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

    Gene ID: 301295, updated on 17-Aug-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
    EnsemblRapid: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 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
      ENSRNOP00000017393.5, ENSRNOT00000017393.9
      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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