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Aplf aprataxin and PNKP like factor [ Mus musculus (house mouse) ]

Gene ID: 72103, updated on 21-Apr-2024

Summary

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Official Symbol
Aplfprovided by MGI
Official Full Name
aprataxin and PNKP like factorprovided by MGI
Primary source
MGI:MGI:1919353
See related
Ensembl:ENSMUSG00000030051 AllianceGenome:MGI:1919353
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Mus musculus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as
2010301N04Rik
Summary
Predicted to enable DNA-(apurinic or apyrimidinic site) endonuclease activity; nuclease activity; and nucleotide binding activity. Acts upstream of or within double-strand break repair 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
Ubiquitous expression in liver E14 (RPKM 3.4), liver E14.5 (RPKM 3.0) and 28 other tissues See more
Orthologs
human all
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Genomic context

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Location:
6 D1; 6 38.52 cM
Exon count:
11
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 6 NC_000072.7 (87605407..87649244, complement)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 6 NC_000072.6 (87628425..87672237, complement)

Chromosome 6 - NC_000072.7Genomic Context describing neighboring genes Neighboring gene prokineticin receptor 1 Neighboring gene predicted gene, 34222 Neighboring gene predicted gene, 34312 Neighboring gene STARR-seq mESC enhancer starr_16560 Neighboring gene STARR-seq mESC enhancer starr_16563 Neighboring gene predicted gene, 46964 Neighboring gene predicted gene, 38852 Neighboring gene RIKEN cDNA E230015B07 gene Neighboring gene STARR-positive B cell enhancer ABC_E9276 Neighboring gene predicted gene, 44097 Neighboring gene STARR-positive B cell enhancer ABC_E1067 Neighboring gene cilia and flagella associated protein 92 Neighboring gene STARR-seq mESC enhancer starr_16564 Neighboring gene STARR-positive B cell enhancer ABC_E9277 Neighboring gene EF hand and coiled-coil domain containing 1 Neighboring gene predicted gene, 34414

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: Mouse ENCODE transcriptome data
  • Description: RNA profiling data sets generated by the Mouse ENCODE project.
  • BioProject: PRJNA66167
  • Publication: PMID 25409824
  • Analysis date: n/a

Bibliography

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Related articles in PubMed

  1. Histone chaperone APLF regulates induction of pluripotency in murine fibroblasts. Syed KM, et al. J Cell Sci, 2016 Dec 15. PMID 27875275, Free PMC Article
  2. Histone chaperone APLF level dictates the implantation of mouse embryos. Varghese PC, et al. J Cell Sci, 2021 Jan 13. PMID 33277378
  3. PARP-3 and APLF function together to accelerate nonhomologous end-joining. Rulten SL, et al. Mol Cell, 2011 Jan 7. PMID 21211721
  4. Quantitative genetics of age-related retinal degeneration: a second F1 intercross between the A/J and C57BL/6 strains. Danciger M, et al. Mol Vis, 2007 Jan 25. PMID 17277741, Free PMC Article
  5. Interactome of vertebrate GAF/ThPOK reveals its diverse functions in gene regulation and DNA repair. Srivastava A, et al. J Biosci, 2020. PMID 32098917

See all (20) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Histone chaperone APLF level dictates the implantation of mouse embryos.
    Title: Histone chaperone APLF level dictates the implantation of mouse embryos.
  2. the downregulation of histone chaperone Aprataxin PNK-like factor (APLF) promotes reprogramming by augmenting the expression of E-cadherin.
    Title: Histone chaperone APLF regulates induction of pluripotency in murine fibroblasts.
  3. APLF has a role in chromosomal DNA double-strand break repair.
    Title: PARP-3 and APLF function together to accelerate nonhomologous end-joining.
Submit: New GeneRIF Correction

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)
  • Gene trapped (1) 
  • Targeted (1)  1 citation
  • Endonuclease-mediated (2) 

