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NECAB3 N-terminal EF-hand calcium binding protein 3 [ Homo sapiens (human) ]

Gene ID: 63941, updated on 9-Feb-2020

Summary

Official Symbol
NECAB3provided by HGNC
Official Full Name
N-terminal EF-hand calcium binding protein 3provided by HGNC
Primary source
HGNC:HGNC:15851
See related
Ensembl:ENSG00000125967 MIM:612478
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
NIP1; XB51; STIP3; EFCBP3; SYTIP2; APBA2BP; dJ63M2.4; dJ63M2.5
Summary
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]
Expression
Broad expression in prostate (RPKM 16.7), adrenal (RPKM 15.0) and 25 other tissues See more
Orthologs

Genomic context

See NECAB3 in Genome Data Viewer
Location:
20q11.22
Exon count:
16
Annotation release Status Assembly Chr Location
109.20191205 current GRCh38.p13 (GCF_000001405.39) 20 NC_000020.11 (33657087..33674428, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (32244893..32262264, complement)

Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene VISTA enhancer hs2173 Neighboring gene syntrophin alpha 1 Neighboring gene CBFA2/RUNX1 partner transcriptional co-repressor 2 Neighboring gene chromosome 20 open reading frame 144 Neighboring gene actin like 10 Neighboring gene E2F transcription factor 1 Neighboring gene peroxisomal membrane protein 4

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?

HIV-1 interactions

Replication interactions

Interaction Pubs
Knockdown of N-terminal EF-hand calcium binding protein 3 (NECAB3) by siRNA inhibits the early stages of HIV-1 replication in 293T cells infected with VSV-G pseudotyped HIV-1 PubMed

Go to the HIV-1, Human Interaction Database

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
calcium ion binding IEA
Inferred from Electronic Annotation
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
protein metabolic process IDA
Inferred from Direct Assay
more info
PubMed 
protein secretion NAS
Non-traceable Author Statement
more info
PubMed 
regulation of amyloid precursor protein biosynthetic process IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
regulation of amyloid precursor protein biosynthetic process IDA
Inferred from Direct Assay
more info
PubMed 
Component Evidence Code Pubs
Golgi apparatus IDA
Inferred from Direct Assay
more info
 
Golgi cis cisterna IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Golgi cis cisterna IDA
Inferred from Direct Assay
more info
PubMed 
cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
endoplasmic reticulum IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
endoplasmic reticulum membrane IDA
Inferred from Direct Assay
more info
PubMed 
nucleus NAS
Non-traceable Author Statement
more info
PubMed 

General protein information

Preferred Names
N-terminal EF-hand calcium-binding protein 3
Names
EF-hand calcium binding protein 3
Nek2-interacting protein 1
X11L-binding protein 51
amyloid beta (A4) precursor protein-binding, family A, member 2 binding protein
amyloid beta A4 protein-binding family A member 2-binding protein
neuronal calcium-binding protein 3
neuronal calcium-binding protein NECAB3
synaptotagmin interacting protein 2
synaptotagmin interacting protein STIP3

NCBI Reference Sequences (RefSeq)

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_031231.4NP_112508.3  N-terminal EF-hand calcium-binding protein 3 isoform 1

    See identical proteins and their annotated locations for NP_112508.3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1), also known as XB51beta, lacks an alternate in-frame segment compared to variant 2. The resulting isoform (1) is shorter compared to isoform 2.
    Source sequence(s)
    AL121906
    Consensus CDS
    CCDS42867.1
    UniProtKB/Swiss-Prot
    Q96P71
    Related
    ENSP00000364386.4, ENST00000375238.8
    Conserved Domains (3) summary
    pfam03992
    Location:262335
    ABM; Antibiotic biosynthesis monooxygenase
    pfam13499
    Location:3965
    EF-hand_7; EF-hand domain pair
    cl08302
    Location:4183
    EFh; EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to ...
  2. NM_031232.4NP_112509.3  N-terminal EF-hand calcium-binding protein 3 isoform 2

    See identical proteins and their annotated locations for NP_112509.3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2), also known as XB51alpha, represents the longer transcript and encodes the longer isoform (2).
    Source sequence(s)
    AL121906
    Consensus CDS
    CCDS42866.1
    UniProtKB/Swiss-Prot
    Q96P71
    Related
    ENSP00000246190.6, ENST00000246190.10
    Conserved Domains (3) summary
    pfam03992
    Location:296369
    ABM; Antibiotic biosynthesis monooxygenase
    pfam13499
    Location:3965
    EF-hand_7; EF-hand domain pair
    cl08302
    Location:4183
    EFh; EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to ...

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20191205

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000020.11 Reference GRCh38.p13 Primary Assembly

    Range
    33657087..33674428 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005260510.1XP_005260567.1  N-terminal EF-hand calcium-binding protein 3 isoform X1

    Related
    ENSP00000392064.1, ENST00000439478.5
    Conserved Domains (3) summary
    pfam03992
    Location:244317
    ABM; Antibiotic biosynthesis monooxygenase
    pfam13499
    Location:3965
    EF-hand_7; EF-hand domain pair
    cl08302
    Location:4183
    EFh; EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to ...
  2. XM_017028015.1XP_016883504.1  N-terminal EF-hand calcium-binding protein 3 isoform X2

    Conserved Domains (1) summary
    pfam03992
    Location:101174
    ABM; Antibiotic biosynthesis monooxygenase
  3. XM_011528991.1XP_011527293.1  N-terminal EF-hand calcium-binding protein 3 isoform X2

    Conserved Domains (1) summary
    pfam03992
    Location:101174
    ABM; Antibiotic biosynthesis monooxygenase
  4. XM_017028016.1XP_016883505.1  N-terminal EF-hand calcium-binding protein 3 isoform X2

    Conserved Domains (1) summary
    pfam03992
    Location:101174
    ABM; Antibiotic biosynthesis monooxygenase
  5. XM_011528992.2XP_011527294.1  N-terminal EF-hand calcium-binding protein 3 isoform X3

    Related
    ENSP00000475369.1, ENST00000485399.5
    Conserved Domains (2) summary
    pfam13499
    Location:3965
    EF-hand_7; EF-hand domain pair
    cl08302
    Location:4183
    EFh; EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to ...

RNA

  1. XR_002958502.1 RNA Sequence

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