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NECAB2 N-terminal EF-hand calcium binding protein 2 [ Homo sapiens (human) ]

Gene ID: 54550, updated on 5-Mar-2024

Summary

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Official Symbol
NECAB2provided by HGNC
Official Full Name
N-terminal EF-hand calcium binding protein 2provided by HGNC
Primary source
HGNC:HGNC:23746
See related
Ensembl:ENSG00000103154 MIM:618130; AllianceGenome:HGNC:23746
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
EFCBP2; stip-2
Summary
The protein encoded by this gene is a neuronal calcium-binding protein that binds to and modulates the function of at least two receptors, adenosine A(2A) receptor and metabotropic glutamate receptor type 5. [provided by RefSeq, Jul 2016]
Expression
Biased expression in brain (RPKM 9.4), kidney (RPKM 3.0) and 3 other tissues See more
Orthologs
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Genomic context

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Location:
16q23.3
Exon count:
14
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (83965177..84002776)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (90031233..90068832)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (84001849..84036381)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:83841377-83841878 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:83846533-83847044 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:83847045-83847556 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:83847557-83848068 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr16:83850559-83851758 Neighboring gene heat shock factor binding protein 1 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:83873977-83874624 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:83874625-83875272 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:83875273-83875919 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:83879897-83880398 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:83880399-83880898 Neighboring gene MPRA-validated peak2652 silencer Neighboring gene ReSE screen-validated silencer GRCh37_chr16:83912211-83912369 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7769 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7770 Neighboring gene NANOG hESC enhancer GRCh37_chr16:83942352-83942873 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr16:83945234-83946433 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:83947165-83947672 Neighboring gene uncharacterized LOC105371372 Neighboring gene malonyl-CoA decarboxylase Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7771 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:83987658-83988427 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7772 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:84007063-84007564 Neighboring gene Sharpr-MPRA regulatory region 13657 Neighboring gene oxidative stress induced growth inhibitor 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7773 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:84035929-84036711 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7774 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:84050003-84050504 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:84060729-84061230 Neighboring gene solute carrier family 38 member 8 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:84066580-84067080 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:84075154-84075858 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:84075859-84076562 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr16:84076563-84077267 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr16:84077268-84077971 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:84078959-84079731 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:84082148-84083032 Neighboring gene RNA, 5S ribosomal pseudogene 432 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:84088845-84089438 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:84089439-84090031 Neighboring gene membrane bound transcription factor peptidase, site 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7775 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr16:84125154-84126353 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7776

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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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Related articles in PubMed

  1. Comparative anatomical distribution of neuronal calcium-binding protein (NECAB) 1 and -2 in rodent and human spinal cord. Zhang MD, et al. Brain Struct Funct, 2016 Sep. PMID 26843217
  2. The neuronal Ca(2+) -binding protein 2 (NECAB2) interacts with the adenosine A(2A) receptor and modulates the cell surface expression and function of the receptor. Canela L, et al. Mol Cell Neurosci, 2007 Sep. PMID 17689978
  3. The association of metabotropic glutamate receptor type 5 with the neuronal Ca2+-binding protein 2 modulates receptor function. Canela L, et al. J Neurochem, 2009 Oct. PMID 19694902
  4. NECABs: a family of neuronal Ca(2+)-binding proteins with an unusual domain structure and a restricted expression pattern. Sugita S, et al. Neuroscience, 2002. PMID 12044471
  5. Isolation and characterization of a downstream target of Pax6 in the mammalian retinal primordium. Bernier G, et al. Development, 2001 Oct. PMID 11641222

