LOCUS       NM_001399197            2888 bp    mRNA    linear   ROD 01-APR-2024
DEFINITION  Rattus norvegicus autophagy related 4B, cysteine peptidase (Atg4b),
            mRNA.
ACCESSION   NM_001399197 XM_006245533
VERSION     NM_001399197.1
KEYWORDS    RefSeq; RefSeq Select.
SOURCE      Rattus norvegicus (Norway rat)
  ORGANISM  Rattus norvegicus
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
            Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha;
            Muroidea; Muridae; Murinae; Rattus.
REFERENCE   1  (bases 1 to 2888)
  AUTHORS   Vicinanza,M., Korolchuk,V.I., Ashkenazi,A., Puri,C., Menzies,F.M.,
            Clarke,J.H. and Rubinsztein,D.C.
  TITLE     PI(5)P regulates autophagosome biogenesis
  JOURNAL   Mol Cell 57 (2), 219-234 (2015)
   PUBMED   25578879
REFERENCE   2  (bases 1 to 2888)
  AUTHORS   Dowdle,W.E., Nyfeler,B., Nagel,J., Elling,R.A., Liu,S.,
            Triantafellow,E., Menon,S., Wang,Z., Honda,A., Pardee,G.,
            Cantwell,J., Luu,C., Cornella-Taracido,I., Harrington,E.,
            Fekkes,P., Lei,H., Fang,Q., Digan,M.E., Burdick,D., Powers,A.F.,
            Helliwell,S.B., D'Aquin,S., Bastien,J., Wang,H., Wiederschain,D.,
            Kuerth,J., Bergman,P., Schwalb,D., Thomas,J., Ugwonali,S.,
            Harbinski,F., Tallarico,J., Wilson,C.J., Myer,V.E., Porter,J.A.,
            Bussiere,D.E., Finan,P.M., Labow,M.A., Mao,X., Hamann,L.G.,
            Manning,B.D., Valdez,R.A., Nicholson,T., Schirle,M., Knapp,M.S.,
            Keaney,E.P. and Murphy,L.O.
  TITLE     Selective VPS34 inhibitor blocks autophagy and uncovers a role for
            NCOA4 in ferritin degradation and iron homeostasis in vivo
  JOURNAL   Nat Cell Biol 16 (11), 1069-1079 (2014)
   PUBMED   25327288
REFERENCE   3  (bases 1 to 2888)
  AUTHORS   Li,M., Hou,Y., Wang,J., Chen,X., Shao,Z.M. and Yin,X.M.
  TITLE     Kinetics comparisons of mammalian Atg4 homologues indicate
            selective preferences toward diverse Atg8 substrates
  JOURNAL   J Biol Chem 286 (9), 7327-7338 (2011)
   PUBMED   21177865
REFERENCE   4  (bases 1 to 2888)
  AUTHORS   Ketteler,R., Sun,Z., Kovacs,K.F., He,W.W. and Seed,B.
  TITLE     A pathway sensor for genome-wide screens of intracellular
            proteolytic cleavage
  JOURNAL   Genome Biol 9 (4), R64 (2008)
   PUBMED   18387192
  REMARK    Publication Status: Online-Only
REFERENCE   5  (bases 1 to 2888)
  AUTHORS   Yoshimura,K., Shibata,M., Koike,M., Gotoh,K., Fukaya,M.,
            Watanabe,M. and Uchiyama,Y.
  TITLE     Effects of RNA interference of Atg4B on the limited proteolysis of
            LC3 in PC12 cells and expression of Atg4B in various rat tissues
  JOURNAL   Autophagy 2 (3), 200-208 (2006)
   PUBMED   16874114
REFERENCE   6  (bases 1 to 2888)
  AUTHORS   Tanida,I., Ueno,T. and Kominami,E.
