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    ncln nicalin [ Danio rerio (zebrafish) ]

    Gene ID: 336844, updated on 2-Nov-2024

    Summary

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    Official Symbol
    nclnprovided by ZNC
    Official Full Name
    nicalinprovided by ZNC
    Primary source
    ZFIN:ZDB-GENE-030131-8788
    See related
    Ensembl:ENSDARG00000058861 AllianceGenome:ZFIN:ZDB-GENE-030131-8788
    Gene type
    protein coding
    RefSeq status
    PROVISIONAL
    Organism
    Danio rerio
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
    Also known as
    ncl1; zgc:77236; wu:fb07e09; wu:fk52a06
    Summary
    Predicted to enable ribosome binding activity. Involved in determination of left/right asymmetry in lateral mesoderm and negative regulation of nodal signaling pathway. Acts upstream of or within enteric nervous system development and regulation of signal transduction. Located in endoplasmic reticulum membrane. Is expressed in central nervous system and intestine. Orthologous to human NCLN (nicalin). [provided by Alliance of Genome Resources, Nov 2024]
    Orthologs
    human mouse all
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    Genomic context

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    See ncln in Genome Data Viewer
    Location:
    chromosome: 22
    Exon count:
    15
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCz11 (GCF_000002035.6) 22 NC_007133.7 (5233396..5252014, complement)
    105 previous assembly GRCz10 (GCF_000002035.5) 22 NC_007133.6 (4849018..4867672, complement)

    Chromosome 22 - NC_007133.7Genomic Context describing neighboring genes Neighboring gene tumor necrosis factor, alpha-induced protein 8-like 1 Neighboring gene ceramide synthase 1 Neighboring gene microRNA 27e Neighboring gene microRNA 23a-1

    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. The biochemical and genetic odyssey to the function of a nicastrin-like protein. Haffner C, et al. Neurodegener Dis, 2004. PMID 16908989
    2. Cellular functions of gamma-secretase-related proteins. Haffner C, et al. Neurodegener Dis, 2006. PMID 17047369
    3. Transmembrane protein 147 (TMEM147) is a novel component of the Nicalin-NOMO protein complex. Dettmer U, et al. J Biol Chem, 2010 Aug 20. PMID 20538592, Free PMC Article
    4. Analysis of nicastrin gene phylogeny and expression in zebrafish. Lim A, et al. Dev Genes Evol, 2015 Jun. PMID 25940938
    5. Whole exome sequencing coupled with unbiased functional analysis reveals new Hirschsprung disease genes. Gui H, et al. Genome Biol, 2017 Mar 8. PMID 28274275, Free PMC Article

    See all (15) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. nicalin is associated with protein complexes involved in cell fate decisions during early embryonic development--{review}
      Title: The biochemical and genetic odyssey to the function of a nicastrin-like protein.
    2. Nicalin/Nodal modulator complex antagonizes Nodal signaling during mesendodermal patterning in zebrafish
      Title: Nicalin and its binding partner Nomo are novel Nodal signaling antagonists.
    Submit: New GeneRIF Correction

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by ZFIN

    Function Evidence Code Pubs
    enables ribosome binding ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Process Evidence Code Pubs
    involved_in determination of left/right asymmetry in lateral mesoderm IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within enteric nervous system development IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in multi-pass transmembrane protein insertion into ER membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in negative regulation of nodal signaling pathway IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in regulation of signal transduction IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within regulation of signal transduction IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    acts_upstream_of_or_within regulation of signal transduction IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within regulation of signal transduction IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in endoplasmic reticulum IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in endoplasmic reticulum membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in endoplasmic reticulum membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    part_of multi-pass translocon complex ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  

    General protein information

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    Preferred Names
    BOS complex subunit ncln
    Names
    nicalin-1
    nicastrin-like protein 1

    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_207057.1 → NP_996940.1  BOS complex subunit ncln precursor

      See identical proteins and their annotated locations for NP_996940.1

      Status: PROVISIONAL

      Source sequence(s)
      BC066393
      UniProtKB/Swiss-Prot
      Q6NZ07, Q6PHK1
      Related
      ENSDARP00000076240.3, ENSDART00000081801.4
      Conserved Domains (1) summary
      cd03882
      Location:123 → 437
      M28_nicalin_like; M28 Zn-Peptidase Nicalin, Nicastrin-like protein

    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_007133.7 Reference GRCz11 Primary Assembly

      Range
      5233396..5252014 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_005161591.5 → XP_005161648.1  BOS complex subunit ncln isoform X3

      UniProtKB/TrEMBL
      A0A8M2B8R6
      Conserved Domains (1) summary
      cd03882
      Location:123 → 422
      M28_nicalin_like; M28 Zn-Peptidase Nicalin, Nicastrin-like protein

    2. XM_005161590.5 → XP_005161647.1  BOS complex subunit ncln isoform X2

      UniProtKB/TrEMBL
      A0A8M2B8L1
      Conserved Domains (1) summary
      cd03882
      Location:123 → 422
      M28_nicalin_like; M28 Zn-Peptidase Nicalin, Nicastrin-like protein

    3. XM_005161589.5 → XP_005161646.1  BOS complex subunit ncln isoform X1

      See identical proteins and their annotated locations for XP_005161646.1

      UniProtKB/Swiss-Prot
      Q6NZ07
      Related
      ENSDARP00000122266.1, ENSDART00000132942.3
      Conserved Domains (1) summary
      cd03882
      Location:123 → 437
      M28_nicalin_like; M28 Zn-Peptidase Nicalin, Nicastrin-like protein
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q6NZ07.1 GenPept UniProtKB/Swiss-Prot:Q6NZ07

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