forester/java/src/org/forester/ws/seqdb/EbiDbEntry.java

   1 // $Id:
   2 // forester -- software libraries and applications
   3 // for genomics and evolutionary biology research.
   4 //
   5 // Copyright (C) 2010 Christian M Zmasek
   6 // Copyright (C) 2010 Sanford-Burnham Medical Research Institute
   7 // All rights reserved
   8 //
   9 // This library is free software; you can redistribute it and/or
  10 // modify it under the terms of the GNU Lesser General Public
  11 // License as published by the Free Software Foundation; either
  12 // version 2.1 of the License, or (at your option) any later version.
  13 //
  14 // This library is distributed in the hope that it will be useful,
  15 // but WITHOUT ANY WARRANTY; without even the implied warranty of
  16 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
  17 // Lesser General Public License for more details.
  18 //
  19 // You should have received a copy of the GNU Lesser General Public
  20 // License along with this library; if not, write to the Free Software
  21 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
  22 //
  23 // Contact: phylosoft @ gmail . com
  24 // WWW: https://sites.google.com/site/cmzmasek/home/software/forester
  25
  26 package org.forester.ws.seqdb;
  27
  28 import java.util.List;
  29
  30 import org.forester.go.GoTerm;
  31 import org.forester.phylogeny.data.Accession;
  32 import org.forester.util.ForesterUtil;
  33
  34 public final class EbiDbEntry implements SequenceDatabaseEntry {
  35
  36     // FIXME actually this is NCBI entry
  37     //http://www.ebi.ac.uk/Tools/dbfetch/dbfetch/emb/AAR37336/
  38     private String _pa;
  39     private String _de;
  40     private String _os;
  41     private String _tax_id;
  42     private String _symbol;
  43     private String _provider;
  44
  45     // TODO  PUBMED   15798186
  46     //TODO  (FEATURES)
  47     // source /db_xref="taxon:9606"
  48     // gene            1..2881
  49     // /gene="RBM39"
  50     //
  51     // /db_xref="MIM:604739"
  52     // CDS
  53     // /gene="RBM39"
  54     // /db_xref="MIM:604739"
  55     // /db_xref="InterPro:IPR002475"
  56     // /product="Bcl-2"
  57     // /protein_id="NP_909122.1"
  58     // /db_xref="UniProtKB/TrEMBL:Q5J7V1" <- reparse?
  59     //
  60     // Protein
  61     /*
  62     LOCUS       NM_184234               2881 bp    mRNA    linear   PRI 16-JUN-2013
  63     DEFINITION  Homo sapiens RNA binding motif protein 39 (RBM39), transcript
  64             variant 1, mRNA.
  65     ACCESSION   NM_184234
  66     VERSION     NM_184234.2  GI:336176061
  67     KEYWORDS    RefSeq.
  68     SOURCE      Homo sapiens (human)
  69     ORGANISM  Homo sapiens
  70             Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
  71             Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
  72             Catarrhini; Hominidae; Homo.
  73     REFERENCE   1  (bases 1 to 2881)
  74     AUTHORS   Sillars-Hardebol,A.H., Carvalho,B., Belien,J.A., de Wit,M.,
  75             Delis-van Diemen,P.M., Tijssen,M., van de Wiel,M.A., Ponten,F.,
  76             Meijer,G.A. and Fijneman,R.J.
  77     TITLE     CSE1L, DIDO1 and RBM39 in colorectal adenoma to carcinoma
  78             progression
  79     JOURNAL   Cell Oncol (Dordr) 35 (4), 293-300 (2012)
  80     PUBMED   22711543
  81     REMARK    GeneRIF: Data show that CSE1L, DIDO1 and RBM39 mRNA expression
  82             levels correlated with chromosome 20q DNA copy number status.
