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    LRFN1 leucine rich repeat and fibronectin type III domain containing 1 [ Homo sapiens (human) ]

    Gene ID: 57622, updated on 2-May-2024

    Summary

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    Official Symbol
    LRFN1provided by HGNC
    Official Full Name
    leucine rich repeat and fibronectin type III domain containing 1provided by HGNC
    Primary source
    HGNC:HGNC:29290
    See related
    Ensembl:ENSG00000128011 MIM:612807; AllianceGenome:HGNC:29290
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    SALM2
    Summary
    Predicted to be involved in regulation of postsynaptic density assembly. Predicted to be located in plasma membrane. Predicted to be active in cell surface. Predicted to be integral component of postsynaptic density membrane. [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Broad expression in brain (RPKM 2.1), spleen (RPKM 1.1) and 18 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See LRFN1 in Genome Data Viewer
    Location:
    19q13.2
    Exon count:
    5
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (39306566..39320863, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (42110835..42125134, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (39797206..39811503, complement)

    Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene interferon lambda 2 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:39798467-39798968 Neighboring gene interferon lambda 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10596 Neighboring gene glia maturation factor gamma Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10597 Neighboring gene sterile alpha motif domain containing 4B Neighboring gene RNA, 7SL, cytoplasmic 566, pseudogene

    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 a Set of Genes Improving Survival Prediction in Kidney Renal Clear Cell Carcinoma through Integrative Reanalysis of Transcriptomic Data. Ruan B, et al. Dis Markers, 2020. PMID 33110456, Free PMC Article
    2. Comparative analysis of structure, expression and PSD95-binding capacity of Lrfn, a novel family of neuronal transmembrane proteins. Morimura N, et al. Gene, 2006 Oct 1. PMID 16828986
    3. Prediction of the coding sequences of unidentified human genes. XVII. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro. Nagase T, et al. DNA Res, 2000 Apr 28. PMID 10819331
    4. Cell Surface Proteomic Map of HIV Infection Reveals Antagonism of Amino Acid Metabolism by Vpu and Nef. Matheson NJ, et al. Cell Host Microbe, 2015 Oct 14. PMID 26439863, Free PMC Article
    5. SNX27-driven membrane localisation of OTULIN antagonises linear ubiquitination and NF-κB signalling activation. Shi R, et al. Cell Biosci, 2021 Jul 27. PMID 34315543, Free PMC Article

    See all (14) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Identification of a Set of Genes Improving Survival Prediction in Kidney Renal Clear Cell Carcinoma through Integrative Reanalysis of Transcriptomic Data.
      Title: Identification of a Set of Genes Improving Survival Prediction in Kidney Renal Clear Cell Carcinoma through Integrative Reanalysis of Transcriptomic Data.
    Submit: New GeneRIF Correction

    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

    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

    HIV-1 interactions

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    Replication interactions

    Interaction Pubs
    HIV-1 infection (VSV-G pseudotyped) of CEMT4 T cells downregulates plasma membrane expression of LRFN1 PubMed

    Go to the HIV-1, Human Interaction Database

    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

    Clone Names

    • KIAA1484

    Gene Ontology Provided by GOA

    Process Evidence Code Pubs
    involved_in regulation of postsynaptic density assembly IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    is_active_in cell surface IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in plasma membrane TAS
    Traceable Author Statement
    more info
    		  
    is_active_in postsynaptic density membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    is_active_in presynaptic active zone membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    leucine-rich repeat and fibronectin type III domain-containing protein 1
    Names
    CTC-246B18.8
    synaptic adhesion-like molecule 2

    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_020862.2 → NP_065913.1  leucine-rich repeat and fibronectin type III domain-containing protein 1 precursor

      See identical proteins and their annotated locations for NP_065913.1

      Status: VALIDATED

      Source sequence(s)
      AC011445
      Consensus CDS
      CCDS46071.1
      UniProtKB/Swiss-Prot
      Q8TBS9, Q9P244
      Related
      ENSP00000248668.4, ENST00000248668.5
      Conserved Domains (8) summary
      smart00082
      Location:252 → 284
      LRRCT; Leucine rich repeat C-terminal domain
      smart00410
      Location:310 → 385
      IG_like; Immunoglobulin like
      cd00116
      Location:65 → 174
      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 ...
      sd00033
      Location:67 → 90
      LRR_RI; leucine-rich repeat [structural motif]
      pfam00041
      Location:426 → 500
      fn3; Fibronectin type III domain
      pfam12799
      Location:165 → 203
      LRR_4; Leucine Rich repeats (2 copies)
      pfam13855
      Location:65 → 125
      LRR_8; Leucine rich repeat
      cl11960
      Location:314 → 387
      Ig; Immunoglobulin domain

    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_000019.10 Reference GRCh38.p14 Primary Assembly

      Range
      39306566..39320863 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017027033.2 → XP_016882522.1  leucine-rich repeat and fibronectin type III domain-containing protein 1 isoform X1

      UniProtKB/Swiss-Prot
      Q8TBS9, Q9P244
      Conserved Domains (8) summary
      smart00082
      Location:252 → 284
      LRRCT; Leucine rich repeat C-terminal domain
      smart00410
      Location:310 → 385
      IG_like; Immunoglobulin like
      cd00116
      Location:65 → 174
      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 ...
      sd00033
      Location:67 → 90
      LRR_RI; leucine-rich repeat [structural motif]
      pfam00041
      Location:426 → 500
      fn3; Fibronectin type III domain
      pfam12799
      Location:165 → 203
      LRR_4; Leucine Rich repeats (2 copies)
      pfam13855
      Location:65 → 125
      LRR_8; Leucine rich repeat
      cl11960
      Location:314 → 387
      Ig; Immunoglobulin domain

    Reference GRCh38.p14 PATCHES

    Genomic

    1. NW_025791808.1 Reference GRCh38.p14 PATCHES

      Range
      86948..101245 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054333248.1 → XP_054189223.1  leucine-rich repeat and fibronectin type III domain-containing protein 1 isoform X1

      UniProtKB/Swiss-Prot
      Q8TBS9, Q9P244

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060943.1 Alternate T2T-CHM13v2.0

      Range
      42110835..42125134 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054321546.1 → XP_054177521.1  leucine-rich repeat and fibronectin type III domain-containing protein 1 isoform X1

      UniProtKB/Swiss-Prot
      Q8TBS9, Q9P244
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9P244.2 GenPept UniProtKB/Swiss-Prot:Q9P244

    Gene LinkOut

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

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