LOCUS       NM_173545               3823 bp    mRNA    linear   PRI 19-SEP-2024
DEFINITION  Homo sapiens aprataxin and PNKP like factor (APLF), mRNA.
ACCESSION   NM_173545
VERSION     NM_173545.3
KEYWORDS    RefSeq; MANE Select.
SOURCE      Homo sapiens (human)
  ORGANISM  Homo sapiens
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
            Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
            Catarrhini; Hominidae; Homo.
REFERENCE   1  (bases 1 to 3823)
  AUTHORS   Huttlin,E.L., Bruckner,R.J., Navarrete-Perea,J., Cannon,J.R.,
            Baltier,K., Gebreab,F., Gygi,M.P., Thornock,A., Zarraga,G., Tam,S.,
            Szpyt,J., Gassaway,B.M., Panov,A., Parzen,H., Fu,S., Golbazi,A.,
            Maenpaa,E., Stricker,K., Guha Thakurta,S., Zhang,T., Rad,R.,
            Pan,J., Nusinow,D.P., Paulo,J.A., Schweppe,D.K., Vaites,L.P.,
            Harper,J.W. and Gygi,S.P.
  TITLE     Dual proteome-scale networks reveal cell-specific remodeling of the
            human interactome
  JOURNAL   Cell 184 (11), 3022-3040 (2021)
   PUBMED   33961781
REFERENCE   2  (bases 1 to 3823)
  AUTHORS   Richter,C., Marquardt,S., Li,F., Spitschak,A., Murr,N.,
            Edelhauser,B.A.H., Iliakis,G., Putzer,B.M. and Logotheti,S.
  TITLE     Rewiring E2F1 with classical NHEJ via APLF suppression promotes
            bladder cancer invasiveness
  JOURNAL   J Exp Clin Cancer Res 38 (1), 292 (2019)
   PUBMED   31287003
  REMARK    GeneRIF: MIR888-dependent inhibition of APLF by E2F1 was
            demonstrated using overexpression and knockdown experiments, in
            combination with luciferase assays.
            Publication Status: Online-Only
REFERENCE   3  (bases 1 to 3823)
  AUTHORS   Nemoz,C., Ropars,V., Frit,P., Gontier,A., Drevet,P., Yu,J.,
            Guerois,R., Pitois,A., Comte,A., Delteil,C., Barboule,N.,
            Legrand,P., Baconnais,S., Yin,Y., Tadi,S., Barbet-Massin,E.,
            Berger,I., Le Cam,E., Modesti,M., Rothenberg,E., Calsou,P. and
            Charbonnier,J.B.
  TITLE     XLF and APLF bind Ku80 at two remote sites to ensure DNA repair by
            non-homologous end joining
  JOURNAL   Nat Struct Mol Biol 25 (10), 971-980 (2018)
   PUBMED   30291363
  REMARK    GeneRIF: The crystal structures of the Ku-binding motifs (KBM) of
            the non-homologous end joining (NHEJ) proteins APLF (A-KBM) and XLF
            (X-KBM) bound to a Ku-DNA complex are discussed.
REFERENCE   4  (bases 1 to 3823)
  AUTHORS   Corbeski,I., Dolinar,K., Wienk,H., Boelens,R. and van Ingen,H.
  TITLE     DNA repair factor APLF acts as a H2A-H2B histone chaperone through
            binding its DNA interaction surface
  JOURNAL   Nucleic Acids Res 46 (14), 7138-7152 (2018)
   PUBMED   29905837
  REMARK    GeneRIF: The acidic domain of APLF is a histone chaperone that can
            bind both the histone H2A-H2B dimer and H3-H4 tetramer.
REFERENCE   5  (bases 1 to 3823)
  AUTHORS   Chen,Q., Kassab,M.A., Dantzer,F. and Yu,X.
  TITLE     PARP2 mediates branched poly ADP-ribosylation in response to DNA
            damage
  JOURNAL   Nat Commun 9 (1), 3233 (2018)
   PUBMED   30104678
  REMARK    Publication Status: Online-Only
REFERENCE   6  (bases 1 to 3823)
  AUTHORS   Macrae,C.J., McCulloch,R.D., Ylanko,J., Durocher,D. and Koch,C.A.