  83     REFERENCE   2  (bases 1 to 2881)
  84     AUTHORS   Huang,G., Zhou,Z., Wang,H. and Kleinerman,E.S.
  85     TITLE     CAPER-alpha alternative splicing regulates the expression of
  86             vascular endothelial growth factor(1)(6)(5) in Ewing sarcoma cells
  87     JOURNAL   Cancer 118 (8), 2106-2116 (2012)
  88     PUBMED   22009261
  89     REMARK    GeneRIF: Increased VEGF(165) expression is secondary to the
  90             down-regulation of CAPER-alpha by EWS/FLI-1. CAPER-alpha mediates
  91             alternative splicing and controls the shift from VEGF(189) to
  92             VEGF(165) .
  93     REFERENCE   3  (bases 1 to 2881)
  94     AUTHORS   Han,B., Stockwin,L.H., Hancock,C., Yu,S.X., Hollingshead,M.G. and
  95             Newton,D.L.
  96     TITLE     Proteomic analysis of nuclei isolated from cancer cell lines
  97             treated with indenoisoquinoline NSC 724998, a novel topoisomerase I
  98             inhibitor
  99     JOURNAL   J. Proteome Res. 9 (8), 4016-4027 (2010)
 100     PUBMED   20515076
 101     REMARK    Erratum:[J Proteome Res. 2011 Apr 1;10(4):2128]
 102     REFERENCE   4  (bases 1 to 2881)
 103     AUTHORS   Zhang,J.Y., Looi,K.S. and Tan,E.M.
 104     TITLE     Identification of tumor-associated antigens as diagnostic and
 105             predictive biomarkers in cancer
 106     JOURNAL   Methods Mol. Biol. 520, 1-10 (2009)
 107     PUBMED   19381943
 108     REFERENCE   5  (bases 1 to 2881)
 109     AUTHORS   Dutta,J., Fan,G. and Gelinas,C.
 110     TITLE     CAPERalpha is a novel Rel-TAD-interacting factor that inhibits
 111             lymphocyte transformation by the potent Rel/NF-kappaB oncoprotein
 112             v-Rel
 113     JOURNAL   J. Virol. 82 (21), 10792-10802 (2008)
 114     PUBMED   18753212
 115     REMARK    GeneRIF: this study identifies CAPERalpha (RNA binding motif
 116             protein 39) as a new transcriptional coregulator for v-Rel and
 117             reveals an important role in modulating Rel's oncogenic activity.
