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    NCLN nicalin [ Homo sapiens (human) ]

    Gene ID: 56926, updated on 7-Apr-2024

    Summary

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    Official Symbol
    NCLNprovided by HGNC
    Official Full Name
    nicalinprovided by HGNC
    Primary source
    HGNC:HGNC:26923
    See related
    Ensembl:ENSG00000125912 MIM:609156; AllianceGenome:HGNC:26923
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    NET59
    Summary
    Enables ribosome binding activity. Involved in protein stabilization; regulation of protein complex stability; and regulation of protein-containing complex assembly. Located in endoplasmic reticulum membrane. Part of protein-containing complex. [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Ubiquitous expression in colon (RPKM 14.1), duodenum (RPKM 12.9) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    19p13.3
    Exon count:
    15
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (3185930..3209575)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (3160750..3184441)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (3185928..3209573)

    Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:3141544-3142044 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:3154789-3155746 Neighboring gene GNA15 divergent transcript Neighboring gene Sharpr-MPRA regulatory region 13242 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:3163409-3164269 Neighboring gene G protein subunit alpha 15 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:3176749-3177631 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9831 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13727 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13728 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13729 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13730 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:3185006-3185888 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9832 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:3189343-3189846 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:3189847-3190350 Neighboring gene sphingosine-1-phosphate receptor 4 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9833 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:3227850-3228390 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:3228391-3228930 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:3229472-3230011 Neighboring gene CUGBP Elav-like family member 5 Neighboring gene MPRA-validated peak3244 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9834 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9835 Neighboring gene uncharacterized LOC105372244 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:3301113-3301307 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9836 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9837 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9838 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13732 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9839 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9840 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9841 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9842 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9843 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13733 Neighboring gene skeletal muscle cis-regulatory module in NFIC intron Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:3389688-3390265 Neighboring gene nuclear factor I C Neighboring gene Sharpr-MPRA regulatory region 10296 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:3434103-3434880 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:3434881-3435658 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:3445307-3445848 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9844 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:3462537-3463072 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:3463073-3463608 Neighboring gene MPRA-validated peak3246 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:3465190-3465690 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:3465691-3466191 Neighboring gene Sharpr-MPRA regulatory region 13615

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Bibliography

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    Related articles in PubMed

    1. Identification of the soluble EphA7-interacting protein Nicalin as a regulator of EphA7 expression. Wang X, et al. Mol Cell Biochem, 2021 Jan. PMID 32914261
    2. The Nicastrin-like protein Nicalin regulates assembly and stability of the Nicalin-nodal modulator (NOMO) membrane protein complex. Haffner C, et al. J Biol Chem, 2007 Apr 6. PMID 17261586
    3. Substrate-driven assembly of a translocon for multipass membrane proteins. Sundaram A, et al. Nature, 2022 Nov. PMID 36261522, Free PMC Article
    4. 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
    5. An ER translocon for multi-pass membrane protein biogenesis. McGilvray PT, et al. Elife, 2020 Aug 21. PMID 32820719, Free PMC Article

    See all (79) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Identification of the soluble EphA7-interacting protein Nicalin as a regulator of EphA7 expression.
      Title: Identification of the soluble EphA7-interacting protein Nicalin as a regulator of EphA7 expression.
    Submit: New GeneRIF Correction

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables ribosome binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in determination of left/right asymmetry in lateral mesoderm ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in multi-pass transmembrane protein insertion into ER membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in negative regulation of nodal signaling pathway ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in protein stabilization IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in regulation of protein complex stability IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in regulation of protein-containing complex assembly IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in regulation of signal transduction IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    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 HDA PubMed 
    part_of multi-pass translocon complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of protein-containing complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    BOS complex subunit NCLN
    Names
    nicalin homolog
    nicastrin-like protein

    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_001321463.2 → NP_001308392.1  BOS complex subunit NCLN isoform 2 precursor

      Status: VALIDATED

      Source sequence(s)
      AC011547, BC025926, BG420915, BU508470, GD158011
      UniProtKB/TrEMBL
      B2RA56
      Conserved Domains (1) summary
      cd03882
      Location:130 → 429
      M28_nicalin_like; M28 Zn-Peptidase Nicalin, Nicastrin-like protein

    2. NM_020170.4 → NP_064555.2  BOS complex subunit NCLN isoform 1 precursor

      See identical proteins and their annotated locations for NP_064555.2

      Status: VALIDATED

      Source sequence(s)
      AL136567, AL365369, BC003076, BC007275, BC008920, BC010064, BC013283, BC025926
      Consensus CDS
      CCDS32869.1
      UniProtKB/Swiss-Prot
      D6W613, O75252, Q6FI60, Q6ZMB7, Q8TAT7, Q969V3, Q96H48, Q96IS7, Q9BQH9, Q9BTX4, Q9NPP2
      UniProtKB/TrEMBL
      B2RA56
      Related
      ENSP00000246117.3, ENST00000246117.9
      Conserved Domains (1) summary
      cd03882
      Location:127 → 429
      M28_nicalin_like; M28 Zn-Peptidase Nicalin, Nicastrin-like protein

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000019.10 Reference GRCh38.p14 Primary Assembly

      Range
      3185930..3209575
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060943.1 Alternate T2T-CHM13v2.0

      Range
      3160750..3184441
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q969V3.2 GenPept UniProtKB/Swiss-Prot:Q969V3

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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