  TITLE     APLF (C2orf13) facilitates nonhomologous end-joining and undergoes
            ATM-dependent hyperphosphorylation following ionizing radiation
  JOURNAL   DNA Repair (Amst) 7 (2), 292-302 (2008)
   PUBMED   18077224
  REMARK    GeneRIF: APLF is an ATM target that is involved in nonhomologous
            end-joining and facilitates double-strand break repair, likely via
            interactions with Ku and XRCC4-DNA ligase IV.
REFERENCE   7  (bases 1 to 3823)
  AUTHORS   Ahel,I., Ahel,D., Matsusaka,T., Clark,A.J., Pines,J., Boulton,S.J.
            and West,S.C.
  TITLE     Poly(ADP-ribose)-binding zinc finger motifs in DNA
            repair/checkpoint proteins
  JOURNAL   Nature 451 (7174), 81-85 (2008)
   PUBMED   18172500
  REMARK    GeneRIF: interaction of poly(ADP-ribose) with a PBZ motif in two
            representative human proteins, APLF (aprataxin PNK-like factor) and
            CHFR (checkpoint protein with FHA and RING domains)
REFERENCE   8  (bases 1 to 3823)
  AUTHORS   Bekker-Jensen,S., Fugger,K., Danielsen,J.R., Gromova,I.,
            Sehested,M., Celis,J., Bartek,J., Lukas,J. and Mailand,N.
  TITLE     Human Xip1 (C2orf13) is a novel regulator of cellular responses to
            DNA strand breaks
  JOURNAL   J Biol Chem 282 (27), 19638-19643 (2007)
   PUBMED   17507382
REFERENCE   9  (bases 1 to 3823)
  AUTHORS   Iles,N., Rulten,S., El-Khamisy,S.F. and Caldecott,K.W.
  TITLE     APLF (C2orf13) is a novel human protein involved in the cellular
            response to chromosomal DNA strand breaks
  JOURNAL   Mol Cell Biol 27 (10), 3793-3803 (2007)
   PUBMED   17353262
  REMARK    GeneRIF: These data identify APLF as a novel component of the
            cellular response to DNA strand breaks in human cells.
            Erratum:[Mol Cell Biol. 2008 May;28(10):3561]
REFERENCE   10 (bases 1 to 3823)
  AUTHORS   Kanno,S., Kuzuoka,H., Sasao,S., Hong,Z., Lan,L., Nakajima,S. and
            Yasui,A.
  TITLE     A novel human AP endonuclease with conserved zinc-finger-like
            motifs involved in DNA strand break responses
  JOURNAL   EMBO J 26 (8), 2094-2103 (2007)
   PUBMED   17396150
  REMARK    GeneRIF: PALF is novel human AP endonuclease with conserved
            zinc-finger-like motifs involved in DNA strand break responses.
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            DA641644.1 and BC041144.1.
            
            On Nov 23, 2018 this sequence version replaced NM_173545.2.
            
            Publication Note:  This RefSeq record includes a subset of the
            publications that are available for this gene. Please see the Gene
            record to access additional publications.
            
            ##Evidence-Data-START##
            Transcript exon combination :: BC041144.1, SRR1660809.68342.1
                                           [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA1968540, SAMEA1968968
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000303795.9/ ENSP00000307004.4
            RefSeq Select criteria :: based on single protein-coding transcript
            ##RefSeq-Attributes-END##
            COMPLETENESS: full length.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-25                DA641644.1         27-51
            26-3823             BC041144.1         1-3798
FEATURES             Location/Qualifiers
     source          1..3823
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="2"
                     /map="2p13.3"
     gene            1..3823
                     /gene="APLF"
                     /gene_synonym="APFL; C2orf13; PALF; Xip1; ZCCHH1"
