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EFCAB3 EF-hand calcium binding domain 3 [ Homo sapiens (human) ]

Gene ID: 146779, updated on 28-Oct-2024

Summary

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Official Symbol
EFCAB3provided by HGNC
Official Full Name
EF-hand calcium binding domain 3provided by HGNC
Primary source
HGNC:HGNC:26379
See related
Ensembl:ENSG00000172421 MIM:619567; AllianceGenome:HGNC:26379
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Summary
Predicted to enable calcium ion binding activity. [provided by Alliance of Genome Resources, Oct 2024]
Expression
Restricted expression toward testis (RPKM 2.1) See more
Orthologs
mouse all
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Genomic context

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See EFCAB3 in Genome Data Viewer
Location:
17q23.2
Exon count:
14
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (62370218..62416480)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (63240163..63286406)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (60447579..60493841)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene ribosomal protein L36a pseudogene 47 Neighboring gene uncharacterized LOC105371936 Neighboring gene uncharacterized LOC105371854 Neighboring gene RNA, U7 small nuclear 52 pseudogene Neighboring gene ribosomal protein lateral stalk subunit P2 pseudogene 5 Neighboring gene ribosomal protein S23 pseudogene 7 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:60500991-60501521 Neighboring gene methyltransferase 2A, tRNA N3-cytidine Neighboring gene uncharacterized LOC112268200 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:60541227-60541728

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 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. Sixteen diverse laboratory mouse reference genomes define strain-specific haplotypes and novel functional loci. Lilue J, et al. Nat Genet, 2018 Nov. PMID 30275530, Free PMC Article
  2. A Global Analysis of the Receptor Tyrosine Kinase-Protein Phosphatase Interactome. Yao Z, et al. Mol Cell, 2017 Jan 19. PMID 28065597, Free PMC Article
  3. Protein interaction landscapes revealed by advanced in vivo cross-linking-mass spectrometry. Wheat A, et al. Proc Natl Acad Sci U S A, 2021 Aug 10. PMID 34349018, Free PMC Article
  4. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. Rose JE, et al. Mol Med, 2010 Jul-Aug. PMID 20379614, Free PMC Article
  5. A reference map of the human binary protein interactome. Luck K, et al. Nature, 2020 Apr. PMID 32296183, Free PMC Article

See all (8) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. 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.
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

Pathways from PubChem

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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

Homology

Clone Names

  • FLJ25818, MGC126801, MGC126827

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 

General protein information

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Preferred Names
EF-hand calcium-binding domain-containing protein 3

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_001144933.2 → NP_001138405.1  EF-hand calcium-binding domain-containing protein 3 isoform a

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (a).
    Source sequence(s)
    AC008026, AI218847, AK098684, EG327376
    Consensus CDS
    CCDS45751.1
    UniProtKB/Swiss-Prot
    Q8N7B9
    Related
    ENSP00000403932.2, ENST00000450662.7
    Conserved Domains (1) summary
    pfam13833
    Location:115 → 167
    EF-hand_8; EF-hand domain pair

  2. NM_173503.4 → NP_775774.1  EF-hand calcium-binding domain-containing protein 3 isoform b

    See identical proteins and their annotated locations for NP_775774.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR and lacks three exons in the 5' coding region, compared to variant 1. These differences cause translation initiation at a downstream AUG and result in an isoform (b) with a shorter N-terminus compared to isoform a.
    Source sequence(s)
    AC008026, AI218847, AK098684
    Consensus CDS
    CCDS11632.1
    UniProtKB/Swiss-Prot
    J3KQM8, Q8N7B9
    Related
    ENSP00000302649.3, ENST00000305286.8
    Conserved Domains (1) summary
    pfam13833
    Location:63 → 115
    EF-hand_8; EF-hand domain pair

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000017.11 Reference GRCh38.p14 Primary Assembly

    Range
    62370218..62416480
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011524380.2 → XP_011522682.1  EF-hand calcium-binding domain-containing protein 3 isoform X2

    See identical proteins and their annotated locations for XP_011522682.1

    UniProtKB/Swiss-Prot
    J3KQM8, Q8N7B9
    Conserved Domains (1) summary
    pfam13833
    Location:63 → 115
    EF-hand_8; EF-hand domain pair

  2. XM_011524381.3 → XP_011522683.2  EF-hand calcium-binding domain-containing protein 3 isoform X1

    Conserved Domains (1) summary
    pfam13833
    Location:85 → 136
    EF-hand_8; EF-hand domain pair

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    63240163..63286406
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054315160.1 → XP_054171135.1  EF-hand calcium-binding domain-containing protein 3 isoform X2

    UniProtKB/Swiss-Prot
    J3KQM8, Q8N7B9

  2. XM_054315159.1 → XP_054171134.1  EF-hand calcium-binding domain-containing protein 3 isoform X1

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q8N7B9.1 GenPept UniProtKB/Swiss-Prot:Q8N7B9

Gene LinkOut

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

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