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Aliases for NECAB3 Gene

Aliases for NECAB3 Gene

  • N-Terminal EF-Hand Calcium Binding Protein 3 2 3 5
  • Amyloid Beta (A4) Precursor Protein-Binding, Family A, Member 2 Binding Protein 2 3
  • Amyloid Beta A4 Protein-Binding Family A Member 2-Binding Protein 3 4
  • Neuronal Calcium-Binding Protein 3 3 4
  • EF-Hand Calcium Binding Protein 3 2 3
  • Nek2-Interacting Protein 1 3 4
  • X11L-Binding Protein 51 3 4
  • APBA2BP 3 4
  • SYTIP2 3 4
  • NIP1 3 4
  • XB51 3 4
  • N-Terminal EF-Hand Calcium-Binding Protein 3 3
  • Neuronal Calcium-Binding Protein NECAB3 3
  • Synaptotagmin Interacting Protein STIP3 3
  • Synaptotagmin Interacting Protein 2 3
  • DJ63M2.4 3
  • DJ63M2.5 3
  • EFCBP3 3
  • STIP3 3

External Ids for NECAB3 Gene

Previous HGNC Symbols for NECAB3 Gene

  • SYTIP2

Previous GeneCards Identifiers for NECAB3 Gene

  • GC20M031709
  • GC20M032244
  • GC20M029030

Summaries for NECAB3 Gene

Entrez Gene Summary for NECAB3 Gene

  • The protein encoded by this gene interacts with the amino-terminal domain of the neuron-specific X11-like protein (X11L), inhibits the association of X11L with amyloid precursor protein through a non-competitive mechanism, and abolishes the suppression of beta-amyloid production by X11L. This protein, together with X11L, may play an important role in the regulatory system of amyloid precursor protein metabolism and beta-amyloid generation. The protein is phosphorylated by NIMA-related expressed kinase 2, and localizes to the Golgi apparatus. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

GeneCards Summary for NECAB3 Gene

NECAB3 (N-Terminal EF-Hand Calcium Binding Protein 3) is a Protein Coding gene. GO annotations related to this gene include calcium ion binding. An important paralog of this gene is NECAB1.

UniProtKB/Swiss-Prot for NECAB3 Gene

  • Inhibits the interaction of APBA2 with beta-amyloid precursor protein (APP), and hence allows formation of beta-amyloid.

Gene Wiki entry for NECAB3 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for NECAB3 Gene

Genomics for NECAB3 Gene

Regulatory Elements for NECAB3 Gene

Enhancers for NECAB3 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
GH20G033553 1.9 FANTOM5 Ensembl ENCODE dbSUPER 10.9 +119.5 119520 3.1 HDGF PKNOX1 FOXA2 ATF1 MLX SIN3A ZNF48 YY1 ELK1 NFYC CBFA2T2 C20orf144 ACTL10 NECAB3 PXMP4 ZNF341 ENSG00000229188 CDK5RAP1 CHMP4B BPIFB4
GH20G033520 1.2 dbSUPER 14.9 +152.7 152703 3.2 CREB3L1 ZFP64 DMAP1 YY1 SLC30A9 ZNF143 ZNF263 SP3 NFYC TBX21 CBFA2T2 NECAB3 C20orf144 ACTL10 PXMP4 ZNF341 ENSG00000229188 GC20P033491 GC20P033492 GC20P033562
GH20G033561 1.5 Ensembl ENCODE dbSUPER 11 +112.1 112114 1.2 FOXA2 ATF1 ARID4B SIN3A DMAP1 ZNF2 ZNF48 YY1 TCF12 SLC30A9 CBFA2T2 C20orf144 ACTL10 NECAB3 PXMP4 ZNF341 ENSG00000229188 GC20P033562 GC20P033492 GC20P033491
GH20G033567 1.4 Ensembl ENCODE dbSUPER 11 +105.0 105017 3.4 PKNOX1 FOXA2 ATF1 ARID4B ETS1 FOS PAF1 MXD4 REST MIER2 CBFA2T2 C20orf144 ACTL10 NECAB3 SNTA1 E2F1 GC20P033562 GC20M033592
GH20G033539 1.1 Ensembl ENCODE 11.7 +135.2 135202 0.5 FOXA2 INSM2 ARID4B ZSCAN9 RARA FOS CREM THAP11 CEBPA ZNF580 CBFA2T2 ACTL10 C20orf144 NECAB3 GC20P033562 GC20P033491 GC20P033492
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around NECAB3 on UCSC Golden Path with GeneCards custom track

