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

Summary

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 regulation of amyloid precursor protein biosynthetic process. Located in Golgi cis cisterna and endoplasmic reticulum. Is expressed in nervous system. Orthologous to human NECAB3 (N-terminal EF-hand calcium binding protein 3). [provided by Alliance of Genome Resources, Nov 2024]
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

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_000068.8 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Mouse ENCODE transcriptome data 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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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.
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 (2)

General gene information

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Markers

NoName (e-PCR)
- UniSTS:489234

AI853434 (e-PCR)
- UniSTS:178746

E2f1 (e-PCR), detects polymorphism
- UniSTS:527319

Gene Ontology Provided by MGI

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	ISO Inferred from Sequence Orthology more info
involved_in protein metabolic process	ISS Inferred from Sequence or Structural Similarity 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	IEA Inferred from Electronic Annotation 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
located_in Golgi cis cisterna	ISS Inferred from Sequence or Structural Similarity 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
located_in cytoplasm	ISS Inferred from Sequence or Structural Similarity 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
located_in endoplasmic reticulum membrane	ISS Inferred from Sequence or Structural Similarity 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)

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 ...
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 ...
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 ...
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

NC_000068.8 Reference GRCm39 C57BL/6J

Range

154386311..154401326 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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
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
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
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
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