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    EFCAB5 EF-hand calcium binding domain 5 [ Homo sapiens (human) ]

    Gene ID: 374786, updated on 2-Nov-2024

    Summary

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    Official Symbol
    EFCAB5provided by HGNC
    Official Full Name
    EF-hand calcium binding domain 5provided by HGNC
    Primary source
    HGNC:HGNC:24801
    See related
    Ensembl:ENSG00000176927 AllianceGenome:HGNC:24801
    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, Nov 2024]
    Expression
    Restricted expression toward testis (RPKM 5.1) See more
    Orthologs
    mouse all
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    Genomic context

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    See EFCAB5 in Genome Data Viewer
    Location:
    17q11.2
    Exon count:
    29
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (29929903..30108452)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (30873230..31053011)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (28256921..28435470)

    Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene slingshot protein phosphatase 2 Neighboring gene small nucleolar RNA U13 Neighboring gene ribosomal protein L9 pseudogene 30 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8388 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8389 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8390 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8391 Neighboring gene Sharpr-MPRA regulatory region 3195 Neighboring gene Sharpr-MPRA regulatory region 15362 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr17:28367348-28368547 Neighboring gene RNY4 pseudogene 13 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8392 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:28432062-28432163 Neighboring gene syntaxin 18 pseudogene 1 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr17:28443345-28444544 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:28468415-28468916 Neighboring gene microRNA 3184 Neighboring gene microRNA 423 Neighboring gene nuclear speckle splicing regulatory protein 1 Neighboring gene uncharacterized LOC124903970 Neighboring gene solute carrier family 6 member 4

    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. Genome-wide meta-analysis identifies six novel loci associated with habitual coffee consumption. Coffee and Caffeine Genetics Consortium, et al. Mol Psychiatry, 2015 May. PMID 25288136, Free PMC Article
    2. Differential expression of a set of genes in follicular and classic variants of papillary thyroid carcinoma. Igci YZ, et al. Endocr Pathol, 2011 Jun. PMID 21509594
    3. Regulation of ETAA1-mediated ATR activation couples DNA replication fidelity and genome stability. Achuthankutty D, et al. J Cell Biol, 2019 Dec 2. PMID 31615875, Free PMC Article
    4. USP7 targets XIAP for cancer progression: Establishment of a p53-independent therapeutic avenue for glioma. Saha G, et al. Oncogene, 2022 Nov. PMID 36243803
    5. TRIM21 ameliorates hepatic glucose and lipid metabolic disorders in type 2 diabetes mellitus by ubiquitination of PEPCK1 and FASN. Zhang K, et al. Cell Mol Life Sci, 2023 May 30. PMID 37249651, Free PMC Article

    See all (14) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. EFCAB5 gene expression is decreased in papillary thyroid carcinoma.
      Title: Differential expression of a set of genes in follicular and classic variants of papillary thyroid carcinoma.
    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

    EBI GWAS Catalog

    Description
    Genome-wide meta-analysis identifies six novel loci associated with habitual coffee consumption.
    EBI GWAS Catalog

    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

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ46247, DKFZp434G2420, DKFZp686I0638

    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 calcium-binding domain-containing protein 5

    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_001145053.2 → NP_001138525.2  EF-hand calcium-binding domain-containing protein 5 isoform b

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR, 3' UTR and coding region compared to variant 1. These differences cause translation initiation at a downstream in-frame AUG and a frame shift at the 3' coding region. The resulting isoform (b) is shorter at both termini and has a distinct C-terminus, compared to isoform a.
      Source sequence(s)
      AC104982, AC104996
      Consensus CDS
      CCDS54103.1
      Related
      ENSP00000440619.2, ENST00000536908.6
      Conserved Domains (1) summary
      pfam05186
      Location:115 → 167
      Dpy-30; Dpy-30 motif

    2. NM_198529.4 → NP_940931.3  EF-hand calcium-binding domain-containing protein 5 isoform a

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longer isoform (a).
      Source sequence(s)
      AC104982, AC104984, AC104996
      Consensus CDS
      CCDS11254.2
      UniProtKB/Swiss-Prot
      A4FU69, B2RPN0, B4DS75, B4DZR5, F5GYL2, Q0VD68, Q6ZRM6, Q8NDG9
      Related
      ENSP00000378312.3, ENST00000394835.8
      Conserved Domains (2) summary
      smart00065
      Location:1059 → 1151
      GAF; Domain present in phytochromes and cGMP-specific phosphodiesterases
      pfam05186
      Location:171 → 223
      Dpy-30; Dpy-30 motif

    RNA

    1. NR_026738.2 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) differs in the 3' UTR and 3' coding region, compared to variant 1. This variant is represented as non-coding because the use of the 5' most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AC104982, AC104996
      Related
      ENST00000440741.7