  TITLE     LC3 conjugation system in mammalian autophagy
  JOURNAL   Int J Biochem Cell Biol 36 (12), 2503-2518 (2004)
   PUBMED   15325588
  REMARK    Review article
REFERENCE   7  (bases 1 to 2888)
  AUTHORS   Kabeya,Y., Mizushima,N., Yamamoto,A., Oshitani-Okamoto,S.,
            Ohsumi,Y. and Yoshimori,T.
  TITLE     LC3, GABARAP and GATE16 localize to autophagosomal membrane
            depending on form-II formation
  JOURNAL   J Cell Sci 117 (Pt 13), 2805-2812 (2004)
   PUBMED   15169837
REFERENCE   8  (bases 1 to 2888)
  AUTHORS   Hemelaar,J., Lelyveld,V.S., Kessler,B.M. and Ploegh,H.L.
  TITLE     A single protease, Apg4B, is specific for the autophagy-related
            ubiquitin-like proteins GATE-16, MAP1-LC3, GABARAP, and Apg8L
  JOURNAL   J Biol Chem 278 (51), 51841-51850 (2003)
   PUBMED   14530254
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            JAXUCZ010000009.1.
            
            On Jan 4, 2022 this sequence version replaced XM_006245533.4.
            
            Sequence Note: The RefSeq transcript and protein were derived from
            genomic sequence to make the sequence consistent with the reference
            genome assembly. The genomic coordinates used for the transcript
            record were based on alignments.
            
            ##Evidence-Data-START##
            Transcript exon combination :: SRR26360172.2085858.1,
                                           SRR26360190.2090021.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA5760383, SAMEA5760386
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            RefSeq Select criteria :: based on conservation, expression,
                                      longest protein
            ##RefSeq-Attributes-END##
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-33                JAXUCZ010000009.1  101729889-101729921
            34-135              JAXUCZ010000009.1  101742053-101742154
            136-207             JAXUCZ010000009.1  101742252-101742323
            208-306             JAXUCZ010000009.1  101747223-101747321
            307-408             JAXUCZ010000009.1  101748552-101748653
            409-481             JAXUCZ010000009.1  101749046-101749118
            482-561             JAXUCZ010000009.1  101752346-101752425
            562-755             JAXUCZ010000009.1  101754849-101755042
            756-834             JAXUCZ010000009.1  101756401-101756479
            835-980             JAXUCZ010000009.1  101756743-101756888
            981-1037            JAXUCZ010000009.1  101758004-101758060
            1038-1131           JAXUCZ010000009.1  101758628-101758721
            1132-2888           JAXUCZ010000009.1  101759700-101761456
FEATURES             Location/Qualifiers
     source          1..2888
                     /organism="Rattus norvegicus"
                     /mol_type="mRNA"
                     /strain="BN"
                     /db_xref="taxon:10116"
                     /chromosome="9"
                     /map="9q36"
     gene            1..2888
                     /gene="Atg4b"
                     /gene_synonym="Apg4b"
                     /note="autophagy related 4B, cysteine peptidase"
                     /db_xref="GeneID:316640"
                     /db_xref="RGD:1309664"
     exon            1..33
                     /gene="Atg4b"
                     /gene_synonym="Apg4b"
