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Aliases for NCALD Gene

Aliases for NCALD Gene

  • Neurocalcin Delta 2 3 5
  • Neurocalcin-Delta 3

External Ids for NCALD Gene

Previous GeneCards Identifiers for NCALD Gene

  • GC08M102766
  • GC08M102367
  • GC08M102655
  • GC08M102767
  • GC08M097897
  • GC08M102698

Summaries for NCALD Gene

Entrez Gene Summary for NCALD Gene

  • This gene encodes a member of the neuronal calcium sensor (NCS) family of calcium-binding proteins. The protein contains an N-terminal myristoylation signal and four EF-hand calcium binding loops. The protein is cytosolic at resting calcium levels; however, elevated intracellular calcium levels induce a conformational change that exposes the myristoyl group, resulting in protein association with membranes and partial co-localization with the perinuclear trans-golgi network. The protein is thought to be a regulator of G protein-coupled receptor signal transduction. Several alternatively spliced variants of this gene have been determined, all of which encode the same protein; additional variants may exist but their biological validity has not been determined. [provided by RefSeq, Jul 2008]

GeneCards Summary for NCALD Gene

NCALD (Neurocalcin Delta) is a Protein Coding gene. Among its related pathways are Presynaptic function of Kainate receptors and Transmission across Chemical Synapses. GO annotations related to this gene include calcium ion binding and clathrin binding. An important paralog of this gene is HPCAL1.

UniProtKB/Swiss-Prot for NCALD Gene

  • May be involved in the calcium-dependent regulation of rhodopsin phosphorylation. Binds three calcium ions.

Additional gene information for NCALD Gene

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

Genomics for NCALD Gene

Regulatory Elements for NCALD Gene

Enhancers for NCALD 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
GH08H102094 1.5 FANTOM5 ENCODE dbSUPER 20 +28.0 28001 4 HDGF PKNOX1 RB1 BMI1 YBX1 ZNF143 ZNF207 ATF7 ETV6 RUNX3 NCALD ZNF706 UBR5 LOC104054148
GH08H102120 1.4 FANTOM5 ENCODE dbSUPER 9.5 +1.8 1834 4 TBL1XR1 SIN3A RAD21 ZNF143 ATF7 RUNX3 IKZF2 SMARCA5 CBFB ZNF398 NCALD UBR5 LOC104054148
GH08H101332 1.4 FANTOM5 Ensembl ENCODE 9.5 +791.8 791801 1 HDGF PKNOX1 TBL1XR1 NFIB ZBTB40 RAD21 ELK1 HSF1 ZNF143 SMARCA5 LOC101927172 GRHL2 NCALD ENSG00000271560 RNU7-67P
GH08H101967 1.1 Ensembl ENCODE 10.8 +157.2 157225 1 HDGF PKNOX1 FOXA2 NFIB MAX FEZF1 BATF RAD21 YY1 CTBP1 NCALD LOC104054148 PDCL3P2
GH08H102127 1.3 FANTOM5 Ensembl ENCODE 7.8 -4.3 -4276 2 PKNOX1 EBF1 RELA POLR2A EED ATF7 IKZF2 CHD2 SMARCE1 ZNF687 NCALD GC08P102128 ENSG00000254492
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around NCALD on UCSC Golden Path with GeneCards custom track

Promoters for NCALD Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000228179 1007 1401 CTCF TBL1XR1 SIN3A CHD4 RAD21 PATZ1 SMC3 ZNF143 RUNX3 IKZF2

Genomic Location for NCALD Gene

Chromosome:
8
Start:
101,686,542 bp from pter
End:
102,124,907 bp from pter
Size:
438,366 bases
Orientation:
Minus strand

Genomic View for NCALD Gene

Genes around NCALD on UCSC Golden Path with GeneCards custom track

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

RefSeq DNA sequence for NCALD Gene

Proteins for NCALD Gene

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

    Protein Symbol:
    P61601-NCALD_HUMAN
    Recommended name:
    Neurocalcin-delta
    Protein Accession:
    P61601
    Secondary Accessions:
    • P29554
    • Q8IYC3
    • Q9H0W2

    Protein attributes for NCALD Gene

    Size:
    193 amino acids
    Molecular mass:
    22245 Da
    Quaternary structure:
    No Data Available

neXtProt entry for NCALD Gene

Post-translational modifications for NCALD Gene

  • Ubiquitination at Lys50
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for NCALD Gene

Domains & Families for NCALD Gene

Gene Families for NCALD Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for NCALD Gene

Suggested Antigen Peptide Sequences for NCALD Gene

Graphical View of Domain Structure for InterPro Entry

P61601

UniProtKB/Swiss-Prot:

NCALD_HUMAN :
  • Belongs to the recoverin family.
Family:
  • Belongs to the recoverin family.
genes like me logo Genes that share domains with NCALD: view

Function for NCALD Gene

Molecular function for NCALD Gene

UniProtKB/Swiss-Prot Function:
May be involved in the calcium-dependent regulation of rhodopsin phosphorylation. Binds three calcium ions.

