LOCUS       NM_053798               3443 bp    mRNA    linear   ROD 30-MAR-2024
DEFINITION  Rattus norvegicus SAC1 like phosphatidylinositide phosphatase
            (Sacm1l), transcript variant 1, mRNA.
ACCESSION   NM_053798 XM_346842
VERSION     NM_053798.3
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 3443)
  AUTHORS   Miao,G., Zhang,Y., Chen,D. and Zhang,H.
  TITLE     The ER-Localized Transmembrane Protein TMEM39A/SUSR2 Regulates
            Autophagy by Controlling the Trafficking of the PtdIns(4)P
            Phosphatase SAC1
  JOURNAL   Mol Cell 77 (3), 618-632 (2020)
   PUBMED   31806350
REFERENCE   2  (bases 1 to 3443)
  AUTHORS   Venditti,R., Masone,M.C., Rega,L.R., Di Tullio,G., Santoro,M.,
            Polishchuk,E., Serrano,I.C., Olkkonen,V.M., Harada,A., Medina,D.L.,
            La Montagna,R. and De Matteis,M.A.
  TITLE     The activity of Sac1 across ER-TGN contact sites requires the
            four-phosphate-adaptor-protein-1
  JOURNAL   J Cell Biol 218 (3), 783-797 (2019)
   PUBMED   30659099
REFERENCE   3  (bases 1 to 3443)
  AUTHORS   Zewe,J.P., Wills,R.C., Sangappa,S., Goulden,B.D. and Hammond,G.R.
  TITLE     SAC1 degrades its lipid substrate PtdIns4P in the endoplasmic
            reticulum to maintain a steep chemical gradient with donor
            membranes
  JOURNAL   Elife 7, e35588 (2018)
   PUBMED   29461204
  REMARK    Publication Status: Online-Only
REFERENCE   4  (bases 1 to 3443)
  AUTHORS   Dickson,E.J., Jensen,J.B., Vivas,O., Kruse,M., Traynor-Kaplan,A.E.
            and Hille,B.
  TITLE     Dynamic formation of ER-PM junctions presents a lipid phosphatase
            to regulate phosphoinositides
  JOURNAL   J Cell Biol 213 (1), 33-48 (2016)
   PUBMED   27044890
REFERENCE   5  (bases 1 to 3443)
  AUTHORS   Loughran,G., Chou,M.Y., Ivanov,I.P., Jungreis,I., Kellis,M.,
            Kiran,A.M., Baranov,P.V. and Atkins,J.F.
  TITLE     Evidence of efficient stop codon readthrough in four mammalian
            genes
  JOURNAL   Nucleic Acids Res 42 (14), 8928-8938 (2014)
   PUBMED   25013167
REFERENCE   6  (bases 1 to 3443)
  AUTHORS   Mesmin,B., Bigay,J., Moser von Filseck,J., Lacas-Gervais,S.,
            Drin,G. and Antonny,B.
  TITLE     A four-step cycle driven by PI(4)P hydrolysis directs sterol/PI(4)P
            exchange by the ER-Golgi tether OSBP
  JOURNAL   Cell 155 (4), 830-843 (2013)
   PUBMED   24209621
REFERENCE   7  (bases 1 to 3443)
  AUTHORS   Yang,G., Zhou,X., Zhu,J., Liu,R., Zhang,S., Coquinco,A., Chen,Y.,
            Wen,Y., Kojic,L., Jia,W. and Cynader,M.S.
  TITLE     JNK3 couples the neuronal stress response to inhibition of
            secretory trafficking
  JOURNAL   Sci Signal 6 (283), ra57 (2013)
   PUBMED   23838184
  REMARK    Publication Status: Online-Only
REFERENCE   8  (bases 1 to 3443)
  AUTHORS   Nemoto,Y., Kearns,B.G., Wenk,M.R., Chen,H., Mori,K., Alb,J.G. Jr.,
            De Camilli,P. and Bankaitis,V.A.
  TITLE     Functional characterization of a mammalian Sac1 and mutants
            exhibiting substrate-specific defects in phosphoinositide
            phosphatase activity
  JOURNAL   J Biol Chem 275 (44), 34293-34305 (2000)
   PUBMED   10887188
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from JAXUCZ010000008.1, FM060902.1,
            FM108115.1, FM108005.1, FM134775.1 and FM095674.1.
            
            On Oct 27, 2017 this sequence version replaced NM_053798.2.
