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ncln nicalin [ Danio rerio (zebrafish) ]

Gene ID: 336844, updated on 9-Dec-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, Dec 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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