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

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; AllianceGenome:HGNC:15851
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: mouse all
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Genomic context

Location:: 20q11.22

Exon count:: 15

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	20	NC_000020.11 (33657087..33675348, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	20	NC_060944.1 (35383618..35401879, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	20	NC_000020.10 (32244893..32262234, complement)

Chromosome 20 - NC_000020.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

GNAS-AS1/miR-4319/NECAB3 axis promotes tumor progression of non-small cell lung cancer by altering macrophage polarization.
Title: GNAS-AS1/miR-4319/NECAB3 axis promotes migration and invasion of non-small cell lung cancer cells by altering macrophage polarization.
Results suggest that NECAB3, a novel Mint3-binding protein, activates HIF-1 to promote normoxic glycolysis and tumorigenicity by forming a ternary complex with Mint3 and FIH-1.
Title: NECAB3 Promotes Activation of Hypoxia-inducible factor-1 during Normoxia and Enhances Tumourigenicity of Cancer Cells.
Observational study of gene-disease association and gene-environment interaction. (HuGE Navigator)
Title: Single nucleotide polymorphisms of matrix metalloproteinase 9 (MMP9) and tumor protein 73 (TP73) interact with Epstein-Barr virus in chronic lymphocytic leukemia: results from the European case-control study EpiLymph.
Observational study of gene-disease association. (HuGE Navigator)
Title: New genetic associations detected in a host response study to hepatitis B vaccine.
xb51 may be required for maturation and maintenance of xb51-expressing neurons in the forebrain
Title: Isolation and expression analysis of Alzheimer's disease-related gene xb51 in zebrafish.
hXB51 isoforms regulate Abeta generation differently, either enhancing it by modifying the association of X11L with APP or suppressing it in an X11L-independent manner
Title: XB51 isoforms mediate Alzheimer's beta-amyloid peptide production by X11L (X11-like protein)-dependent and -independent mechanisms.

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Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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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

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Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

AF021113 (e-PCR)
- UniSTS:54021

PMC344741P1 (e-PCR)
- UniSTS:273209

A006D04 (e-PCR)
- UniSTS:43345

RH78379 (e-PCR)
- UniSTS:57989

RH12699 (e-PCR)
- UniSTS:15567

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables calcium ion binding	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in protein metabolic process	IDA Inferred from Direct Assay more info	PubMed
involved_in protein secretion	NAS Non-traceable Author Statement more info	PubMed
involved_in regulation of amyloid precursor protein biosynthetic process	IBA Inferred from Biological aspect of Ancestor more info
involved_in regulation of amyloid precursor protein biosynthetic process	IDA Inferred from Direct Assay more info	PubMed

Component	Evidence Code	Pubs
located_in Golgi apparatus	IDA Inferred from Direct Assay more info
is_active_in Golgi cis cisterna	IBA Inferred from Biological aspect of Ancestor more info
located_in Golgi cis cisterna	IDA Inferred from Direct Assay more info	PubMed
is_active_in cytoplasm	IBA Inferred from Biological aspect of Ancestor more info
located_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
is_active_in endoplasmic reticulum	IBA Inferred from Biological aspect of Ancestor more info
located_in endoplasmic reticulum membrane	IDA Inferred from Direct Assay more info	PubMed
located_in nucleus	NAS Non-traceable Author Statement more info	PubMed

General protein information

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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)

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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)

NM_031231.4 → NP_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/TrEMBL

U3KQ06

Related

ENSP00000364386.4, ENST00000375238.8

Conserved Domains (3) summary

pfam03992
Location:262 → 335

ABM; Antibiotic biosynthesis monooxygenase

pfam13499
Location:39 → 65

EF-hand_7; EF-hand domain pair

cl08302
Location:41 → 83

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 ...
NM_031232.4 → NP_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

A8K780, E1P5N2, Q5JWF5, Q5JWF6, Q5JWF7, Q86VV1, Q96P71, Q9H433, Q9H8G8, Q9HBW7, Q9HCQ9

Related

ENSP00000246190.6, ENST00000246190.11

Conserved Domains (3) summary

pfam03992
Location:296 → 369

ABM; Antibiotic biosynthesis monooxygenase

pfam13499
Location:39 → 65

EF-hand_7; EF-hand domain pair

cl08302
Location:41 → 83

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: 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

NC_000020.11 Reference GRCh38.p14 Primary Assembly

Range

33657087..33675348 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047440370.1 → XP_047296326.1 N-terminal EF-hand calcium-binding protein 3 isoform X3
XM_047440369.1 → XP_047296325.1 N-terminal EF-hand calcium-binding protein 3 isoform X2
XM_005260510.1 → XP_005260567.1 N-terminal EF-hand calcium-binding protein 3 isoform X1

UniProtKB/TrEMBL

U3KQ06

Related

ENSP00000392064.1, ENST00000439478.5

Conserved Domains (3) summary

pfam03992
Location:244 → 317

ABM; Antibiotic biosynthesis monooxygenase

pfam13499
Location:39 → 65

EF-hand_7; EF-hand domain pair

cl08302
Location:41 → 83

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 ...
XM_011528991.2 → XP_011527293.1 N-terminal EF-hand calcium-binding protein 3 isoform X4

Conserved Domains (1) summary

pfam03992
Location:101 → 174

ABM; Antibiotic biosynthesis monooxygenase
XM_017028016.2 → XP_016883505.1 N-terminal EF-hand calcium-binding protein 3 isoform X4

Conserved Domains (1) summary

pfam03992
Location:101 → 174

ABM; Antibiotic biosynthesis monooxygenase
XM_011528992.3 → XP_011527294.1 N-terminal EF-hand calcium-binding protein 3 isoform X5

UniProtKB/TrEMBL

U3KPZ3

Related

ENSP00000475369.1, ENST00000485399.5

Conserved Domains (2) summary

pfam13499
Location:39 → 65

EF-hand_7; EF-hand domain pair

cl08302
Location:41 → 83

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 ...

Alternate T2T-CHM13v2.0

Genomic

NC_060944.1 Alternate T2T-CHM13v2.0

Range

35383618..35401879 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054323828.1 → XP_054179803.1 N-terminal EF-hand calcium-binding protein 3 isoform X3
XM_054323827.1 → XP_054179802.1 N-terminal EF-hand calcium-binding protein 3 isoform X2
XM_054323826.1 → XP_054179801.1 N-terminal EF-hand calcium-binding protein 3 isoform X1
XM_054323829.1 → XP_054179804.1 N-terminal EF-hand calcium-binding protein 3 isoform X4
XM_054323830.1 → XP_054179805.1 N-terminal EF-hand calcium-binding protein 3 isoform X4
XM_054323831.1 → XP_054179806.1 N-terminal EF-hand calcium-binding protein 3 isoform X5