            
            Summary: This gene encodes an integral membrane protein, which is
            localized to the endoplasmic reticulum, and functions as a
            phosphoinositide phosphatase that hydrolyzes phosphatidylinositol
            3-phosphate, phosphatidylinositol 4-phosphate, and
            phosphatidylinositol 3,5-bisphosphate. Deletion of this gene in
            mouse results in preimplantation lethality. Other studies suggest
            that this gene is also involved in the organization of golgi
            membranes and mitotic spindles. Two isoforms are predicted to be
            produced from the same mRNA by the use of alternative in-frame
            translation termination codons via a stop codon readthrough
            mechanism. [provided by RefSeq, Dec 2017].
            
            Transcript Variant: This variant (1) represents the predominant
            transcript and encodes two isoforms, which result from the use of
            alternative in-frame translation termination codons. The shorter
            isoform (1) results from translation termination at the upstream
            UGA stop codon, while the longer isoform (1x) results from UGA stop
            codon readthrough to the downstream UGA termination codon. This
            RefSeq represents the shorter isoform (1).
            
            ##Evidence-Data-START##
            Transcript exon combination :: SRR26360176.1046445.1,
                                           SRR26360194.288225.1 [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##
            COMPLETENESS: complete on the 3' end.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-124               JAXUCZ010000008.1  132053465-132053588
            125-222             JAXUCZ010000008.1  132064592-132064689
            223-297             JAXUCZ010000008.1  132068271-132068345
            298-425             JAXUCZ010000008.1  132069989-132070116
            426-575             JAXUCZ010000008.1  132075967-132076116
            576-635             JAXUCZ010000008.1  132081646-132081705
            636-669             JAXUCZ010000008.1  132083277-132083310
            670-771             JAXUCZ010000008.1  132086947-132087048
            772-857             JAXUCZ010000008.1  132089456-132089541
            858-944             JAXUCZ010000008.1  132090467-132090553
            945-992             JAXUCZ010000008.1  132091007-132091054
            993-1543            FM060902.1         1-551
            1544-1907           FM108115.1         241-604
            1908-2357           FM108005.1         66-515
            2358-2741           FM134775.1         292-675
            2742-2881           FM095674.1         239-378
            2882-3443           JAXUCZ010000008.1  132109296-132109857
FEATURES             Location/Qualifiers
     source          1..3443
                     /organism="Rattus norvegicus"
                     /mol_type="mRNA"
                     /strain="BN"
                     /db_xref="taxon:10116"
                     /chromosome="8"
                     /map="8q32"
     gene            1..3443
                     /gene="Sacm1l"
                     /gene_synonym="Sac1"
                     /note="SAC1 like phosphatidylinositide phosphatase"
                     /db_xref="GeneID:116482"
                     /db_xref="RGD:69223"
     exon            1..124
                     /gene="Sacm1l"
                     /gene_synonym="Sac1"
                     /inference="alignment:Splign:2.1.0"
     CDS             93..1856
                     /gene="Sacm1l"
                     /gene_synonym="Sac1"
                     /EC_number="3.1.3.64"
                     /note="isoform 1 is encoded by transcript variant 1;
                     phosphatidylinositide phosphatase SAC1; suppressor of
                     actin mutations 1-like protein;
                     phosphatidylinositol-4-phosphate phosphatase; SAC1
                     suppressor of actin mutations 1-like;
                     phosphatidylinositol-3-phosphatase SAC1"
                     /codon_start=1
                     /product="phosphatidylinositol-3-phosphatase SAC1 isoform
                     1"
