisome2
    cytosol1
    lysosome1
    mitochondrion1

    Gene Ontology (GO): 2 cellular component terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005578proteinaceous extracellular matrix NAS10644439
    GO:0005887integral component of plasma membrane NAS10644439

    Find genes that share ontologies with FLRT1           About GenesLikeMe


    (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 FLRT1
    Interactions:

        Search GeneGlobe Interaction Network for FLRT1

    STRING Interaction Network Preview (showing 5 interactants - click image to see 6)

    Selected Interacting proteins for FLRT1 (Q9NZU12, 3 ENSP000002468414) via UniProtKB, MINT, STRING, and/or I2D (see all 7)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    FLRT2O431552, 3, ENSP000003328794MINT-1778563 I2D: score=1 STRING: ENSP00000332879
    UNC5BENSP000003343294STRING: ENSP00000334329
    UNC5CENSP000004060224STRING: ENSP00000406022
    CAB39ENSP000002584184STRING: ENSP00000258418
    CAB39LENSP000002616694STRING: ENSP00000261669
    About this table

    Gene Ontology (GO): 3 biological process terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0007155cell adhesion IEA--
    GO:0008150biological_process ND--
    GO:0035556intracellular signal transduction NAS10644439

    Find genes that share ontologies with FLRT1           About GenesLikeMe



    (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 FLRT1



    (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,
    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, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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    REFSEQ mRNAs for FLRT1 gene: 
    NM_013280.4  

    Unigene Cluster for FLRT1:

    Fibronectin leucine rich transmembrane protein 1
    Hs.584876  [show with all ESTs]
    Unigene Representative Sequence: AY358308
    1 Ensembl transcript including schematic representation, and UCSC links where relevant:
    ENST00000246841(uc001nyi.1)
    miRNA
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    8 qRT-PCR Assays for microRNAs that regulate FLRT1:
    hsa-miR-502-5p hsa-miR-196a hsa-miR-544 hsa-miR-196b hsa-miR-654-3p hsa-miR-145 hsa-miR-205* hsa-miR-552
    SwitchGear 3'UTR luciferase reporter plasmidFLRT1 3' UTR sequence
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    Primer
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    OriGene qPCR primer pairs and template standards for FLRT1
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      QuantiTect SYBR Green Assays in human, mouse, rat FLRT1
      QuantiFast Probe-based Assays in human, mouse, rat FLRT1

    Additional mRNA sequence: 

    AF007139.1 AF169675.1 AK289931.1 AY358308.1 BC018370.1 

    3 DOTS entries:

    DT.97770464  DT.210792  DT.120741897 

    Selected AceView cDNA sequences (see all 37):

    BM710660 BX951900 AI494233 F04546 Z40799 BM674096 BF530310 BF437742 
    BM667377 BM728867 AY358308 CD624700 BU742770 BX090702 AI362924 F08324 
    AF169675 NM_013280 BM715659 Z45074 BC018370 AF007139 CD624699 BG913718 

    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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    FLRT1 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: TAGTCGATTA
    FLRT1 Expression
    About this image


    FLRT1 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     
     Brain (Nervous System)    fully expand to see all 18 entries
             Thalamus
             Septum   
    FLRT1 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    FLRT1 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.584876

    UniProtKB/Swiss-Prot: FLRT1_HUMAN, Q9NZU1
    Tissue specificity: Expressed in kidney and brain

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    (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 chordates.

    Orthologs for FLRT1 gene from Selected species (see all 12)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Flrt11 , 5 fibronectin leucine rich transmembrane protein 11, 5 89.27(n)1
    96.14(a)1
      19 (5.20 cM)5
    3961841  NM_201411.21  NP_958813.11 
     70920145 
    chicken
    (Gallus gallus)
    Aves --
    Uncharacterized protein
    23(a)
    many ↔ many
    3(62789352-62799720) ENSGALG00000014900
    lizard
    (Anolis carolinensis)
    Reptilia FLRT16
    fibronectin leucine rich transmembrane protein 1
    87(a)
    1 ↔ 1
    GL343555.1(263570-311098)
    tropical clawed frog
    (Xenopus tropicalis)
    Amphibia flrt11 fibronectin leucine rich transmembrane protein 1 71.9(n)
    84.91(a)
      100486965  XM_002940222.2  XP_002940268.1 
    zebrafish
    (Danio rerio)
    Actinopterygii flrt1a1 fibronectin leucine rich transmembrane 1a 60.91(n)
    63.61(a)
      100144402  XM_005168654.1  XP_005168711.1 


