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    FLRT1 fibronectin leucine rich transmembrane protein 1 [ Homo sapiens (human) ]

    Gene ID: 23769, updated on 5-Mar-2024

    Summary

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    Official Symbol
    FLRT1provided by HGNC
    Official Full Name
    fibronectin leucine rich transmembrane protein 1provided by HGNC
    Primary source
    HGNC:HGNC:3760
    See related
    Ensembl:ENSG00000126500 MIM:604806; AllianceGenome:HGNC:3760
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    SPG68
    Summary
    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]
    Expression
    Broad expression in brain (RPKM 4.3), adrenal (RPKM 3.2) and 14 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    11q13.1
    Exon count:
    6
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (64035931..64119171)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (64025770..64109031)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (63803403..63886643)

    Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3453 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:63764275-63765212 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:63766149-63767086 Neighboring gene H3K27ac-H3K4me1 hESC enhancers GRCh37_chr11:63767087-63768022 and GRCh37_chr11:63768035-63768542 Neighboring gene OTU deubiquitinase, ubiquitin aldehyde binding 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:63775344-63775934 Neighboring gene mono-ADP ribosylhydrolase 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:63789022-63789720 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:63789721-63790419 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:63791118-63791816 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:63795215-63796016 Neighboring gene uncharacterized LOC124902685 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:63803443-63804345 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:63804346-63805247 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:63815687-63816245 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:63816558-63817058 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:63820013-63820556 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:63820557-63821100 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:63821645-63822187 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:63826482-63827200 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3456 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:63836633-63837360 Neighboring gene ReSE screen-validated silencer GRCh37_chr11:63840775-63840963 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:63860723-63861393 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:63861723-63862230 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:63877842-63878622 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:63889359-63890290 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:63896949-63897542 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:63913439-63913940 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:63919856-63920851 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:63920852-63921846 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:63933104-63933604 Neighboring gene uncharacterized LOC105369339 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3460 Neighboring gene MPRA-validated peak1294 silencer Neighboring gene uncharacterized LOC124902686 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:63948751-63949252 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:63949253-63949752 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:63951637-63952142 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4883 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3461 Neighboring gene stress induced phosphoprotein 1

    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. Identification of FLRT1, FLRT2, and FLRT3: a novel family of transmembrane leucine-rich repeat proteins. Lacy SE, et al. Genomics, 1999 Dec 15. PMID 10644439
    2. Critical role of FLRT1 phosphorylation in the interdependent regulation of FLRT1 function and FGF receptor signalling. Wheldon LM, et al. PLoS One, 2010 Apr 22. PMID 20421966, Free PMC Article
    3. Yeast Two-Hybrid Screening for Proteins that Interact with the Extracellular Domain of Amyloid Precursor Protein. Yu Y, et al. Neurosci Bull, 2016 Apr. PMID 26960425, Free PMC Article
    4. Exome sequencing links corticospinal motor neuron disease to common neurodegenerative disorders. Novarino G, et al. Science, 2014 Jan 31. PMID 24482476, Free PMC Article
    5. The gluconeogenic enzyme PCK1 phosphorylates INSIG1/2 for lipogenesis. Xu D, et al. Nature, 2020 Apr. PMID 32322062

    See all (15) 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
    Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease.
    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

    Clone Names

    • MGC21624

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein-macromolecule adaptor activity NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in cell adhesion IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in dendrite development ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in fibroblast growth factor receptor signaling pathway ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in neuron projection extension ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Component Evidence Code Pubs
    located_in cell-cell junction ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in cytoplasmic vesicle ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in cytoplasmic vesicle membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in endoplasmic reticulum membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in extracellular matrix NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    is_active_in extracellular space IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    colocalizes_with focal adhesion ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in neuron projection terminus ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in neuronal cell body membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in perinuclear region of cytoplasm ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in plasma membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in plasma membrane NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    located_in plasma membrane TAS
    Traceable Author Statement
    more info
    		  

