LOCUS       NM_153583               3024 bp    mRNA    linear   ROD 10-FEB-2025
DEFINITION  Mus musculus autophagy related 4D, cysteine peptidase (Atg4d),
            mRNA.
ACCESSION   NM_153583
VERSION     NM_153583.10
KEYWORDS    RefSeq; RefSeq Select.
SOURCE      Mus musculus (house mouse)
  ORGANISM  Mus musculus
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
            Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha;
            Muroidea; Muridae; Murinae; Mus; Mus.
REFERENCE   1  (bases 1 to 3024)
  AUTHORS   Tamargo-Gomez,I., Martinez-Garcia,G.G., Suarez,M.F., Rey,V.,
            Fueyo,A., Codina-Martinez,H., Bretones,G., Caravia,X.M., Morel,E.,
            Dupont,N., Cabo,R., Tomas-Zapico,C., Souquere,S., Pierron,G.,
            Codogno,P., Lopez-Otin,C., Fernandez,A.F. and Marino,G.
  TITLE     ATG4D is the main ATG8 delipidating enzyme in mammalian cells and
            protects against cerebellar neurodegeneration
  JOURNAL   Cell Death Differ 28 (9), 2651-2672 (2021)
   PUBMED   33795848
  REMARK    Erratum:[Cell Death Differ. 2021 Nov;28(11):3197. doi:
            10.1038/s41418-021-00783-2.. PMID: 33893394]
REFERENCE   2  (bases 1 to 3024)
  AUTHORS   Chai,G., Webb,A., Li,C., Antaki,D., Lee,S., Breuss,M.W., Lang,N.,
            Stanley,V., Anzenberg,P., Yang,X., Marshall,T., Gaffney,P.,
            Wierenga,K.J., Chung,B.H., Tsang,M.H., Pais,L.S., Lovgren,A.K.,
            VanNoy,G.E., Rehm,H.L., Mirzaa,G., Leon,E., Diaz,J., Neumann,A.,
            Kalverda,A.P., Manfield,I.W., Parry,D.A., Logan,C.V., Johnson,C.A.,
            Bonthron,D.T., Valleley,E.M.A., Issa,M.Y., Abdel-Ghafar,S.F.,
            Abdel-Hamid,M.S., Jennings,P., Zaki,M.S., Sheridan,E. and
            Gleeson,J.G.
  TITLE     Mutations in Spliceosomal Genes PPIL1 and PRP17 Cause
            Neurodegenerative Pontocerebellar Hypoplasia with Microcephaly
  JOURNAL   Neuron 109 (2), 241-256 (2021)
   PUBMED   33220177
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            BB857077.1, AK036571.1 and AK036282.1.
            
            On Nov 28, 2013 this sequence version replaced NM_153583.9.
            
            ##Evidence-Data-START##
            Transcript exon combination :: AK036282.1, AK036571.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMN00849374, SAMN00849375
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            gene product(s) localized to mito. :: inferred from homology
            RefSeq Select criteria             :: based on conservation,
                                                  expression, longest protein
            ##RefSeq-Attributes-END##
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-14                BB857077.1         3-16
            15-2555             AK036571.1         4-2544
            2556-3024           AK036282.1         2544-3012
FEATURES             Location/Qualifiers
     source          1..3024
                     /organism="Mus musculus"
                     /mol_type="mRNA"
                     /strain="C57BL/6"
                     /db_xref="taxon:10090"
                     /chromosome="9"
                     /map="9 7.75 cM"
     gene            1..3024
                     /gene="Atg4d"
                     /gene_synonym="9830134P12Rik; APG4-D; Apg4d; Atg4dl;
                     Autl4"
                     /note="autophagy related 4D, cysteine peptidase"
                     /db_xref="GeneID:235040"
                     /db_xref="MGI:MGI:2444308"
     exon            1..433
                     /gene="Atg4d"
                     /gene_synonym="9830134P12Rik; APG4-D; Apg4d; Atg4dl;
                     Autl4"
                     /inference="alignment:Splign:2.1.0"
     CDS             199..1623
                     /gene="Atg4d"
                     /gene_synonym="9830134P12Rik; APG4-D; Apg4d; Atg4dl;
                     Autl4"
                     /note="cysteine protease involved in autophagy APG4-D;
                     cysteine protease ATG4D; autophagin-4; autophagy-related
                     4D; autophagy-related protein 4 homolog D;
                     autophagy-related cysteine endopeptidase 4; AUT-like 4,
                     cysteine endopeptidase; APG4 (ATG4) autophagy-related
