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Aliases for NCDN Gene

Aliases for NCDN Gene

  • Neurochondrin 2 3 3 5
  • KIAA0607 4

External Ids for NCDN Gene

Previous GeneCards Identifiers for NCDN Gene

  • GC01P035844
  • GC01P035080
  • GC01P035449
  • GC01P035451
  • GC01P035692
  • GC01P035795
  • GC01P036023
  • GC01P034141

Summaries for NCDN Gene

Entrez Gene Summary for NCDN Gene

  • 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]

GeneCards Summary for NCDN Gene

NCDN (Neurochondrin) is a Protein Coding gene.

UniProtKB/Swiss-Prot for NCDN Gene

  • Probably involved in signal transduction, in the nervous system, via increasing cell surface localization of GRM5 and positively regulating its signaling (By similarity). Required for the spatial learning process. Acts as a negative regulator of Ca(2+)-calmodulin-dependent protein kinase 2 (CaMK2) phosphorylation. May play a role in modulating melanin-concentrating hormone-mediated functions via its interaction with MCHR1 that interferes with G protein-coupled signal transduction. May be involved in bone metabolism. May also be involved in neurite outgrowth.

Gene Wiki entry for NCDN Gene

Additional gene information for NCDN Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for NCDN Gene

Genomics for NCDN Gene

Regulatory Elements for NCDN Gene

Enhancers for NCDN Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH01H035444 1.4 Ensembl ENCODE dbSUPER 11.7 -107.8 -107762 11 HDGF FOXA2 PKNOX1 TBL1XR1 RB1 ARNT ARID4B RAD21 YY1 ZNF143 NCDN KIAA0319L ENSG00000232335 CLSPN ZMYM4 GC01P035455 GC01M035428
GH01H035505 1.3 Ensembl ENCODE 11.4 -50.2 -50195 3 HDGF PKNOX1 ATF1 FEZF1 ZNF2 GLIS2 GATA2 FOS ATF7 RUNX3 ZMYM6 ZMYM4 AGO3 KIAA0319L ZMYM1 SFPQ NCDN LOC653160 LOC100419802 GC01P035467
GH01H035706 1.4 FANTOM5 Ensembl ENCODE 10.4 +150.4 150447 2 KLF17 BATF GLIS2 KLF7 EGR2 SP3 ZNF398 ZNF610 GLIS1 KDM1A LOC105378645 TFAP2E ENSG00000232335 CLSPN KIAA0319L NCDN TEKT2 AGO1 GC01M035706 PIR49848
GH01H035636 1.1 Ensembl ENCODE 10.4 +80.4 80444 2 HDAC1 HDGF TBL1XR1 NFRKB FEZF1 ZBTB40 GATA2 SCRT2 HCFC1 CEBPB C1orf216 LOC105378645 TFAP2E KIAA0319L NCDN ENSG00000232335 CLSPN PSMB2 DLGAP3 GC01P035622
GH01H035287 0.8 Ensembl ENCODE 9.6 -269.0 -268996 2 JUND JUN CEBPB HMBOX1 FOS PRDM1 KIAA0319L ENSG00000201542 ENSG00000201868 SFPQ LOC653160 TMEM35B NCDN RN7SL503P ZMYM4
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around NCDN on UCSC Golden Path with GeneCards custom track

Promoters for NCDN Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000004685 127 2001 HDGF PKNOX1 ARNT ARID4B SIN3A FEZF1 DMAP1 YBX1 ZNF2 YY1

Genomic Location for NCDN Gene

Chromosome:
1
Start:
35,557,473 bp from pter
End:
35,567,274 bp from pter
Size:
9,802 bases
Orientation:
Plus strand

Genomic View for NCDN Gene

Genes around NCDN on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
NCDN Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for NCDN Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for NCDN Gene

Proteins for NCDN Gene

  • Protein details for NCDN Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9UBB6-NCDN_HUMAN
    Recommended name:
    Neurochondrin
    Protein Accession:
    Q9UBB6
    Secondary Accessions:
    • D3DPR9
    • Q9UBY2
    • Q9Y4A6
    • Q9Y4D9

    Protein attributes for NCDN Gene

    Size:
    729 amino acids
    Molecular mass:
    78864 Da
    Quaternary structure:
    • Interacts with SEMA4C, DIAPH1 (via FH3 domain) and GRM5 (By similarity). Interacts with MCHR1.
    SequenceCaution:
    • Sequence=AAD05029.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};

