LOCUS       NM_012268               2137 bp    mRNA    linear   PRI 09-FEB-2025
DEFINITION  Homo sapiens phospholipase D family member 3 (PLD3), transcript
            variant 2, mRNA.
ACCESSION   NM_012268
VERSION     NM_012268.4
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 2137)
  AUTHORS   Roske,Y., Cappel,C., Cremer,N., Hoffmann,P., Koudelka,T.,
            Tholey,A., Heinemann,U., Daumke,O. and Damme,M.
  TITLE     Structural analysis of PLD3 reveals insights into the mechanism of
            lysosomal 5' exonuclease-mediated nucleic acid degradation
  JOURNAL   Nucleic Acids Res 52 (1), 370-384 (2024)
   PUBMED   37994783
  REMARK    GeneRIF: Structural analysis of PLD3 reveals insights into the
            mechanism of lysosomal 5' exonuclease-mediated nucleic acid
            degradation.
REFERENCE   2  (bases 1 to 2137)
  AUTHORS   Nackenoff,A.G., Hohman,T.J., Neuner,S.M., Akers,C.S., Weitzel,N.C.,
            Shostak,A., Ferguson,S.M., Mobley,B., Bennett,D.A., Schneider,J.A.,
            Jefferson,A.L., Kaczorowski,C.C. and Schrag,M.S.
  TITLE     PLD3 is a neuronal lysosomal phospholipase D associated with
            beta-amyloid plaques and cognitive function in Alzheimer's disease
  JOURNAL   PLoS Genet 17 (4), e1009406 (2021)
   PUBMED   33830999
  REMARK    GeneRIF: PLD3 is a neuronal lysosomal phospholipase D associated
            with beta-amyloid plaques and cognitive function in Alzheimer's
            disease.
            Publication Status: Online-Only
REFERENCE   3  (bases 1 to 2137)
  AUTHORS   Luck,K., Kim,D.K., Lambourne,L., Spirohn,K., Begg,B.E., Bian,W.,
            Brignall,R., Cafarelli,T., Campos-Laborie,F.J., Charloteaux,B.,
            Choi,D., Cote,A.G., Daley,M., Deimling,S., Desbuleux,A., Dricot,A.,
            Gebbia,M., Hardy,M.F., Kishore,N., Knapp,J.J., Kovacs,I.A.,
            Lemmens,I., Mee,M.W., Mellor,J.C., Pollis,C., Pons,C.,
            Richardson,A.D., Schlabach,S., Teeking,B., Yadav,A., Babor,M.,
            Balcha,D., Basha,O., Bowman-Colin,C., Chin,S.F., Choi,S.G.,
            Colabella,C., Coppin,G., D'Amata,C., De Ridder,D., De Rouck,S.,
            Duran-Frigola,M., Ennajdaoui,H., Goebels,F., Goehring,L., Gopal,A.,
            Haddad,G., Hatchi,E., Helmy,M., Jacob,Y., Kassa,Y., Landini,S.,
            Li,R., van Lieshout,N., MacWilliams,A., Markey,D., Paulson,J.N.,
            Rangarajan,S., Rasla,J., Rayhan,A., Rolland,T., San-Miguel,A.,
            Shen,Y., Sheykhkarimli,D., Sheynkman,G.M., Simonovsky,E., Tasan,M.,
            Tejeda,A., Tropepe,V., Twizere,J.C., Wang,Y., Weatheritt,R.J.,
            Weile,J., Xia,Y., Yang,X., Yeger-Lotem,E., Zhong,Q., Aloy,P.,
            Bader,G.D., De Las Rivas,J., Gaudet,S., Hao,T., Rak,J.,
            Tavernier,J., Hill,D.E., Vidal,M., Roth,F.P. and Calderwood,M.A.
  TITLE     A reference map of the human binary protein interactome
  JOURNAL   Nature 580 (7803), 402-408 (2020)
   PUBMED   32296183
REFERENCE   4  (bases 1 to 2137)
  AUTHORS   Demirev,A.V., Song,H.L., Cho,M.H., Cho,K., Peak,J.J., Yoo,H.J.,
            Kim,D.H. and Yoon,S.Y.
  TITLE     V232M substitution restricts a distinct O-glycosylation of PLD3 and
            its neuroprotective function
  JOURNAL   Neurobiol Dis 129, 182-194 (2019)
   PUBMED   31121321
  REMARK    GeneRIF: the V232M mutation of PLD3 may affect Alzheimer's disease
            pathogenesis
REFERENCE   5  (bases 1 to 2137)
  AUTHORS   Gonzalez,A.C., Stroobants,S., Reisdorf,P., Gavin,A.L., Nemazee,D.,
            Schwudke,D., D'Hooge,R., Saftig,P. and Damme,M.
