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    Egflam EGF-like, fibronectin type III and laminin G domains [ Rattus norvegicus (Norway rat) ]

    Gene ID: 365691, updated on 9-Dec-2024

    Summary

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    Official Symbol
    Egflamprovided by RGD
    Official Full Name
    EGF-like, fibronectin type III and laminin G domainsprovided by RGD
    Primary source
    RGD:1306592
    See related
    EnsemblRapid:ENSRNOG00000012058 AllianceGenome:RGD:1306592
    Gene type
    protein coding
    RefSeq status
    PROVISIONAL
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Also known as
    RGD1306592
    Summary
    Predicted to enable glycosaminoglycan binding activity. Predicted to act upstream of or within extracellular matrix organization and positive regulation of cell-substrate adhesion. Predicted to be located in basement membrane; cell surface; and interstitial matrix. Predicted to be active in photoreceptor ribbon synapse. Orthologous to human EGFLAM (EGF like, fibronectin type III and laminin G domains). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in Uterus (RPKM 43.6), Adrenal (RPKM 27.4) and 8 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Egflam in Genome Data Viewer
    Location:
    2q16
    Exon count:
    23
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 2 NC_086020.1 (58029934..58204010, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 2 NC_051337.1 (56301945..56476665, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 2 NC_005101.4 (56503002..56681334, complement)

    Chromosome 2 - NC_086020.1Genomic Context describing neighboring genes Neighboring gene ribosomal protein L21, pseudogene 11 Neighboring gene LIF receptor subunit alpha Neighboring gene uncharacterized LOC108349957 Neighboring gene U4 spliceosomal RNA Neighboring gene FKBP prolyl isomerase 3, pseudogene 1 Neighboring gene ribosomal protein S9, pseudogene 4 Neighboring gene 40S ribosomal protein S6 pseudogene

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Bibliography

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    Related articles in PubMed

    1. Cell specific post-translational processing of pikachurin, a protein involved in retinal synaptogenesis. Han J, et al. PLoS One, 2012. PMID 23226524, Free PMC Article
    2. Transcriptome-based systematic identification of extracellular matrix proteins. Manabe R, et al. Proc Natl Acad Sci U S A, 2008 Sep 2. PMID 18757743, Free PMC Article
    3. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, et al. Proc Natl Acad Sci U S A, 2002 Dec 24. PMID 12477932, Free PMC Article
    4. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, et al. Brief Bioinform, 2011 Sep. PMID 21873635, Free PMC Article

    GeneRIFs: Gene References Into Functions

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by RGD

    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 glycosaminoglycan binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    Process Evidence Code Pubs
    involved_in extracellular matrix organization IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within extracellular matrix organization ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of cell-substrate adhesion IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within positive regulation of cell-substrate adhesion ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    located_in basement membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in basement membrane ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in cell junction IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in cell projection IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in cell surface ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in extracellular matrix ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in interstitial matrix IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in interstitial matrix ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in photoreceptor ribbon synapse IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in photoreceptor ribbon synapse ISO
    Inferred from Sequence Orthology
    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

    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_001108938.2 → NP_001102408.2  pikachurin precursor

      See identical proteins and their annotated locations for NP_001102408.2

      Status: PROVISIONAL

      Source sequence(s)
      BC168173
      UniProtKB/Swiss-Prot
      B4F785
      UniProtKB/TrEMBL
      A6KGG7, G3V7M7
      Related
      ENSRNOP00000016722.3, ENSRNOT00000016722.6
      Conserved Domains (4) summary
      cd00054
      Location:786 → 816
      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:142 → 236
      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:387 → 537
      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:856 → 981
      Laminin_G_2; Laminin G domain

    RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCr8

    Genomic

    1. NC_086020.1 Reference GRCr8

      Range
      58029934..58204010 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006232013.5 → XP_006232075.1  pikachurin isoform X1

      UniProtKB/TrEMBL
      A0A8I6GJD5, A6KGG7, G3V7M7
      Related
      ENSRNOP00000091969.1, ENSRNOT00000104810.2
      Conserved Domains (4) summary
      cd00054
      Location:786 → 816
      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:142 → 236
      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:387 → 537
      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:864 → 989
      Laminin_G_2; Laminin G domain

    2. XM_017590987.3 → XP_017446476.1  pikachurin isoform X2

      UniProtKB/TrEMBL
      A6KGG7, G3V7M7
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    B4F785.1 GenPept UniProtKB/Swiss-Prot:B4F785

    Gene LinkOut

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

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