Phenotypes From GWAS Catalog for NCALD Gene

Gene Ontology (GO) - Molecular Function for NCALD Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003779 actin binding IDA 11964161
GO:0005509 calcium ion binding IEA --
GO:0005515 protein binding IPI 16189514
GO:0015276 ligand-gated ion channel activity TAS --
GO:0015631 tubulin binding IDA 11964161
genes like me logo Genes that share ontologies with NCALD: view
genes like me logo Genes that share phenotypes with NCALD: view

Animal Models for NCALD Gene

MGI Knock Outs for NCALD:

Animal Model Products

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for NCALD
  • 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 NCALD Gene

Localization for NCALD Gene

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 NCALD gene
Compartment Confidence
extracellular 5
cytosol 5
golgi apparatus 5
nucleus 2
cytoskeleton 1

Gene Ontology (GO) - Cellular Components for NCALD Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005622 intracellular IDA --
GO:0005829 cytosol TAS --
GO:0030130 clathrin coat of trans-Golgi network vesicle NAS 11964161
GO:0070062 extracellular exosome IDA 23376485
genes like me logo Genes that share ontologies with NCALD: view

No data available for Subcellular locations from UniProtKB/Swiss-Prot and Subcellular locations from the Human Protein Atlas (HPA) for NCALD Gene

Pathways & Interactions for NCALD Gene

genes like me logo Genes that share pathways with NCALD: view

Gene Ontology (GO) - Biological Process for NCALD Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003073 regulation of systemic arterial blood pressure IEA --
GO:0016192 vesicle-mediated transport NAS 11964161
GO:0019722 calcium-mediated signaling IEA --
GO:0034220 ion transmembrane transport IEA --
genes like me logo Genes that share ontologies with NCALD: view

No data available for SIGNOR curated interactions for NCALD Gene

Drugs & Compounds for NCALD Gene

(1) Drugs for NCALD Gene - From: HMDB and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
calcium Nutra 0
genes like me logo Genes that share compounds with NCALD: view

Transcripts for NCALD Gene

Unigene Clusters for NCALD Gene

Neurocalcin delta:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

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

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

ExUns: 1a · 1b ^ 2a · 2b · 2c ^ 3 ^ 4 ^ 5 ^ 6a · 6b ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13 ^ 14 ^ 15 ^ 16 ^ 17a · 17b · 17c ^ 18 ^ 19 ^ 20 ^
SP1: - - -
SP2: - - - - - - - - - - - - - - - - - -
SP3: - - - - - - - - - - - - - - - -
SP4: - - - - - - - - - - - - - - -
SP5: - - - - - - - - - - - - - - - - - - -
SP6: - - - - - - - - - - - - - - - -
SP7: - - - - - - - - - - - - - -
SP8: - - - - - - - - - - - - - -
SP9: - - - - - - -
SP10: - - -
SP11: - - -
SP12: - - - - - - - - - - - - - - - - - -
SP13: - - - - - - - - - - - - - - -
SP14: - - - - - - - - - - - - - - - -
SP15: - - - - - - - - - - - - - - - - - - - - - - -
SP16: - - - - - - - - - - - - - - - - - - - - -
SP17: - -
SP18: -
SP19: - -
SP20:
SP21:

ExUns: 21a · 21b ^ 22a · 22b · 22c · 22d · 22e · 22f ^ 23 ^ 24a · 24b · 24c ^ 25 ^ 26
SP1:
SP2: - -
SP3: - -
SP4:
SP5: -
SP6:
SP7:
SP8: -
SP9: - -
SP10: - -
SP11: -
SP12: -
SP13:
SP14:
SP15:
SP16: -
SP17:
SP18:
SP19:
SP20: -
SP21:

Relevant External Links for NCALD Gene

GeneLoc Exon Structure for
NCALD
ECgene alternative splicing isoforms for
NCALD

Expression for NCALD Gene

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

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

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

This gene is overexpressed in Brain - Cortex (x7.8), Brain - Frontal Cortex (BA9) (x7.3), and Brain - Anterior cingulate cortex (BA24) (x4.5).

Protein differential expression in normal tissues from HIPED for NCALD Gene

This gene is overexpressed in Frontal cortex (26.4), Salivary gland (11.7), and Brain (7.3).

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



Protein tissue co-expression partners for NCALD Gene

NURSA nuclear receptor signaling pathways regulating expression of NCALD Gene:

NCALD

SOURCE GeneReport for Unigene cluster for NCALD Gene:

Hs.492427

mRNA Expression by UniProt/SwissProt for NCALD Gene:

P61601-NCALD_HUMAN
Tissue specificity: Retina, cerebrum, cerebellum, brain stem, spinal cord, testis, ovary and small intestine.

Evidence on tissue expression from TISSUES for NCALD Gene

  • Nervous system(5)
genes like me logo Genes that share expression patterns with NCALD: view

Primer Products

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

Orthologs for NCALD Gene

This gene was present in the common ancestor of animals.

