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    Aplf aprataxin and PNKP like factor [ Rattus norvegicus (Norway rat) ]

    Gene ID: 500247, updated on 9-Dec-2024

    Summary

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    Official Symbol
    Aplfprovided by RGD
    Official Full Name
    aprataxin and PNKP like factorprovided by RGD
    Primary source
    RGD:1565557
    See related
    EnsemblRapid:ENSRNOG00000043059 AllianceGenome:RGD:1565557
    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
    Also known as
    RGD1565557
    Summary
    Predicted to enable several functions, including ADP-D-ribose modification-dependent protein binding activity; nuclease activity; and poly-ADP-D-ribose binding activity. Predicted to be involved in several processes, including DNA repair; DNA repair-dependent chromatin remodeling; and embryo implantation. Predicted to act upstream of or within positive regulation of DNA ligation and regulation of isotype switching. Predicted to be located in nucleoplasm. Predicted to be active in cytosol; nucleus; and site of double-strand break. Orthologous to human APLF (aprataxin and PNKP like factor). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in Thymus (RPKM 134.3), Kidney (RPKM 92.4) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Aplf in Genome Data Viewer
    Location:
    4q34
    Exon count:
    12
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 4 NC_086022.1 (121627800..121679980, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 4 NC_051339.1 (120070471..120122656, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 4 NC_005103.4 (119514822..119568764, complement)

    Chromosome 4 - NC_086022.1Genomic Context describing neighboring genes Neighboring gene Rho GTPase activating protein 25 Neighboring gene prokineticin receptor 1 Neighboring gene uncharacterized LOC120102330 Neighboring gene cilia and flagella associated protein 92 Neighboring gene uncharacterized LOC100910604 Neighboring gene EF-hand and coiled-coil 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. PARP-3 and APLF function together to accelerate nonhomologous end-joining. Rulten SL, et al. Mol Cell, 2011 Jan 7. PMID 21211721
    2. A novel human AP endonuclease with conserved zinc-finger-like motifs involved in DNA strand break responses. Kanno S, et al. EMBO J, 2007 Apr 18. PMID 17396150, Free PMC Article
    3. Histone chaperones in nucleosome assembly and human disease. Burgess RJ, et al. Nat Struct Mol Biol, 2013 Jan. PMID 23288364, Free PMC Article
    4. The mechanism of double-strand DNA break repair by the nonhomologous DNA end-joining pathway. Lieber MR. Annu Rev Biochem, 2010. PMID 20192759, Free PMC Article
    5. Structures and Mechanisms of Enzymes Employed in the Synthesis and Degradation of PARP-Dependent Protein ADP-Ribosylation. Barkauskaite E, et al. Mol Cell, 2015 Jun 18. PMID 26091342

    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 3'-5' exonuclease activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables ADP-D-ribose modification-dependent protein binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables DNA endonuclease activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables DNA-(apurinic or apyrimidinic site) endonuclease activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables DNA-(apurinic or apyrimidinic site) endonuclease activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables histone binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables histone chaperone activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables nucleotide binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables poly-ADP-D-ribose binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables protein folding chaperone ISO
    Inferred from Sequence Orthology
    more info
    		  
    Process Evidence Code Pubs
    involved_in DNA damage response ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in DNA repair ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in DNA repair-dependent chromatin remodeling ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in biological_process ND
    No biological Data available
    more info
    		  
    involved_in double-strand break repair IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within double-strand break repair ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in double-strand break repair ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in double-strand break repair via nonhomologous end joining ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in embryo implantation ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within positive regulation of DNA ligation ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in protein folding IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in protein localization to chromatin ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in regulation of epithelial to mesenchymal transition ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within regulation of isotype switching ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in single strand break repair ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    is_active_in cytosol ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    is_active_in nucleus ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleus ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in site of DNA damage ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in site of DNA damage ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in site of double-strand break IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    is_active_in site of double-strand break ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in site of double-strand break ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    aprataxin and PNK-like factor
    NP_001166853.1
    XP_008761298.1
    XP_017448313.1
    XP_017448314.1
    XP_038964092.1

    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_001173382.1 → NP_001166853.1  aprataxin and PNK-like factor

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000004
      UniProtKB/TrEMBL
      A6IB10
      Conserved Domains (2) summary
      cd00060
      Location:4 → 102
      FHA; Forkhead associated domain (FHA); found in eukaryotic and prokaryotic proteins. Putative nuclear signalling domain. FHA domains may bind phosphothreonine, phosphoserine and sometimes phosphotyrosine. In eukaryotes, many FHA domain-containing proteins ...
      pfam10283
      Location:421 → 442
      zf-CCHH; Zinc-finger (CX5CX6HX5H) motif

    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
      121627800..121679980 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017592824.3 → XP_017448313.1  aprataxin and PNK-like factor isoform X2

      UniProtKB/TrEMBL
      A0A8I6AU35, A6IB10
      Related
      ENSRNOP00000095757.1, ENSRNOT00000117709.2

    2. XM_008763076.3 → XP_008761298.1  aprataxin and PNK-like factor isoform X1

      UniProtKB/TrEMBL
      A6IB10, F6Q5G6
      Related
      ENSRNOP00000043929.5, ENSRNOT00000041234.7
      Conserved Domains (2) summary
      cd00060
      Location:4 → 102
      FHA; Forkhead associated domain (FHA); found in eukaryotic and prokaryotic proteins. Putative nuclear signalling domain. FHA domains may bind phosphothreonine, phosphoserine and sometimes phosphotyrosine. In eukaryotes, many FHA domain-containing proteins ...
      pfam10283
      Location:424 → 445
      zf-CCHH; Zinc-finger (CX5CX6HX5H) motif

    3. XM_039108164.2 → XP_038964092.1  aprataxin and PNK-like factor isoform X4

      Conserved Domains (1) summary
      pfam10283
      Location:93 → 118
      zf-CCHH; Zinc-finger (CX5CX6HX5H) motif

    4. XM_017592825.3 → XP_017448314.1  aprataxin and PNK-like factor isoform X3

      UniProtKB/TrEMBL
      A6IB10

    RNA

    1. XR_005503300.1 RNA Sequence

    Nucleotide Protein Strain
    Heading Accession and Version

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