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    si:ch211-282j22.3 si:ch211-282j22.3 [ Danio rerio (zebrafish) ]

    Gene ID: 562939, updated on 18-Sep-2024

    Summary

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    Official Symbol
    si:ch211-282j22.3provided by ZNC
    Official Full Name
    si:ch211-282j22.3provided by ZNC
    Primary source
    ZFIN:ZDB-GENE-091113-49
    See related
    Ensembl:ENSDARG00000010524 AllianceGenome:ZFIN:ZDB-GENE-091113-49
    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
    Summary
    Predicted to enable calcium ion binding activity; hydrolase activity, hydrolyzing O-glycosyl compounds; and lytic transglycosylase activity. Predicted to act upstream of or within carbohydrate metabolic process and mannose trimming involved in glycoprotein ERAD pathway. Predicted to be located in membrane. Human ortholog(s) of this gene implicated in congenital disorder of glycosylation type II. Orthologous to human EDEM3 (ER degradation enhancing alpha-mannosidase like protein 3). [provided by Alliance of Genome Resources, Apr 2022]
    Orthologs
    all
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    Genomic context

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    See si:ch211-282j22.3 in Genome Data Viewer
    Location:
    chromosome: 21
    Exon count:
    20
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCz11 (GCF_000002035.6) 21 NC_007132.7 (13759926..13785324, complement)
    105 previous assembly GRCz10 (GCF_000002035.5) 21 NC_007132.6 (13663498..13688608, complement)

    Chromosome 21 - NC_007132.7Genomic Context describing neighboring genes Neighboring gene POU domain, class 5, transcription factor 3 Neighboring gene neural proliferation, differentiation and control, 1a Neighboring gene solute carrier family 31 member 2 Neighboring gene niban apoptosis regulator 2a

    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 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. RFX transcription factors are essential for hearing in mice. Elkon R, et al. Nat Commun, 2015 Oct 15. PMID 26469318, Free PMC Article
    2. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, et al. Brief Bioinform, 2011 Sep. PMID 21873635, Free PMC Article
    3. Gene evolution and gene expression after whole genome duplication in fish: the PhyloFish database. Pasquier J, et al. BMC Genomics, 2016 May 18. PMID 27189481, Free PMC Article

    GeneRIFs: Gene References Into Functions

    General gene information

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    Homology

    Gene Ontology Provided by ZFIN

    Function Evidence Code Pubs
    enables calcium ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables hydrolase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables hydrolase activity, acting on glycosyl bonds IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables hydrolase activity, hydrolyzing O-glycosyl compounds IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables mannosyl-oligosaccharide 1,2-alpha-mannosidase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables mannosyl-oligosaccharide 1,2-alpha-mannosidase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    acts_upstream_of_or_within carbohydrate metabolic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within endoplasmic reticulum mannose trimming IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in endoplasmic reticulum unfolded protein response IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in mannoprotein catabolic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within mannose trimming involved in glycoprotein ERAD pathway IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in ubiquitin-dependent glycoprotein ERAD pathway IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    is_active_in endoplasmic reticulum IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in endoplasmic reticulum IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in membrane IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    ER degradation-enhancing alpha-mannosidase-like protein 3

    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_007132.7 Reference GRCz11 Primary Assembly

      Range
      13759926..13785324 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_003200833.6 → XP_003200881.1  ER degradation-enhancing alpha-mannosidase-like protein 3 isoform X1

      UniProtKB/TrEMBL
      A0A8M1RMX5, E7F7X8
      Related
      ENSDARP00000002926.6, ENSDART00000024720.7
      Conserved Domains (2) summary
      cd02126
      Location:642 → 768
      PA_EDEM3_like; PA_EDEM3_like: protease associated domain (PA) domain-containing EDEM3-like proteins. This group contains various PA domain-containing proteins similar to mouse EDEM3 (ER-degradation-enhancing mannosidase-like 3 protein). EDEM3 contains a region, similar ...
      pfam01532
      Location:55 → 494
      Glyco_hydro_47; Glycosyl hydrolase family 47

    2. XM_021469032.2 → XP_021324707.1  ER degradation-enhancing alpha-mannosidase-like protein 3 isoform X2

      UniProtKB/TrEMBL
      A0A8M9P3N3
      Conserved Domains (2) summary
      cd02126
      Location:642 → 768
      PA_EDEM3_like; protease associated domain (PA) domain-containing EDEM3-like proteins. This group contains various PA domain-containing proteins similar to mouse EDEM3 (ER-degradation-enhancing mannosidase-like 3 protein). EDEM3 contains a region, similar to Class I ...
      pfam01532
      Location:55 → 494
      Glyco_hydro_47; Glycosyl hydrolase family 47
    Nucleotide Protein
    Heading Accession and Version

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