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    EGFLAM EGF like, fibronectin type III and laminin G domains [ Homo sapiens (human) ]

    Gene ID: 133584, updated on 5-Mar-2024

    Summary

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    Official Symbol
    EGFLAMprovided by HGNC
    Official Full Name
    EGF like, fibronectin type III and laminin G domainsprovided by HGNC
    Primary source
    HGNC:HGNC:26810
    See related
    Ensembl:ENSG00000164318 MIM:617683; AllianceGenome:HGNC:26810
    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
    PIKA; AGRNL; AGRINL
    Summary
    Predicted to enable calcium ion binding activity and glycosaminoglycan binding activity. Predicted to be involved in animal organ morphogenesis and tissue development. Predicted to act upstream of or within extracellular matrix organization; peptide cross-linking via chondroitin 4-sulfate glycosaminoglycan; and positive regulation of cell-substrate adhesion. Part of cell surface. [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Broad expression in placenta (RPKM 12.2), fat (RPKM 7.7) and 17 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See EGFLAM in Genome Data Viewer
    Location:
    5p13.2-p13.1
    Exon count:
    24
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (38258559..38465480)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (38507663..38714549)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (38258661..38465582)

    Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene long intergenic non-protein coding RNA 2107 Neighboring gene long intergenic non-protein coding RNA 2119 Neighboring gene peroxiredoxin 4 pseudogene 2 Neighboring gene uncharacterized LOC124900966 Neighboring gene NANOG hESC enhancer GRCh37_chr5:38257291-38257792 Neighboring gene EGFLAM antisense RNA 4 Neighboring gene Sharpr-MPRA regulatory region 7458 Neighboring gene EGFLAM antisense RNA 2 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr5:38426700-38427899 Neighboring gene 60S ribosomal protein L27-like Neighboring gene EGFLAM antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15980 Neighboring gene uncharacterized LOC124900965 Neighboring gene uncharacterized LOC105374732 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr5:38463193-38464392 Neighboring gene uncharacterized LOC124900964 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr5:38466368-38467567 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:38468935-38469806 Neighboring gene LIF receptor subunit alpha Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:38556889-38557672 Neighboring gene LIFR antisense RNA 1 Neighboring gene microRNA 3650

    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. EGFLAM correlates with cell proliferation, migration, invasion and poor prognosis in glioblastoma. Chen J, et al. Cancer Biomark, 2019. PMID 30829611, Free PMC Article
    2. [Model of aberrant DNA methylation patterns and its applications in epithelial ovarian cancer.]. Gu XH, et al. Zhonghua Fu Chan Ke Za Zhi, 2009 Oct. PMID 20078962
    3. Identification of EGFLAM, SPATC1L and RNASE13 as novel susceptibility loci for aortic aneurysm in Japanese individuals by exome-wide association studies. Yamada Y, et al. Int J Mol Med, 2017 May. PMID 28339009, Free PMC Article
    4. Pikachurin interaction with dystroglycan is diminished by defective O-mannosyl glycosylation in congenital muscular dystrophy models and rescued by LARGE overexpression. Hu H, et al. Neurosci Lett, 2011 Feb 1. PMID 21129441, Free PMC Article
    5. Genome-wide pharmacogenomic study of citalopram-induced side effects in STAR*D. Adkins DE, et al. Transl Psychiatry, 2012 Jul 3. PMID 22760553, Free PMC Article

    See all (20) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Structure of the photoreceptor synaptic assembly of the extracellular matrix protein pikachurin with the orphan receptor GPR179.
      Title: Structure of the photoreceptor synaptic assembly of the extracellular matrix protein pikachurin with the orphan receptor GPR179.
    2. this is the first report to describe that EGFLAM promoted the proliferation, migration and invasion of GBM cells via the activation of PI3K/AKT pathway, and predicted poor prognosis in GBM patients.
      Title: EGFLAM correlates with cell proliferation, migration, invasion and poor prognosis in glioblastoma.
    3. rs1465567 of EGFLAM and rs113710653 of SPATC1L may be susceptibility loci for true aortic aneurysm and rs143881017 of RNASE13 may be such a locus for dissecting aortic aneurysm in Japanese individuals.
      Title: Identification of EGFLAM, SPATC1L and RNASE13 as novel susceptibility loci for aortic aneurysm in Japanese individuals by exome-wide association studies.
    4. Strong candidate gene for macular dystrophy, MCDR3 (human 5p15.33-p13.1). Conclusion is based on a massive expression data set for mouse (103 strains) and joint analysis of RetNet database.
      Title: Gene expression in the mouse eye: an online resource for genetics using 103 strains of mice.
    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 pharmacogenomic study of citalopram-induced side effects in STAR*D.
    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

