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    Egflam EGF-like, fibronectin type III and laminin G domains [ Mus musculus (house mouse) ]

    Gene ID: 268780, updated on 9-Dec-2024

    Summary

    Official Symbol
    Egflamprovided by MGI
    Official Full Name
    EGF-like, fibronectin type III and laminin G domainsprovided by MGI
    Primary source
    MGI:MGI:2146149
    See related
    Ensembl:ENSMUSG00000042961 AllianceGenome:MGI:2146149
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
    Also known as
    5930412K08
    Summary
    Enables glycosaminoglycan binding activity. Acts upstream of or within extracellular matrix organization and positive regulation of cell-substrate adhesion. Located in basement membrane and interstitial matrix. Is active in photoreceptor ribbon synapse. Is expressed in hair follicle and rib. Orthologous to human EGFLAM (EGF like, fibronectin type III and laminin G domains). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Broad expression in lung adult (RPKM 9.0), ovary adult (RPKM 6.9) and 16 other tissues See more
    Orthologs
    NEW
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    Try the new Transcript table

    Genomic context

    See Egflam in Genome Data Viewer
    Location:
    15 A1; 15 3.5 cM
    Exon count:
    25
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 15 NC_000081.7 (7235598..7428203, complement)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 15 NC_000081.6 (7206120..7398744, complement)

    Chromosome 15 - NC_000081.7Genomic Context describing neighboring genes Neighboring gene STARR-seq mESC enhancer starr_37875 Neighboring gene STARR-seq mESC enhancer starr_37876 Neighboring gene predicted gene, 30971 Neighboring gene STARR-seq mESC enhancer starr_37878 Neighboring gene LIF receptor alpha Neighboring gene STARR-seq mESC enhancer starr_37880 Neighboring gene FK506 binding protein 3 pseudogene Neighboring gene predicted gene, 41263 Neighboring gene predicted gene, 41262 Neighboring gene STARR-seq mESC enhancer starr_37882 Neighboring gene STARR-seq mESC enhancer starr_37883 Neighboring gene predicted gene, 41264

    Genomic regions, transcripts, and products

    Expression

    • Project title: Mouse ENCODE transcriptome data
    • Description: RNA profiling data sets generated by the Mouse ENCODE project.
    • BioProject: PRJNA66167
    • Publication: PMID 25409824
    • Analysis date: n/a

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Variation

    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    • Endonuclease-mediated (1) 
    • Targeted (1)  1 citation

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General protein information

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

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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_001289496.2NP_001276425.1  pikachurin isoform 1 precursor

      See identical proteins and their annotated locations for NP_001276425.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform.
      Source sequence(s)
      AC109195, AC158747
      Consensus CDS
      CCDS79359.1
      UniProtKB/Swiss-Prot
      B2RWU6, B6JU28, Q4VBE4, Q80WX4, Q8BGP3
      Related
      ENSMUSP00000094238.5, ENSMUST00000096494.5
      Conserved Domains (4) summary
      cd00054
      Location:790820
      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:36133
      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:391541
      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:868993
      Laminin_G_2; Laminin G domain
    2. NM_001289498.1NP_001276427.1  pikachurin isoform 3

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) uses an alternate splice site in the 5' UTR and has multiple coding region differnces compared to variant 1. These differences result in the use of an alternate AUG compared to variant 1. The encoded isoform (3) is shorter and has a distinct N-terminus compared to isoform 1.
      Source sequence(s)
      AC158747, AK158909
      Conserved Domains (4) summary
      cd00054
      Location:640670
      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:3086
      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:241391
      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:718843
      Laminin_G_2; Laminin G domain
    3. NM_001416486.1NP_001403415.1  pikachurin isoform 4 precursor

      Status: VALIDATED

      Source sequence(s)
      AC109195, AC158747
    4. NM_001416487.1NP_001403416.1  pikachurin isoform 2 precursor

      Status: VALIDATED

      Source sequence(s)
      AC109195, AC158747
    5. NM_001416488.1NP_001403417.1  pikachurin isoform 3

      Status: VALIDATED

      Source sequence(s)
      AC109195, AC158747
    6. NM_001416489.1NP_001403418.1  pikachurin isoform 5

      Status: VALIDATED

      Source sequence(s)
      AC109195, AC158747
    7. NM_001416490.1NP_001403419.1  pikachurin isoform 5

      Status: VALIDATED

      Source sequence(s)
      AC105969, AC109195, AC158747
    8. NM_001416491.1NP_001403420.1  pikachurin isoform 5

      Status: VALIDATED

      Source sequence(s)
      AC109195, AC158747
    9. NM_001416492.1NP_001403421.1  pikachurin isoform 5

      Status: VALIDATED

      Source sequence(s)
      AC109195, AC158747
    10. NM_001416493.1NP_001403422.1  pikachurin isoform 5

      Status: VALIDATED

      Source sequence(s)
      AC109195, AC158747
    11. NM_001416494.1NP_001403423.1  pikachurin isoform 5

      Status: VALIDATED

      Source sequence(s)
      AC109195, AC158747
    12. NM_001416495.1NP_001403424.1  pikachurin isoform 6

      Status: VALIDATED

      Source sequence(s)
      AC109195, AC158747
    13. NM_001416496.1NP_001403425.1  pikachurin isoform 7

      Status: VALIDATED

      Source sequence(s)
      AC109195, AC158747
    14. NM_178748.7NP_848863.1  pikachurin isoform 2 precursor

      See identical proteins and their annotated locations for NP_848863.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks an exon in the 3' coding region comapred to variant 1. The encoded isoform (2) is shorter than isoform 1.
      Source sequence(s)
      AC109195, AC158747
      Consensus CDS
      CCDS27370.1
      UniProtKB/Swiss-Prot
      Q4VBE4
      Related
      ENSMUSP00000055599.4, ENSMUST00000058593.10
      Conserved Domains (4) summary
      cd00054
      Location:790820
      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:36133
      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:391541
      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:860985
      Laminin_G_2; Laminin G domain

    RNA

    1. NR_184054.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC109195, AC158747

    RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

    Reference GRCm39 C57BL/6J

    Genomic

    1. NC_000081.7 Reference GRCm39 C57BL/6J

      Range
      7235598..7428203 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_036159432.1XP_036015325.1  pikachurin isoform X3

      Conserved Domains (4) summary
      cd00054
      Location:640670
      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:3086
      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:241391
      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:710835
      Laminin_G_2; Laminin G domain
    2. XM_036159431.1XP_036015324.1  pikachurin isoform X2

      Conserved Domains (1) summary
      pfam02210
      Location:3128
      Laminin_G_2; Laminin G domain