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    Shroom3 shroom family member 3 [ Mus musculus (house mouse) ]

    Gene ID: 27428, updated on 9-Dec-2024

    Summary

    Official Symbol
    Shroom3provided by MGI
    Official Full Name
    shroom family member 3provided by MGI
    Primary source
    MGI:MGI:1351655
    See related
    Ensembl:ENSMUSG00000029381 AllianceGenome:MGI:1351655
    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
    Shrm; Shrm3; D5Ertd287e
    Summary
    Enables actin binding activity. Acts upstream of or within several processes, including columnar/cuboidal epithelial cell development; neural tube closure; and regulation of cell shape. Located in several cellular components, including adherens junction; apical junction complex; and apical plasma membrane. Is expressed in several structures, including central nervous system; gut; heart; paraxial mesenchyme; and sensory organ. Orthologous to human SHROOM3 (shroom family member 3). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Broad expression in colon adult (RPKM 39.5), small intestine adult (RPKM 32.7) and 15 other tissues See more
    Orthologs
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    Genomic context

    See Shroom3 in Genome Data Viewer
    Location:
    5 E2; 5 47.29 cM
    Exon count:
    15
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 5 NC_000071.7 (92831294..93113618)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 5 NC_000071.6 (92683435..92965759)

    Chromosome 5 - NC_000071.7Genomic Context describing neighboring genes Neighboring gene VISTA enhancer mm187 Neighboring gene coiled-coil domain containing 158 Neighboring gene starch binding domain 1 Neighboring gene STARR-seq mESC enhancer starr_13649 Neighboring gene STARR-seq mESC enhancer starr_13650 Neighboring gene STARR-seq mESC enhancer starr_13651 Neighboring gene STARR-seq mESC enhancer starr_13653 Neighboring gene microRNA 1961 Neighboring gene STARR-seq mESC enhancer starr_13654 Neighboring gene STARR-seq mESC enhancer starr_13657 Neighboring gene STARR-seq mESC enhancer starr_13658 Neighboring gene VISTA enhancer mm397 Neighboring gene predicted gene, 36764 Neighboring gene predicted gene, 25521 Neighboring gene ribosomal protein L9 pseudogene

    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)
    • Chemically induced (ENU) (1) 
    • Endonuclease-mediated (4) 
    • Gene trapped (1)  1 citation

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables actin binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables actin filament binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables actin filament binding IEA
    Inferred from Electronic Annotation
    more info
     
    Process Evidence Code Pubs
    acts_upstream_of_or_within actin cytoskeleton organization IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    involved_in actin filament organization IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in apical protein localization ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in cell morphogenesis ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in cellular pigment accumulation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    acts_upstream_of_or_within columnar/cuboidal epithelial cell development IDA
    Inferred from Direct Assay
    more info
    PubMed 
    acts_upstream_of_or_within neural tube closure IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within pattern specification process IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within regulation of cell shape IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Component Evidence Code Pubs
    is_active_in adherens junction IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in adherens junction IDA
    Inferred from Direct Assay
    more info
    PubMed 
    is_active_in apical junction complex IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in apical junction complex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in apical part of cell IDA
    Inferred from Direct Assay
    more info
    PubMed 
    is_active_in apical plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in apical plasma membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    is_active_in cortical actin cytoskeleton IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in cytoplasm IEA
    Inferred from Electronic Annotation
    more info
     
    located_in cytoskeleton IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in microtubule IEA
    Inferred from Electronic Annotation
    more info
     

    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_001077595.2NP_001071063.1  protein Shroom3 isoform 2

      See identical proteins and their annotated locations for NP_001071063.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR and the 5' coding region and initiates translation at a downstream start codon, compared to variant 1. Variants 2 and 3 encode the same isoform (2).
      Source sequence(s)
      AK147493, AK164918, BM942679, CJ103792
      Consensus CDS
      CCDS39155.1
      UniProtKB/Swiss-Prot
      Q3TNX1, Q6ZPP9, Q99L16, Q9QXM9, Q9QXN0
      UniProtKB/TrEMBL
      A0A0R4J1H8
      Related
      ENSMUSP00000108677.3, ENSMUST00000113054.9
      Conserved Domains (3) summary
      PHA03247
      Location:562959
      PHA03247; large tegument protein UL36; Provisional
      pfam08687
      Location:14801764
      ASD2; Apx/Shroom domain ASD2
      pfam08688
      Location:707881
      ASD1; Apx/Shroom domain ASD1
    2. NM_001077596.2NP_001071064.1  protein Shroom3 isoform 2

      See identical proteins and their annotated locations for NP_001071064.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR and the 5' coding region and initiates translation at a downstream start codon, compared to variant 1. Variants 2 and 3 encode the same isoform (2).
      Source sequence(s)
      AK147493, BM942679, CJ045556
      Consensus CDS
      CCDS39155.1
      UniProtKB/Swiss-Prot
      Q3TNX1, Q6ZPP9, Q99L16, Q9QXM9, Q9QXN0
      UniProtKB/TrEMBL
      A0A0R4J1H8
      Related
      ENSMUSP00000108674.3, ENSMUST00000113051.9
      Conserved Domains (3) summary
      PHA03247
      Location:562959
      PHA03247; large tegument protein UL36; Provisional
      pfam08687
      Location:14801764
      ASD2; Apx/Shroom domain ASD2
      pfam08688
      Location:707881
      ASD1; Apx/Shroom domain ASD1
    3. NM_015756.2NP_056571.2  protein Shroom3 isoform 1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longer isoform (1).
      Source sequence(s)
      AC124560, AC125233, AK147493, BM942679
      Consensus CDS
      CCDS39154.1
      UniProtKB/Swiss-Prot
      Q3TNX1, Q6ZPP9, Q99L16, Q9QXM9, Q9QXN0
      UniProtKB/TrEMBL
      E9QMY5
      Related
      ENSMUSP00000108678.3, ENSMUST00000113055.9
      Conserved Domains (3) summary
      cd00992
      Location:32106
      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:16551939
      ASD2; Apx/Shroom domain ASD2
      pfam08688
      Location:8821056
      ASD1; Apx/Shroom domain ASD1

    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_000071.7 Reference GRCm39 C57BL/6J

      Range
      92831294..93113618
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006534966.5XP_006535029.1  protein Shroom3 isoform X1

      UniProtKB/Swiss-Prot
      Q3TNX1, Q6ZPP9, Q99L16, Q9QXM9, Q9QXN0
      UniProtKB/TrEMBL
      A0A286YDQ8
      Related
      ENSMUSP00000153516.2, ENSMUST00000225438.2
      Conserved Domains (3) summary
      PHA03247
      Location:6561053
      PHA03247; large tegument protein UL36; Provisional
      pfam08687
      Location:15741858
      ASD2; Apx/Shroom domain ASD2
      pfam08688
      Location:801975
      ASD1; Apx/Shroom domain ASD1
    2. XM_006534968.4XP_006535031.1  protein Shroom3 isoform X2

      See identical proteins and their annotated locations for XP_006535031.1

      UniProtKB/Swiss-Prot
      Q3TNX1, Q6ZPP9, Q99L16, Q9QXM9, Q9QXN0
      UniProtKB/TrEMBL
      A0A0R4J1H8
      Conserved Domains (3) summary
      PHA03247
      Location:562959
      PHA03247; large tegument protein UL36; Provisional
      pfam08687
      Location:14801764
      ASD2; Apx/Shroom domain ASD2
      pfam08688
      Location:707881
      ASD1; Apx/Shroom domain ASD1