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    Shroom3 shroom family member 3 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 305230, updated on 9-Dec-2024

    Summary

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    Official Symbol
    Shroom3provided by RGD
    Official Full Name
    shroom family member 3provided by RGD
    Primary source
    RGD:1310470
    See related
    EnsemblRapid:ENSRNOG00000002208 AllianceGenome:RGD:1310470
    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
    Shrm; RGD1310470
    Summary
    Predicted to enable actin filament binding activity. Predicted to be involved in actin filament organization. Predicted to act upstream of or within several processes, including columnar/cuboidal epithelial cell development; neural tube closure; and regulation of cell shape. Predicted to be located in apical part of cell and cytoskeleton. Predicted to be active in several cellular components, including adherens junction; apical junction complex; and apical plasma membrane. Orthologous to human SHROOM3 (shroom family member 3). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in Lung (RPKM 39.9), Heart (RPKM 35.1) and 6 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Shroom3 in Genome Data Viewer
    Location:
    14p22
    Exon count:
    12
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 14 NC_086032.1 (15383769..15681158, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 14 NC_051349.1 (15099415..15396832, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 14 NC_005113.4 (16622767..16903265, complement)

    Chromosome 14 - NC_086032.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC134481898 Neighboring gene uncharacterized LOC134481829 Neighboring gene 60S ribosomal protein L12 pseudogene Neighboring gene uncharacterized LOC108352720 Neighboring gene large ribosomal subunit protein uL30m-like Neighboring gene uncharacterized LOC134481722 Neighboring gene uncharacterized LOC120096575 Neighboring gene coiled-coil domain containing 158

    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. Shroom3 contributes to the maintenance of the glomerular filtration barrier integrity. Yeo NC, et al. Genome Res, 2015 Jan. PMID 25273069, Free PMC Article
    2. Shroom regulates epithelial cell shape via the apical positioning of an actomyosin network. Hildebrand JD. J Cell Sci, 2005 Nov 15. PMID 16249236
    3. Shroom, a PDZ domain-containing actin-binding protein, is required for neural tube morphogenesis in mice. Hildebrand JD, et al. Cell, 1999 Nov 24. PMID 10589677
    4. Loss of cell polarity causes severe brain dysplasia in Lgl1 knockout mice. Klezovitch O, et al. Genes Dev, 2004 Mar 1. PMID 15037549, Free PMC Article
    5. 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

    See all (6) citations in PubMed

    GeneRIFs: Gene References Into Functions

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables actin binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables actin filament binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Process Evidence Code Pubs
    acts_upstream_of_or_within actin cytoskeleton organization ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in actin filament organization IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in biological_process ND
    No biological Data available
    more info
    		  
    acts_upstream_of_or_within columnar/cuboidal epithelial cell development ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within neural tube closure ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within pattern specification process ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within regulation of cell shape ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    is_active_in adherens junction IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in adherens junction ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in apical junction complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in apical junction complex ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in apical part of cell ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in apical plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in apical plasma membrane ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in cortical actin cytoskeleton IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytoskeleton ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in microtubule IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    protein Shroom3

    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_001100889.1 → NP_001094359.1  protein Shroom3

      Status: PROVISIONAL

      Source sequence(s)
      JAXUCZ010000014
      UniProtKB/TrEMBL
      A0A8I5XVY8
      Conserved Domains (3) summary
      cd00992
      Location:32 → 106
      PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...
      pfam08687
      Location:1662 → 1945
      ASD2; Apx/Shroom domain ASD2
      pfam08688
      Location:891 → 1070
      ASD1; Apx/Shroom domain ASD1

    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_086032.1 Reference GRCr8

      Range
      15383769..15681158 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006250723.5 → XP_006250785.1  protein Shroom3 isoform X1

      See identical proteins and their annotated locations for XP_006250785.1

      UniProtKB/TrEMBL
      A0A8I5XVY8, A6KK58, F1LP26
      Related
      ENSRNOP00000107290.1, ENSRNOT00000128277.1
      Conserved Domains (3) summary
      cd00992
      Location:32 → 106
      PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...
      pfam08687
      Location:1663 → 1946
      ASD2; Apx/Shroom domain ASD2
      pfam08688
      Location:891 → 1070
      ASD1; Apx/Shroom domain ASD1

    2. XM_039091852.2 → XP_038947780.1  protein Shroom3 isoform X2

      UniProtKB/TrEMBL
      A0A8I5XVY8
      Related
      ENSRNOP00000003001.7, ENSRNOT00000003001.8
      Conserved Domains (3) summary
      PTZ00449
      Location:571 → 830
      PTZ00449; 104 kDa microneme/rhoptry antigen; Provisional
      pfam08687
      Location:1488 → 1771
      ASD2; Apx/Shroom domain ASD2
      pfam08688
      Location:716 → 895
      ASD1; Apx/Shroom domain ASD1
    Nucleotide Protein Strain
    Heading Accession and Version

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