U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Links from GEO Profiles

    • Showing Current items.

    EFCC1 EF-hand and coiled-coil domain containing 1 [ Homo sapiens (human) ]

    Gene ID: 79825, updated on 10-Dec-2024

    Summary

    Go to the top of the page Help
    Official Symbol
    EFCC1provided by HGNC
    Official Full Name
    EF-hand and coiled-coil domain containing 1provided by HGNC
    Primary source
    HGNC:HGNC:25692
    See related
    Ensembl:ENSG00000114654 AllianceGenome:HGNC:25692
    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
    CCDC48; C3orf73
    Summary
    Predicted to enable calcium ion binding activity. [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Broad expression in lung (RPKM 5.0), ovary (RPKM 2.3) and 19 other tissues See more
    Orthologs
    mouse all
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    Go to the top of the page Help
    See EFCC1 in Genome Data Viewer
    Location:
    3q21.3
    Exon count:
    14
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (129001304..129040742)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (131746185..131785616)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (128720147..128759585)

    Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancers GRCh37_chr3:128597333-128598184 and GRCh37_chr3:128598185-128599037 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:128599038-128599889 Neighboring gene ACAD9 divergent transcript Neighboring gene acyl-CoA dehydrogenase family member 9 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr3:128620937-128622136 Neighboring gene cilia and flagella associated protein 92 (putative) Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:128651057-128651558 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:128653559-128654060 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:128654061-128654560 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:128682980-128683974 Neighboring gene MPRA-validated peak4825 silencer Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr3:128705779-128706978 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:128711587-128712348 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14714 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:128734769-128735276 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:128735847-128736348 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14716 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:128752375-128752929 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:128756987-128757962 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:128757963-128758936 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20502 Neighboring gene JMJD4 pseudogene 1 Neighboring gene glycoprotein IX platelet

    Genomic regions, transcripts, and products

    Go to the top of the page Help

    Go to nucleotide: Graphics FASTA GenBank

    Expression

    Go to the top of the page Help
    • 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

    Go to the top of the pageHelp

    Related articles in PubMed

    1. The global gene-expression profiles of U-937 human macrophages treated with Tat peptide and Tat-FITC conjugate. Lin CW, et al. J Drug Target, 2012 Jul. PMID 22632162
    2. The DNA sequence, annotation and analysis of human chromosome 3. Muzny DM, et al. Nature, 2006 Apr 27. PMID 16641997
    3. Dynamics of cullin-RING ubiquitin ligase network revealed by systematic quantitative proteomics. Bennett EJ, et al. Cell, 2010 Dec 10. PMID 21145461, Free PMC Article
    4. EZH2 depletion potentiates MYC degradation inhibiting neuroblastoma and small cell carcinoma tumor formation. Wang L, et al. Nat Commun, 2022 Jan 10. PMID 35013218, Free PMC Article
    5. Complete sequencing and characterization of 21,243 full-length human cDNAs. Ota T, et al. Nat Genet, 2004 Jan. PMID 14702039

    See all (8) citations in PubMed

    GeneRIFs: Gene References Into Functions

    Phenotypes

    Go to the top of the page Help

    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Variation

    Go to the top of the page Help

    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    HIV-1 interactions

    Go to the top of the page Help

    Protein interactions

    Protein Gene Interaction Pubs
    Tat tat Both HIV-1 Tat 47-59 and FITC-labeled Tat 47-59 peptides downregulate gene expression of coiled-coil domain containing 48 (CCDC48) in U-937 macrophages PubMed

    Go to the HIV-1, Human Interaction Database

    Interactions

    Go to the top of the page Help
    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Go to the top of the page Help

    Markers

    Homology

    Clone Names

    • FLJ12053, FLJ12057, MGC138400, DKFZp686B0148

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables calcium ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

    Go to the top of the page Help
    Preferred Names
    EF-hand and coiled-coil domain-containing protein 1
    Names
    EF-hand domain-containing protein ENSP00000381169
    coiled-coil domain containing 48
    coiled-coil domain-containing protein 48

    NCBI Reference Sequences (RefSeq)

    Go to the top of the page Help

    NEW Try the new Transcript table

    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_001377500.1 → NP_001364429.1  EF-hand and coiled-coil domain-containing protein 1 isoform 1

      Status: VALIDATED

      Source sequence(s)
      AC108673, AC112484
      Consensus CDS
      CCDS93371.1
      UniProtKB/TrEMBL
      A0A804HK68
      Related
      ENSP00000507795.1, ENST00000683648.1
      Conserved Domains (1) summary
      pfam15799
      Location:18 → 599
      CCD48; Coiled-coil domain-containing protein 48

    2. NM_001377501.1 → NP_001364430.1  EF-hand and coiled-coil domain-containing protein 1 isoform 3

      Status: VALIDATED

      Source sequence(s)
      AC112484
      Conserved Domains (1) summary
      pfam15799
      Location:18 → 327
      CCD48; Coiled-coil domain-containing protein 48

    3. NM_024768.3 → NP_079044.2  EF-hand and coiled-coil domain-containing protein 1 isoform 2

      See identical proteins and their annotated locations for NP_079044.2

      Status: VALIDATED

      Source sequence(s)
      AC108673, AC112484, BC093800
      Consensus CDS
      CCDS3054.2
      UniProtKB/Swiss-Prot
      A8MYE2, Q9HA90
      Related
      ENSP00000414597.3, ENST00000436022.2
      Conserved Domains (1) summary
      pfam15799
      Location:18 → 598
      CCD48; Coiled-coil domain-containing protein 48

    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
      129001304..129040742
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011513163.4 → XP_011511465.1  EF-hand and coiled-coil domain-containing protein 1 isoform X3

      Conserved Domains (1) summary
      pfam15799
      Location:18 → 326
      CCD48; Coiled-coil domain-containing protein 48

    2. XM_047448963.1 → XP_047304919.1  EF-hand and coiled-coil domain-containing protein 1 isoform X2

    3. XM_011513161.3 → XP_011511463.1  EF-hand and coiled-coil domain-containing protein 1 isoform X1

      Conserved Domains (1) summary
      pfam15799
      Location:3 → 370
      CCD48; Coiled-coil domain-containing protein 48

    4. XM_011513164.3 → XP_011511466.1  EF-hand and coiled-coil domain-containing protein 1 isoform X4

      Conserved Domains (1) summary
      pfam15799
      Location:31 → 303
      CCD48; Coiled-coil domain-containing protein 48

    RNA

    1. XR_924178.4 RNA Sequence

    2. XR_007095727.1 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060927.1 Alternate T2T-CHM13v2.0

      Range
      131746185..131785616
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054347917.1 → XP_054203892.1  EF-hand and coiled-coil domain-containing protein 1 isoform X3

    2. XM_054347916.1 → XP_054203891.1  EF-hand and coiled-coil domain-containing protein 1 isoform X1

    3. XM_054347915.1 → XP_054203890.1  EF-hand and coiled-coil domain-containing protein 1 isoform X5

    4. XM_054347918.1 → XP_054203893.1  EF-hand and coiled-coil domain-containing protein 1 isoform X4

    RNA

    1. XR_008486799.1 RNA Sequence

    2. XR_008486798.1 RNA Sequence

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9HA90.2 GenPept UniProtKB/Swiss-Prot:Q9HA90

    Gene LinkOut

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

    Chemical Information
    Molecular Biology Databases
    Research Materials
    Tools