U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination
    • Showing Current items.

    FLRT3 fibronectin leucine rich transmembrane protein 3 [ Homo sapiens (human) ]

    Gene ID: 23767, updated on 3-Apr-2024

    Summary

    Go to the top of the page Help
    Official Symbol
    FLRT3provided by HGNC
    Official Full Name
    fibronectin leucine rich transmembrane protein 3provided by HGNC
    Primary source
    HGNC:HGNC:3762
    See related
    Ensembl:ENSG00000125848 MIM:604808; AllianceGenome:HGNC:3762
    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
    HH21
    Summary
    This gene encodes a member of the fibronectin leucine rich transmembrane protein (FLRT) family. FLRTs may function in cell adhesion and/or receptor signalling. Their protein structures resemble small leucine-rich proteoglycans found in the extracellular matrix. This gene is expressed in many tissues. Two alternatively spliced transcript variants encoding the same protein have been described for this gene. [provided by RefSeq, Jul 2010]
    Expression
    Broad expression in kidney (RPKM 12.2), lung (RPKM 9.3) and 16 other tissues See more
    Orthologs
    mouse all
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    Go to the top of the page Help
    Location:
    20p12.1
    Exon count:
    4
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (14322985..14337612, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (14372130..14386755, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (14303631..14318258, complement)

    Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene mono-ADP ribosylhydrolase 2 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:14200853-14201581 Neighboring gene aminoacyl tRNA synthetase complex interacting multifunctional protein 1 pseudogene 1 Neighboring gene RNA, 7SL, cytoplasmic 864, pseudogene Neighboring gene RNA, U6 small nuclear 228, pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:14447417-14447918 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:14447919-14448418 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr20:14451799-14452358 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_59600 Neighboring gene uncharacterized LOC124904873

    Genomic regions, transcripts, and products

    Go to the top of the page Help

    Go to nucleotide: Graphics FASTA GenBank

    Expression

    Go to the top of the page Help
    • 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

    Go to the top of the pageHelp

    Related articles in PubMed

    1. TGF-β-Induced FLRT3 Attenuation Is Essential for Cancer-Associated Fibroblast-Mediated Epithelial-Mesenchymal Transition in Colorectal Cancer. Yang M, et al. Mol Cancer Res, 2022 Aug 5. PMID 35560224
    2. Variants in FLRT3 and SLC35E2B identified using exome sequencing in seven high myopia families from Central Europe. Swierkowska J, et al. Adv Med Sci, 2021 Mar. PMID 33711669
    3. Adipose Gene Expression Profile Changes With Lung Allograft Reperfusion. Diamond JM, et al. Am J Transplant, 2017 Jan. PMID 27421969, Free PMC Article
    4. Lack of C20orf133 and FLRT3 mutations in 43 patients with Kabuki syndrome in Japan. Kuniba H, et al. J Med Genet, 2008 Jul. PMID 18593871
    5. FLRT3, a cell surface molecule containing LRR repeats and a FNIII domain, promotes neurite outgrowth. Tsuji L, et al. Biochem Biophys Res Commun, 2004 Jan 23. PMID 14706654

    See all (31) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. FLRT3 and TGF-beta/SMAD4 signalling: Impacts on apoptosis, autophagy and ion channels in supraventricular tachycardia.
      Title: FLRT3 and TGF-β/SMAD4 signalling: Impacts on apoptosis, autophagy and ion channels in supraventricular tachycardia.
    2. TGF-beta-Induced FLRT3 Attenuation Is Essential for Cancer-Associated Fibroblast-Mediated Epithelial-Mesenchymal Transition in Colorectal Cancer.
      Title: TGF-β-Induced FLRT3 Attenuation Is Essential for Cancer-Associated Fibroblast-Mediated Epithelial-Mesenchymal Transition in Colorectal Cancer.
    3. Variants in FLRT3 and SLC35E2B identified using exome sequencing in seven high myopia families from Central Europe.
      Title: Variants in FLRT3 and SLC35E2B identified using exome sequencing in seven high myopia families from Central Europe.
    4. Low FLRT3 expression is associated with lung graft dysfunction.
      Title: Adipose Gene Expression Profile Changes With Lung Allograft Reperfusion.
    5. Results suggest that UNC5 and LPHN3 can simultaneously bind to FLRT3, forming a trimeric complex, and that FLRT3 may form transsynaptic complexes with both LPHN3 and UNC5.
      Title: Structural Basis of Latrophilin-FLRT-UNC5 Interaction in Cell Adhesion.
    6. This study demonistrated that LPHN3 and its ligand FLRT3 play an important role in glutamatergic synapse development.
      Title: FLRT proteins are endogenous latrophilin ligands and regulate excitatory synapse development.
    7. Observational study of gene-disease association. (HuGE Navigator)
      Title: Lack of C20orf133 and FLRT3 mutations in 43 patients with Kabuki syndrome in Japan.
    Submit: New GeneRIF Correction

