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    si:ch211-129c21.1 si:ch211-129c21.1 [ Danio rerio (zebrafish) ]

    Gene ID: 563087, updated on 11-Apr-2024

    Summary

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    Official Symbol
    si:ch211-129c21.1provided by ZNC
    Official Full Name
    si:ch211-129c21.1provided by ZNC
    Primary source
    ZFIN:ZDB-GENE-030131-5796
    See related
    Ensembl:ENSDARG00000024775 AllianceGenome:ZFIN:ZDB-GENE-030131-5796
    Gene type
    protein coding
    RefSeq status
    PREDICTED
    Organism
    Danio rerio
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
    Also known as
    fi18h09; wu:fb73c06; wu:fi18h09
    Summary
    Predicted to enable chemorepellent activity and semaphorin receptor binding activity. Predicted to be involved in several processes, including generation of neurons; negative regulation of alkaline phosphatase activity; and ossification involved in bone maturation. Predicted to be located in membrane. Predicted to be integral component of membrane. Predicted to be active in extracellular space. Predicted to be integral component of plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]
    Orthologs
    all
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    Genomic context

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    See si:ch211-129c21.1 in Genome Data Viewer
    Location:
    chromosome: 22
    Exon count:
    15
    Annotation release Status Assembly Chr Location
    106 current GRCz11 (GCF_000002035.6) 22 NC_007133.7 (22316838..22340793, complement)
    105 previous assembly GRCz10 (GCF_000002035.5) 22 NC_007133.6 (22291686..22315769, complement)

    Chromosome 22 - NC_007133.7Genomic Context describing neighboring genes Neighboring gene chromatin assembly factor 1, subunit A (p150) Neighboring gene secretory carrier membrane protein 4 Neighboring gene calmodulin regulated spectrin-associated protein family, member 2a Neighboring gene DEAD (Asp-Glu-Ala-Asp) box polypeptide 59

    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. Unilateral dampening of Bmp activity by nodal generates cardiac left-right asymmetry. Veerkamp J, et al. Dev Cell, 2013 Mar 25. PMID 23499359
    2. RFX transcription factors are essential for hearing in mice. Elkon R, et al. Nat Commun, 2015 Oct 15. PMID 26469318, Free PMC Article
    3. 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 ZFIN

    Function Evidence Code Pubs
    enables chemorepellent activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables semaphorin receptor binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables semaphorin receptor binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in axon guidance IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in negative chemotaxis IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in neural crest cell migration IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in positive regulation of cell migration IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in semaphorin-plexin signaling pathway IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    located_in membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    semaphorin 4d; uncharacterized protein LOC563087

    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_001045008.1 → NP_001038473.1  uncharacterized protein LOC563087

      Status: PREDICTED

      Source sequence(s)
      BX005201
      UniProtKB/TrEMBL
      A0A8M1N9V0, M9MMA2
      Related
      ENSDARP00000096374.4, ENSDART00000105597.5
      Conserved Domains (4) summary
      cd05873
      Location:542 → 628
      Ig_Sema4D_like; Immunoglobulin (Ig)-like domain of the class IV semaphorin Sema4D
      cd11260
      Location:26 → 482
      Sema_4E; The Sema domain, a protein interacting module, of semaphorin 4E (Sema4E)
      smart00410
      Location:544 → 607
      IG_like; Immunoglobulin like
      smart00423
      Location:483 → 537
      PSI; domain found in Plexins, Semaphorins and Integrins

    RefSeqs of Annotated Genomes: Danio rerio Annotation Release 106 details...Open this link in a new tab

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

    Reference GRCz11 Primary Assembly

    Genomic

    1. NC_007133.7 Reference GRCz11 Primary Assembly

      Range
      22316838..22340793 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_005170470.4 → XP_005170527.1  semaphorin 4d isoform X1

      UniProtKB/TrEMBL
      A0A8M2BHS6
      Conserved Domains (4) summary
      cd05873
      Location:558 → 644
      Ig_Sema4D_like; Immunoglobulin (Ig)-like domain of the class IV semaphorin Sema4D
      cd11260
      Location:42 → 498
      Sema_4E; The Sema domain, a protein interacting module, of semaphorin 4E (Sema4E)
      smart00410
      Location:560 → 623
      IG_like; Immunoglobulin like
      smart00423
      Location:499 → 553
      PSI; domain found in Plexins, Semaphorins and Integrins

    Reference GRCz11 ALT_DRER_TU_1

    Genomic

    1. NW_018395106.1 Reference GRCz11 ALT_DRER_TU_1

      Range
      156795..182211 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein Strain
    Heading Accession and Version

    Gene LinkOut

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