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

Gene ID: 374786, updated on 6-Nov-2022

Summary

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

See EFCAB5 in Genome Data Viewer
Location:
17q11.2
Exon count:
29
Annotation release Status Assembly Chr Location
110 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (29929903..30108452)
110 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 RNY4 pseudogene 13 Neighboring gene syntaxin 18 pseudogene 1 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

Expression

  • 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

Phenotypes

EBI GWAS Catalog

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

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

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

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_001145053.2NP_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:115167
    Dpy-30; Dpy-30 motif
  2. NM_198529.4NP_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
    Q8NDG9
    Related
    ENSP00000378312.3, ENST00000394835.8
    Conserved Domains (2) summary
    smart00065
    Location:10591151
    GAF; Domain present in phytochromes and cGMP-specific phosphodiesterases
    pfam05186
    Location:171223
    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: Homo sapiens Annotation Release 110 details...Open this link in a new tab

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_024450742.1XP_024306510.1  EF-hand calcium-binding domain-containing protein 5 isoform X3

    Conserved Domains (3) summary
    smart00065
    Location:10051097
    GAF; Domain present in phytochromes and cGMP-specific phosphodiesterases
    pfam05186
    Location:115167
    Dpy-30; Dpy-30 motif
    pfam10243
    Location:436684
    MIP-T3; Microtubule-binding protein MIP-T3
  2. XM_024450743.1XP_024306511.1  EF-hand calcium-binding domain-containing protein 5 isoform X4

    Conserved Domains (3) summary
    smart00065
    Location:10031095
    GAF; Domain present in phytochromes and cGMP-specific phosphodiesterases
    pfam05186
    Location:115167
    Dpy-30; Dpy-30 motif
    pfam10243
    Location:434682
    MIP-T3; Microtubule-binding protein MIP-T3
  3. XM_047435947.1XP_047291903.1  EF-hand calcium-binding domain-containing protein 5 isoform X8

  4. XM_011524759.2XP_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:10611153
    GAF; Domain present in phytochromes and cGMP-specific phosphodiesterases
    pfam05186
    Location:171223
    Dpy-30; Dpy-30 motif
  5. XM_011524765.2XP_011523067.1  EF-hand calcium-binding domain-containing protein 5 isoform X6

    Conserved Domains (2) summary
    smart00065
    Location:10611153
    GAF; Domain present in phytochromes and cGMP-specific phosphodiesterases
    pfam05186
    Location:171223
    Dpy-30; Dpy-30 motif
  6. XM_011524763.3XP_011523065.1  EF-hand calcium-binding domain-containing protein 5 isoform X2

    Conserved Domains (2) summary
    smart00065
    Location:10611153
    GAF; Domain present in phytochromes and cGMP-specific phosphodiesterases
    pfam05186
    Location:171223
    Dpy-30; Dpy-30 motif
  7. XM_047435946.1XP_047291902.1  EF-hand calcium-binding domain-containing protein 5 isoform X7

  8. XM_011524768.3XP_011523070.1  EF-hand calcium-binding domain-containing protein 5 isoform X10

  9. XM_047435949.1XP_047291905.1  EF-hand calcium-binding domain-containing protein 5 isoform X11

  10. XM_017024592.2XP_016880081.1  EF-hand calcium-binding domain-containing protein 5 isoform X12

  11. XM_047435945.1XP_047291901.1  EF-hand calcium-binding domain-containing protein 5 isoform X5

  12. XM_017024591.2XP_016880080.1  EF-hand calcium-binding domain-containing protein 5 isoform X5

    Related
    ENSP00000417009.1, ENST00000419434.5
  13. XM_047435948.1XP_047291904.1  EF-hand calcium-binding domain-containing protein 5 isoform X9

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

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

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.