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    Fgd5 FYVE, RhoGEF and PH domain containing 5 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 362402, updated on 27-Nov-2024

    Summary

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    Official Symbol
    Fgd5provided by RGD
    Official Full Name
    FYVE, RhoGEF and PH domain containing 5provided by RGD
    Primary source
    RGD:1305589
    See related
    EnsemblRapid:ENSRNOG00000010213 AllianceGenome:RGD:1305589
    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 guanyl-nucleotide exchange factor activity. Predicted to be located in plasma membrane. Predicted to be active in cytoplasm. Orthologous to human FGD5 (FYVE, RhoGEF and PH domain containing 5). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Biased expression in Lung (RPKM 171.9), Heart (RPKM 109.3) and 8 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Fgd5 in Genome Data Viewer
    Location:
    4q34
    Exon count:
    21
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 4 NC_086022.1 (126054201..126151698)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 4 NC_051339.1 (124497061..124594564)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 4 NC_005103.4 (123865557..123962904)

    Chromosome 4 - NC_086022.1Genomic Context describing neighboring genes Neighboring gene ribosomal protein S11, pseudogene 14 Neighboring gene coiled-coil domain containing 174 Neighboring gene similar to human chromosome 3 open reading frame 20 Neighboring gene uncharacterized LOC102554857 Neighboring gene uncharacterized LOC134486612 Neighboring gene nuclear receptor subfamily 2, group C, member 2 Neighboring gene mitochondrial ribosomal protein S25

    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. Normalization and subtraction: two approaches to facilitate gene discovery. Bonaldo MF, et al. Genome Res, 1996 Sep. PMID 8889548
    2. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, et al. Brief Bioinform, 2011 Sep. PMID 21873635, Free PMC Article

    GeneRIFs: Gene References Into Functions

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables guanyl-nucleotide exchange factor activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytoskeleton IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in plasma membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in plasma membrane ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    FYVE, RhoGEF and PH 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_001108637.2 → NP_001102107.2  FYVE, RhoGEF and PH domain-containing protein 5

      Status: VALIDATED

      Source sequence(s)
      BI289075, JAXUCZ010000004
      UniProtKB/TrEMBL
      A0A8I5ZMC4, F1LTE6
      Related
      ENSRNOP00000040013.5, ENSRNOT00000051022.8
      Conserved Domains (5) summary
      PHA03169
      Location:113 → 324
      PHA03169; hypothetical protein; Provisional
      cd13237
      Location:1424 → 1514
      PH2_FGD5_FGD6; FYVE, RhoGEF and PH domain containing/faciogenital dysplasia proteins 5 and 6 pleckstrin homology (PH) domain, C-terminus
      cl28890
      Location:1294 → 1360
      FYVE_like_SF; FYVE domain like superfamily
      pfam00621
      Location:951 → 1139
      RhoGEF; RhoGEF domain
      cl17171
      Location:1158 → 1280
      PH-like; Pleckstrin homology-like domain

    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_086022.1 Reference GRCr8

      Range
      126054201..126151698
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006236926.5 → XP_006236988.1  FYVE, RhoGEF and PH domain-containing protein 5 isoform X1

      See identical proteins and their annotated locations for XP_006236988.1

      UniProtKB/TrEMBL
      A0A8I5ZMC4
      Related
      ENSRNOP00000101814.1, ENSRNOT00000153524.1
      Conserved Domains (5) summary
      cd13237
      Location:1423 → 1513
      PH2_FGD5_FGD6; FYVE, RhoGEF and PH domain containing/faciogenital dysplasia proteins 5 and 6 pleckstrin homology (PH) domain, C-terminus
      pfam00169
      Location:1172 → 1263
      PH; PH domain
      pfam00621
      Location:951 → 1139
      RhoGEF; RhoGEF domain
      cl17171
      Location:1157 → 1279
      PH-like; Pleckstrin homology-like domain
      cl22851
      Location:1293 → 1359
      PHD_SF; PHD finger superfamily
    Nucleotide Protein Strain
    Heading Accession and Version

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