    Alternative splice isoforms for NCDN Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for NCDN Gene

Post-translational modifications for NCDN Gene

  • Ubiquitination at posLast=272272
  • Modification sites at PhosphoSitePlus

Other Protein References for NCDN Gene

No data available for DME Specific Peptides for NCDN Gene

Domains & Families for NCDN Gene

Gene Families for NCDN Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for NCDN Gene

Suggested Antigen Peptide Sequences for NCDN Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q9UBB6

UniProtKB/Swiss-Prot:

NCDN_HUMAN :
  • Belongs to the neurochondrin family.
Family:
  • Belongs to the neurochondrin family.
genes like me logo Genes that share domains with NCDN: view

Function for NCDN Gene

Molecular function for NCDN Gene

UniProtKB/Swiss-Prot Function:
Probably involved in signal transduction, in the nervous system, via increasing cell surface localization of GRM5 and positively regulating its signaling (By similarity). Required for the spatial learning process. Acts as a negative regulator of Ca(2+)-calmodulin-dependent protein kinase 2 (CaMK2) phosphorylation. May play a role in modulating melanin-concentrating hormone-mediated functions via its interaction with MCHR1 that interferes with G protein-coupled signal transduction. May be involved in bone metabolism. May also be involved in neurite outgrowth.

Phenotypes From GWAS Catalog for NCDN Gene

Gene Ontology (GO) - Molecular Function for NCDN Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 21044950
genes like me logo Genes that share ontologies with NCDN: view
genes like me logo Genes that share phenotypes with NCDN: view

Animal Models for NCDN Gene

MGI Knock Outs for NCDN:

Animal Model Products

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for NCDN
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for NCDN Gene

Localization for NCDN Gene

Subcellular locations from UniProtKB/Swiss-Prot for NCDN Gene

Cytoplasm, cytosol. Cell projection, dendrite. Note=Localizes to somatic regions of neurons.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for NCDN gene
Compartment Confidence
cytosol 5
plasma membrane 3
peroxisome 2

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for NCDN Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 NOT nucleus ISS --
GO:0005737 cytoplasm IEA --
GO:0005829 cytosol ISS --
GO:0016020 membrane IDA 19946888
GO:0030424 NOT axon ISS --
genes like me logo Genes that share ontologies with NCDN: view

Pathways & Interactions for NCDN Gene

No Data Available

Gene Ontology (GO) - Biological Process for NCDN Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0031175 neuron projection development IEA,ISS --
GO:0045453 bone resorption IEA --
GO:0048168 regulation of neuronal synaptic plasticity IEA --
genes like me logo Genes that share ontologies with NCDN: view

No data available for Pathways by source and SIGNOR curated interactions for NCDN Gene

Drugs & Compounds for NCDN Gene

No Compound Related Data Available

Transcripts for NCDN Gene

Unigene Clusters for NCDN Gene

Neurochondrin:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for NCDN
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

Alternative Splicing Database (ASD) splice patterns (SP) for NCDN Gene

ExUns: 1a · 1b ^ 2a · 2b · 2c ^ 3 ^ 4 ^ 5a · 5b ^ 6 ^ 7 ^ 8 ^ 9a · 9b
SP1: - - -
SP2: - - - -
SP3: - -
SP4:
SP5: -

Relevant External Links for NCDN Gene

GeneLoc Exon Structure for
NCDN
ECgene alternative splicing isoforms for
NCDN

Expression for NCDN Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for NCDN Gene

mRNA differential expression in normal tissues according to GTEx for NCDN Gene

This gene is overexpressed in Brain - Nucleus accumbens (basal ganglia) (x9.7), Brain - Putamen (basal ganglia) (x6.7), Brain - Caudate (basal ganglia) (x6.2), and Brain - Cortex (x4.5).

Protein differential expression in normal tissues from HIPED for NCDN Gene

This gene is overexpressed in Frontal cortex (25.6), Brain (18.5), and Bone (12.8).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for NCDN Gene



Protein tissue co-expression partners for NCDN Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of NCDN Gene:

NCDN

SOURCE GeneReport for Unigene cluster for NCDN Gene:

Hs.121870

mRNA Expression by UniProt/SwissProt for NCDN Gene:

Q9UBB6-NCDN_HUMAN
Tissue specificity: Abundantly expressed in whole adult brain and in all individual brain regions examined, including spinal cord. Weakly expressed in ovary, testis, fetal brain and small intestine.