  TITLE     PLD3 and spinocerebellar ataxia
  JOURNAL   Brain 141 (11), e78 (2018)
   PUBMED   30312375
REFERENCE   6  (bases 1 to 2137)
  AUTHORS   Cheng,J., Kapranov,P., Drenkow,J., Dike,S., Brubaker,S., Patel,S.,
            Long,J., Stern,D., Tammana,H., Helt,G., Sementchenko,V.,
            Piccolboni,A., Bekiranov,S., Bailey,D.K., Ganesh,M., Ghosh,S.,
            Bell,I., Gerhard,D.S. and Gingeras,T.R.
  TITLE     Transcriptional maps of 10 human chromosomes at 5-nucleotide
            resolution
  JOURNAL   Science 308 (5725), 1149-1154 (2005)
   PUBMED   15790807
REFERENCE   7  (bases 1 to 2137)
  AUTHORS   Wistow,G., Bernstein,S.L., Wyatt,M.K., Ray,S., Behal,A.,
            Touchman,J.W., Bouffard,G., Smith,D. and Peterson,K.
  TITLE     Expressed sequence tag analysis of human retina for the NEIBank
            Project: retbindin, an abundant, novel retinal cDNA and alternative
            splicing of other retina-preferred gene transcripts
  JOURNAL   Mol Vis 8, 196-204 (2002)
   PUBMED   12107411
  REMARK    Publication Status: Online-Only
REFERENCE   8  (bases 1 to 2137)
  AUTHORS   Pedersen,K.M., Finsen,B., Celis,J.E. and Jensen,N.A.
  TITLE     Expression of a novel murine phospholipase D homolog coincides with
            late neuronal development in the forebrain
  JOURNAL   J Biol Chem 273 (47), 31494-31504 (1998)
   PUBMED   9813063
REFERENCE   9  (bases 1 to 2137)
  AUTHORS   Cao,J.X., Koop,B.F. and Upton,C.
  TITLE     A human homolog of the vaccinia virus HindIII K4L gene is a member
            of the phospholipase D superfamily
  JOURNAL   Virus Res 48 (1), 11-18 (1997)
   PUBMED   9140189
REFERENCE   10 (bases 1 to 2137)
  AUTHORS   Perlman,S.
  TITLE     Hereditary Ataxia Overview
  JOURNAL   (in) Adam MP, Feldman J, Mirzaa GM, Pagon RA, Wallace SE and
            Amemiya A (Eds.);
            GENEREVIEWS(R);
            (1993)
   PUBMED   20301317
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from CX785201.1, BP304863.1,
            BC000553.1 and BQ640152.1.
            This sequence is a reference standard in the RefSeqGene project.
            
            On Nov 22, 2018 this sequence version replaced NM_012268.3.
            
            Summary: This gene encodes a member of the phospholipase D (PLD)
            family of enzymes that catalyze the hydrolysis of membrane
            phospholipids. The encoded protein is a single-pass type II
            membrane protein and contains two PLD phosphodiesterase domains.
            This protein influences processing of amyloid-beta precursor
            protein. Mutations in this gene are associated with Alzheimer
            disease risk. Alternatively spliced transcript variants encoding
            the same protein have been found for this gene. [provided by
            RefSeq, Apr 2014].
            
            Transcript Variant: This variant (2) represents the longer
            transcript. Variants 1, 2 and 3 encode the same protein.