                     /protein_id="NP_446250.1"
                     /db_xref="GeneID:116482"
                     /db_xref="RGD:69223"
                     /translation="MAATAYEHLKLHITPEKFYVEACDDGADDVLIIDRVSTEVTLAV
                     KKDVPPSAVTRPIYGIMGTIHLVAGNYLVVITKKMKVGEFFNHVIWKATDFDVLSYKK
                     TMLHLTDIQLQDNKTFLAMLNHVLSTDGFYFSTTYDLTHTLQRLSNTSPEFQEMSLLE
                     RADQRFVWNGHLLRELSAQPEVHRFALPVLHGFITMHSCSINGKYFDWILISRRSCFR
                     AGVRYYVRGIDSEGHAANFVETEQIVHYSGNRASFVQTRGSIPVFWSQRPNLKYKPDP
                     QINKVANHMDGFQRHFDSQVIIYGKQVIINLVNHKGSEKPLEQTFAKMVSSLGSGMIR
                     YIAFDFHKECKNMRWDRLSILLDQVAEMQDELSYFLVDSAGKVVTNQEGVFRSNCMDC
                     LDRTNVIQSLLARRSLQAQLQRLGVLHVGQKLEEQDEFEKIYKNAWADNANACAKQYA
                     GTGALKTDFTRTGKRTQLGLVMDGFNSLLRYYKNNFSDGFRQDSIDLFLGNYSVDELD
                     SHSPLSVPRDWKFLALPIIMVVAFSMCIICLLMAGDTWTETLAYVLFWGVASIGTFFI
                     ILYNGKDFVDAPRLVQKEKID"
     exon            125..222
                     /gene="Sacm1l"
                     /gene_synonym="Sac1"
                     /inference="alignment:Splign:2.1.0"
     exon            223..297
                     /gene="Sacm1l"
                     /gene_synonym="Sac1"
                     /inference="alignment:Splign:2.1.0"
     exon            298..425
                     /gene="Sacm1l"
                     /gene_synonym="Sac1"
                     /inference="alignment:Splign:2.1.0"
     exon            426..575
                     /gene="Sacm1l"
                     /gene_synonym="Sac1"
                     /inference="alignment:Splign:2.1.0"
     exon            576..635
                     /gene="Sacm1l"
                     /gene_synonym="Sac1"
                     /inference="alignment:Splign:2.1.0"
     exon            636..669
                     /gene="Sacm1l"
                     /gene_synonym="Sac1"
                     /inference="alignment:Splign:2.1.0"
     exon            670..771
                     /gene="Sacm1l"
                     /gene_synonym="Sac1"
                     /inference="alignment:Splign:2.1.0"
     exon            772..857
                     /gene="Sacm1l"
                     /gene_synonym="Sac1"
                     /inference="alignment:Splign:2.1.0"
     exon            858..944
                     /gene="Sacm1l"
                     /gene_synonym="Sac1"
                     /inference="alignment:Splign:2.1.0"
     exon            945..1013
                     /gene="Sacm1l"
                     /gene_synonym="Sac1"
                     /inference="alignment:Splign:2.1.0"
     exon            1014..1093
                     /gene="Sacm1l"
                     /gene_synonym="Sac1"
                     /inference="alignment:Splign:2.1.0"
     exon            1094..1192
                     /gene="Sacm1l"
                     /gene_synonym="Sac1"
                     /inference="alignment:Splign:2.1.0"
     exon            1193..1331
                     /gene="Sacm1l"
                     /gene_synonym="Sac1"
                     /inference="alignment:Splign:2.1.0"
     exon            1332..1401
                     /gene="Sacm1l"
                     /gene_synonym="Sac1"
                     /inference="alignment:Splign:2.1.0"
     exon            1402..1474
                     /gene="Sacm1l"
                     /gene_synonym="Sac1"
                     /inference="alignment:Splign:2.1.0"
     exon            1475..1568
                     /gene="Sacm1l"
                     /gene_synonym="Sac1"
                     /inference="alignment:Splign:2.1.0"
     exon            1569..1661
                     /gene="Sacm1l"
                     /gene_synonym="Sac1"
                     /inference="alignment:Splign:2.1.0"
     exon            1662..1719
                     /gene="Sacm1l"
                     /gene_synonym="Sac1"
                     /inference="alignment:Splign:2.1.0"
     exon            1720..3443
                     /gene="Sacm1l"
                     /gene_synonym="Sac1"
                     /inference="alignment:Splign:2.1.0"
ORIGIN      
        1 tccttggcca ccgcacctgg ggagcggtcg caccggcgcc gtggtggcat cggggtacac
       61 tgcgggtgga gcgaagcgga ggaaggtgca cgatggcggc cacagcctac gagcatctga
