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nalcn sodium leak channel, non-selective [ Danio rerio (zebrafish) ]

Gene ID: 548345, updated on 2-Nov-2024

Summary

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Official Symbol
nalcnprovided by ZNC
Official Full Name
sodium leak channel, non-selectiveprovided by ZNC
Primary source
ZFIN:ZDB-GENE-050410-12
See related
Ensembl:ENSDARG00000001835 AllianceGenome:ZFIN:ZDB-GENE-050410-12
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Danio rerio
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
Also known as
zgc:113349
Summary
Predicted to enable monoatomic cation channel activity. Predicted to be involved in positive regulation of GABAergic synaptic transmission and positive regulation of cholinergic synaptic transmission. Predicted to act upstream of or within monoatomic ion transport and transmembrane transport. Predicted to be located in membrane. Predicted to be active in plasma membrane. Is expressed in central nervous system. Human ortholog(s) of this gene implicated in congenital limbs-face contractures-hypotonia-developmental delay syndrome. Orthologous to human NALCN (sodium leak channel, non-selective). [provided by Alliance of Genome Resources, Nov 2024]
Orthologs
human mouse all
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Genomic context

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See nalcn in Genome Data Viewer
Location:
chromosome: 9
Exon count:
46
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCz11 (GCF_000002035.6) 9 NC_007120.7 (31588672..31747106, complement)
105 previous assembly GRCz10 (GCF_000002035.5) 9 NC_007120.6 (31777920..31936394, complement)

Chromosome 9 - NC_007120.7Genomic Context describing neighboring genes Neighboring gene si:ch211-168k14.2 Neighboring gene transmembrane O-mannosyltransferase targeting cadherins 4 Neighboring gene uncharacterized LOC137496427 Neighboring gene integrin, beta-like 1 Neighboring gene fibroblast growth factor 14

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. Candidate risk genes for bipolar disorder are highly conserved during evolution and highly interconnected. Franklin C, et al. Bipolar Disord, 2021 Jun. PMID 32959503
  2. Evolution of complexity in the zebrafish synapse proteome. Bayés À, et al. Nat Commun, 2017 Mar 2. PMID 28252024, 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

General gene information

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Homology

Gene Ontology Provided by ZFIN

Function Evidence Code Pubs
enables monoatomic cation channel activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables monoatomic cation channel activity IEA
Inferred from Electronic Annotation
more info
  
enables monoatomic ion channel activity IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
acts_upstream_of_or_within monoatomic ion transport IEA
Inferred from Electronic Annotation
more info
  
involved_in positive regulation of synaptic transmission, GABAergic IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in positive regulation of synaptic transmission, cholinergic IBA
Inferred from Biological aspect of Ancestor
more info
  
acts_upstream_of_or_within transmembrane transport IEA
Inferred from Electronic Annotation
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
sodium leak channel NALCN

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_001017549.2 → NP_001017549.2  sodium leak channel NALCN

    Status: VALIDATED

    Source sequence(s)
    BX571700, BX571786
    UniProtKB/TrEMBL
    A0A8M1N575, F1QCP2
    Related
    ENSDARP00000048468.6, ENSDART00000048469.9
    Conserved Domains (1) summary
    pfam00520
    Location:1263 → 1481
    Ion_trans; Ion transport 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_007120.7 Reference GRCz11 Primary Assembly

    Range
    31588672..31747106 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_009304740.4 → XP_009303015.1  sodium leak channel NALCN isoform X2

    See identical proteins and their annotated locations for XP_009303015.1

    UniProtKB/TrEMBL
    A0A8M3B5P5
    Conserved Domains (1) summary
    pfam00520
    Location:1261 → 1479
    Ion_trans; Ion transport protein

  2. XM_005167698.5 → XP_005167755.1  sodium leak channel NALCN isoform X1

    UniProtKB/TrEMBL
    A0A8M2BF56
    Conserved Domains (1) summary
    pfam00520
    Location:1263 → 1481
    Ion_trans; Ion transport protein

  3. XM_009304739.3 → XP_009303014.1  sodium leak channel NALCN isoform X2

    See identical proteins and their annotated locations for XP_009303014.1

    UniProtKB/TrEMBL
    A0A8M3B5P5
    Conserved Domains (1) summary
    pfam00520
    Location:1261 → 1479
    Ion_trans; Ion transport protein

  4. XM_017357669.2 → XP_017213158.1  sodium leak channel NALCN isoform X1

    UniProtKB/TrEMBL
    A0A8M2BF56
    Conserved Domains (1) summary
    pfam00520
    Location:1263 → 1481
    Ion_trans; Ion transport protein
Nucleotide Protein Strain
Heading Accession and Version

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