    Phenotypes

    Go to the top of the page Help

    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Variation

    Go to the top of the page Help

    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    Pathways from PubChem

    Go to the top of the page

    Interactions

    Go to the top of the page Help
    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Go to the top of the page Help

    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables chemorepellent activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables fibroblast growth factor receptor binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables protein homodimerization activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables protein-macromolecule adaptor activity NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in axon guidance IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in cell-cell adhesion via plasma-membrane adhesion molecules IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in embryonic morphogenesis 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 head development ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in heart development ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in negative chemotaxis IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in neuron projection development ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in neuron projection extension IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in neuron projection extension ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in positive regulation of synapse assembly IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in proepicardium cell migration involved in pericardium morphogenesis ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in response to axon injury ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in synapse assembly ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in synaptic membrane adhesion IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in axon terminus ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in axonal growth cone ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in cell junction IDA
    Inferred from Direct Assay
    more info
    		  
    located_in cell-cell junction IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in cytosol IDA
    Inferred from Direct Assay
    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
    		  
    located_in focal adhesion IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in glutamatergic synapse IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in growth cone membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in plasma membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in plasma membrane NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    located_in plasma membrane TAS
    Traceable Author Statement
    more info
    		  
    located_in postsynaptic density IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in postsynaptic membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in synaptic membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  

    General protein information

    Go to the top of the page Help
    Preferred Names
    leucine-rich repeat transmembrane protein FLRT3
    Names
    fibronectin-like domain-containing leucine-rich transmembrane protein 3

    NCBI Reference Sequences (RefSeq)

    Go to the top of the page Help

    NEW Try the new Transcript table

    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.

    Genomic

    1. NG_033913.1 RefSeqGene

      Range
      5056..19683
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_013281.4 → NP_037413.1  leucine-rich repeat transmembrane protein FLRT3 precursor

      See identical proteins and their annotated locations for NP_037413.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) differs in the 5' UTR, compared to variant 2. Variants 1 and 2 encode the same isoform.
      Source sequence(s)
      AB040902, AL132826, BC020870, DA502792
      Consensus CDS
      CCDS13121.1
      UniProtKB/Swiss-Prot
      D3DW20, Q542Z9, Q96K39, Q96K42, Q96KB1, Q9NZU0, Q9P259
      UniProtKB/TrEMBL
      Q8NC95
      Related
      ENSP00000367292.3, ENST00000378053.3
      Conserved Domains (8) summary
      smart00013
      Location:31 → 61
      LRRNT; Leucine rich repeat N-terminal domain
      smart00082
      Location:305 → 356
      LRRCT; Leucine rich repeat C-terminal domain
      cd00116
      Location:120 → 259
      LRR_RI; Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond ...
      sd00031
      Location:61 → 84
      LRR_1; leucine-rich repeat [structural motif]
      sd00033
      Location:85 → 104
      LRR_RI; leucine-rich repeat [structural motif]
      pfam00041
      Location:413 → 478
      fn3; Fibronectin type III domain
      pfam12799
      Location:247 → 287
      LRR_4; Leucine Rich repeats (2 copies)
      pfam13855
      Location:247 → 306
      LRR_8; Leucine rich repeat

    2. NM_198391.3 → NP_938205.1  leucine-rich repeat transmembrane protein FLRT3 precursor

      See identical proteins and their annotated locations for NP_938205.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) is the longer transcript. Variants 1 and 2 encode the same isoform.
      Source sequence(s)
      AB040902, AL132826, AL529481, BC020870
      Consensus CDS
      CCDS13121.1
      UniProtKB/Swiss-Prot
      D3DW20, Q542Z9, Q96K39, Q96K42, Q96KB1, Q9NZU0, Q9P259
      UniProtKB/TrEMBL
      Q8NC95
      Related
      ENSP00000339912.4, ENST00000341420.5
      Conserved Domains (8) summary
      smart00013
      Location:31 → 61
      LRRNT; Leucine rich repeat N-terminal domain
      smart00082
      Location:305 → 356
      LRRCT; Leucine rich repeat C-terminal domain
      cd00116
      Location:120 → 259
      LRR_RI; Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond ...
      sd00031
      Location:61 → 84
      LRR_1; leucine-rich repeat [structural motif]
      sd00033
      Location:85 → 104
      LRR_RI; leucine-rich repeat [structural motif]
      pfam00041
      Location:413 → 478
      fn3; Fibronectin type III domain
      pfam12799
      Location:247 → 287
      LRR_4; Leucine Rich repeats (2 copies)
      pfam13855
      Location:247 → 306
      LRR_8; Leucine rich repeat

