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    Necab3 N-terminal EF-hand calcium binding protein 3 [ Mus musculus (house mouse) ]

    Gene ID: 56846, updated on 5-Mar-2024

    Summary

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    Official Symbol
    Necab3provided by MGI
    Official Full Name
    N-terminal EF-hand calcium binding protein 3provided by MGI
    Primary source
    MGI:MGI:1861721
    See related
    Ensembl:ENSMUSG00000027489 AllianceGenome:MGI:1861721
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
    Also known as
    Nip1; XB51; Apba2bp; 2900010M17Rik
    Summary
    Predicted to enable calcium ion binding activity. Predicted to be involved in protein metabolic process and regulation of amyloid precursor protein biosynthetic process. Located in Golgi cis cisterna and endoplasmic reticulum. Is expressed in brain; dorsal root ganglion; and spinal cord. Orthologous to human NECAB3 (N-terminal EF-hand calcium binding protein 3). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Biased expression in frontal lobe adult (RPKM 19.4), cortex adult (RPKM 18.6) and 8 other tissues See more
    Orthologs
    human all
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    Genomic context

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    Location:
    2 H1; 2 76.79 cM
    Exon count:
    16
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 2 NC_000068.8 (154386311..154401326, complement)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 2 NC_000068.7 (154544391..154559406, complement)

    Chromosome 2 - NC_000068.8Genomic Context describing neighboring genes Neighboring gene VISTA enhancer mm1461 Neighboring gene STARR-seq mESC enhancer starr_06124 Neighboring gene predicted gene, 52564 Neighboring gene CBFA2/RUNX1 translocation partner 2 Neighboring gene STARR-seq mESC enhancer starr_06127 Neighboring gene zinc finger, FYVE domain containing 21 pseudogene Neighboring gene RIKEN cDNA 1700003F12 gene Neighboring gene actin-like 10 Neighboring gene STARR-positive B cell enhancer ABC_E816 Neighboring gene STARR-seq mESC enhancer starr_06129 Neighboring gene E2F transcription factor 1 Neighboring gene STARR-seq mESC enhancer starr_06130 Neighboring gene predicted gene, 39963 Neighboring gene peroxisomal membrane protein 4

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Mouse ENCODE transcriptome data
    • Description: RNA profiling data sets generated by the Mouse ENCODE project.
    • BioProject: PRJNA66167
    • Publication: PMID 25409824
    • Analysis date: n/a

    Bibliography

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    Related articles in PubMed

    1. Expression of the calcium binding proteins Necab-1,-2 and -3 in the adult mouse hippocampus and dentate gyrus. Zimmermann B, et al. Brain Res, 2013 Aug 28. PMID 23850650
    2. NIP1/XB51/NECAB3 is a potential substrate of Nek2, suggesting specific roles of Nek2 in Golgi. Yoo JC, et al. Exp Cell Res, 2004 Jan 15. PMID 14697346
    3. Regulation of X11L-dependent amyloid precursor protein metabolism by XB51, a novel X11L-binding protein. Lee DS, et al. J Biol Chem, 2000 Jul 28. PMID 10833507
    4. Isolation and expression analysis of Alzheimer's disease-related gene xb51 in zebrafish. Kim HT, et al. Dev Dyn, 2008 Dec. PMID 19035353
    5. BGEM: an in situ hybridization database of gene expression in the embryonic and adult mouse nervous system. Magdaleno S, et al. PLoS Biol, 2006 Apr. PMID 16602821, Free PMC Article

    See all (17) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. The genes for the three Necab's, including Necab-3, were expressed in specific, non-overlapping areas of the hippocampus.
      Title: Expression of the calcium binding proteins Necab-1,-2 and -3 in the adult mouse hippocampus and dentate gyrus.
    2. 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.
    3. Physical interactions of Nek2 with NIP1 were confirmed. In fact, Nek2 can phosphorylate NIP1 in vivo. Immunostaining experiments revealed that NIP1 is a Golgi protein.
      Title: NIP1/XB51/NECAB3 is a potential substrate of Nek2, suggesting specific roles of Nek2 in Golgi.
    Submit: New GeneRIF Correction

    Variation

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    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    • Endonuclease-mediated (1) 

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables calcium ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables metal 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 ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within protein metabolic process TAS
    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 ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    located_in Golgi apparatus ISO
    Inferred from Sequence Orthology
    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 
    located_in Golgi cis cisterna ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in endoplasmic reticulum IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in endoplasmic reticulum IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in endoplasmic reticulum membrane ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    N-terminal EF-hand calcium-binding protein 3
    Names
    X11L-binding protein 51
    amyloid beta (A4) precursor protein-binding family A member 1 binding protein
    amyloid beta (A4) precursor protein-binding, family A, member 2 binding protein
    amyloid beta A4 protein-binding family A member 2-binding protein
    mXB51