    • FLJ39155

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables calcium ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables glycosaminoglycan binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in extracellular matrix organization IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in positive regulation of cell-substrate adhesion IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in basement membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in cell projection IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in interstitial matrix IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in photoreceptor ribbon synapse IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in presynaptic active zone IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in synaptic cleft IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    pikachurin
    Names
    EGF-like, fibronectin type-III and laminin G-like domain-containing protein
    agrin-like protein

    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_001205301.2 → NP_001192230.1  pikachurin isoform 5 precursor

      See identical proteins and their annotated locations for NP_001192230.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (5) contains an alternate in-frame exon in the coding region, compared to variant 1. The encoded isoform (5) is longer than isoform 1.
      Source sequence(s)
      AC010338, AC010457, AC091839
      Consensus CDS
      CCDS56363.1
      UniProtKB/Swiss-Prot
      A8K6D7, Q5U643, Q63HQ2, Q6P3V1, Q8N124, Q8N197, Q8N7Y0, Q8N8N5, Q8NAL2
      Related
      ENSP00000346964.3, ENST00000354891.7
      Conserved Domains (4) summary
      cd00054
      Location:792 → 820
      EGF_CA; Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the ...
      cd00063
      Location:36 → 133
      FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...
      cd00110
      Location:391 → 541
      LamG; Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of ...
      pfam02210
      Location:868 → 993
      Laminin_G_2; Laminin G domain

    2. NM_152403.4 → NP_689616.2  pikachurin isoform 1 precursor

      See identical proteins and their annotated locations for NP_689616.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes isoform 1.
      Source sequence(s)
      AC010338, AC010457, AC091839
      Consensus CDS
      CCDS3924.1
      UniProtKB/Swiss-Prot
      Q63HQ2
      Related
      ENSP00000313084.5, ENST00000322350.10
      Conserved Domains (4) summary
      cd00054
      Location:792 → 820
      EGF_CA; Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the ...
      cd00063
      Location:36 → 133
      FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...
      cd00110
      Location:391 → 541
      LamG; Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of ...
      pfam02210
      Location:860 → 985
      Laminin_G_2; Laminin G domain

    3. NM_182798.3 → NP_877950.1  pikachurin isoform 2

      See identical proteins and their annotated locations for NP_877950.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (2) has a distinct N-terminus and is shorter than isoform 1.
      Source sequence(s)
      AC010457, AC091839, AK097549
      Consensus CDS
      CCDS3925.1
      UniProtKB/Swiss-Prot
      Q63HQ2
      Related
      ENSP00000337607.6, ENST00000336740.10
      Conserved Domains (3) summary
      cd00054
      Location:558 → 586
      EGF_CA; Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the ...
      cd00110
      Location:157 → 307
      LamG; Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of ...
      pfam02210
      Location:626 → 751
      Laminin_G_2; Laminin G domain

    4. NM_182801.3 → NP_877953.1  pikachurin isoform 4

      See identical proteins and their annotated locations for NP_877953.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at a downstream, in-frame start codon, compared to variant 1. The encoded isoform (4) has a shorter N-terminus, compared to isoform 1.
      Source sequence(s)
      AC010457, BC033188, DN995271
      Consensus CDS
      CCDS47199.1
      UniProtKB/Swiss-Prot
      Q63HQ2
      Related
      ENSP00000380393.3, ENST00000397210.7
      Conserved Domains (1) summary
      pfam02210
      Location:3 → 128
      Laminin_G_2; Laminin G 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_000005.10 Reference GRCh38.p14 Primary Assembly

      Range
      38258559..38465480
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060929.1 Alternate T2T-CHM13v2.0

      Range
      38507663..38714549
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_182799.1: Suppressed sequence

      Description
      NM_182799.1: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q63HQ2.2 GenPept UniProtKB/Swiss-Prot:Q63HQ2

    Gene LinkOut

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

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