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Aliases for APLF Gene

Aliases for APLF Gene

  • Aprataxin And PNKP Like Factor 2 3 5
  • XRCC1-Interacting Protein 1 2 3 4
  • PNK And APTX-Like FHA Domain-Containing Protein 3 4
  • Zinc Finger, CX5CX6HX5H Motif Containing 1 2 3
  • Apurinic-Apyrimidinic Endonuclease APLF 3 4
  • C2orf13 3 4
  • Xip1 3 4
  • PALF 3 4
  • Chromosome 2 Open Reading Frame 13 2
  • Aprataxin- And PNK-Like Factor 3
  • PNK And APTX-Like FHA Protein 3
  • Aprataxin And PNK-Like Factor 3
  • EC 4.2.99.18 4
  • ZCCHH1 3
  • APFL 3

External Ids for APLF Gene

Previous HGNC Symbols for APLF Gene

  • C2orf13

Previous GeneCards Identifiers for APLF Gene

  • GC02P068548
  • GC02P068694

Summaries for APLF Gene

Entrez Gene Summary for APLF Gene

  • C2ORF13 is a component of the cellular response to chromosomal DNA single- and double-strand breaks (Iles et al., 2007 [PubMed 17353262]).[supplied by OMIM, Mar 2008]

GeneCards Summary for APLF Gene

APLF (Aprataxin And PNKP Like Factor) is a Protein Coding gene. GO annotations related to this gene include G-protein coupled receptor activity and 3-5 exonuclease activity.

UniProtKB/Swiss-Prot for APLF Gene

  • Nuclease involved in single-strand and double-strand DNA break repair. Recruited to sites of DNA damage through interaction with poly(ADP-ribose), a polymeric post-translational modification synthesized transiently at sites of chromosomal damage to accelerate DNA strand break repair reactions. Displays apurinic-apyrimidinic (AP) endonuclease and 3-5 exonuclease activities in vitro. Also able to introduce nicks at hydroxyuracil and other types of pyrimidine base damage.

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for APLF Gene

Genomics for APLF Gene

Regulatory Elements for APLF Gene

Enhancers for APLF Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH02G068761 1.7 FANTOM5 ENCODE dbSUPER 15.7 +301.8 301821 16.7 PKNOX1 FOXA2 ATF1 CREB3L1 ZNF133 YY1 ZNF766 GATA2 ELK1 CBX5 ARHGAP25 FBXO48 APLF LINC01888 PLEK LOC105374790
GH02G068833 1.7 FANTOM5 Ensembl ENCODE dbSUPER 13.4 +367.6 367642 2.8 FOXA2 RAD21 RARA FOS CEBPB ZNF592 CEBPA RCOR2 HNF4A ILK FBXO48 PLEK LINC01890 APLF ARHGAP25 LINC01888
GH02G068906 1.5 Ensembl ENCODE dbSUPER 11 +440.6 440609 2.9 ATF1 TCF12 ZNF766 GATA2 ELK1 FOS DEK SP3 ZNF592 MEF2D BMP10 LINC01888 APLF FBXO48 GKN2 GKN3P LOC105374792
GH02G068714 1.4 Ensembl ENCODE dbSUPER 11.5 +248.2 248178 2.4 ELF3 TBL1XR1 MLX ARID4B THRB RAD21 ZNF143 IKZF2 MIXL1 ZNF654 FBXO48 APLF LINC01888 ARHGAP25 LOC105374790
GH02G068750 1.4 Ensembl ENCODE dbSUPER 10.6 +285.5 285464 4.7 ELF3 CBX3 RB1 PLRG1 ZNF48 RAD21 CHAMP1 YY1 ZNF366 ELK1 LINC01888 WDR92 APLF FBXO48 ARHGAP25 LOC105374790
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around APLF on UCSC Golden Path with GeneCards custom track

Promoters for APLF Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000118402 -159 2001 HDGF PKNOX1 CREB3L1 ZFP64 ARID4B SIN3A FEZF1 YY1 SLC30A9 ZNF766

Genomic Location for APLF Gene

Chromosome:
2
Start:
68,467,559 bp from pter
End:
68,655,862 bp from pter
Size:
188,304 bases
Orientation:
Plus strand

Genomic View for APLF Gene

Genes around APLF on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
APLF Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for APLF Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for APLF Gene

Proteins for APLF Gene

  • Protein details for APLF Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q8IW19-APLF_HUMAN
    Recommended name:
    Aprataxin and PNK-like factor
    Protein Accession:
    Q8IW19
    Secondary Accessions:
    • A8K476
    • Q53P47
    • Q53PB9
    • Q53QU0