                     /note="aprataxin and PNKP like factor"
                     /db_xref="GeneID:200558"
                     /db_xref="HGNC:HGNC:28724"
                     /db_xref="MIM:611035"
     exon            1..243
                     /gene="APLF"
                     /gene_synonym="APFL; C2orf13; PALF; Xip1; ZCCHH1"
                     /inference="alignment:Splign:2.1.0"
     CDS             148..1683
                     /gene="APLF"
                     /gene_synonym="APFL; C2orf13; PALF; Xip1; ZCCHH1"
                     /EC_number="4.2.99.18"
                     /note="aprataxin- and PNK-like factor; XRCC1-interacting
                     protein 1; PNK and APTX-like FHA protein;
                     apurinic-apyrimidinic endonuclease APLF; PNK and APTX-like
                     FHA domain-containing protein; zinc finger, CX5CX6HX5H
                     motif containing 1"
                     /codon_start=1
                     /product="aprataxin and PNK-like factor"
                     /protein_id="NP_775816.1"
                     /db_xref="CCDS:CCDS1888.1"
                     /db_xref="GeneID:200558"
                     /db_xref="HGNC:HGNC:28724"
                     /db_xref="MIM:611035"
                     /translation="MSGGFELQPRDGGPRVALAPGETVIGRGPLLGITDKRVSRRHAI
                     LEVAGGQLRIKPIHTNPCFYQSSEKSQLLPLKPNLWCYLNPGDSFSLLVDKYIFRILS
                     IPSEVEMQCTLRNSQVLDEDNILNETPKSPVINLPHETTGASQLEGSTEIAKTQMTPT
                     NSVSFLGENRDCNKQQPILAERKRILPTWMLAEHLSDQNLSVPAISGGNVIQGSGKEE
                     ICKDKSQLNTTQQGRRQLISSGSSENTSAEQDTGEECKNTDQEESTISSKEMPQSFSA
                     ITLSNTEMNNIKTNAQRNKLPIEELGKVSKHKIATKRTPHKEDEAMSCSENCSSAQGD
                     SLQDESQGSHSESSSNPSNPETLHAKATDSVLQGSEGNKVKRTSCMYGANCYRKNPVH
                     FQHFSHPGDSDYGGVQIVGQDETDDRPECPYGPSCYRKNPQHKIEYRHNTLPVRNVLD
                     EDNDNVGQPNEYDLNDSFLDDEEEDYEPTDEDSDWEPGKEDEEKEDVEELLKEAKRFM
                     KRK"
     exon            244..315
                     /gene="APLF"
                     /gene_synonym="APFL; C2orf13; PALF; Xip1; ZCCHH1"
                     /inference="alignment:Splign:2.1.0"
     exon            316..488
                     /gene="APLF"
                     /gene_synonym="APFL; C2orf13; PALF; Xip1; ZCCHH1"
                     /inference="alignment:Splign:2.1.0"
     exon            489..636
                     /gene="APLF"
                     /gene_synonym="APFL; C2orf13; PALF; Xip1; ZCCHH1"
                     /inference="alignment:Splign:2.1.0"
     exon            637..769
                     /gene="APLF"
                     /gene_synonym="APFL; C2orf13; PALF; Xip1; ZCCHH1"
                     /inference="alignment:Splign:2.1.0"
     exon            770..951
                     /gene="APLF"
                     /gene_synonym="APFL; C2orf13; PALF; Xip1; ZCCHH1"
                     /inference="alignment:Splign:2.1.0"
     exon            952..1307
                     /gene="APLF"
                     /gene_synonym="APFL; C2orf13; PALF; Xip1; ZCCHH1"
                     /inference="alignment:Splign:2.1.0"
     exon            1308..1433
                     /gene="APLF"
                     /gene_synonym="APFL; C2orf13; PALF; Xip1; ZCCHH1"
                     /inference="alignment:Splign:2.1.0"
     exon            1434..1480
                     /gene="APLF"
                     /gene_synonym="APFL; C2orf13; PALF; Xip1; ZCCHH1"
                     /inference="alignment:Splign:2.1.0"
     exon            1481..3823
                     /gene="APLF"
