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="

MDAATLTYDTLRFAEFEDFPETSEPVWILGRKYSIFTEKDEILSDVASRLWFTYRRNFPAIGGTGPTSDTGWGCMLRCGQMIFAQALVCRHLGRDWRWTQRKRQPDSYFSVLNAFLDRKDSYYSIHQIAQMGVGEGKSIGQWYGPNTVAQVLKKLAVFDTWSSLAVHIAMDNTVVMEEIRRLCRASLPCAGAAALSMESERHCNGLPAGAEVTNRPLAWRPLVLLIPLRLGLTDINEAYVETLKHCFMMPQSLGVIGGKPNSAHYFIGYVGEELIYLDPHTTQPAVELTDSCFIPDESFHCQHPPCRMGIGELDPSIAVGFFCKTEEDFNDWCQQVKKLSQLGGALPMFELVEQQPSHLACQDVLNLSLDSSDVERLERFFDSEDEDFEILSL"

     misc_feature    24..26
                     /gene="Atg4b"
                     /gene_synonym="Apg4b"
                     /note="N-acetylmethionine.
                     /evidence=ECO:0000250|UniProtKB:Q9Y4P1; propagated from
                     UniProtKB/Swiss-Prot (A0A0G2QC33.1); acetylation site"
     misc_feature    123..125
                     /gene="Atg4b"
                     /gene_synonym="Apg4b"
                     /note="Phosphoserine.
                     /evidence=ECO:0000250|UniProtKB:Q9Y4P1; propagated from
                     UniProtKB/Swiss-Prot (A0A0G2QC33.1); phosphorylation site"
     misc_feature    138..1028
                     /gene="Atg4b"
                     /gene_synonym="Apg4b"
                     /note="Peptidase family C54; Region: Peptidase_C54;
                     pfam03416"
                     /db_xref="CDD:460915"
     misc_feature    969..971
                     /gene="Atg4b"
                     /gene_synonym="Apg4b"
                     /note="Phosphoserine.
                     /evidence=ECO:0000250|UniProtKB:Q9Y4P1; propagated from
                     UniProtKB/Swiss-Prot (A0A0G2QC33.1); phosphorylation site"
     misc_feature    1110..1196
                     /gene="Atg4b"
                     /gene_synonym="Apg4b"
                     /note="ATG4, F-type LIR motif; Region: ATG4_LIR;
                     pfam20166"
                     /db_xref="CDD:466317"
     misc_feature    1170..1172
                     /gene="Atg4b"
                     /gene_synonym="Apg4b"
                     /note="Phosphoserine.
                     /evidence=ECO:0000250|UniProtKB:Q9Y4P1; propagated from
                     UniProtKB/Swiss-Prot (A0A0G2QC33.1); phosphorylation site"
     misc_feature    1185..1196
                     /gene="Atg4b"
                     /gene_synonym="Apg4b"
                     /note="propagated from UniProtKB/Swiss-Prot
                     (A0A0G2QC33.1); Region: LIR.
                     /evidence=ECO:0000250|UniProtKB:Q9Y4P1"
     misc_feature    1197..1199
                     /gene="Atg4b"
                     /gene_synonym="Apg4b"
                     /note="Phosphoserine.
                     /evidence=ECO:0000250|UniProtKB:Q9Y4P1; propagated from
                     UniProtKB/Swiss-Prot (A0A0G2QC33.1); phosphorylation site"
     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      