See all (29) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. NECAB2 is an endosomal protein important for striatal function.
    Title: NECAB2 is an endosomal protein important for striatal function.
  2. Study suggests that the phenotypic segregation of Neuronal calcium-binding protein 1 and -2 (NECAB1 and -2) to respective excitatory and inhibitory spinal systems can underpin functional modalities in determining the fidelity of synaptic neurotransmission and neuronal responsiveness, and might bear translational relevance to humans.
    Title: Comparative anatomical distribution of neuronal calcium-binding protein (NECAB) 1 and -2 in rodent and human spinal cord.
  3. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
    Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
  4. Clinical trial and genome-wide association study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
    Title: Molecular genetics of successful smoking cessation: convergent genome-wide association study results.
  5. NECAB2 by its physical interaction with mGlu(5b) receptor modulates receptor function
    Title: The association of metabotropic glutamate receptor type 5 with the neuronal Ca2+-binding protein 2 modulates receptor function.
Submit: New GeneRIF Correction

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)

Genotypes

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables A2A adenosine receptor binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables calcium ion binding IEA
Inferred from Electronic Annotation
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables type 5 metabotropic glutamate receptor binding IDA
Inferred from Direct Assay
more info
 PubMed 
Process Evidence Code Pubs
involved_in negative regulation of G protein-coupled receptor internalization IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in positive regulation of ERK1 and ERK2 cascade IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in positive regulation of adenosine receptor signaling pathway IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in positive regulation of glutamate receptor signaling pathway IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in positive regulation of protein localization to membrane IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in regulation of amyloid precursor protein biosynthetic process IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
located_in axon IEA
Inferred from Electronic Annotation
more info
  
is_active_in cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in dendrite IEA
Inferred from Electronic Annotation
more info
  
located_in plasma membrane IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
N-terminal EF-hand calcium-binding protein 2
Names
EF-hand calcium-binding protein 2
neuronal calcium binding 2
neuronal calcium-binding protein 2
synaptotagmin-interacting protein 2

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)

  1. NM_001329748.1 → NP_001316677.1  N-terminal EF-hand calcium-binding protein 2 isoform 2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an alternate in-frame exon in the 3' end compared to variant 1. The resulting isoform (2) has the same N- and C-termini but is shorter compared to isoform 1.
    Source sequence(s)
    AC040169

  2. NM_001329749.2 → NP_001316678.1  N-terminal EF-hand calcium-binding protein 2 isoform 3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) lacks an alternate coding exon compared to variant 1. The resulting isoform (3) has a shorter and distinct N-terminus compared to isoform 1.
    Source sequence(s)
    AC040169
    Consensus CDS
    CCDS82019.1
    UniProtKB/Swiss-Prot
    Q7Z6G3
    Conserved Domains (1) summary
    pfam03992
    Location:205 → 275
    ABM; Antibiotic biosynthesis monooxygenase

  3. NM_019065.3 → NP_061938.2  N-terminal EF-hand calcium-binding protein 2 isoform 1

    See identical proteins and their annotated locations for NP_061938.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
    Source sequence(s)
    AC040169
    Consensus CDS
    CCDS10940.1
    UniProtKB/Swiss-Prot
    A2RRG3, H3BTW2, O75547, Q6ZSK0, Q7Z6G3
    Related
    ENSP00000307449.4, ENST00000305202.9
    Conserved Domains (3) summary
    PTZ00440
    Location:79 → 211
    PTZ00440; reticulocyte binding protein 2-like protein; Provisional
    pfam03992
    Location:288 → 358
    ABM; Antibiotic biosynthesis monooxygenase
    pfam13499
    Location:64 → 123
    EF-hand_7; EF-hand domain pair

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

  1. NC_000016.10 Reference GRCh38.p14 Primary Assembly

    Range
    83965177..84002776
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047434240.1 → XP_047290196.1  N-terminal EF-hand calcium-binding protein 2 isoform X1

    Related
    ENSP00000457354.1, ENST00000565691.5

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060940.1 Alternate T2T-CHM13v2.0

    Range
    90031233..90068832
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054380512.1 → XP_054236487.1  N-terminal EF-hand calcium-binding protein 2 isoform X1

  2. XM_054380513.1 → XP_054236488.1  N-terminal EF-hand calcium-binding protein 2 isoform X2

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q7Z6G3.1 GenPept UniProtKB/Swiss-Prot:Q7Z6G3

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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