                     /gene_synonym="APFL; C2orf13; PALF; Xip1; ZCCHH1"
                     /inference="alignment:Splign:2.1.0"
     regulatory      1976..1981
                     /regulatory_class="polyA_signal_sequence"
                     /gene="APLF"
                     /gene_synonym="APFL; C2orf13; PALF; Xip1; ZCCHH1"
                     /note="hexamer: AGTAAA"
     polyA_site      2000
                     /gene="APLF"
                     /gene_synonym="APFL; C2orf13; PALF; Xip1; ZCCHH1"
                     /note="major polyA site"
     regulatory      2346..2351
                     /regulatory_class="polyA_signal_sequence"
                     /gene="APLF"
                     /gene_synonym="APFL; C2orf13; PALF; Xip1; ZCCHH1"
                     /note="hexamer: AGTAAA"
     regulatory      2383..2388
                     /regulatory_class="polyA_signal_sequence"
                     /gene="APLF"
                     /gene_synonym="APFL; C2orf13; PALF; Xip1; ZCCHH1"
                     /note="hexamer: ACTAAA"
     polyA_site      2388
                     /gene="APLF"
                     /gene_synonym="APFL; C2orf13; PALF; Xip1; ZCCHH1"
     polyA_site      2408
                     /gene="APLF"
                     /gene_synonym="APFL; C2orf13; PALF; Xip1; ZCCHH1"
     regulatory      2732..2737
                     /regulatory_class="polyA_signal_sequence"
                     /gene="APLF"
                     /gene_synonym="APFL; C2orf13; PALF; Xip1; ZCCHH1"
                     /note="hexamer: CATAAA"
     polyA_site      2751
                     /gene="APLF"
                     /gene_synonym="APFL; C2orf13; PALF; Xip1; ZCCHH1"
     regulatory      3616..3621
                     /regulatory_class="polyA_signal_sequence"
                     /gene="APLF"
                     /gene_synonym="APFL; C2orf13; PALF; Xip1; ZCCHH1"
                     /note="hexamer: AATAAA"
     polyA_site      3639
                     /gene="APLF"
                     /gene_synonym="APFL; C2orf13; PALF; Xip1; ZCCHH1"
     regulatory      3802..3807
                     /regulatory_class="polyA_signal_sequence"
                     /gene="APLF"
                     /gene_synonym="APFL; C2orf13; PALF; Xip1; ZCCHH1"
                     /note="hexamer: AATAAA"
     polyA_site      3823
                     /gene="APLF"
                     /gene_synonym="APFL; C2orf13; PALF; Xip1; ZCCHH1"
ORIGIN      
        1 gagaggaccg gcgcagccgc ggggagcctt tgaggccctc cctcggtgtt ttttcccagg
       61 gcgtgggctt gccccgcgcg tgtctgtgga gggcggaaac agcggagggg ccagtctcct
      121 ggcgaagggg cctaatcctt gcccgccatg tccgggggct tcgagctgca gccgcgggac
      181 ggcggtcccc gggtggccct ggcgcccggg gagacggtga tcggccgcgg gccgctgctg
      241 ggaataacag acaagagagt atccagaaga catgccattc ttgaggtggc aggtggtcag
      301 ctgcgaatca aaccgataca cacaaatcca tgtttttacc agtcttcaga gaagagtcag
      361 ctcttaccat tgaagccaaa tctatggtgc tatttgaatc ctggagacag cttttctttg
      421 ttagttgaca aatacatttt ccgcattctc tctataccct ctgaagtgga aatgcaatgt
      481 accttaagaa acagtcaagt gcttgatgaa gataatatat tgaatgaaac accaaaatcc
      541 cccgtgatta atttacctca tgagactact ggtgcctcac aactggaagg aagcacagaa
      601 atagccaaga cccagatgac tcccacaaat agtgtgtctt tcctaggtga aaatagagac
      661 tgcaataagc agcagccaat ccttgccgag aggaaaagaa tccttccaac ttggatgtta
      721 gcagaacatt taagtgatca aaacctttca gtaccagcaa tcagtggagg taatgtaatc
      781 cagggaagtg gaaaagaaga aatctgcaaa gataaatccc agctaaacac aacccagcaa
      841 ggaagaaggc aattaatttc atcaggaagt tcagaaaata catcagcaga acaagacaca
      901 ggagaagagt gcaaaaatac tgatcaggaa gagtctacca tttcatccaa ggaaatgcca
