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

Gene ID: 365691, updated on 2-Nov-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, Nov 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 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 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

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