    Protein attributes for APLF Gene

    Size:
    511 amino acids
    Molecular mass:
    56956 Da
    Quaternary structure:
    • Interacts with LIG4, PARP1, XRCC1, XRCC4 and XRCC5.
    SequenceCaution:
    • Sequence=AAY14945.1; Type=Erroneous initiation; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for APLF Gene

neXtProt entry for APLF Gene

Post-translational modifications for APLF Gene

  • Phosphorylated in an ATM-dependent manner upon double-strand DNA break.
  • Poly-ADP-ribosylated. In addition to binding non covalently poly(ADP-ribose) via its PBZ-type zinc fingers, the protein is also covalently poly-ADP-ribosylated by PARP1.
  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for APLF Gene

No data available for DME Specific Peptides for APLF Gene

Domains & Families for APLF Gene

Gene Families for APLF Gene

Protein Domains for APLF Gene

Suggested Antigen Peptide Sequences for APLF Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q8IW19

UniProtKB/Swiss-Prot:

APLF_HUMAN :
  • The PBZ-type zinc fingers (also named CYR) mediate non-covalent poly(ADP-ribose)-binding. Poly(ADP-ribose)-binding is dependent on the presence of zinc and promotes its recruitment to DNA damage sites.
  • Belongs to the APLF family.
Domain:
  • The PBZ-type zinc fingers (also named CYR) mediate non-covalent poly(ADP-ribose)-binding. Poly(ADP-ribose)-binding is dependent on the presence of zinc and promotes its recruitment to DNA damage sites.
  • The FHA-like domain mediates interaction with XRCC1 and XRCC4.
Family:
  • Belongs to the APLF family.
genes like me logo Genes that share domains with APLF: view

Function for APLF Gene

Molecular function for APLF Gene

UniProtKB/Swiss-Prot CatalyticActivity:
The C-O-P bond 3 to the apurinic or apyrimidinic site in DNA is broken by a beta-elimination reaction, leaving a 3-terminal unsaturated sugar and a product with a terminal 5-phosphate.
UniProtKB/Swiss-Prot Function:
Nuclease involved in single-strand and double-strand DNA break repair. Recruited to sites of DNA damage through interaction with poly(ADP-ribose), a polymeric post-translational modification synthesized transiently at sites of chromosomal damage to accelerate DNA strand break repair reactions. Displays apurinic-apyrimidinic (AP) endonuclease and 3-5 exonuclease activities in vitro. Also able to introduce nicks at hydroxyuracil and other types of pyrimidine base damage.

Enzyme Numbers (IUBMB) for APLF Gene

Gene Ontology (GO) - Molecular Function for APLF Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000166 nucleotide binding IEA,IDA 18172500
GO:0003906 DNA-(apurinic or apyrimidinic site) lyase activity IEA,IDA 17396150
GO:0004520 endodeoxyribonuclease activity IDA 17396150
GO:0005515 protein binding IPI 17353262
GO:0008408 3-5 exonuclease activity IDA 17396150
genes like me logo Genes that share ontologies with APLF: view
genes like me logo Genes that share phenotypes with APLF: view

Animal Model Products

CRISPR Products

Inhibitory RNA Products

Clone Products

No data available for Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for APLF Gene

Localization for APLF Gene

Subcellular locations from UniProtKB/Swiss-Prot for APLF Gene

Nucleus. Cytoplasm, cytosol. Note=Localizes to DNA damage sites. Accumulates at single-strand breaks and double-strand breaks via the PBZ-type zinc fingers.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for APLF gene
Compartment Confidence
nucleus 5
cytosol 5
endosome 1

Gene Ontology (GO) - Cellular Components for APLF Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA,IDA 17396150
GO:0005654 nucleoplasm IDA --
GO:0005737 cytoplasm IEA --
GO:0005829 cytosol IEA --
GO:0035861 site of double-strand break IDA 21211721
genes like me logo Genes that share ontologies with APLF: view

Pathways & Interactions for APLF Gene

No Data Available

Gene Ontology (GO) - Biological Process for APLF Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000012 single strand break repair IMP 17396150
GO:0006281 DNA repair IEA --
GO:0006302 double-strand break repair IMP 17396150
GO:0006974 cellular response to DNA damage stimulus IDA,IEA 17396150
GO:0045191 regulation of isotype switching IEA --
genes like me logo Genes that share ontologies with APLF: view

No data available for Pathways by source and SIGNOR curated interactions for APLF Gene

Drugs & Compounds for APLF Gene

(1) Drugs for APLF Gene - From: PharmGKB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Platinum compounds Pharma 0
genes like me logo Genes that share compounds with APLF: view

Transcripts for APLF Gene

Unigene Clusters for APLF Gene

Aprataxin and PNKP like factor:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for APLF Gene

ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10a · 10b ^ 11 ^ 12 ^ 13 ^ 14a · 14b
SP1: - - - -
SP2: -
SP3:

Relevant External Links for APLF Gene

GeneLoc Exon Structure for
APLF
ECgene alternative splicing isoforms for
APLF

Expression for APLF Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for APLF Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for APLF Gene

This gene is overexpressed in Serum (68.5).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for APLF Gene



Protein tissue co-expression partners for APLF Gene

NURSA nuclear receptor signaling pathways regulating expression of APLF Gene:

APLF

SOURCE GeneReport for Unigene cluster for APLF Gene:

Hs.720369

Evidence on tissue expression from TISSUES for APLF Gene

  • Liver(4.1)
genes like me logo Genes that share expression patterns with APLF: view

Primer Products

No data available for mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for APLF Gene

Orthologs for APLF Gene

This gene was present in the common ancestor of animals.