      961 caatcatttt ctgcaatcac attaagtaac acagagatga ataatattaa gactaatgca
     1021 cagagaaaca aacttccaat agaggaactt ggtaaagttt ctaaacataa aattgccact
     1081 aaaagaacac cacataaaga agatgaggca atgagctgtt ctgaaaattg ttcgagtgcc
     1141 cagggcgact cacttcagga tgagtctcaa gggtctcatt ctgagtccag ctctaatccc
     1201 tccaatcctg aaactttgca tgcaaaggca actgattcag ttctacaagg ttctgaagga
     1261 aacaaggtca agaggacatc ctgcatgtat ggggcaaact gctataggaa gaatcctgtt
     1321 cattttcaac attttagcca tcctggtgat agtgattatg gaggtgtaca aatcgtgggc
     1381 caagatgaga ctgatgaccg gcctgaatgt ccctatggac catcctgtta taggaagaat
     1441 ccccagcaca agatagaata tagacataat acgcttccag tgagaaatgt tttagatgaa
     1501 gataatgata atgttgggca acccaatgag tatgacctga acgacagctt tctagatgat
     1561 gaggaagaag actatgagcc aacagatgaa gattctgact gggaaccagg aaaggaagat
     1621 gaagagaagg aagatgtgga agagcttttg aaagaagcaa aaaggtttat gaaaagaaaa
     1681 tagtaactaa cttctgtagt catatctgcc ttacatttac tttttctttg tgggaaaaca
     1741 tttatgaact aaggaggtac ttaagtgaca gttattttcc ttcttttgat agttaatgac
     1801 ttttactact gactctttac aaatgagaca ttgaaacgtc agccttcagt ataatagatg
     1861 gaattttttg ttgccttgcc ttttctttcc tacttaaagc atctggaaat aggaagacag
     1921 agaaggtaga gtaaaaatgg atatttttta tgtactttgt atattggtaa taaaaagtaa
     1981 aagccatagg ttgcataaaa ctttggtctt tttaaatttt tttccaaaga ttatggagta
     2041 ctctgcaagt ataaccaggc aaagtacatg aaaacatgcc tcttttcatt gttactgaag
     2101 taattctgta agcagaacca ggctttaaaa aatgcagcca ttacataatg gcgttttttt
     2161 tctagtacct tagatgtgag ctttgcaatt tcacttacta cttttatcct tcaaaacttg
     2221 ggaagattgg ttccaaatgg gtactgaaaa tagattcaac taggctgtag aagagaaatg
     2281 ttcaccatgt agggaatgtt attttgtgtt ccacatctgc aatttactgt atgtttgaat
     2341 ttaaaagtaa aaaaactcaa aaaacttgac cttttttttc aaactaaagt cctagctgat
     2401 tattttaact ctcagtgtgc tgtctttata ttaagaatag agaaacgaca taactttctc
     2461 aaatggcatt agttttgcct tagttttttt gacctcagat gaaagtagca agttgtttgc
     2521 cagttgaaag ttcaagattc tggcctccca tatcaagaag aaaccactta ttctccagtt
     2581 ttacaaagta tctttctgta tttctgttct aaaactactt taagccctat aatgctcttc
     2641 atattacgtg actttgaatt gttaaaatgt agtttagaat ctttaataac agttgggttg
     2701 tgtacacaga gcaggagata tttattgaaa tcataaatca ctaagccaaa agaatctttg
     2761 ttaaatgcta ttattttcta ctctaaagga acctaaaaat ttatatctta aaagatcaaa
     2821 acatatttat aataatattt tctcattgct ttaaaatata tctcccagta attatacaat
     2881 atttaatatt tacttaaact ggaacaagaa taagataaac atttctctag actataacct
     2941 attattctga tttttatctc ttattgttat ttgggaacta tttttcccct tataatgtcc
     3001 ctttagcctt ggtagtataa caaatctacg aatgtaatat ttaacttatt ctcatccctg
     3061 ccactaactt aatccttgaa gtgttacata atctactcct aggtatatac ccagaggaat
     3121 tgaaaacatt tccacataaa aactgtacac aatgtcaata gaagcattat tcttaacagc
     3181 caaaaagtat aaacacccaa agtctatcaa ctatcaactg ggtgaatgga taagcaaaac
     3241 gtggtatatc tgtgcaatgg aatattattt ggtcataaaa aggaataaag tactgataca
     3301 tgctacaaga tagatgaacc ttgaaggcaa gtaaaagaag ccagacacaa aaggccacat
     3361 actgtatgaa ctcatttata tgaaatttcc aaaacaggca aatccataaa gacagaaagc
     3421 aaatttgtgg ttgccaggga cttggggagg aagaatgggg agtgactgct aatgagtata
     3481 ggatttcctt ttgagtgata aaaatgttct aagattagat ggcagtgatg gttgcacaac
     3541 tctgtaaata tattacaaac aatgcattgt acactttcaa agggtagatt tcattgcacg
     3601 tgaactatat atttcaataa atctgtcaca aaaaagtaat gcaaagggta ataccagtct
     3661 tttagaagga aaaaaatatt taatatcaaa ggatattctt cgtagtaatg taatagttca
     3721 tggtagctgc ttttaacgat acagttttaa tgcaactttc ataatcatcc tgaagacact
     3781 tttgagtata actattgtat aaataaatgt atagcttaat tga
//