Promoters for NECAB3 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000136284 263 1201 MLX AGO1 ARID4B SIN3A DMAP1 ZNF2 SP3 MXD4 REST ZNF592

Genomic Location for NECAB3 Gene

33,657,087 bp from pter
33,674,463 bp from pter
17,377 bases
Minus strand

Genomic View for NECAB3 Gene

Genes around NECAB3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
NECAB3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for NECAB3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for NECAB3 Gene

Proteins for NECAB3 Gene

  • Protein details for NECAB3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    N-terminal EF-hand calcium-binding protein 3
    Protein Accession:
    Secondary Accessions:
    • A8K780
    • E1P5N2
    • Q5JWF5
    • Q5JWF6
    • Q5JWF7
    • Q86VV1
    • Q9H433
    • Q9H8G8
    • Q9HBW7
    • Q9HCQ9

    Protein attributes for NECAB3 Gene

    396 amino acids
    Molecular mass:
    44350 Da
    Quaternary structure:
    • Interacts with the N-terminal domain of APBA2. Interacts with NEK2.
    • Sequence=BAB14649.1; Type=Frameshift; Positions=56; Evidence={ECO:0000305}; Sequence=BAB16413.1; Type=Erroneous initiation; Evidence={ECO:0000305};

    Alternative splice isoforms for NECAB3 Gene


neXtProt entry for NECAB3 Gene

Post-translational modifications for NECAB3 Gene

No data available for DME Specific Peptides for NECAB3 Gene

Domains & Families for NECAB3 Gene

Suggested Antigen Peptide Sequences for NECAB3 Gene

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with NECAB3: view

No data available for UniProtKB/Swiss-Prot for NECAB3 Gene

Function for NECAB3 Gene

Molecular function for NECAB3 Gene

UniProtKB/Swiss-Prot Function:
Inhibits the interaction of APBA2 with beta-amyloid precursor protein (APP), and hence allows formation of beta-amyloid.

Gene Ontology (GO) - Molecular Function for NECAB3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005509 calcium ion binding IEA --
GO:0005515 protein binding IPI 10833507
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with NECAB3: view
genes like me logo Genes that share phenotypes with NECAB3: view

Animal Model Products

CRISPR Products

miRNA for NECAB3 Gene

miRTarBase miRNAs that target NECAB3

Inhibitory RNA Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for NECAB3 Gene

Localization for NECAB3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for NECAB3 Gene

Golgi apparatus.

Subcellular locations from

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 NECAB3 gene
Compartment Confidence
nucleus 5
endoplasmic reticulum 5
golgi apparatus 5
extracellular 3
mitochondrion 1
cytosol 1
lysosome 1

Gene Ontology (GO) - Cellular Components for NECAB3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000137 Golgi cis cisterna IDA 10833507
GO:0005634 nucleus NAS 10833507
GO:0005737 cytoplasm IDA 10833507
GO:0005783 endoplasmic reticulum IEA --
GO:0005789 endoplasmic reticulum membrane IDA 10833507
genes like me logo Genes that share ontologies with NECAB3: view

Pathways & Interactions for NECAB3 Gene

SuperPathways for NECAB3 Gene

No Data Available

Interacting Proteins for NECAB3 Gene

Gene Ontology (GO) - Biological Process for NECAB3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0009306 protein secretion NAS 12780348
GO:0019538 protein metabolic process IDA 12780348
GO:0042984 regulation of amyloid precursor protein biosynthetic process IDA 10833507
genes like me logo Genes that share ontologies with NECAB3: view

No data available for Pathways by source and SIGNOR curated interactions for NECAB3 Gene

Drugs & Compounds for NECAB3 Gene

No Compound Related Data Available

Transcripts for NECAB3 Gene

Unigene Clusters for NECAB3 Gene

N-terminal EF-hand calcium binding protein 3:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Alternative Splicing Database (ASD) splice patterns (SP) for NECAB3 Gene

ExUns: 1 ^ 2 ^ 3a · 3b ^ 4 ^ 5a · 5b ^ 6a · 6b ^ 7a · 7b ^ 8 ^ 9 ^ 10 ^ 11 ^ 12a · 12b
SP1: - - -
SP2: - -
SP3: - -
SP4: - - -
SP5: - -
SP6: - - - - -
SP7: - -

Relevant External Links for NECAB3 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for NECAB3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for NECAB3 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

NURSA nuclear receptor signaling pathways regulating expression of NECAB3 Gene:


SOURCE GeneReport for Unigene cluster for NECAB3 Gene:


mRNA Expression by UniProt/SwissProt for NECAB3 Gene:

Tissue specificity: Strongly expressed in heart and skeletal muscle, moderately in brain and pancreas.