cagtcggcggccggacagggaagatggacgcagccactttgacatatgatactctccggtttgccgaatttgaagatttccccgagacctcagagcctgtttggattctgggcagaaaatacagcattttcacagagaaggatgagatcttgtctgatgttgcatccagactttggtttacgtacaggagaaactttccagctattgggggaactggccctacctcagacacaggctggggttgcatgcttcggtgtggacagatgatctttgcccaggccctggtgtgccggcacttaggtcgagattggagatggactcagcggaagagacagcctgacagctacttcagtgtcctcaacgctttcctcgacaggaaggacagctactattccatccaccagatagcgcaaatgggagttggcgaaggcaagtctataggccagtggtacgggccgaacactgttgcccaggtcctcaagaaactggctgtattcgacacatggagctccctggctgttcacatagcaatggacaacactgtggtgatggaggaaatcagaagattgtgcagggccagccttccctgtgccggggccgctgcactatccatggagtcagagaggcactgtaacgggctccctgctggagctgaagtcaccaacaggcccttggcctggagaccattagtgcttctcatccctcttcgcctgggactgacagacatcaatgaggcctatgtggagacgctgaagcactgtttcatgatgccccagtccctgggtgttattggagggaagcccaacagtgcccactactttattggctacgttggtgaggagctcatctatctggatccccatactacacagcctgcagtggagctgacagacagctgctttatccccgacgagagcttccactgccaacaccctccctgtcggatgggcattggggagcttgacccatccattgccgtggggtttttctgtaagaccgaggaagactttaatgactggtgccagcaagtcaaaaagctgtcccagcttggaggtgccctgcccatgtttgagttggtggaacagcagccttcccatctggcctgccaggatgtcctgaacctgtccctagattcttctgatgtagagagactggagaggttctttgactctgaggatgaagactttgaaatcttatccctctgaaaatcctggggttgggggatggcctccatggccctcattggggtgcgttgagaacccagacctgccttgggcactcagtgtcaccgcattccatccacccagcccaccctgctgagtgctgtccgcctgtgccacctctgtcccgagggcctgctctgctcatggaccaaggactgtggtgcctggaggccttactgcttggagtcagactgcctaagcccaaacacacaagggcctgtccacatgaaggcgctcaccagaaggcctagtcaggaagagcagtgggtcgggagcgcccagcattctccactcgacactgccagccctggtcagcgcatcagcttggttctgctttctcctgggcacctgggtctgtggtttatttggaattaaagccctgtttgaagttgtttaacaaagacatgaatttctggggcacttcccaggtcagtcttagaagatctgcaggttggcgtgtacagagtgacagccacatcatggcctcataactgctgggcagggtgagcttttgtgctgtctcctctgcccagtgtgattatcaagggctacctcagtgggaaagcatatggagagaatcccagcaaggctgctatttgctttggagaaaaagtattcttgtggggcatttggaaaatccaaagataccagtgtgcatgggcacaatatggacacctgaaccttggagcagctgacaagtttctagtgcttctggagttgtggtcttgaggttctccattaggccctcactagggaagagctatgtctcctatatggggttgatgggtttcatgacacgctgcctgctgctgttagcttgccacccagcttccctctgggaggaaagggagggggggagcagagctgttctttgcttgtgacactgtgcccactggtagtagggcacacactgctatttgagccttcctccatgttctttcccttctcagaaaccctcctgggacataggaaattttagatggtttggggccaacaaggtaaaagtactgcagctttcggtgcagagtagacatttagacagagcaggtagctccaggcaccagtgggtgaagagttcagctctccttggcactcatttccatacctgccacctaaccttggcttcctgggccttcaagctttgggtgctctaggtctgctgtcttagaaaagcacctttcctccccctagataggaaacagggtatggcattgtggggaggcccatgcaacaaacagcctttgctaaaaatcctccccaagagcctgtagatgggtgaggctggagctactccagatacagcagctctaagtagcccacgaggtagcaagagatcctgcctatcaacatcagatatgttgatgacatatttatttcatcttattcctctctcccgtatcttgtcccttgacttcagatggggtgggacaggaagactagggcaattcccattcctctggagcttgcttcctggtccaggagccattgtgctgttgtcgactagggtcttgttgtaactcctgctgttggtagcaagggtggatgtctggaacccgacaacctgaaggacctctcagggctcaagaaaggcctcctgaggttgttcattcttcgtagtgtagtttgcaatccttaacagtaaataataagtttcagtagaaaaca

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