                     homolog D"
                     /codon_start=1
                     /product="cysteine protease ATG4D precursor"
                     /protein_id="NP_705811.8"
                     /db_xref="CCDS:CCDS22899.1"
                     /db_xref="GeneID:235040"
                     /db_xref="MGI:MGI:2444308"
                     /translation="MNSVSPAAAQYRSGSSEDARRADCRRPRGQTRIPDPSNLGPSGS
                     GVAALGSSGTDPAEPDEVDKFKAKFLTAWNNVKYGWAVKSRTSFSKISTVHLCGRCYH
                     FEGEGDIQRFQRDFVSRLWLTYRRDFPPLAGGSLTSDCGWGCMLRSGQMMLAQGLLLH
                     FLPRDWRWVEGTGLASSEMPGPASPSRCRGPGRRGPPRWTQGALEMEQDRWHRRIVSW
                     FADHPRAPFGLHRLVELGRSSGKKAGDWYGPSVVAHILRKAVESCSEVSRLVVYVSQD
                     CTVYKADVARLLSWPDPTAEWKSVVILVPVRLGGETLNPVYVPCVKELLRSELCLGIM
                     GGKPRHSLYFIGYQDDFLLYLDPHYCQPTVDVSQPSFPLESFHCTSPRKMAFAKMDPS
                     CTVGFYAGNRKEFETLCSELMRILSSSSVTERYPMFTVAEGHAQDHSLDALCTQLSQP
                     TLRLPCTGRLLKAKRPSSEDFVFL"
     exon            434..517
                     /gene="Atg4d"
                     /gene_synonym="9830134P12Rik; APG4-D; Apg4d; Atg4dl;
                     Autl4"
                     /inference="alignment:Splign:2.1.0"
     exon            518..691
                     /gene="Atg4d"
                     /gene_synonym="9830134P12Rik; APG4-D; Apg4d; Atg4dl;
                     Autl4"
                     /inference="alignment:Splign:2.1.0"
     exon            692..968
                     /gene="Atg4d"
                     /gene_synonym="9830134P12Rik; APG4-D; Apg4d; Atg4dl;
                     Autl4"
                     /inference="alignment:Splign:2.1.0"
     exon            969..1033
                     /gene="Atg4d"
                     /gene_synonym="9830134P12Rik; APG4-D; Apg4d; Atg4dl;
                     Autl4"
                     /inference="alignment:Splign:2.1.0"
     exon            1034..1164
                     /gene="Atg4d"
                     /gene_synonym="9830134P12Rik; APG4-D; Apg4d; Atg4dl;
                     Autl4"
                     /inference="alignment:Splign:2.1.0"
     exon            1165..1243
                     /gene="Atg4d"
                     /gene_synonym="9830134P12Rik; APG4-D; Apg4d; Atg4dl;
                     Autl4"
                     /inference="alignment:Splign:2.1.0"
     exon            1244..1320
                     /gene="Atg4d"
                     /gene_synonym="9830134P12Rik; APG4-D; Apg4d; Atg4dl;
                     Autl4"
                     /inference="alignment:Splign:2.1.0"
     exon            1321..1440
                     /gene="Atg4d"
                     /gene_synonym="9830134P12Rik; APG4-D; Apg4d; Atg4dl;
                     Autl4"
                     /inference="alignment:Splign:2.1.0"
     exon            1441..3024
                     /gene="Atg4d"
                     /gene_synonym="9830134P12Rik; APG4-D; Apg4d; Atg4dl;
                     Autl4"
                     /inference="alignment:Splign:2.1.0"
     regulatory      1915..1920
                     /regulatory_class="polyA_signal_sequence"
                     /gene="Atg4d"
                     /gene_synonym="9830134P12Rik; APG4-D; Apg4d; Atg4dl;
                     Autl4"
                     /note="hexamer: GATAAA"
     polyA_site      1934
                     /gene="Atg4d"
                     /gene_synonym="9830134P12Rik; APG4-D; Apg4d; Atg4dl;
                     Autl4"
                     /note="major polyA site"
     polyA_site      2557
                     /gene="Atg4d"
                     /gene_synonym="9830134P12Rik; APG4-D; Apg4d; Atg4dl;
                     Autl4"
     regulatory      2956..2961
                     /regulatory_class="polyA_signal_sequence"
                     /gene="Atg4d"
                     /gene_synonym="9830134P12Rik; APG4-D; Apg4d; Atg4dl;
                     Autl4"
                     /note="hexamer: AACAAG"
     polyA_site      2965
                     /gene="Atg4d"
                     /gene_synonym="9830134P12Rik; APG4-D; Apg4d; Atg4dl;
                     Autl4"
     regulatory      3003..3008
                     /regulatory_class="polyA_signal_sequence"