                     /inference="alignment:Splign:2.1.0"
     CDS             24..1205
                     /gene="Atg4b"
                     /gene_synonym="Apg4b"
                     /note="autophagy-related 4B; ATG4 autophagy related 4
                     homolog B; autophagy-related protein 4 homolog B"
                     /codon_start=1
                     /product="cysteine protease ATG4B"
                     /protein_id="NP_001386126.1"
                     /db_xref="GeneID:316640"
                     /db_xref="RGD:1309664"
                     /translation="MDAATLTYDTLRFAEFEDFPETSEPVWILGRKYSIFTEKDEILS
                     DVASRLWFTYRRNFPAIGGTGPTSDTGWGCMLRCGQMIFAQALVCRHLGRDWRWTQRK
                     RQPDSYFSVLNAFLDRKDSYYSIHQIAQMGVGEGKSIGQWYGPNTVAQVLKKLAVFDT
                     WSSLAVHIAMDNTVVMEEIRRLCRASLPCAGAAALSMESERHCNGLPAGAEVTNRPLA
                     WRPLVLLIPLRLGLTDINEAYVETLKHCFMMPQSLGVIGGKPNSAHYFIGYVGEELIY
                     LDPHTTQPAVELTDSCFIPDESFHCQHPPCRMGIGELDPSIAVGFFCKTEEDFNDWCQ
                     QVKKLSQLGGALPMFELVEQQPSHLACQDVLNLSLDSSDVERLERFFDSEDEDFEILS
                     L"
     exon            34..135
                     /gene="Atg4b"
                     /gene_synonym="Apg4b"
                     /inference="alignment:Splign:2.1.0"
     exon            136..207
                     /gene="Atg4b"
                     /gene_synonym="Apg4b"
                     /inference="alignment:Splign:2.1.0"
     exon            208..306
                     /gene="Atg4b"
                     /gene_synonym="Apg4b"
                     /inference="alignment:Splign:2.1.0"
     exon            307..408
                     /gene="Atg4b"
                     /gene_synonym="Apg4b"
                     /inference="alignment:Splign:2.1.0"
     exon            409..481
                     /gene="Atg4b"
                     /gene_synonym="Apg4b"
                     /inference="alignment:Splign:2.1.0"
     exon            482..561
                     /gene="Atg4b"
                     /gene_synonym="Apg4b"
                     /inference="alignment:Splign:2.1.0"
     exon            562..755
                     /gene="Atg4b"
                     /gene_synonym="Apg4b"
                     /inference="alignment:Splign:2.1.0"
     exon            756..834
                     /gene="Atg4b"
                     /gene_synonym="Apg4b"
                     /inference="alignment:Splign:2.1.0"
     exon            835..980
                     /gene="Atg4b"
                     /gene_synonym="Apg4b"
                     /inference="alignment:Splign:2.1.0"
     exon            981..1037
                     /gene="Atg4b"
                     /gene_synonym="Apg4b"
                     /inference="alignment:Splign:2.1.0"
     exon            1038..1131
                     /gene="Atg4b"
                     /gene_synonym="Apg4b"
                     /inference="alignment:Splign:2.1.0"
     exon            1132..2888
                     /gene="Atg4b"
                     /gene_synonym="Apg4b"
                     /inference="alignment:Splign:2.1.0"
ORIGIN      
        1 cagtcggcgg ccggacaggg aagatggacg cagccacttt gacatatgat actctccggt
       61 ttgccgaatt tgaagatttc cccgagacct cagagcctgt ttggattctg ggcagaaaat
      121 acagcatttt cacagagaag gatgagatct tgtctgatgt tgcatccaga ctttggttta
      181 cgtacaggag aaactttcca gctattgggg gaactggccc tacctcagac acaggctggg