 118     REFERENCE   6  (bases 1 to 2881)
 119     AUTHORS   Cazalla,D., Newton,K. and Caceres,J.F.
 120     TITLE     A novel SR-related protein is required for the second step of
 121             Pre-mRNA splicing
 122     JOURNAL   Mol. Cell. Biol. 25 (8), 2969-2980 (2005)
 123     PUBMED   15798186
 124     REFERENCE   7  (bases 1 to 2881)
 125     AUTHORS   Dowhan,D.H., Hong,E.P., Auboeuf,D., Dennis,A.P., Wilson,M.M.,
 126             Berget,S.M. and O'Malley,B.W.
 127     TITLE     Steroid hormone receptor coactivation and alternative RNA splicing
 128             by U2AF65-related proteins CAPERalpha and CAPERbeta
 129     JOURNAL   Mol. Cell 17 (3), 429-439 (2005)
 130     PUBMED   15694343
 131     REFERENCE   8  (bases 1 to 2881)
 132     AUTHORS   Sun,N.N., Fastje,C.D., Wong,S.S., Sheppard,P.R., Macdonald,S.J.,
 133             Ridenour,G., Hyde,J.D. and Witten,M.L.
 134     TITLE     Dose-dependent transcriptome changes by metal ores on a human acute
 135             lymphoblastic leukemia cell line
 136     JOURNAL   Toxicol Ind Health 19 (7-10), 157-163 (2003)
 137     PUBMED   15747776
 138     REMARK    GeneRIF: 10 genes were down-regulated following treatment of the
 139             T-ALL cells with 0.15 and 1.5 microg/mL of metal ores at 72 h
 140     REFERENCE   9  (bases 1 to 2881)
 141     AUTHORS   Jung,D.J., Na,S.Y., Na,D.S. and Lee,J.W.
 142     TITLE     Molecular cloning and characterization of CAPER, a novel
 143             coactivator of activating protein-1 and estrogen receptors
 144     JOURNAL   J. Biol. Chem. 277 (2), 1229-1234 (2002)
 145     PUBMED   11704680
 146     REMARK    GeneRIF: This paper describes the mouse gene.
 147     REFERENCE   10 (bases 1 to 2881)
 148     AUTHORS   Imai,H., Chan,E.K., Kiyosawa,K., Fu,X.D. and Tan,E.M.
 149     TITLE     Novel nuclear autoantigen with splicing factor motifs identified
 150             with antibody from hepatocellular carcinoma
 151     JOURNAL   J. Clin. Invest. 92 (5), 2419-2426 (1993)
 152     PUBMED   8227358
 153     COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
 154             reference sequence was derived from DC346351.1, BC141835.1 and
 155             C75555.1.
 156             On Jun 16, 2011 this sequence version replaced gi:35493810.
 157
 158             Summary: This gene encodes a member of the U2AF65 family of
 159             proteins. The encoded protein is found in the nucleus, where it
 160             co-localizes with core spliceosomal proteins. It has been shown to
 161             play a role in both steroid hormone receptor-mediated transcription
 162             and alternative splicing, and it is also a transcriptional
 163             coregulator of the viral oncoprotein v-Rel. Multiple transcript
 164             variants have been observed for this gene. A related pseudogene has
 165             been identified on chromosome X. [provided by RefSeq, Aug 2011].
 166
 167             Transcript Variant: This variant (1) encodes the longest isoform
 168             (a, also called CC1.4).
 169
 170             Publication Note:  This RefSeq record includes a subset of the
 171             publications that are available for this gene. Please see the Gene
 172             record to access additional publications.
 173
 174             ##Evidence-Data-START##
 175             Transcript exon combination :: BC141835.1, L10911.1 [ECO:0000332]
 176             RNAseq introns              :: mixed/partial sample support
 177                                            ERS025081, ERS025082 [ECO:0000350]
 178             ##Evidence-Data-END##
 179             COMPLETENESS: complete on the 3' end.
 180     PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
 181             1-578               DC346351.1         3-580
 182             579-2872            BC141835.1         429-2722
 183             2873-2881           C75555.1           1-9                 c
 184     FEATURES             Location/Qualifiers
 185      source          1..2881
 186                      /organism="Homo sapiens"
 187                      /mol_type="mRNA"
 188                      /db_xref="taxon:9606"
 189                      /chromosome="20"
 190                      /map="20q11.22"
 191      gene            1..2881
 192                      /gene="RBM39"
 193                      /gene_synonym="CAPER; CAPERalpha; FSAP59; HCC1; RNPC2"
 194                      /note="RNA binding motif protein 39"
 195                      /db_xref="GeneID:9584"
 196                      /db_xref="HGNC:15923"
 197                      /db_xref="HPRD:09201"
 198                      /db_xref="MIM:604739"
 199      exon            1..396