                     /gene="Atg4d"
                     /gene_synonym="9830134P12Rik; APG4-D; Apg4d; Atg4dl;
                     Autl4"
                     /note="hexamer: GATAAA"
     polyA_site      3022
                     /gene="Atg4d"
                     /gene_synonym="9830134P12Rik; APG4-D; Apg4d; Atg4dl;
                     Autl4"
ORIGIN      
        1 agcccaccgt atccgggtgc tctgggccac caagatggcg ctggctgtgg gagcccgggt
       61 atccgctgcg gccagagccg gacccgggag cccggctctg agtatagagt aacactgtgc
      121 tggccgcggg gctgctcccg agcgttcgca gttccccgga cctcggggac acctgcgtcc
      181 ttcctctccg gcgggtccat gaactccgtg tcgccggctg cggcgcagta ccgcagcggg
      241 agctcggagg acgcgcgccg ggccgattgt cgccggccga ggggacaaac ccgtatcccg
      301 gatcctagca acctgggacc ttcggggtcc ggagtggcag ctctcggttc atctgggaca
      361 gaccccgccg agcccgacga ggtggacaag ttcaaagcca agttcctgac agcctggaac
      421 aacgtcaagt atggttgggc agttaaaagc cggaccagct tcagcaagat ctccactgtt
      481 cacctctgcg ggcgatgcta ccatttcgag ggagagggtg acatccagcg gtttcaaagg
      541 gactttgtat ctcgactatg gctcacatat cgccgggact tcccacccct tgctggaggc
      601 agcctgacct cagactgtgg ctggggatgt atgttacgaa gtggtcagat gatgctggcc
      661 cagggcctgc tcctgcattt tctgcctaga gactggaggt gggtggaagg cacaggcctg
      721 gcttcctctg agatgccagg gccagcctct cccagtcgct gccgagggcc tggtcgtcgt
      781 gggcccccaa gatggacaca gggtgcactg gagatggagc aggaccgttg gcaccggcgg
      841 attgtttcct ggttcgctga tcatccacgg gcccccttcg gtctacatcg gctagtggag
      901 cttgggcgga gctcgggcaa gaaggcagga gactggtacg ggccctctgt ggtggcacac
      961 atcctcagga aagctgtgga gagttgctca gaagtcagcc gcctggtggt gtacgtctct
     1021 caggactgca cagtgtacaa ggcagatgta gcacgcctgc tgtcctggcc agatcctaca
     1081 gcggagtgga aatctgtggt catcctggtg cctgtacgac tgggcgggga gacccttaac
     1141 cctgtgtacg tgccctgtgt gaaggagctt ctgcgttcag aactctgtct gggcatcatg
     1201 ggcggcaagc cccggcattc actgtacttc attggctatc aggatgactt tctgctctac
     1261 ctggatcctc actactgcca gcccacagtg gatgtcagcc agcccagctt ccccctggag
     1321 tcctttcact gcacctcgcc ccgcaagatg gcctttgcca agatggaccc cagctgtacc
     1381 gtggggttct atgctgggaa caggaaggag tttgagacac tctgctcgga gctgatgagg
     1441 atcctcagct cctcctcagt cacggaacgg taccccatgt tcacagtggc tgaaggccac
     1501 gctcaggacc acagcctgga tgccctctgc acccagctgt cccagcccac actgcggcta
     1561 ccttgcacag gacgactact caaggccaaa aggcccagct ccgaggactt tgtgttttta
     1621 taatgggaag ggatggggaa agatgccaga ctatttattt ttttatttat gtcatgtcag
     1681 gtatgggatc tgcaactcca gtggtggtgc tggacccctg tcctcatgtc cccgtcctcc
     1741 ccaacacagc tgagacctat ctgggccccc agctgcccct gcctcctcag gagccaggga
     1801 aggagagtgg gctccagggc actcactcag ggcctaattc aagttctgta gcctgcattg
     1861 ggtcactggt cccaaggtcc caaaggtcct gtcctgggag aactgactgt ggctgataaa
     1921 gatgcagact tgaacatgcc tggcgttgtt gacatttcag gctgtctgtg gagaagacag
     1981 tgctctggta gcctcatttc aaagcttagg aacagcagtg ccctctcctg caggtagctt
     2041 tcgtaggctg ccaggcagag tttggtcagc agcttagttg tagaggcagg ttggctccct
     2101 gtggccctca ggagtggctc tgctgtttct tccgttggcg gcctaactgg cggaagtgca
     2161 gccttttggg gttgagacca aaggcctgca atctctgtct gctgaacttg tgacctccaa
     2221 gtgtcaccgt gggacccagc agcctggcct tcttgctctt ctgcttctgg gatgctggct
     2281 tctctgggca ggatgtgtgg gccaacccct cttccttgga tactaaggtc tcagcctggg
     2341 gtgtcttctg gtcagctcca ttgggtgtga acaactgtac ttgtgggctg gccttgctct
     2401 gtgactttcc tgtggcttct gtggacattt ccatcctaca gggagaaaag tcaaggctta
     2461 ggtcagcctg ctgttctgtt cagaaaggat ttcccccact ctgccctttt tgtttgagaa
     2521 gggggttcat gactggcctt aaactctatg tacccaagat gacctgtaac tatttttaaa
     2581 gcaggatgga gtgatacagc ctcactatgt agctctggct gtgccggaac tcactgtaag
     2641 accacactgg ccttgaactc agagctcttc aggggttttt atacagtgct aacatagagc
     2701 ccaggccatt agacatgcca cggaagcact ctgcccactc agccaaaacc ctggtcttgt
     2761 tgtctcacta cagaacccag atggcctcag cttcctgaga taactttcat aaataggaca
     2821 actacagatt agttggacca gcggaagcca tttatgtcag tcaactcctt gtgcctttag
     2881 tgcagctgcc atgtctgtca caactgaggg tctaggtcct agactctagg ggatgatggt
     2941 aacaactgtc cttgtaacaa gcctataagg tacttgtaag aatttatttt gttcaggctt
     3001 gggataaaac tcaggatttt aatc
//