    ENSEMBL Gene Tree for FLRT1 (if available)
    TreeFam Gene Tree for FLRT1 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for FLRT1 gene
    PODN2  PODNL12  FMOD2  KERA2  PRELP2  FLRT32  OMD2  ASPN2  
    BGN2  DCN2  FLRT22  ECM22  LOC1005090912  LUM2  
    2 SIMAP similar genes for FLRT1 using alignment to 1 protein entry:     FLRT1_HUMAN:
    FLRT3    FLRT2

    Find genes that share paralogs with FLRT1           About GenesLikeMe



    (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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    Structural Variations
         Database of Genomic Variants (DGV) 9 variations for FLRT1:    About this table    
    Variant IDTypeSubtypePubMed ID
    esv2744613CNV Deletion23290073
    dgv1155n71CNV Loss21882294
    nsv356CNV Loss18451855
    dgv15n68CNV Loss17160897
    dgv1156n71CNV Loss21882294
    dgv1163n71CNV Loss21882294
    dgv1160n71CNV Loss21882294
    nsv469961CNV Loss18288195
    dgv1162n71CNV Gain21882294

    Site Specific Mutation Identification with PCR Assays
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    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    OMIM gene information: 604806    OMIM disorders: --

    1 disease for FLRT1:    
    About MalaCards
    autosomal recessive spastic paraplegia type 68


    Find genes that share disorders with FLRT1           About GenesLikeMe


    Export disorders for FLRT1 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 FLRT1 gene, integrated from 10 sources (see all 11):
    (articles sorted by number of sources associating them with FLRT1)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Identification of FLRT1, FLRT2, and FLRT3: a novel family of transmembrane leucine-rich repeat proteins. (PubMed id 10644439)1, 2, 3 Lacy S.E.... Kunkel L.M. (Genomics 1999)
    2. Exome sequencing links corticospinal motor neuron disease to common neurodegenerative disorders. (PubMed id 24482476)1, 3 Novarino G....Gleeson J.G. (Science 2014)
    3. The secreted protein discovery initiative (SPDI), a large-scale effort to identify novel human secreted and transmembrane proteins: a bioinformatics assessment. (PubMed id 12975309)1, 2 Clark H.F.... Gray A.M. (Genome Res. 2003)
    4. Critical role of FLRT1 phosphorylation in the interdependent regulation of FLRT1 function and FGF receptor signalling. (PubMed id 20421966)1, 9 Wheldon L.M....Heath J.K. (PLoS ONE 2010)
    5. Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease. (PubMed id 23128233)1 Jostins L....Cho J.H. (Nature 2012)
    6. Human chromosome 11 DNA sequence and analysis including novel gene identification. (PubMed id 16554811)2 Taylor T.D....Sakaki Y. (Nature 2006)
    7. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)2 Gerhard D.S.... Malek J. (Genome Res. 2004)
    8. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)2 Ota T.... Sugano S. (Nat. Genet. 2004)
    9. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1 Strausberg R.L....Marra M.A. (Proc. Natl. Acad. Sci. U.S.A. 2002)
    10. Large-scale concatenation cDNA sequencing. (PubMed id 9110174)1 Yu W.... Gibbs R.A. (Genome Res. 1997)

    (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: 23769 HGNC: 3760 AceView: FLRT1 Ensembl:ENSG00000126500 euGenes: HUgn23769
    ECgene: FLRT1 H-InvDB: FLRT1

    (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 FLRT1 Pharmacogenomics, SNPs, Pathways
    ATLAS Chromosomes in Cancer entry for FLRT1 Genetics and Cytogenetics in Oncology and Haematology

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for FLRT1 gene:
    Search GeneIP for patents involving FLRT1

    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, eBioscience, antibodies-online, and/or others, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Addgene, Cell lines from GenScript, and ESI BIO, Flow cytometery from eBioscience, 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 genOway)
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