      241 gttgcatgct tcggtgtgga cagatgatct ttgcccaggc cctggtgtgc cggcacttag
      301 gtcgagattg gagatggact cagcggaaga gacagcctga cagctacttc agtgtcctca
      361 acgctttcct cgacaggaag gacagctact attccatcca ccagatagcg caaatgggag
      421 ttggcgaagg caagtctata ggccagtggt acgggccgaa cactgttgcc caggtcctca
      481 agaaactggc tgtattcgac acatggagct ccctggctgt tcacatagca atggacaaca
      541 ctgtggtgat ggaggaaatc agaagattgt gcagggccag ccttccctgt gccggggccg
      601 ctgcactatc catggagtca gagaggcact gtaacgggct ccctgctgga gctgaagtca
      661 ccaacaggcc cttggcctgg agaccattag tgcttctcat ccctcttcgc ctgggactga
      721 cagacatcaa tgaggcctat gtggagacgc tgaagcactg tttcatgatg ccccagtccc
      781 tgggtgttat tggagggaag cccaacagtg cccactactt tattggctac gttggtgagg
      841 agctcatcta tctggatccc catactacac agcctgcagt ggagctgaca gacagctgct
      901 ttatccccga cgagagcttc cactgccaac accctccctg tcggatgggc attggggagc
      961 ttgacccatc cattgccgtg gggtttttct gtaagaccga ggaagacttt aatgactggt
     1021 gccagcaagt caaaaagctg tcccagcttg gaggtgccct gcccatgttt gagttggtgg
     1081 aacagcagcc ttcccatctg gcctgccagg atgtcctgaa cctgtcccta gattcttctg
     1141 atgtagagag actggagagg ttctttgact ctgaggatga agactttgaa atcttatccc
     1201 tctgaaaatc ctggggttgg gggatggcct ccatggccct cattggggtg cgttgagaac
     1261 ccagacctgc cttgggcact cagtgtcacc gcattccatc cacccagccc accctgctga
     1321 gtgctgtccg cctgtgccac ctctgtcccg agggcctgct ctgctcatgg accaaggact
     1381 gtggtgcctg gaggccttac tgcttggagt cagactgcct aagcccaaac acacaagggc
     1441 ctgtccacat gaaggcgctc accagaaggc ctagtcagga agagcagtgg gtcgggagcg
     1501 cccagcattc tccactcgac actgccagcc ctggtcagcg catcagcttg gttctgcttt
     1561 ctcctgggca cctgggtctg tggtttattt ggaattaaag ccctgtttga agttgtttaa
     1621 caaagacatg aatttctggg gcacttccca ggtcagtctt agaagatctg caggttggcg
     1681 tgtacagagt gacagccaca tcatggcctc ataactgctg ggcagggtga gcttttgtgc
     1741 tgtctcctct gcccagtgtg attatcaagg gctacctcag tgggaaagca tatggagaga
     1801 atcccagcaa ggctgctatt tgctttggag aaaaagtatt cttgtggggc atttggaaaa
     1861 tccaaagata ccagtgtgca tgggcacaat atggacacct gaaccttgga gcagctgaca
     1921 agtttctagt gcttctggag ttgtggtctt gaggttctcc attaggccct cactagggaa
     1981 gagctatgtc tcctatatgg ggttgatggg tttcatgaca cgctgcctgc tgctgttagc
     2041 ttgccaccca gcttccctct gggaggaaag ggaggggggg agcagagctg ttctttgctt
     2101 gtgacactgt gcccactggt agtagggcac acactgctat ttgagccttc ctccatgttc
     2161 tttcccttct cagaaaccct cctgggacat aggaaatttt agatggtttg gggccaacaa
     2221 ggtaaaagta ctgcagcttt cggtgcagag tagacattta gacagagcag gtagctccag
     2281 gcaccagtgg gtgaagagtt cagctctcct tggcactcat ttccatacct gccacctaac
     2341 cttggcttcc tgggccttca agctttgggt gctctaggtc tgctgtctta gaaaagcacc
     2401 tttcctcccc ctagatagga aacagggtat ggcattgtgg ggaggcccat gcaacaaaca
     2461 gcctttgcta aaaatcctcc ccaagagcct gtagatgggt gaggctggag ctactccaga
     2521 tacagcagct ctaagtagcc cacgaggtag caagagatcc tgcctatcaa catcagatat
     2581 gttgatgaca tatttatttc atcttattcc tctctcccgt atcttgtccc ttgacttcag
     2641 atggggtggg acaggaagac tagggcaatt cccattcctc tggagcttgc ttcctggtcc
     2701 aggagccatt gtgctgttgt cgactagggt cttgttgtaa ctcctgctgt tggtagcaag
     2761 ggtggatgtc tggaacccga caacctgaag gacctctcag ggctcaagaa aggcctcctg
     2821 aggttgttca ttcttcgtag tgtagtttgc aatccttaac agtaaataat aagtttcagt
     2881 agaaaaca
//
