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

    Gene ID: 90288, updated on 3-Apr-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
    mouse all
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    Genomic context

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    Location:
    3q21.3
    Exon count:
    9
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (129401321..129428636, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (132146154..132175347, complement)
    105.20220307 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
    • 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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    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

    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_2023_10

    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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