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by MGI

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 hydrolase activity IEA
Inferred from Electronic Annotation
more info
  
enables metal ion binding IEA
Inferred from Electronic Annotation
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 double-strand break repair IBA
Inferred from Biological aspect of Ancestor
more info
  
acts_upstream_of_or_within double-strand break repair IMP
Inferred from Mutant Phenotype
more info
 PubMed 
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 IMP
Inferred from Mutant Phenotype
more info
 PubMed 
acts_upstream_of_or_within positive regulation of DNA ligation ISO
Inferred from Sequence Orthology
more info
  
involved_in protein localization to chromatin ISO
Inferred from Sequence Orthology
more info
  
involved_in regulation of epithelial to mesenchymal transition IMP
Inferred from Mutant Phenotype
more info
 PubMed 
acts_upstream_of_or_within regulation of isotype switching IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in single strand break repair ISO
Inferred from Sequence Orthology
more info
  
Component Evidence Code Pubs
located_in chromosome IEA
Inferred from Electronic Annotation
more info
  
located_in cytoplasm IEA
Inferred from Electronic Annotation
more info
  
is_active_in cytosol IDA
Inferred from Direct Assay
more info
 PubMed 
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 IDA
Inferred from Direct Assay
more info
 PubMed 
located_in nucleus ISO
Inferred from Sequence Orthology
more info
  
is_active_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
  
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
Names
apurinic-apyrimidinic endonuclease APLF
NP_001163960.1
NP_001359261.1
NP_077213.2
XP_006506719.1
XP_006506720.1

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_001170489.1 → NP_001163960.1  aprataxin and PNK-like factor isoform 1

    See identical proteins and their annotated locations for NP_001163960.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
    Source sequence(s)
    AC125171, AK008513
    Consensus CDS
    CCDS51839.1
    UniProtKB/Swiss-Prot
    Q8BZL5, Q99LX6, Q9D842
    Related
    ENSMUSP00000032130.3, ENSMUST00000032130.8
    Conserved Domains (2) summary
    cd00060
    Location:5 → 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:414 → 435
    zf-CCHH; Zinc-finger (CX5CX6HX5H) motif

  2. NM_001372332.1 → NP_001359261.1  aprataxin and PNK-like factor isoform 3

    Status: VALIDATED

    Source sequence(s)
    AC125171, AC158626
    Conserved Domains (2) summary
    pfam10283
    Location:413 → 435
    zf-CCHH; Zinc-finger (CX5CX6HX5H) motif
    pfam17913
    Location:6 → 100
    FHA_2; FHA domain

  3. NM_024251.4 → NP_077213.2  aprataxin and PNK-like factor isoform 2

    See identical proteins and their annotated locations for NP_077213.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR and coding sequence and in the 3' UTR and coding sequence compared to variant 1. The resulting isoform (2) has distinct N- and C-termini and is shorter compared to isoform 1.
    Source sequence(s)
    AC125171, AK008513, AK034191
    Consensus CDS
    CCDS20324.1
    UniProtKB/Swiss-Prot
    Q9D842
    Related
    ENSMUSP00000066232.3, ENSMUST00000065997.5
    Conserved Domains (1) summary
    pfam10283
    Location:393 → 414
    zf-CCHH; Zinc-finger (CX5CX6HX5H) motif

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCm39 C57BL/6J

Genomic

  1. NC_000072.7 Reference GRCm39 C57BL/6J

    Range
    87605407..87649244 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006506656.5 → XP_006506719.1  aprataxin and PNK-like factor isoform X1

    See identical proteins and their annotated locations for XP_006506719.1

    Conserved Domains (1) summary
    pfam10283
    Location:339 → 361
    zf-CCHH; Zinc-finger (CX5CX6HX5H) motif

  2. XM_006506657.5 → XP_006506720.1  aprataxin and PNK-like factor isoform X1

    See identical proteins and their annotated locations for XP_006506720.1

    Conserved Domains (1) summary
    pfam10283
    Location:339 → 361
    zf-CCHH; Zinc-finger (CX5CX6HX5H) motif
Nucleotide Protein Strain
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9D842.2 GenPept UniProtKB/Swiss-Prot:Q9D842

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