 200                      /gene="RBM39"
 201                      /gene_synonym="CAPER; CAPERalpha; FSAP59; HCC1; RNPC2"
 202                      /inference="alignment:Splign:1.39.8"
 203      STS             35..262
 204                      /gene="RBM39"
 205                      /gene_synonym="CAPER; CAPERalpha; FSAP59; HCC1; RNPC2"
 206                      /standard_name="REN58946"
 207                      /db_xref="UniSTS:383746"
 208      misc_feature    221..223
 209                      /gene="RBM39"
 210                      /gene_synonym="CAPER; CAPERalpha; FSAP59; HCC1; RNPC2"
 211                      /note="upstream in-frame stop codon"
 212      STS             299..453
 213                      /gene="RBM39"
 214                      /gene_synonym="CAPER; CAPERalpha; FSAP59; HCC1; RNPC2"
 215                      /standard_name="G64285"
 216                      /db_xref="UniSTS:158667"
 217      exon            397..460
 218                      /gene="RBM39"
 219                      /gene_synonym="CAPER; CAPERalpha; FSAP59; HCC1; RNPC2"
 220                      /inference="alignment:Splign:1.39.8"
 221      CDS             410..2002
 222                      /gene="RBM39"
 223                      /gene_synonym="CAPER; CAPERalpha; FSAP59; HCC1; RNPC2"
 224                      /note="isoform a is encoded by transcript variant 1;
 225                      coactivator of activating protein-1 and estrogen
 226                      receptors; functional spliceosome-associated protein 59;
 227                      RNA-binding region (RNP1, RRM) containing 2;
 228                      hepatocellular carcinoma protein 1; splicing factor HCC1"
 229                      /codon_start=1
 230                      /product="RNA-binding protein 39 isoform a"
 231                      /protein_id="NP_909122.1"
 232                      /db_xref="GI:35493811"
 233                      /db_xref="CCDS:CCDS13266.1"
 234                      /db_xref="GeneID:9584"
 235                      /db_xref="HGNC:15923"
 236                      /db_xref="HPRD:09201"
 237                      /db_xref="MIM:604739"
 238                      /translation="MADDIDIEAMLEAPYKKDENKLSSANGHEERSKKRKKSKSRSRS
 239                      HERKRSKSKERKRSRDRERKKSKSRERKRSRSKERRRSRSRSRDRRFRGRYRSPYSGP
 240                      KFNSAIRGKIGLPHSIKLSRRRSRSKSPFRKDKSPVREPIDNLTPEERDARTVFCMQL
 241                      AARIRPRDLEEFFSTVGKVRDVRMISDRNSRRSKGIAYVEFVDVSSVPLAIGLTGQRV
 242                      LGVPIIVQASQAEKNRAAAMANNLQKGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRI
 243                      ESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPMKVGHVTERTDASS
 244                      ASSFLDSDELERTGIDLGTTGRLQLMARLAEGTGLQIPPAAQQALQMSGSLAFGAVAE
 245                      FSFVIDLQTRLSQQTEASALAAAASVQPLATQCFQLSNMFNPQTEEEVGWDTEIKDDV
 246                      IEECNKHGGVIHIYVDKNSAQGNVYVKCPSIAAAIAAVNALHGRWFAGKMITAAYVPL
 247                      PTYHNLFPDSMTATQLLVPSRR"
 248      misc_feature    413..415
 249                      /gene="RBM39"
 250                      /gene_synonym="CAPER; CAPERalpha; FSAP59; HCC1; RNPC2"
 251                      /experiment="experimental evidence, no additional details
 252                      recorded"
 253                      /note="N-acetylalanine; propagated from
 254                      UniProtKB/Swiss-Prot (Q14498.2); acetylation site"
 255      misc_feature    692..694
 256                      /gene="RBM39"
 257                      /gene_synonym="CAPER; CAPERalpha; FSAP59; HCC1; RNPC2"
 258                      /experiment="experimental evidence, no additional details
 259                      recorded"
 260                      /note="Phosphotyrosine; propagated from
 261                      UniProtKB/Swiss-Prot (Q14498.2); phosphorylation site"
 262      misc_feature    698..700
 263                      /gene="RBM39"
 264                      /gene_synonym="CAPER; CAPERalpha; FSAP59; HCC1; RNPC2"
 265                      /experiment="experimental evidence, no additional details
 266                      recorded"
 267                      /note="Phosphoserine; propagated from UniProtKB/Swiss-Prot
 268                      (Q14498.2); phosphorylation site"
 269      misc_feature    707..709
 270                      /gene="RBM39"
 271                      /gene_synonym="CAPER; CAPERalpha; FSAP59; HCC1; RNPC2"
 272                      /experiment="experimental evidence, no additional details
 273                      recorded"
 274                      /note="Phosphoserine; propagated from UniProtKB/Swiss-Prot
 275                      (Q14498.2); phosphorylation site"
