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    ELFN2 extracellular leucine rich repeat and fibronectin type III domain containing 2 [ Homo sapiens (human) ]

    Gene ID: 114794, updated on 28-Oct-2024

    Summary

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    Official Symbol
    ELFN2provided by HGNC
    Official Full Name
    extracellular leucine rich repeat and fibronectin type III domain containing 2provided by HGNC
    Primary source
    HGNC:HGNC:29396
    See related
    Ensembl:ENSG00000166897 MIM:620223; AllianceGenome:HGNC:29396
    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
    LRRC62; PPP1R29
    Summary
    Predicted to enable protein phosphatase inhibitor activity. Predicted to be involved in synaptic membrane adhesion. Located in extracellular space. [provided by Alliance of Genome Resources, Oct 2024]
    Expression
    Biased expression in brain (RPKM 10.0) and testis (RPKM 1.9) See more
    Orthologs
    mouse all
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    Genomic context

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    See ELFN2 in Genome Data Viewer
    Location:
    22q13.1
    Exon count:
    5
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 22 NC_000022.11 (37340644..37427479, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 22 NC_060946.1 (37801164..37887955, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 22 NC_000022.10 (37736685..37823514, complement)

    Chromosome 22 - NC_000022.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107985576 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:37656641-37657180 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18960 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18961 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18962 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18963 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18964 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18965 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13684 Neighboring gene Sharpr-MPRA regulatory region 14238 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18966 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18967 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18968 Neighboring gene cytohesin 4 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:37705193-37705774 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18970 Neighboring gene uncharacterized LOC105373024 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr22:37707125-37708324 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:37713975-37714832 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr22:37723358-37724557 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:37725005-37725650 Neighboring gene Sharpr-MPRA regulatory region 3535 Neighboring gene uncharacterized LOC100506271 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:37751415-37751915 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:37750914-37751414 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:37764078-37765044 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:37774300-37774868 Neighboring gene uncharacterized LOC124905114 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:37782078-37782616 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:37798615-37799363 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:37806589-37807090 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:37812286-37812830 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:37815805-37816474 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:37816475-37817143 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:37863012-37863625 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:37865281-37865782 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:37880249-37880758 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18973 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18974 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:37882293-37882802 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:37882803-37883314 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:37883315-37883824 Neighboring gene MFNG O-fucosylpeptide 3-beta-N-acetylglucosaminyltransferase Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:37898069-37898668 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:37898669-37899266 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:37904132-37904960 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:37904961-37905787 Neighboring gene caspase recruitment domain family member 10 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:37907945-37908458

    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. Identification of Key Prognostic-Related miRNA-mRNA Pairs in the Progression of Endometrial Carcinoma. Dong Y, et al. Gynecol Obstet Invest, 2022. PMID 35081534
    2. ELFN2 is a postsynaptic cell adhesion molecule with essential roles in controlling group III mGluRs in the brain and neuropsychiatric behavior. Dunn HA, et al. Mol Psychiatry, 2019 Dec. PMID 31485013, Free PMC Article
    3. The extracellular leucine-rich repeat superfamily; a comparative survey and analysis of evolutionary relationships and expression patterns. Dolan J, et al. BMC Genomics, 2007 Sep 14. PMID 17868438, Free PMC Article
    4. Genome-wide data reveal novel genes for methotrexate response in a large cohort of juvenile idiopathic arthritis cases. Cobb J, et al. Pharmacogenomics J, 2014 Aug. PMID 24709693, Free PMC Article
    5. Prediction of the coding sequences of unidentified human genes. XXI. The complete sequences of 60 new cDNA clones from brain which code for large proteins. Nagase T, et al. DNA Res, 2001 Aug 31. PMID 11572484

    See all (24) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Identification of Key Prognostic-Related miRNA-mRNA Pairs in the Progression of Endometrial Carcinoma.
      Title: Identification of Key Prognostic-Related miRNA-mRNA Pairs in the Progression of Endometrial Carcinoma.
    2. Authors conclude that extracellular transsynaptic scaffolding by ELFN2 in the brain is a cardinal organizational feature of group III mGluRs essential for their signaling properties and brain function.
      Title: ELFN2 is a postsynaptic cell adhesion molecule with essential roles in controlling group III mGluRs in the brain and neuropsychiatric behavior.
    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

    EBI GWAS Catalog

    Description
    Genome-wide data reveal novel genes for methotrexate response in a large cohort of juvenile idiopathic arthritis cases.
    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

    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 ELFN2 PubMed

    Go to the HIV-1, Human Interaction Database

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ30913, KIAA1904

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein phosphatase inhibitor activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in synaptic membrane adhesion IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    is_active_in extracellular matrix IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in extracellular space HDA PubMed 
    is_active_in extracellular space IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in postsynaptic density membrane IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    protein phosphatase 1 regulatory subunit 29
    Names
    dJ63G5.3 (putative Leucine rich protein)
    leucine-rich repeat and fibronectin type-III domain-containing protein 6
    leucine-rich repeat-containing protein 62

    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_052906.5 → NP_443138.2  protein phosphatase 1 regulatory subunit 29 precursor

      See identical proteins and their annotated locations for NP_443138.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer trancript and encodes the protein.
      Source sequence(s)
      AB067491, BC032082, DA398675, FP325335, Z94160
      Consensus CDS
      CCDS33642.1
      UniProtKB/Swiss-Prot
      Q5R3F8, Q96PY3
      Related
      ENSP00000385277.1, ENST00000402918.7
      Conserved Domains (4) summary
      TIGR00864
      Location:157 → 227
      PCC; polycystin cation channel protein
      sd00031
      Location:60 → 80
      LRR_1; leucine-rich repeat [structural motif]
      sd00033
      Location:200 → 226
      LRR_RI; leucine-rich repeat [structural motif]
      pfam13855
      Location:80 → 139
      LRR_8; Leucine rich repeat

    RNA

    1. NR_110512.2 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks two exons and contains two alternate 3' terminal exons, compared to variant 1. This variant is represented as non-coding because it lacks the entire coding region found in variant 1.
      Source sequence(s)
      DA365834, DA398675, FP325335, Z94160

    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_000022.11 Reference GRCh38.p14 Primary Assembly

      Range
      37340644..37427479 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060946.1 Alternate T2T-CHM13v2.0

      Range
      37801164..37887955 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q5R3F8.1 GenPept UniProtKB/Swiss-Prot:Q5R3F8

    Gene LinkOut

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

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