    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_000020.11 Reference GRCh38.p14 Primary Assembly

      Range
      14322985..14337612 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011529205.3 → XP_011527507.1  leucine-rich repeat transmembrane protein FLRT3 isoform X1

      See identical proteins and their annotated locations for XP_011527507.1

      UniProtKB/Swiss-Prot
      D3DW20, Q542Z9, Q96K39, Q96K42, Q96KB1, Q9NZU0, Q9P259
      UniProtKB/TrEMBL
      Q8NC95
      Conserved Domains (8) summary
      smart00013
      Location:31 → 61
      LRRNT; Leucine rich repeat N-terminal domain
      smart00082
      Location:305 → 356
      LRRCT; Leucine rich repeat C-terminal domain
      cd00116
      Location:120 → 259
      LRR_RI; Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond ...
      sd00031
      Location:61 → 84
      LRR_1; leucine-rich repeat [structural motif]
      sd00033
      Location:85 → 104
      LRR_RI; leucine-rich repeat [structural motif]
      pfam00041
      Location:413 → 478
      fn3; Fibronectin type III domain
      pfam12799
      Location:247 → 287
      LRR_4; Leucine Rich repeats (2 copies)
      pfam13855
      Location:247 → 306
      LRR_8; Leucine rich repeat

    2. XM_005260682.5 → XP_005260739.1  leucine-rich repeat transmembrane protein FLRT3 isoform X1

      See identical proteins and their annotated locations for XP_005260739.1

      UniProtKB/Swiss-Prot
      D3DW20, Q542Z9, Q96K39, Q96K42, Q96KB1, Q9NZU0, Q9P259
      UniProtKB/TrEMBL
      Q8NC95
      Conserved Domains (8) summary
      smart00013
      Location:31 → 61
      LRRNT; Leucine rich repeat N-terminal domain
      smart00082
      Location:305 → 356
      LRRCT; Leucine rich repeat C-terminal domain
      cd00116
      Location:120 → 259
      LRR_RI; Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond ...
      sd00031
      Location:61 → 84
      LRR_1; leucine-rich repeat [structural motif]
      sd00033
      Location:85 → 104
      LRR_RI; leucine-rich repeat [structural motif]
      pfam00041
      Location:413 → 478
      fn3; Fibronectin type III domain
      pfam12799
      Location:247 → 287
      LRR_4; Leucine Rich repeats (2 copies)
      pfam13855
      Location:247 → 306
      LRR_8; Leucine rich repeat

    3. XM_011529204.3 → XP_011527506.1  leucine-rich repeat transmembrane protein FLRT3 isoform X1

      See identical proteins and their annotated locations for XP_011527506.1

      UniProtKB/Swiss-Prot
      D3DW20, Q542Z9, Q96K39, Q96K42, Q96KB1, Q9NZU0, Q9P259
      UniProtKB/TrEMBL
      Q8NC95
      Conserved Domains (8) summary
      smart00013
      Location:31 → 61
      LRRNT; Leucine rich repeat N-terminal domain
      smart00082
      Location:305 → 356
      LRRCT; Leucine rich repeat C-terminal domain
      cd00116
      Location:120 → 259
      LRR_RI; Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond ...
      sd00031
      Location:61 → 84
      LRR_1; leucine-rich repeat [structural motif]
      sd00033
      Location:85 → 104
      LRR_RI; leucine-rich repeat [structural motif]
      pfam00041
      Location:413 → 478
      fn3; Fibronectin type III domain
      pfam12799
      Location:247 → 287
      LRR_4; Leucine Rich repeats (2 copies)
      pfam13855
      Location:247 → 306
      LRR_8; Leucine rich repeat

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060944.1 Alternate T2T-CHM13v2.0

      Range
      14372130..14386755 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054323308.1 → XP_054179283.1  leucine-rich repeat transmembrane protein FLRT3 isoform X1

    2. XM_054323306.1 → XP_054179281.1  leucine-rich repeat transmembrane protein FLRT3 isoform X1

    3. XM_054323307.1 → XP_054179282.1  leucine-rich repeat transmembrane protein FLRT3 isoform X1

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9NZU0.1 GenPept UniProtKB/Swiss-Prot:Q9NZU0

    Gene LinkOut

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

    Chemical Information
    Molecular Biology Databases
    Research Materials
    Tools
    Miscellaneous