 276      misc_feature    815..817
 277                      /gene="RBM39"
 278                      /gene_synonym="CAPER; CAPERalpha; FSAP59; HCC1; RNPC2"
 279                      /experiment="experimental evidence, no additional details
 280                      recorded"
 281                      /note="Phosphoserine; propagated from UniProtKB/Swiss-Prot
 282                      (Q14498.2); phosphorylation site"
 283      misc_feature    845..847
 284                      /gene="RBM39"
 285                      /gene_synonym="CAPER; CAPERalpha; FSAP59; HCC1; RNPC2"
 286                      /experiment="experimental evidence, no additional details
 287                      recorded"
 288                      /note="Phosphothreonine; propagated from
 289                      UniProtKB/Swiss-Prot (Q14498.2); phosphorylation site"
 290      misc_feature    1280..1627
 291                      /gene="RBM39"
 292                      /gene_synonym="CAPER; CAPERalpha; FSAP59; HCC1; RNPC2"
 293                      /inference="non-experimental evidence, no additional
 294                      details recorded"
 295                      /note="propagated from UniProtKB/Swiss-Prot (Q14498.2);
 296                      Region: Interaction with JUN (By similarity)"
 297      misc_feature    1280..1474
 298                      /gene="RBM39"
 299                      /gene_synonym="CAPER; CAPERalpha; FSAP59; HCC1; RNPC2"
 300                      /inference="non-experimental evidence, no additional
 301                      details recorded"
 302                      /note="propagated from UniProtKB/Swiss-Prot (Q14498.2);
 303                      Region: Activating domain (By similarity)"
 304      misc_feature    1409..1411
 305                      /gene="RBM39"
 306                      /gene_synonym="CAPER; CAPERalpha; FSAP59; HCC1; RNPC2"
 307                      /experiment="experimental evidence, no additional details
 308                      recorded"
 309                      /note="Phosphoserine; propagated from UniProtKB/Swiss-Prot
 310                      (Q14498.2); phosphorylation site"
 311      misc_feature    1418..1420
 312                      /gene="RBM39"
 313                      /gene_synonym="CAPER; CAPERalpha; FSAP59; HCC1; RNPC2"
 314                      /experiment="experimental evidence, no additional details
 315                      recorded"
 316                      /note="Phosphoserine; propagated from UniProtKB/Swiss-Prot
 317                      (Q14498.2); phosphorylation site"
 318      misc_feature    1430..1432
 319                      /gene="RBM39"
 320                      /gene_synonym="CAPER; CAPERalpha; FSAP59; HCC1; RNPC2"
 321                      /experiment="experimental evidence, no additional details
 322                      recorded"
 323                      /note="Phosphoserine; propagated from UniProtKB/Swiss-Prot
 324                      (Q14498.2); phosphorylation site"
 325      misc_feature    1472..1627
 326                      /gene="RBM39"
 327                      /gene_synonym="CAPER; CAPERalpha; FSAP59; HCC1; RNPC2"
 328                      /inference="non-experimental evidence, no additional
 329                      details recorded"
 330                      /note="propagated from UniProtKB/Swiss-Prot (Q14498.2);
 331                      Region: Interaction with ESR1 and ESR2 (By similarity)"
 332      misc_feature    1625..1999
 333                      /gene="RBM39"
 334                      /gene_synonym="CAPER; CAPERalpha; FSAP59; HCC1; RNPC2"
 335                      /inference="non-experimental evidence, no additional
 336                      details recorded"
 337                      /note="propagated from UniProtKB/Swiss-Prot (Q14498.2);
 338                      Region: Interaction with NCOA6 (By similarity)"
 339      exon            461..510
 340                      /gene="RBM39"
 341                      /gene_synonym="CAPER; CAPERalpha; FSAP59; HCC1; RNPC2"
 342                      /inference="alignment:Splign:1.39.8"
 343      exon            511..705
 344                      /gene="RBM39"
 345                      /gene_synonym="CAPER; CAPERalpha; FSAP59; HCC1; RNPC2"
 346                      /inference="alignment:Splign:1.39.8"
 347      exon            706..771
 348                      /gene="RBM39"
 349                      /gene_synonym="CAPER; CAPERalpha; FSAP59; HCC1; RNPC2"
 350                      /inference="alignment:Splign:1.39.8"
 351      exon            772..825
 352                      /gene="RBM39"
 353                      /gene_synonym="CAPER; CAPERalpha; FSAP59; HCC1; RNPC2"
 354                      /inference="alignment:Splign:1.39.8"
