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    Def8 differentially expressed in FDCP 8 homolog [ Rattus norvegicus (Norway rat) ]

    Gene ID: 307973, updated on 9-Dec-2024

    Summary

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    Official Symbol
    Def8provided by RGD
    Official Full Name
    differentially expressed in FDCP 8 homologprovided by RGD
    Primary source
    RGD:1309008
    See related
    EnsemblRapid:ENSRNOG00000000264 AllianceGenome:RGD:1309008
    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 metal ion binding activity. Predicted to be involved in lysosome localization; positive regulation of bone resorption; and positive regulation of ruffle assembly. Orthologous to human DEF8 (differentially expressed in FDCP 8 homolog). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in Kidney (RPKM 177.3), Liver (RPKM 95.3) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Def8 in Genome Data Viewer
    Location:
    19q12
    Exon count:
    13
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 19 NC_086037.1 (68383293..68404133)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 19 NC_051354.1 (51474783..51495638)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 19 NC_005118.4 (56238353..56259867)

    Chromosome 19 - NC_086037.1Genomic Context describing neighboring genes Neighboring gene melanocortin 1 receptor Neighboring gene tubulin, beta 3 class III Neighboring gene U5 spliceosomal RNA Neighboring gene AFG3 (ATPase family gene 3)-like 1 Neighboring gene dysbindin domain containing 1

    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. PLEKHM1/DEF8/RAB7 complex regulates lysosome positioning and bone homeostasis. Fujiwara T, et al. JCI Insight, 2016 Oct 20. PMID 27777970, Free PMC Article
    2. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, et al. Proc Natl Acad Sci U S A, 2002 Dec 24. PMID 12477932, 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 metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in lysosome localization ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in lysosome localization ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in positive regulation of bone resorption ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of bone resorption ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in positive regulation of ruffle assembly ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of ruffle assembly ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  

    General protein information

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    Preferred Names
    differentially expressed in FDCP 8 homolog
    Names
    DEF-8

    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_001024774.1 → NP_001019945.1  differentially expressed in FDCP 8 homolog

      See identical proteins and their annotated locations for NP_001019945.1

      Status: PROVISIONAL

      Source sequence(s)
      BC097376
      UniProtKB/Swiss-Prot
      Q4V8I4
      UniProtKB/TrEMBL
      A6IZY4
      Conserved Domains (2) summary
      pfam13901
      Location:236 → 433
      zf-RING_9; Putative zinc-RING and/or ribbon
      cd20819
      Location:134 → 194
      C1_DEF8; protein kinase C conserved region 1 (C1 domain) found in differentially expressed in FDCP 8 (DEF-8) and similar proteins

    2. NM_001434577.1 → NP_001421506.1  differentially expressed in FDCP 8 homolog

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000019
      UniProtKB/Swiss-Prot
      Q4V8I4
      UniProtKB/TrEMBL
      A6IZY4

    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_086037.1 Reference GRCr8

      Range
      68383293..68404133
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006255769.3 → XP_006255831.1  differentially expressed in FDCP 8 homolog isoform X1

      Related
      ENSRNOP00000109709.1, ENSRNOT00000145122.1
      Conserved Domains (2) summary
      pfam13901
      Location:236 → 433
      zf-RING_9; Putative zinc-RING and/or ribbon
      cd20819
      Location:134 → 194
      C1_DEF8; protein kinase C conserved region 1 (C1 domain) found in differentially expressed in FDCP 8 (DEF-8) and similar proteins
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q4V8I4.1 GenPept UniProtKB/Swiss-Prot:Q4V8I4

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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