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EFCAB12 EF-hand calcium binding domain 12 [ Homo sapiens (human) ]

Gene ID: 90288, updated on 10-Oct-2024

Summary

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Official Symbol
EFCAB12provided by HGNC
Official Full Name
EF-hand calcium binding domain 12provided by HGNC
Primary source
HGNC:HGNC:28061
See related
Ensembl:ENSG00000172771 AllianceGenome:HGNC:28061
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
Also known as
C3orf25
Summary
Predicted to enable calcium ion binding activity. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Broad expression in testis (RPKM 1.8), prostate (RPKM 1.5) and 14 other tissues See more
Orthologs
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Genomic context

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See EFCAB12 in Genome Data Viewer
Location:
3q21.3
Exon count:
9
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (129401321..129428636, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (132146154..132175347, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (129120164..129147479, complement)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:129066385-129066884 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:129072356-129072856 Neighboring gene MARK2 pseudogene 19 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:129076650-129077534 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:129084869-129085400 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:129085401-129085930 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr3:129107257-129108456 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:129113559-129114255 Neighboring gene ribosomal protein L32 pseudogene 3 Neighboring gene small nucleolar RNA, H/ACA box 7B Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:129129626-129130126 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:129137243-129137742 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20511 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14724 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20512 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20513 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20514 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20515 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20516 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20517 Neighboring gene Sharpr-MPRA regulatory region 8693 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:129168229-129168945 Neighboring gene methyl-CpG binding domain 4, DNA glycosylase Neighboring gene intraflagellar transport 122 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:129200162-129201039 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:129208521-129208729 Neighboring gene Sharpr-MPRA regulatory region 10640 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr3:129213542-129214741

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. A genome-wide RNAi screen identifies multiple synthetic lethal interactions with the Ras oncogene. Luo J, et al. Cell, 2009 May 29. PMID 19490893, Free PMC Article
  2. Genome-scale RNAi screen for host factors required for HIV replication. Zhou H, et al. Cell Host Microbe, 2008 Nov 13. PMID 18976975
  3. SR protein kinases promote splicing of nonconsensus introns. Lipp JJ, et al. Nat Struct Mol Biol, 2015 Aug. PMID 26167880
  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. Histone Interaction Landscapes Visualized by Crosslinking Mass Spectrometry in Intact Cell Nuclei. Fasci D, et al. Mol Cell Proteomics, 2018 Oct. PMID 30021884, Free PMC Article

See all (9) 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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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

HIV-1 interactions

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Replication interactions

Interaction Pubs
Knockdown of chromosome 3 open reading frame 25 (C3orf25) by siRNA inhibits HIV-1 replication in HeLa P4/R5 cells PubMed

Go to the HIV-1, Human Interaction Database

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 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 12
Names
EF-hand domain-containing protein C3orf25

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_207307.3 → NP_997190.1  EF-hand calcium-binding domain-containing protein 12

    See identical proteins and their annotated locations for NP_997190.1

    Status: VALIDATED

    Source sequence(s)
    AK127968, BC066975
    Consensus CDS
    CCDS54638.1
    UniProtKB/Swiss-Prot
    Q69YX4, Q6NXP0
    UniProtKB/TrEMBL
    B3KXU6
    Related
    ENSP00000420854.1, ENST00000505956.6

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_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    129401321..129428636 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    132146154..132175347 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054348318.1 → XP_054204293.1  EF-hand calcium-binding domain-containing protein 12 isoform X2

  2. XM_054348319.1 → XP_054204294.1  EF-hand calcium-binding domain-containing protein 12 isoform X3

  3. XM_054348321.1 → XP_054204296.1  EF-hand calcium-binding domain-containing protein 12 isoform X5

  4. XM_054348320.1 → XP_054204295.1  EF-hand calcium-binding domain-containing protein 12 isoform X4

  5. XM_054348317.1 → XP_054204292.1  EF-hand calcium-binding domain-containing protein 12 isoform X1

  6. XM_054348323.1 → XP_054204298.1  EF-hand calcium-binding domain-containing protein 12 isoform X7

  7. XM_054348322.1 → XP_054204297.1  EF-hand calcium-binding domain-containing protein 12 isoform X6

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q6NXP0.1 GenPept UniProtKB/Swiss-Prot:Q6NXP0

Gene LinkOut

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