    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
      29929903..30108452
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_024450742.1 → XP_024306510.1  EF-hand calcium-binding domain-containing protein 5 isoform X10

      UniProtKB/TrEMBL
      H0Y843
      Conserved Domains (3) summary
      smart00065
      Location:1005 → 1097
      GAF; Domain present in phytochromes and cGMP-specific phosphodiesterases
      pfam05186
      Location:115 → 167
      Dpy-30; Dpy-30 motif
      pfam10243
      Location:436 → 684
      MIP-T3; Microtubule-binding protein MIP-T3

    2. XM_024450743.1 → XP_024306511.1  EF-hand calcium-binding domain-containing protein 5 isoform X11

      UniProtKB/TrEMBL
      H0Y843
      Conserved Domains (3) summary
      smart00065
      Location:1003 → 1095
      GAF; Domain present in phytochromes and cGMP-specific phosphodiesterases
      pfam05186
      Location:115 → 167
      Dpy-30; Dpy-30 motif
      pfam10243
      Location:434 → 682
      MIP-T3; Microtubule-binding protein MIP-T3

    3. XM_047435947.1 → XP_047291903.1  EF-hand calcium-binding domain-containing protein 5 isoform X12

    4. XM_011524759.2 → XP_011523061.1  EF-hand calcium-binding domain-containing protein 5 isoform X1

      See identical proteins and their annotated locations for XP_011523061.1

      Conserved Domains (2) summary
      smart00065
      Location:1061 → 1153
      GAF; Domain present in phytochromes and cGMP-specific phosphodiesterases
      pfam05186
      Location:171 → 223
      Dpy-30; Dpy-30 motif

    5. XM_011524765.2 → XP_011523067.1  EF-hand calcium-binding domain-containing protein 5 isoform X4

      Conserved Domains (2) summary
      smart00065
      Location:1061 → 1153
      GAF; Domain present in phytochromes and cGMP-specific phosphodiesterases
      pfam05186
      Location:171 → 223
      Dpy-30; Dpy-30 motif

    6. XM_011524763.3 → XP_011523065.1  EF-hand calcium-binding domain-containing protein 5 isoform X2

      Conserved Domains (2) summary
      smart00065
      Location:1061 → 1153
      GAF; Domain present in phytochromes and cGMP-specific phosphodiesterases
      pfam05186
      Location:171 → 223
      Dpy-30; Dpy-30 motif

    7. XM_047435946.1 → XP_047291902.1  EF-hand calcium-binding domain-containing protein 5 isoform X5

    8. XM_011524768.3 → XP_011523070.1  EF-hand calcium-binding domain-containing protein 5 isoform X7

    9. XM_047435949.1 → XP_047291905.1  EF-hand calcium-binding domain-containing protein 5 isoform X8

    10. XM_017024592.2 → XP_016880081.1  EF-hand calcium-binding domain-containing protein 5 isoform X9

    11. XM_047435945.1 → XP_047291901.1  EF-hand calcium-binding domain-containing protein 5 isoform X3

    12. XM_017024591.2 → XP_016880080.1  EF-hand calcium-binding domain-containing protein 5 isoform X3

      UniProtKB/TrEMBL
      H0Y843
      Related
      ENSP00000417009.1, ENST00000419434.5

    13. XM_047435948.1 → XP_047291904.1  EF-hand calcium-binding domain-containing protein 5 isoform X6

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060941.1 Alternate T2T-CHM13v2.0

      Range
      30873230..31053011
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054315994.1 → XP_054171969.1  EF-hand calcium-binding domain-containing protein 5 isoform X1

    2. XM_054315998.1 → XP_054171973.1  EF-hand calcium-binding domain-containing protein 5 isoform X4

    3. XM_054315995.1 → XP_054171970.1  EF-hand calcium-binding domain-containing protein 5 isoform X2

    4. XM_054315999.1 → XP_054171974.1  EF-hand calcium-binding domain-containing protein 5 isoform X5

    5. XM_054316001.1 → XP_054171976.1  EF-hand calcium-binding domain-containing protein 5 isoform X7

    6. XM_054316002.1 → XP_054171977.1  EF-hand calcium-binding domain-containing protein 5 isoform X8

    7. XM_054316003.1 → XP_054171978.1  EF-hand calcium-binding domain-containing protein 5 isoform X9

    8. XM_054315996.1 → XP_054171971.1  EF-hand calcium-binding domain-containing protein 5 isoform X3

    9. XM_054315997.1 → XP_054171972.1  EF-hand calcium-binding domain-containing protein 5 isoform X3

    10. XM_054316000.1 → XP_054171975.1  EF-hand calcium-binding domain-containing protein 5 isoform X6

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_001033562.1: Suppressed sequence

      Description
      NM_001033562.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    A4FU69.3 GenPept UniProtKB/Swiss-Prot:A4FU69

    Gene LinkOut

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

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