      121 agctgcatat tacacctgaa aagttttatg tggaagcttg tgatgatgga gcagatgatg
      181 tactcatcat tgaccgcgtg tctacagagg tcacccttgc agtcaaaaaa gatgttcccc
      241 cttctgctgt tacaagacca atatatggga taatgggcac aatccatctg gtggcaggca
      301 attatcttgt tgtcattacc aaaaagatga aagtaggtga attttttaat catgtaatct
      361 ggaaagccac agattttgat gttctttctt ataagaagac aatgttacac ttaactgata
      421 ttcagttaca agataataaa actttcctag caatgctaaa ccatgtcttg agtacggatg
      481 gattttactt ttcaacaaca tatgacttga cccatacttt gcaacggcta tctaacacga
      541 gtccagaatt ccaagaaatg agtctcctag aaagggcaga tcagcggttt gtatggaacg
      601 ggcatctgct cagagaactg tctgctcagc cagaggtcca tcggtttgct cttcctgtgt
      661 tgcatggctt tattactatg cattcatgtt ctattaacgg gaaatatttt gattggattc
      721 tcatctcccg gaggagttgt ttcagagccg gtgtgcgtta ttatgtgaga ggaattgatt
      781 ctgaaggcca cgcagctaac tttgtagaaa cagaacagat tgtgcactac agtgggaaca
      841 gggcttcatt tgtacagact cgaggatcaa tacctgtttt ctggtcacaa agaccaaatc
      901 taaagtacaa accagatcca cagatcaaca aagtagcaaa tcacatggat ggtttccaaa
      961 ggcattttga ttcacaagta attatttatg gaaaacaagt aataattaat ctggtgaacc
     1021 ataagggatc agagaaacca cttgagcaaa catttgcaaa aatggtgtca tccttgggaa
     1081 gtgggatgat cagatatatt gcctttgact tccataagga gtgtaaaaat atgagatggg
     1141 atcgactgag tattttattg gatcaagtag cagaaatgca ggatgaatta agttattttt
     1201 tagtagactc tgctggcaag gtggtgacaa accaggaagg agttttccgc agcaactgta
     1261 tggattgtct agacagaacg aatgtgatac agagtttatt agctcggcgt tcccttcagg
     1321 cacagctgca gagactagga gttttgcatg tgggacaaaa gcttgaagaa caagatgagt
     1381 ttgagaagat ttacaaaaat gcctgggccg ataatgctaa tgcttgtgcc aaacagtatg
     1441 caggaaccgg tgccttgaag actgacttta caagaactgg aaaaagaact cagttgggac
     1501 tggtaatgga tggcttcaac tcattattac ggtactacaa aaacaacttt tctgatggat
     1561 ttagacaaga ttctatagac ttatttcttg gaaactactc agtggatgaa ttagactctc
     1621 acagtccttt aagtgttcca agggactgga aattcctggc gttgcctatc atcatggttg
     1681 ttgccttttc aatgtgcatc atctgtttgc ttatggctgg tgacacttgg acagaaacac
     1741 tggcatatgt cctcttctgg ggagttgcaa gcattggaac attttttatt attctttaca
     1801 atggcaaaga ttttgttgat gctcccagac ttgtacagaa agaaaagata gactgaattt
     1861 gtgtttgtgg aaagcggctt ggcttggaag actccatgat gcagaactgg agtctttact
     1921 gacctgcttt ccacatgaac cccaaggtct tcttaaagcc tttatccaaa agtacctctt
     1981 gtgatttggg ctgggtgata tcttagaatt gatctgatat tactgctttg atgatctctt
     2041 tactgttggg atggttatat ttataatttg aagctatagt ataattaaaa tgtagcttaa
     2101 attcagctca cagaacagaa gaaatctatt cactgtcaag tcagaagttc acagataagt
     2161 aatatatttt aaaaaattta acttctttca ttatttaaaa caaaattatt tttctagctc
     2221 tgtttcatta ttgccattgt aaagcagtca ctgttagcaa gcattttttc catgtatctt
     2281 tgggcttttc ttaagagttt aataatatgc taattctact atgcttagag aatgtctctt
     2341 aaaggtcagg cagtttgcta agctgtgatt tcacagtgag ggagaggaga atgggatcta
     2401 gagtcatttg aaattgcttg agctgctagc agcttaaatg tcatgaaaag ttcagatata
     2461 ttttatcttt tttaaatggt ataaatgaaa tcaaagaatg taaagtctgt ctcttatgct
     2521 aaaggtccaa agtcacctct ttttaagaac tgcttcattg tggaaaatac actagactgc
     2581 cagctgctgc ttctcatatc ttgtaggatt ttattattgg ttgctcattg agacatgcag
     2641 acctcagaga aggtcttgtg ctagacttga ttcacacttg gggtagcagt tgcttttcct
     2701 gcatggcact ctggctttat caccctgaca aggtttgtat tcactgtcaa taagtgtctg
     2761 aaatttagtg cttccaggta gccatagttc tccaaatcaa ggaccaactt taatttatgc
     2821 ataaacagac tgaaaaccac gcttcagagc tgtgcatagt tgtgagacag gttatatatt
     2881 aaaattgtaa ttatgaggtt tagatattag aacagtgtat aaggtagtat cactgcgcta
     2941 tcttagaaca attcagttaa acactgctat gctatatcag tgttttgctt taaaatatgt
     3001 ggtttttttt tctaatagta ccttatgtta aatatttcta aaagcgcctt taacattacc
     3061 tttttttcaa cattatcttt tataaacaat aagttattgc ttttagaaac tctgggaaaa
     3121 tcctgtgtag tttaaaatca gtcattaaag ctcactatag ggtagtaaat agagccgcct
     3181 gctctgacac gtgtaagcag tttgttccaa gatgaaacat gaagccacgt ctgctgtgat
     3241 gtgctattca gaagctgctg ggcattttac agtgagcact tcatgccaac accacgtgga
     3301 accagtagtg tggctgcttt gcaaggagta atgtcagagg gttaggctgc aagtgatcag
     3361 tgtttgagag ccctgcagtg atcttgttta actcatttac tgtacatcca tatgcaaaaa
     3421 taaaatgcca tattcttttc taa
//
