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    NCDN neurochondrin [ Homo sapiens (human) ]

    Gene ID: 23154, updated on 5-Mar-2024

    Summary

    Official Symbol
    NCDNprovided by HGNC
    Official Full Name
    neurochondrinprovided by HGNC
    Primary source
    HGNC:HGNC:17597
    See related
    Ensembl:ENSG00000020129 MIM:608458; AllianceGenome:HGNC:17597
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    NEDIES
    Summary
    This gene encodes a leucine-rich cytoplasmic protein, which is highly similar to a mouse protein that negatively regulates Ca/calmodulin-dependent protein kinase II phosphorylation and may be essential for spatial learning processes. Several alternatively spliced transcript variants of this gene have been described. [provided by RefSeq, Jul 2008]
    Expression
    Biased expression in brain (RPKM 97.7), adrenal (RPKM 7.8) and 6 other tissues See more
    Orthologs
    NEW
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    Try the new Transcript table

    Genomic context

    See NCDN in Genome Data Viewer
    Location:
    1p34.3
    Exon count:
    8
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (35557799..35566779)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (35420844..35429828)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (36023400..36032380)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene KIAA0319 like Neighboring gene RNY5 pseudogene 1 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:35916701-35916880 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 728 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:35931229-35931375 Neighboring gene Sharpr-MPRA regulatory region 12145 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 729 Neighboring gene zinc finger protein 485 pseudogene Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:35996497-35996998 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:35996999-35997498 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 730 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 731 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 640 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:36019721-36020677 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:36020678-36021633 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:36022434-36023161 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:36023162-36023888 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 643 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:36024616-36025341 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:36025798-36026432 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:36035818-36035919 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:36038879-36039378 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:36039620-36040366 Neighboring gene TFAP2E antisense RNA 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:36042064-36042916 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:36042917-36043769 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:36055869-36056370 Neighboring gene transcription factor AP-2 epsilon Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:36056371-36056870 Neighboring gene proteasome 20S subunit beta 2 Neighboring gene Sharpr-MPRA regulatory region 1763 Neighboring gene MPRA-validated peak173 silencer Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancers GRCh37_chr1:36106102-36107067 and GRCh37_chr1:36107068-36108032

    Genomic regions, transcripts, and products

    Expression

    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • KIAA0607

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in bone resorption IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in neuron projection development IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in neuron projection development ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in regulation of neuronal synaptic plasticity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    Component Evidence Code Pubs
    NOT located_in axon ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in cytosol ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    is_active_in dendrite IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in dendrite ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in endosome membrane IEA
    Inferred from Electronic Annotation
    more info
     
    located_in membrane HDA PubMed 
    located_in membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in neuronal cell body ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    NOT located_in nucleus ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in perikaryon IEA
    Inferred from Electronic Annotation
    more info
     
    located_in postsynapse IEA
    Inferred from Electronic Annotation
    more info
     

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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_001014839.2NP_001014839.1  neurochondrin isoform 1

      See identical proteins and their annotated locations for NP_001014839.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1), also known as NCDN-1, encodes the longer isoform (1).
      Source sequence(s)
      AB018739, AL536768, AW207151, BC024592
      Consensus CDS
      CCDS392.1
      UniProtKB/Swiss-Prot
      D3DPR9, Q9UBB6, Q9UBY2, Q9Y4A6, Q9Y4D9
      Related
      ENSP00000348394.4, ENST00000356090.8
      Conserved Domains (1) summary
      pfam05536
      Location:30637
      Neurochondrin
    2. NM_001014841.2NP_001014841.1  neurochondrin isoform 2

      See identical proteins and their annotated locations for NP_001014841.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2), also known as NCDN-2, contains a distinct 5' UTR and lacks an in-frame portion of the 5' coding region, compared to variant 1. The resulting isoform (2) has a shorter N-terminus when compared to isoform 1.
      Source sequence(s)
      AB018740, AL536768, AW207151, BC024592
      Consensus CDS
      CCDS30672.1
      UniProtKB/Swiss-Prot
      Q9UBB6
      Related
      ENSP00000362350.3, ENST00000373253.7
      Conserved Domains (1) summary
      pfam05536
      Location:13620
      Neurochondrin
    3. NM_014284.3NP_055099.1  neurochondrin isoform 1

      See identical proteins and their annotated locations for NP_055099.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR compared to variant 1. Variants 1 and 3 encode the same isoform (1).
      Source sequence(s)
      AL536768, AW207151, BC024592, BI545092
      Consensus CDS
      CCDS392.1
      UniProtKB/Swiss-Prot
      D3DPR9, Q9UBB6, Q9UBY2, Q9Y4A6, Q9Y4D9
      Related
      ENSP00000362340.2, ENST00000373243.7
      Conserved Domains (1) summary
      pfam05536
      Location:30637
      Neurochondrin

    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_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      35557799..35566779
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      35420844..35429828
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)