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

Gene ID: 79825, updated on 27-Nov-2024

Summary

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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, Nov 2024]
Expression
Broad expression in lung (RPKM 5.0), ovary (RPKM 2.3) and 19 other tissues See more
Orthologs
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Genomic context

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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

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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. 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

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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)

HIV-1 interactions

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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

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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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

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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)

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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_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

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