Evidence on tissue expression from TISSUES for NECAB3 Gene

  • Nervous system(4.7)
  • Muscle(4.3)
  • Liver(4.1)
genes like me logo Genes that share expression patterns with NECAB3: view

Primer Products

No data available for mRNA differential expression in normal tissues , Protein differential expression in normal tissues , Protein expression , Protein tissue co-expression partners and Phenotype-based relationships between genes and organs from Gene ORGANizer for NECAB3 Gene

Orthologs for NECAB3 Gene

This gene was present in the common ancestor of chordates.

Orthologs for NECAB3 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia NECAB3 34 35
  • 98.25 (n)
(Canis familiaris)
Mammalia NECAB3 34 35
  • 88.49 (n)
(Bos Taurus)
Mammalia NECAB3 34 35
  • 87.15 (n)
(Mus musculus)
Mammalia Necab3 34 16 35
  • 85.17 (n)
(Rattus norvegicus)
Mammalia Necab3 34
  • 84.69 (n)
(Monodelphis domestica)
Mammalia NECAB3 35
  • 60 (a)
(Ornithorhynchus anatinus)
Mammalia NECAB3 35
  • 43 (a)
(Gallus gallus)
Aves NECAB3 34 35
  • 67.05 (n)
(Anolis carolinensis)
Reptilia NECAB3 35
  • 55 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia LOC100497938 34
  • 58.2 (n)
(Danio rerio)
Actinopterygii NECAB3 35
  • 44 (a)
Species where no ortholog for NECAB3 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)
  • fruit fly (Drosophila melanogaster)
  • 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 NECAB3 Gene

Gene Tree for NECAB3 (if available)
Gene Tree for NECAB3 (if available)

Paralogs for NECAB3 Gene

Paralogs for NECAB3 Gene

(3) SIMAP similar genes for NECAB3 Gene using alignment to 8 proteins:

genes like me logo Genes that share paralogs with NECAB3: view

Variants for NECAB3 Gene

Sequence variations from dbSNP and Humsavar for NECAB3 Gene

SNP ID Clin Chr 20 pos Sequence Context AA Info Type
rs1000188291 -- 33,673,307(+) CCCCC(A/T)CCAGG intron-variant
rs1000197218 -- 33,660,914(+) TCTCA(C/G)TCAGA intron-variant, upstream-variant-2KB
rs1000223854 -- 33,670,716(+) AACAG(C/T)TCCTG reference, synonymous-codon
rs1000243510 -- 33,671,998(+) AAGTT(C/G)GAGCC intron-variant
rs1000357529 -- 33,667,458(+) GTGGC(A/G)GAGCT intron-variant, upstream-variant-2KB, utr-variant-5-prime

Structural Variations from Database of Genomic Variants (DGV) for NECAB3 Gene

Variant ID Type Subtype PubMed ID
dgv7560n54 CNV loss 21841781
nsv1065189 CNV loss 25217958
nsv482067 CNV gain 20164927
nsv585927 CNV loss 21841781
nsv833960 CNV loss 17160897
nsv833961 CNV loss 17160897
nsv954024 CNV deletion 24416366

Variation tolerance for NECAB3 Gene

Residual Variation Intolerance Score: 77.1% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.74; 46.84% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for NECAB3 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for NECAB3 Gene

Disorders for NECAB3 Gene

Relevant External Links for NECAB3

Human Genome Epidemiology (HuGE) Navigator
Atlas of Genetics and Cytogenetics in Oncology and Haematology:

No disorders were found for NECAB3 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for NECAB3 Gene

Publications for NECAB3 Gene

  1. Regulation of X11L-dependent amyloid precursor protein metabolism by XB51, a novel X11L-binding protein. (PMID: 10833507) Lee D.-S. … Suzuki T. (J. Biol. Chem. 2000) 2 3 4 22 64
  2. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T. … Sugano S. (Nat. Genet. 2004) 3 4 64
  3. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard D.S. … Malek J. (Genome Res. 2004) 3 4 64
  4. NIP1/XB51/NECAB3 is a potential substrate of Nek2, suggesting specific roles of Nek2 in Golgi. (PMID: 14697346) Yoo J.C. … Rhee K. (Exp. Cell Res. 2004) 3 4 64
  5. XB51 isoforms mediate Alzheimer's beta-amyloid peptide production by X11L (X11-like protein)-dependent and -independent mechanisms. (PMID: 12780348) Sumioka A. … Suzuki T. (Biochem. J. 2003) 3 22 64

Products for NECAB3 Gene

Sources for NECAB3 Gene

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