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

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

Summary

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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
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Genomic context

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See FLRT3 in Genome Data Viewer
Location:
20p12.1
Exon count:
4
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (14322985..14337612, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (14372130..14386755, complement)
RS_2024_09 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

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues 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. 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. 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
  3. 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
  4. Adipose Gene Expression Profile Changes With Lung Allograft Reperfusion. Diamond JM, et al. Am J Transplant, 2017 Jan. PMID 27421969, Free PMC Article
  5. 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

See all (35) 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

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Review eQTL and phenotype association data in this region using PheGenI

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

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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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 membrane IEA
Inferred from Electronic Annotation
more info
  
located_in synaptic membrane ISS
Inferred from Sequence or Structural Similarity
more info
  

General protein information

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Preferred Names
leucine-rich repeat transmembrane protein FLRT3
Names
fibronectin-like domain-containing leucine-rich transmembrane protein 3

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.

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_2024_08

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

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