Orthologs for NCALD Gene

Organism Taxonomy Gene Similarity Type Details
oppossum
(Monodelphis domestica)
Mammalia NCALD 34
  • 100 (a)
OneToOne
chimpanzee
(Pan troglodytes)
Mammalia NCALD 33 34
  • 99.48 (n)
dog
(Canis familiaris)
Mammalia NCALD 33 34
  • 95.34 (n)
cow
(Bos Taurus)
Mammalia NCALD 33 34
  • 93.09 (n)
rat
(Rattus norvegicus)
Mammalia Ncald 33
  • 93.09 (n)
mouse
(Mus musculus)
Mammalia Ncald 33 16 34
  • 92.57 (n)
chicken
(Gallus gallus)
Aves NCALD 33 34
  • 86.36 (n)
lizard
(Anolis carolinensis)
Reptilia NCALD 34
  • 100 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia ncald 33
  • 84.11 (n)
Str.14728 33
zebrafish
(Danio rerio)
Actinopterygii ncaldb 34
  • 94 (a)
OneToMany
ncalda 33 34
  • 81.35 (n)
fruit fly
(Drosophila melanogaster)
Insecta Nca 35
  • 87 (a)
CG7646 35
  • 47 (a)
worm
(Caenorhabditis elegans)
Secernentea ncs-3 35
  • 58 (a)
ncs-2 35
  • 50 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 77 (a)
OneToMany
Species where no ortholog for NCALD was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • 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)
  • platypus (Ornithorhynchus anatinus)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • 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)

Evolution for NCALD Gene

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

Paralogs for NCALD Gene

Variants for NCALD Gene

Sequence variations from dbSNP and Humsavar for NCALD Gene

SNP ID Clin Chr 08 pos Sequence Context AA Info Type
rs1000000130 -- 101,944,508(+) TCTCT(A/G)CAAAG intron-variant
rs1000008228 -- 101,940,667(+) AACAG(A/G)CAACC intron-variant
rs1000024989 -- 101,805,843(+) ATTCC(A/T)GGGAT intron-variant
rs1000025054 -- 101,846,529(+) ATCAG(A/G)AACCT intron-variant
rs1000038500 -- 101,933,606(+) CATCC(C/T)GCAAC intron-variant

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

Variant ID Type Subtype PubMed ID
dgv466n21 CNV loss 19592680
esv21888 CNV loss 19812545
esv2421949 CNV deletion 20811451
esv2605083 CNV insertion 19546169
esv2662515 CNV deletion 23128226
esv2664408 CNV deletion 23128226
esv2737371 CNV deletion 23290073
esv2761453 CNV loss 21179565
esv3310355 CNV mobile element insertion 20981092
esv3431444 CNV duplication 20981092
esv3448877 CNV insertion 20981092
esv3543934 CNV deletion 23714750
esv3618213 CNV loss 21293372
esv3618214 CNV loss 21293372
esv3618216 CNV loss 21293372
esv3618217 CNV loss 21293372
esv3891452 CNV loss 25118596
nsv1020359 CNV gain 25217958
nsv1030076 CNV loss 25217958
nsv1076099 CNV deletion 25765185
nsv1137618 CNV deletion 24896259
nsv1139941 CNV duplication 24896259
nsv1152951 CNV deletion 26484159
nsv438074 CNV loss 16468122
nsv465749 CNV loss 19166990
nsv507478 OTHER sequence alteration 20534489
nsv517149 CNV loss 19592680
nsv517893 CNV loss 19592680
nsv523654 CNV gain 19592680
nsv611819 CNV loss 21841781
nsv611820 CNV loss 21841781
nsv818646 CNV loss 17921354
nsv831411 CNV gain 17160897
nsv8371 CNV loss 18304495
nsv981971 CNV duplication 23825009

Variation tolerance for NCALD Gene

Residual Variation Intolerance Score: 37.7% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.50; 10.82% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for NCALD Gene

Human Gene Mutation Database (HGMD)
NCALD
SNPedia medical, phenotypic, and genealogical associations of SNPs for
NCALD

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

Disorders for NCALD Gene

Relevant External Links for NCALD

Genetic Association Database (GAD)
NCALD
Human Genome Epidemiology (HuGE) Navigator
NCALD
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
NCALD

No disorders were found for NCALD Gene.

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

Publications for NCALD Gene

  1. Molecular cloning, mapping and characterization of the human neurocalcin delta gene (NCALD). (PMID: 11267673) Wang W … Mao Y (Biochimica et biophysica acta 2001) 2 3 4 22 60
  2. Polymorphisms in the 3' UTR in the neurocalcin delta gene affect mRNA stability, and confer susceptibility to diabetic nephropathy. (PMID: 17671797) Kamiyama M … Maeda S (Human genetics 2007) 3 22 45 60
  3. Genome-wide association analysis of coffee drinking suggests association with CYP1A1/CYP1A2 and NRCAM. (PMID: 21876539) Amin N … van Duijn CM (Molecular psychiatry 2012) 3 45 60
  4. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose JE … Uhl GR (Molecular medicine (Cambridge, Mass.) 2010) 3 45 60
  5. Common genetic variation and performance on standardized cognitive tests. (PMID: 20125193) Cirulli ET … Goldstein DB (European journal of human genetics : EJHG 2010) 3 45 60

Products for NCALD Gene

Sources for NCALD Gene

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