Evidence on tissue expression from TISSUES for NCDN Gene

  • Nervous system(4.8)
genes like me logo Genes that share expression patterns with NCDN: view

Primer Products

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for NCDN Gene

Orthologs for NCDN Gene

This gene was present in the common ancestor of animals.

Orthologs for NCDN Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia NCDN 33 34
  • 99.77 (n)
oppossum
(Monodelphis domestica)
Mammalia NCDN 34
  • 95 (a)
OneToOne
cow
(Bos Taurus)
Mammalia NCDN 33 34
  • 92.59 (n)
dog
(Canis familiaris)
Mammalia NCDN 33 34
  • 91.68 (n)
mouse
(Mus musculus)
Mammalia Ncdn 33 16 34
  • 90.76 (n)
rat
(Rattus norvegicus)
Mammalia Ncdn 33
  • 90.67 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia NCDN 34
  • 59 (a)
OneToOne
chicken
(Gallus gallus)
Aves NCDN 33 34
  • 64.36 (n)
lizard
(Anolis carolinensis)
Reptilia NCDN 34
  • 58 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia ncdn 33
  • 55.21 (n)
zebrafish
(Danio rerio)
Actinopterygii ncdn 33 34
  • 50.27 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP013338 33
  • 47.48 (n)
fruit fly
(Drosophila melanogaster)
Insecta Neurochondrin 33 34
  • 47.21 (n)
Species where no ortholog for NCDN was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for NCDN Gene

ENSEMBL:
Gene Tree for NCDN (if available)
TreeFam:
Gene Tree for NCDN (if available)

Paralogs for NCDN Gene

No data available for Paralogs for NCDN Gene

Variants for NCDN Gene

Sequence variations from dbSNP and Humsavar for NCDN Gene

SNP ID Clin Chr 01 pos Sequence Context AA Info Type
rs753974779 A colorectal cancer sample 35,562,423(+) CTTTG(A/T)GTTTG reference, missense
VAR_039850 A colorectal cancer sample
rs1000343223 -- 35,558,064(+) TTTTT(-/G)TTTTT intron-variant, upstream-variant-2KB, utr-variant-5-prime
rs1000465360 -- 35,559,709(+) TGGGG(A/G)CAGCA intron-variant
rs1000797640 -- 35,567,240(+) AGTAA(C/T)TATCT downstream-variant-500B

Structural Variations from Database of Genomic Variants (DGV) for NCDN Gene

Variant ID Type Subtype PubMed ID
nsv1012556 CNV gain 25217958

Variation tolerance for NCDN Gene

Residual Variation Intolerance Score: 2.49% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.60; 12.98% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for NCDN Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
NCDN

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for NCDN Gene

Disorders for NCDN Gene

Relevant External Links for NCDN

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
NCDN

No disorders were found for NCDN Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for NCDN Gene

Publications for NCDN Gene

  1. Molecular cloning and expression of human neurochondrin-1 and -2. (PMID: 10524216) Mochizuki R … Murakami K (Biochimica et biophysica acta 1999) 3 4 22 60
  2. Interaction of neurochondrin with the melanin-concentrating hormone receptor 1 interferes with G protein-coupled signal transduction but not agonist-mediated internalization. (PMID: 16945926) Francke F … Bächner D (The Journal of biological chemistry 2006) 4 22 60
  3. Corrigendum to 'Molecular cloning and expression of human neurochondrin-1 and -2'(1). (PMID: 10684983) Mochizuki R … Fukamizu A (Biochimica et biophysica acta 2000) 3 4 60
  4. Prediction of the coding sequences of unidentified human genes. IX. The complete sequences of 100 new cDNA clones from brain which can code for large proteins in vitro. (PMID: 9628581) Nagase T … Ohara O (DNA research : an international journal for rapid publication of reports on genes and genomes 1998) 3 4 60
  5. Architecture of the human interactome defines protein communities and disease networks. (PMID: 28514442) Huttlin EL … Harper JW (Nature 2017) 3 60

Products for NCDN Gene

Sources for NCDN Gene

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