    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_001379147.1 → NP_001366076.1  N-terminal EF-hand calcium-binding protein 3 isoform 2

      Status: VALIDATED

      Source sequence(s)
      AL772292
      Related
      ENSMUSP00000105338.3, ENSMUST00000109716.9
      Conserved Domains (3) summary
      cl28895
      Location:36 → 148
      EFh_PI-PLC; EF-hand motif found in eukaryotic phosphoinositide-specific phospholipase C (PI-PLC, EC 3.1.4.11) isozymes
      pfam03992
      Location:234 → 301
      ABM; Antibiotic biosynthesis monooxygenase
      cl08302
      Location:32 → 74
      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_001379148.1 → NP_001366077.1  N-terminal EF-hand calcium-binding protein 3 isoform 4

      Status: VALIDATED

      Source sequence(s)
      AL772292
      Conserved Domains (3) summary
      cl28895
      Location:36 → 148
      EFh_PI-PLC; EF-hand motif found in eukaryotic phosphoinositide-specific phospholipase C (PI-PLC, EC 3.1.4.11) isozymes
      pfam03992
      Location:265 → 337
      ABM; Antibiotic biosynthesis monooxygenase
      cl08302
      Location:32 → 74
      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 ...

    3. NM_001379149.1 → NP_001366078.1  N-terminal EF-hand calcium-binding protein 3 isoform 1

      Status: VALIDATED

      Source sequence(s)
      AL772292
      Conserved Domains (2) summary
      pfam03992
      Location:222 → 294
      ABM; Antibiotic biosynthesis monooxygenase
      cl08302
      Location:4 → 43
      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 ...

    4. NM_021546.3 → NP_067521.2  N-terminal EF-hand calcium-binding protein 3 isoform 3

      See identical proteins and their annotated locations for NP_067521.2

      Status: VALIDATED

      Source sequence(s)
      AK158225
      Consensus CDS
      CCDS50766.1
      UniProtKB/Swiss-Prot
      A1L0S0, A1L0S1, A2AKE8, A2AKE9, Q3TYZ9, Q9D6J4, Q9ESR0
      Related
      ENSMUSP00000000895.7, ENSMUST00000000895.13
      Conserved Domains (3) summary
      pfam03992
      Location:253 → 326
      ABM; Antibiotic biosynthesis monooxygenase
      pfam13499
      Location:30 → 56
      EF-hand_7; EF-hand domain pair
      cl08302
      Location:32 → 74
      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_000001635.27-RS_2024_02

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

    Reference GRCm39 C57BL/6J

    Genomic

    1. NC_000068.8 Reference GRCm39 C57BL/6J

      Range
      154386311..154401326 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_036162417.1 → XP_036018310.1  N-terminal EF-hand calcium-binding protein 3 isoform X4

      Conserved Domains (1) summary
      pfam03992
      Location:139 → 211
      ABM; Antibiotic biosynthesis monooxygenase

    2. XM_036162416.1 → XP_036018309.1  N-terminal EF-hand calcium-binding protein 3 isoform X3

      Conserved Domains (1) summary
      pfam03992
      Location:151 → 223
      ABM; Antibiotic biosynthesis monooxygenase

    3. XM_030251902.2 → XP_030107762.1  N-terminal EF-hand calcium-binding protein 3 isoform X4

      Conserved Domains (1) summary
      pfam03992
      Location:139 → 211
      ABM; Antibiotic biosynthesis monooxygenase

    4. XM_011239713.1 → XP_011238015.1  N-terminal EF-hand calcium-binding protein 3 isoform X2

      Conserved Domains (1) summary
      pfam03992
      Location:274 → 345
      ABM; Antibiotic biosynthesis monooxygenase

    5. XM_011239712.1 → XP_011238014.1  N-terminal EF-hand calcium-binding protein 3 isoform X1

      Conserved Domains (1) summary
      pfam03992
      Location:286 → 357
      ABM; Antibiotic biosynthesis monooxygenase

    RNA

    1. XR_001783157.1 RNA Sequence

    2. XR_001783156.1 RNA Sequence

    3. XR_001783155.1 RNA Sequence

    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9D6J4.2 GenPept UniProtKB/Swiss-Prot:Q9D6J4

    Gene LinkOut

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