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    shroom4 shroom family member 4 [ Danio rerio (zebrafish) ]

    Gene ID: 559035, updated on 9-Dec-2024

    Summary

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    Official Symbol
    shroom4provided by ZNC
    Official Full Name
    shroom family member 4provided by ZNC
    Primary source
    ZFIN:ZDB-GENE-041111-246
    See related
    Ensembl:ENSDARG00000079900 AllianceGenome:ZFIN:ZDB-GENE-041111-246
    Gene type
    protein coding
    RefSeq status
    MODEL
    Organism
    Danio rerio
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
    Also known as
    im:7145757; wu:fe05h01; zgc:194172; zgc:194173
    Summary
    Predicted to enable actin filament binding activity. Acts upstream of or within peristalsis. Predicted to be located in cytoplasm. Predicted to be active in several cellular components, including adherens junction; apical junction complex; and apical plasma membrane. Is expressed in brain; gut; head; heart; and pectoral fin bud. Orthologous to human SHROOM4 (shroom family member 4). [provided by Alliance of Genome Resources, Dec 2024]
    Orthologs
    human mouse all
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    Genomic context

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    See shroom4 in Genome Data Viewer
    Location:
    chromosome: 7
    Exon count:
    12
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCz11 (GCF_000002035.6) 7 NC_007118.7 (24729599..24812648)
    105 previous assembly GRCz10 (GCF_000002035.5) 7 NC_007118.6 (24458406..24541861)

    Chromosome 7 - NC_007118.7Genomic Context describing neighboring genes Neighboring gene calbindin 2b Neighboring gene cap methyltransferase 2 Neighboring gene si:ch211-226l4.6 Neighboring gene OTU deubiquitinase, ubiquitin aldehyde binding 1b

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
    • Description: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
    • BioProject: PRJEB1986
    • Analysis date: Fri Dec 8 19:48:10 2017

    Bibliography

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    Related articles in PubMed

    1. X-linked variations in SHROOM4 are implicated in congenital anomalies of the urinary tract and the anorectal, cardiovascular and central nervous systems. Kolvenbach CM, et al. J Med Genet, 2023 Jun. PMID 36379543, Free PMC Article
    2. RESA identifies mRNA-regulatory sequences at high resolution. Yartseva V, et al. Nat Methods, 2017 Feb. PMID 28024160, Free PMC Article
    3. RFX transcription factors are essential for hearing in mice. Elkon R, et al. Nat Commun, 2015 Oct 15. PMID 26469318, Free PMC Article
    4. 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
    5. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, et al. Brief Bioinform, 2011 Sep. PMID 21873635, Free PMC Article

    See all (6) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. X-linked variations in SHROOM4 are implicated in congenital anomalies of the urinary tract and the anorectal, cardiovascular and central nervous systems.
      Title: X-linked variations in SHROOM4 are implicated in congenital anomalies of the urinary tract and the anorectal, cardiovascular and central nervous systems.
    Submit: New GeneRIF Correction

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by ZFIN

    Function Evidence Code Pubs
    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
    involved_in actin filament organization IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within peristalsis IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    is_active_in adherens junction IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    is_active_in apical junction complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    is_active_in apical plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    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
    		  

    General protein information

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    Preferred Names
    protein Shroom4; shroom family member 4

    NCBI Reference Sequences (RefSeq)

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    RefSeqs of Annotated Genomes: GCF_000002035.6-RS_2024_08

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

    Reference GRCz11 Primary Assembly

    Genomic

    1. NC_007118.7 Reference GRCz11 Primary Assembly

      Range
      24729599..24812648
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_005172333.5 → XP_005172390.1  protein Shroom4 isoform X1

      UniProtKB/TrEMBL
      A0A8M2BJN6, F1Q6C1
      Related
      ENSDARP00000103889.3, ENSDART00000111542.5
      Conserved Domains (2) summary
      cd00992
      Location:12 → 91
      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:1372 → 1622
      ASD2; Apx/Shroom domain ASD2

    2. XM_068222593.1 → XP_068078694.1  protein Shroom4 isoform X3

    3. XM_682334.10 → XP_687426.5  protein Shroom4 isoform X2

      UniProtKB/TrEMBL
      A0A8N7TES2
      Conserved Domains (1) summary
      pfam08687
      Location:1246 → 1496
      ASD2; Apx/Shroom domain ASD2
    Nucleotide Protein Strain
    Heading Accession and Version

    Gene LinkOut

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