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Efhc1 EF-hand domain containing 1 [ Rattus norvegicus (Norway rat) ]

Gene ID: 301295, updated on 4-Apr-2024

Summary

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Official Symbol
Efhc1provided by RGD
Official Full Name
EF-hand domain containing 1provided by RGD
Primary source
RGD:1587365
See related
Ensembl:ENSRNOG00000042729 AllianceGenome:RGD:1587365
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Rattus norvegicus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Summary
Predicted to enable alpha-tubulin binding activity and protein C-terminus binding activity. Predicted to be involved in several processes, including cerebral cortex cell migration; cilium-dependent cell motility; and mitotic spindle organization. Predicted to be located in cilium; microtubule cytoskeleton; and neuronal cell body. Predicted to be active in axoneme and mitotic spindle. Human ortholog(s) of this gene implicated in juvenile absence epilepsy 1 and juvenile myoclonic epilepsy. Orthologous to human EFHC1 (EF-hand domain containing 1). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Biased expression in Testes (RPKM 404.1), Lung (RPKM 49.3) and 1 other tissue See more
Orthologs
human mouse all
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Genomic context

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See Efhc1 in Genome Data Viewer
Location:
9q13
Exon count:
11
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCr8 (GCF_036323735.1) 9 NC_086027.1 (30872238..30910703)
RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 9 NC_051344.1 (23375815..23414283)
106 previous assembly Rnor_6.0 (GCF_000001895.5) 9 NC_005108.4 (27068505..27107713)

Chromosome 9 - NC_086027.1Genomic Context describing neighboring genes Neighboring gene small nucleolar RNA SNORA17 Neighboring gene progestin and adipoQ receptor family member 8 Neighboring gene small nucleolar RNA SNORA17 Neighboring gene uncharacterized LOC102549795 Neighboring gene translocation associated membrane protein 2 Neighboring gene uncharacterized LOC102549948

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
  • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
  • BioProject: PRJNA238328
  • Publication: PMID 24510058
  • Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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Related articles in PubMed

  1. Microtubule-associated defects caused by EFHC1 mutations in juvenile myoclonic epilepsy. Raju PK, et al. Hum Mutat, 2017 Jul. PMID 28370826
  2. EFHC1 interacts with microtubules to regulate cell division and cortical development. de Nijs L, et al. Nat Neurosci, 2009 Oct. PMID 19734894
  3. Expression profile and distribution of Efhc1 gene transcript during rodent brain development. Conte FF, et al. J Mol Neurosci, 2009 Sep. PMID 19191033
  4. Mutations of EFHC1, linked to juvenile myoclonic epilepsy, disrupt radial and tangential migrations during brain development. de Nijs L, et al. Hum Mol Genet, 2012 Dec 1. PMID 22926142, Free PMC Article
  5. The mouse ortholog of EFHC1 implicated in juvenile myoclonic epilepsy is an axonemal protein widely conserved among organisms with motile cilia and flagella. Ikeda T, et al. FEBS Lett, 2005 Jan 31. PMID 15670853

See all (8) citations in PubMed

GeneRIFs: Gene References Into Functions

General gene information

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Markers

Homology

Gene Ontology Provided by RGD

Function Evidence Code Pubs
enables alpha-tubulin binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables alpha-tubulin binding ISO
Inferred from Sequence Orthology
more info
  
enables calcium ion binding IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
involved_in cerebral cortex cell migration ISO
Inferred from Sequence Orthology
more info
  
involved_in cilium-dependent cell motility IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in mitotic cytokinesis IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in mitotic cytokinesis ISO
Inferred from Sequence Orthology
more info
  
involved_in mitotic spindle organization IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in mitotic spindle organization ISO
Inferred from Sequence Orthology
more info
  
involved_in regulation of cell division ISO
Inferred from Sequence Orthology
more info
  
Component Evidence Code Pubs
is_active_in axonemal A tubule inner sheath ISO
Inferred from Sequence Orthology
more info
  
located_in axonemal microtubule ISO
Inferred from Sequence Orthology
more info
  
is_active_in axoneme IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in axoneme ISO
Inferred from Sequence Orthology
more info
  
located_in centrosome ISO
Inferred from Sequence Orthology
more info
  
located_in cilium ISO
Inferred from Sequence Orthology
more info
  
is_active_in mitotic spindle IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in mitotic spindle ISO
Inferred from Sequence Orthology
more info
  
located_in neuronal cell body ISO
Inferred from Sequence Orthology
more info
  
located_in spindle pole ISO
Inferred from Sequence Orthology
more info
  

General protein information

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Preferred Names
EF-hand domain-containing protein 1
Names
EF-hand domain (C-terminal) containing 1

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_001122947.4 → NP_001116419.2  EF-hand domain-containing protein 1

    Status: VALIDATED

    Source sequence(s)
    JAXUCZ010000009
    UniProtKB/TrEMBL
    A6JJ88, D3ZD71
    Related
    ENSRNOP00000017393.4, ENSRNOT00000017393.8
    Conserved Domains (4) summary
    smart00676
    Location:93 → 198
    DM10; Domains in hypothetical proteins in Drosophila, C. elegans and mammals. Occurs singly in some nucleoside diphosphate kinases
    cd00051
    Location:587 → 647
    EFh; EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to ...
    pfam06565
    Location:439 → 471
    DUF1126; Repeat of unknown function (DUF1126)
    pfam13499
    Location:587 → 646
    EF-hand_7; EF-hand domain pair

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCr8

Genomic

  1. NC_086027.1 Reference GRCr8

    Range
    30872238..30910703
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_039083193.2 → XP_038939121.1  EF-hand domain-containing protein 1 isoform X1

    UniProtKB/TrEMBL
    A6JJ88
    Conserved Domains (3) summary
    smart00676
    Location:93 → 198
    DM10; Domains in hypothetical proteins in Drosophila, C. elegans and mammals. Occurs singly in some nucleoside diphosphate kinases
    COG5126
    Location:567 → 637
    FRQ1; Ca2+-binding protein, EF-hand superfamily [Signal transduction mechanisms]
    pfam06565
    Location:232 → 351
    DUF1126; DUF1126 PH-like domain
Nucleotide Protein Strain
Heading Accession and Version

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