            
            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 :: SRR3476690.655781.1,
                                           SRR3476690.105080.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA1966682, SAMEA1968189
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000409735.9/ ENSP00000386938.3
            RefSeq Select criteria :: based on conservation, expression,
                                      longest protein
            ##RefSeq-Attributes-END##
            COMPLETENESS: full length.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-239               CX785201.1         103-341
            240-781             BP304863.1         26-567
            782-2135            BC000553.1         298-1651
            2136-2137           BQ640152.1         461-462
FEATURES             Location/Qualifiers
     source          1..2137
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="19"
                     /map="19q13.2"
     gene            1..2137
                     /gene="PLD3"
                     /gene_synonym="AD19; HU-K4; HUK4; SCA46"
                     /note="phospholipase D family member 3"
                     /db_xref="GeneID:23646"
                     /db_xref="HGNC:HGNC:17158"
                     /db_xref="MIM:615698"
     exon            1..74
                     /gene="PLD3"
                     /gene_synonym="AD19; HU-K4; HUK4; SCA46"
                     /inference="alignment:Splign:2.1.0"
     exon            75..287
                     /gene="PLD3"
                     /gene_synonym="AD19; HU-K4; HUK4; SCA46"
                     /inference="alignment:Splign:2.1.0"
     exon            288..379
                     /gene="PLD3"
                     /gene_synonym="AD19; HU-K4; HUK4; SCA46"
                     /inference="alignment:Splign:2.1.0"
     CDS             353..1825
                     /gene="PLD3"
                     /gene_synonym="AD19; HU-K4; HUK4; SCA46"
                     /EC_number="3.1.16.1"
                     /note="phosphatidylcholine-hydrolyzing phospholipase D3;
                     choline phosphatase 3; hindIII K4L homolog;
                     (S,S)-bis(monoacylglycero)phosphate synthase PLD3"
                     /codon_start=1
                     /product="5'-3' exonuclease PLD3"
                     /protein_id="NP_036400.2"
                     /db_xref="CCDS:CCDS33027.1"
                     /db_xref="GeneID:23646"
                     /db_xref="HGNC:HGNC:17158"
                     /db_xref="MIM:615698"
                     /translation="MKPKLMYQELKVPAEEPANELPMNEIEAWKAAEKKARWVLLVLI
                     LAVVGFGALMTQLFLWEYGDLHLFGPNQRPAPCYDPCEAVLVESIPEGLDFPNASTGN
                     PSTSQAWLGLLAGAHSSLDIASFYWTLTNNDTHTQEPSAQQGEEVLRQLQTLAPKGVN
                     VRIAVSKPSGPQPQADLQALLQSGAQVRMVDMQKLTHGVLHTKFWVVDQTHFYLGSAN
                     MDWRSLTQVKELGVVMYNCSCLARDLTKIFEAYWFLGQAGSSIPSTWPRFYDTRYNQE
                     TPMEICLNGTPALAYLASAPPPLCPSGRTPDLKALLNVVDNARSFIYVAVMNYLPTLE
                     FSHPHRFWPAIDDGLRRATYERGVKVRLLISCWGHSEPSMRAFLLSLAALRDNHTHSD
                     IQVKLFVVPADEAQARIPYARVNHNKYMVTERATYIGTSNWSGNYFTETAGTSLLVTQ
                     NGRGGLRSQLEAIFLRDWDSPYSHDLDTSADSVGNACRLL"
     exon            380..454
                     /gene="PLD3"
                     /gene_synonym="AD19; HU-K4; HUK4; SCA46"
                     /inference="alignment:Splign:2.1.0"
     exon            455..597
                     /gene="PLD3"
                     /gene_synonym="AD19; HU-K4; HUK4; SCA46"
                     /inference="alignment:Splign:2.1.0"
     exon            598..781
                     /gene="PLD3"
                     /gene_synonym="AD19; HU-K4; HUK4; SCA46"
                     /inference="alignment:Splign:2.1.0"
     exon            782..902
                     /gene="PLD3"
                     /gene_synonym="AD19; HU-K4; HUK4; SCA46"
                     /inference="alignment:Splign:2.1.0"
     exon            903..1030
                     /gene="PLD3"
                     /gene_synonym="AD19; HU-K4; HUK4; SCA46"
