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

Gene ID: 500247, updated on 30-Mar-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
Ensembl: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 DNA-(apurinic or apyrimidinic site) endonuclease activity; nuclease activity; and nucleotide binding activity. Predicted to be involved in double-strand break repair via nonhomologous end joining and single strand break repair. 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 nucleus and site of double-strand break. Orthologous to human APLF (aprataxin and PNKP like factor). [provided by Alliance of Genome Resources, Apr 2022]
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

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

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

    UniProtKB/TrEMBL
    A6IB10, F6Q5G6
    Related
    ENSRNOP00000043929.5, ENSRNOT00000041234.6
    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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