Orthologs for APLF Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia APLF 35
  • 98 (a)
OneToOne
cow
(Bos Taurus)
Mammalia APLF 34 35
  • 83.99 (n)
dog
(Canis familiaris)
Mammalia APLF 34 35
  • 81.79 (n)
mouse
(Mus musculus)
Mammalia Aplf 34 16 35
  • 74.71 (n)
rat
(Rattus norvegicus)
Mammalia Aplf 34
  • 74.21 (n)
oppossum
(Monodelphis domestica)
Mammalia APLF 35
  • 53 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia APLF 35
  • 46 (a)
OneToOne
chicken
(Gallus gallus)
Aves APLF 34 35
  • 58.27 (n)
lizard
(Anolis carolinensis)
Reptilia APLF 35
  • 38 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia aplf 34
  • 50.08 (n)
zebrafish
(Danio rerio)
Actinopterygii APLF 35
  • 32 (a)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta CG6171 35
  • 22 (a)
OneToOne
Species where no ortholog for APLF was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for APLF Gene

ENSEMBL:
Gene Tree for APLF (if available)
TreeFam:
Gene Tree for APLF (if available)

Paralogs for APLF Gene

No data available for Paralogs for APLF Gene

Variants for APLF Gene

Sequence variations from dbSNP and Humsavar for APLF Gene

SNP ID Clin Chr 02 pos Sequence Context AA Info Type
rs1000044288 -- 68,493,930(+) GGTGA(A/T)ACCCC intron-variant
rs1000045105 -- 68,572,759(+) ACTTG(A/C)GCCCA intron-variant
rs1000107075 -- 68,579,063(+) TATTT(A/G)TTGAA utr-variant-3-prime
rs1000125900 -- 68,468,988(+) TAAAG(C/G)GGTGT intron-variant, upstream-variant-2KB
rs1000139647 -- 68,578,817(+) TTTTG(C/T)CTTAG utr-variant-3-prime

Structural Variations from Database of Genomic Variants (DGV) for APLF Gene

Variant ID Type Subtype PubMed ID
dgv1929n106 CNV duplication 24896259
dgv44n82 CNV duplication 23825009
esv1006357 CNV insertion 20482838
esv2525478 CNV insertion 19546169
esv2576058 CNV loss 19546169
esv2671612 CNV deletion 23128226
esv3382557 CNV insertion 20981092
esv33850 CNV gain+loss 17666407
esv3591168 CNV loss 21293372
esv3591169 CNV loss 21293372
esv3892603 CNV loss 25118596
nsv1003470 CNV gain 25217958
nsv1120374 CNV tandem duplication 24896259
nsv1123333 CNV deletion 24896259
nsv1125691 CNV tandem duplication 24896259
nsv1138780 CNV deletion 24896259
nsv1151026 CNV duplication 26484159

Variation tolerance for APLF Gene

Residual Variation Intolerance Score: 77.9% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 9.98; 89.95% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for APLF Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
APLF

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for APLF Gene

Disorders for APLF Gene

Relevant External Links for APLF

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
APLF

No disorders were found for APLF Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for APLF Gene

Publications for APLF Gene

  1. APLF (C2orf13) facilitates nonhomologous end-joining and undergoes ATM-dependent hyperphosphorylation following ionizing radiation. (PMID: 18077224) Macrae C.J. … Koch C.A. (DNA Repair 2008) 2 3 4 64
  2. APLF (C2orf13) is a novel component of poly(ADP-ribose) signaling in mammalian cells. (PMID: 18474613) Rulten S.L. … Caldecott K.W. (Mol. Cell. Biol. 2008) 2 3 4 64
  3. APLF (C2orf13) is a novel human protein involved in the cellular response to chromosomal DNA strand breaks. (PMID: 17353262) Iles N. … Caldecott K.W. (Mol. Cell. Biol. 2007) 2 3 4 64
  4. Solution structures of the two PBZ domains from human APLF and their interaction with poly(ADP-ribose). (PMID: 20098424) Eustermann S. … Neuhaus D. (Nat. Struct. Mol. Biol. 2010) 3 4 64
  5. Poly(ADP-ribose)-binding zinc finger motifs in DNA repair/checkpoint proteins. (PMID: 18172500) Ahel I. … West S.C. (Nature 2008) 3 4 64

Products for APLF Gene

Sources for APLF Gene

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