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

Gene ID: 374786, updated on 3-Apr-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, Apr 2022]
Expression
Restricted expression toward testis (RPKM 5.1) See more
Orthologs
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Genomic context

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Location:
17q11.2
Exon count:
29
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (29929903..30108452)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (30873230..31053011)
105.20220307 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
  • 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. Shotgun sequencing of the human transcriptome with ORF expressed sequence tags. Dias Neto E, et al. Proc Natl Acad Sci U S A, 2000 Mar 28. PMID 10737800, Free PMC Article

See all (11) 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_2023_10

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

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