                     /inference="alignment:Splign:2.1.0"
     exon            1031..1231
                     /gene="PLD3"
                     /gene_synonym="AD19; HU-K4; HUK4; SCA46"
                     /inference="alignment:Splign:2.1.0"
     exon            1232..1371
                     /gene="PLD3"
                     /gene_synonym="AD19; HU-K4; HUK4; SCA46"
                     /inference="alignment:Splign:2.1.0"
     exon            1372..1537
                     /gene="PLD3"
                     /gene_synonym="AD19; HU-K4; HUK4; SCA46"
                     /inference="alignment:Splign:2.1.0"
     exon            1538..1637
                     /gene="PLD3"
                     /gene_synonym="AD19; HU-K4; HUK4; SCA46"
                     /inference="alignment:Splign:2.1.0"
     exon            1638..2137
                     /gene="PLD3"
                     /gene_synonym="AD19; HU-K4; HUK4; SCA46"
                     /inference="alignment:Splign:2.1.0"
     regulatory      2117..2122
                     /regulatory_class="polyA_signal_sequence"
                     /gene="PLD3"
                     /gene_synonym="AD19; HU-K4; HUK4; SCA46"
                     /note="hexamer: AGTAAA"
     polyA_site      2137
                     /gene="PLD3"
                     /gene_synonym="AD19; HU-K4; HUK4; SCA46"
                     /note="major polyA site"
ORIGIN      
        1 gggccgtcag gcggggatac agcctggaag gtgcgtgtgg ggctgggtct cggagtggga
       61 gacgtggagt gcaggctgga gcgaccgtgt ctggggagcc gagccccgct tctcgctgcg
      121 gtgagcccgg actggggcac gcactgcgca gactccccgc tgcagtgggc ggagctccca
      181 caggccccgc cccctcctcc caccctcgtt cagcctgtcc agacagaagc tggggcccac
      241 cggaggtagc tgcagacgcc tgagagcgag gccgaggccc ctcagggttt ggagaccctg
      301 acacacccac cttctcacct gggctctgcg tatcccccag ccttgaggga agatgaagcc
      361 taaactgatg taccaggagc tgaaggtgcc tgcagaggag cccgccaatg agctgcccat
      421 gaatgagatt gaggcgtgga aggctgcgga aaagaaagcc cgctgggtcc tgctggtcct
      481 cattctggcg gttgtgggct tcggagccct gatgactcag ctgtttctat gggaatacgg
      541 cgacttgcat ctctttgggc ccaaccagcg cccagccccc tgctatgacc cttgcgaagc
      601 agtgctggtg gaaagcattc ctgagggcct ggacttcccc aatgcctcca cggggaaccc
      661 ttccaccagc caggcctggc tgggcctgct cgccggtgcg cacagcagcc tggacatcgc
      721 ctccttctac tggaccctca ccaacaatga cacccacacg caggagccct ctgcccagca
      781 gggtgaggag gtcctccggc agctgcagac cctggcacca aagggcgtga acgtccgcat
      841 cgctgtgagc aagcccagcg ggccccagcc acaggcggac ctgcaggctc tgctgcagag
      901 cggtgcccag gtccgcatgg tggacatgca gaagctgacc catggcgtcc tgcataccaa
      961 gttctgggtg gtggaccaga cccacttcta cctgggcagt gccaacatgg actggcgttc
     1021 actgacccag gtcaaggagc tgggcgtggt catgtacaac tgcagctgcc tggctcgaga
     1081 cctgaccaag atctttgagg cctactggtt cctgggccag gcaggcagct ccatcccatc
     1141 aacttggccc cggttctatg acacccgcta caaccaagag acaccaatgg agatctgcct
     1201 caatggaacc cctgctctgg cctacctggc gagtgcgccc ccacccctgt gtccaagtgg
     1261 ccgcactcca gacctgaagg ctctactcaa cgtggtggac aatgcccgga gtttcatcta
     1321 cgtcgctgtc atgaactacc tgcccactct ggagttctcc caccctcaca ggttctggcc
     1381 tgccattgac gatgggctgc ggcgggccac ctacgagcgt ggcgtcaagg tgcgcctgct
     1441 catcagctgc tggggacact cggagccatc catgcgggcc ttcctgctct ctctggctgc
     1501 cctgcgtgac aaccataccc actctgacat ccaggtgaaa ctctttgtgg tccccgcgga
     1561 tgaggcccag gctcgaatcc catatgcccg tgtcaaccac aacaagtaca tggtgactga
     1621 acgcgccacc tacatcggaa cctccaactg gtctggcaac tacttcacgg agacggcggg
     1681 cacctcgctg ctggtgacgc agaatgggag gggcggcctg cggagccagc tggaggccat
     1741 tttcctgagg gactgggact ccccttacag ccatgacctt gacacctcag ctgacagcgt
     1801 gggcaacgcc tgccgcctgc tctgaggccc gatccagtgg gcaggccaag gcctgctggg
     1861 cccccgcgga cccaggtgct ctgggtcacg gtccctgtcc ccgcgccccc gcttctgtct
     1921 gccccattgt ggctcctcag gctctctccc ctgctctccc acctctacct ccacccccac
     1981 cggcctgacg ctgtggcccc gggacccagc agagctgggg gagggatcag cccccaaaga
     2041 aatgggggtg catgctgggc ctggccccct ggcccacccc cactttccag ggcaaaaagg
     2101 gcccagggtt ataataagta aataacttgt ctgtaca
//