    General protein information

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    Preferred Names
    leucine-rich repeat transmembrane protein FLRT1
    Names
    fibronectin-like domain-containing leucine-rich transmembrane 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_001384466.1 → NP_001371395.1  leucine-rich repeat transmembrane protein FLRT1 isoform 1

      Status: REVIEWED

      Source sequence(s)
      AP000721, AP006333
      Consensus CDS
      CCDS8057.1
      UniProtKB/Swiss-Prot
      A0A6E1VY70, Q8WVA2, Q9NZU1
      Conserved Domains (4) summary
      PRK15370
      Location:58 → 329
      PRK15370; type III secretion system effector E3 ubiquitin transferase SlrP
      TIGR00864
      Location:300 → 406
      PCC; polycystin cation channel protein
      smart00060
      Location:441 → 505
      FN3; Fibronectin type 3 domain
      sd00033
      Location:108 → 128
      LRR_RI; leucine-rich repeat [structural motif]

    2. NM_001423967.1 → NP_001410896.1  leucine-rich repeat transmembrane protein FLRT1 isoform 2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) has the same exon combination as variant 1 and uses a downstream start codon compared to variant 1. The encoded isoform (2) has a shorter N-terminus compared to isoform 1
      Source sequence(s)
      AP000721, AP006333

    3. NM_013280.5 → NP_037412.2  leucine-rich repeat transmembrane protein FLRT1 isoform 1

      See identical proteins and their annotated locations for NP_037412.2

      Status: REVIEWED

      Source sequence(s)
      AP000721, AP006333
      Consensus CDS
      CCDS8057.1
      UniProtKB/Swiss-Prot
      A0A6E1VY70, Q8WVA2, Q9NZU1
      Related
      ENSP00000507207.1, ENST00000682287.1
      Conserved Domains (4) summary
      PRK15370
      Location:58 → 329
      PRK15370; type III secretion system effector E3 ubiquitin transferase SlrP
      TIGR00864
      Location:300 → 406
      PCC; polycystin cation channel protein
      smart00060
      Location:441 → 505
      FN3; Fibronectin type 3 domain
      sd00033
      Location:108 → 128
      LRR_RI; leucine-rich repeat [structural motif]

    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_000011.10 Reference GRCh38.p14 Primary Assembly

      Range
      64035931..64119171
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047426696.1 → XP_047282652.1  leucine-rich repeat transmembrane protein FLRT1 isoform X1

      UniProtKB/Swiss-Prot
      A0A6E1VY70, Q8WVA2, Q9NZU1

    2. XM_047426698.1 → XP_047282654.1  leucine-rich repeat transmembrane protein FLRT1 isoform X1

      UniProtKB/Swiss-Prot
      A0A6E1VY70, Q8WVA2, Q9NZU1

    3. XM_047426699.1 → XP_047282655.1  leucine-rich repeat transmembrane protein FLRT1 isoform X1

      UniProtKB/Swiss-Prot
      A0A6E1VY70, Q8WVA2, Q9NZU1

    4. XM_047426697.1 → XP_047282653.1  leucine-rich repeat transmembrane protein FLRT1 isoform X1

      UniProtKB/Swiss-Prot
      A0A6E1VY70, Q8WVA2, Q9NZU1
      Related
      ENSP00000246841.3, ENST00000246841.3

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060935.1 Alternate T2T-CHM13v2.0

      Range
      64025770..64109031
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054368272.1 → XP_054224247.1  leucine-rich repeat transmembrane protein FLRT1 isoform X1

      UniProtKB/Swiss-Prot
      A0A6E1VY70, Q8WVA2, Q9NZU1

    2. XM_054368271.1 → XP_054224246.1  leucine-rich repeat transmembrane protein FLRT1 isoform X1

      UniProtKB/Swiss-Prot
      A0A6E1VY70, Q8WVA2, Q9NZU1
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9NZU1.4 GenPept UniProtKB/Swiss-Prot:Q9NZU1

    Gene LinkOut

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

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