 355      exon            826..943
 356                      /gene="RBM39"
 357                      /gene_synonym="CAPER; CAPERalpha; FSAP59; HCC1; RNPC2"
 358                      /inference="alignment:Splign:1.39.8"
 359      exon            944..1096
 360                      /gene="RBM39"
 361                      /gene_synonym="CAPER; CAPERalpha; FSAP59; HCC1; RNPC2"
 362                      /inference="alignment:Splign:1.39.8"
 363      exon            1097..1234
 364                      /gene="RBM39"
 365                      /gene_synonym="CAPER; CAPERalpha; FSAP59; HCC1; RNPC2"
 366                      /inference="alignment:Splign:1.39.8"
 367      exon            1235..1300
 368                      /gene="RBM39"
 369                      /gene_synonym="CAPER; CAPERalpha; FSAP59; HCC1; RNPC2"
 370                      /inference="alignment:Splign:1.39.8"
 371      exon            1301..1505
 372                      /gene="RBM39"
 373                      /gene_synonym="CAPER; CAPERalpha; FSAP59; HCC1; RNPC2"
 374                      /inference="alignment:Splign:1.39.8"
 375      exon            1506..1583
 376                      /gene="RBM39"
 377                      /gene_synonym="CAPER; CAPERalpha; FSAP59; HCC1; RNPC2"
 378                      /inference="alignment:Splign:1.39.8"
 379      exon            1584..1634
 380                      /gene="RBM39"
 381                      /gene_synonym="CAPER; CAPERalpha; FSAP59; HCC1; RNPC2"
 382                      /inference="alignment:Splign:1.39.8"
 383      exon            1635..1716
 384                      /gene="RBM39"
 385                      /gene_synonym="CAPER; CAPERalpha; FSAP59; HCC1; RNPC2"
 386                      /inference="alignment:Splign:1.39.8"
 387      exon            1717..1822
 388                      /gene="RBM39"
 389                      /gene_synonym="CAPER; CAPERalpha; FSAP59; HCC1; RNPC2"
 390                      /inference="alignment:Splign:1.39.8"
 391      exon            1823..1901
 392                      /gene="RBM39"
 393                      /gene_synonym="CAPER; CAPERalpha; FSAP59; HCC1; RNPC2"
 394                      /inference="alignment:Splign:1.39.8"
 395      exon            1902..2874
 396                      /gene="RBM39"
 397                      /gene_synonym="CAPER; CAPERalpha; FSAP59; HCC1; RNPC2"
 398                      /inference="alignment:Splign:1.39.8"
 399      STS             1956..2182
 400                      /gene="RBM39"
 401                      /gene_synonym="CAPER; CAPERalpha; FSAP59; HCC1; RNPC2"
 402                      /standard_name="REN58786"
 403                      /db_xref="UniSTS:383586"
 404      STS             2104..2148
 405                      /gene="RBM39"
 406                      /gene_synonym="CAPER; CAPERalpha; FSAP59; HCC1; RNPC2"
 407                      /standard_name="D19S1033"
 408                      /db_xref="UniSTS:154759"
 409      STS             2145..2400
 410                      /gene="RBM39"
 411                      /gene_synonym="CAPER; CAPERalpha; FSAP59; HCC1; RNPC2"
 412                      /standard_name="REN58785"
 413                      /db_xref="UniSTS:383585"
 414      STS             2349..2590
 415                      /gene="RBM39"
 416                      /gene_synonym="CAPER; CAPERalpha; FSAP59; HCC1; RNPC2"
 417                      /standard_name="REN58784"
 418                      /db_xref="UniSTS:383584"
 419      STS             2450..2669
 420                      /gene="RBM39"
 421                      /gene_synonym="CAPER; CAPERalpha; FSAP59; HCC1; RNPC2"
 422                      /standard_name="RH69003"
 423                      /db_xref="UniSTS:85360"
 424      STS             2579..2828
 425                      /gene="RBM39"
 426                      /gene_synonym="CAPER; CAPERalpha; FSAP59; HCC1; RNPC2"
 427                      /standard_name="REN58783"
 428                      /db_xref="UniSTS:383583"
 429      STS             2639..2728
 430                      /gene="RBM39"
 431                      /gene_synonym="CAPER; CAPERalpha; FSAP59; HCC1; RNPC2"
 432                      /standard_name="RH67917"
 433                      /db_xref="UniSTS:84037"
 434      polyA_signal    2851..2856
 435                      /gene="RBM39"
 436                      /gene_synonym="CAPER; CAPERalpha; FSAP59; HCC1; RNPC2"
 437      polyA_site      2874
 438                      /gene="RBM39"
 439                      /gene_synonym="CAPER; CAPERalpha; FSAP59; HCC1; RNPC2"
 440     ORIGIN
 441         1 atttggagct tggggcagct tctcgcgaga gcccgtgctg agggctctgt gaggccccgt
 442        61 gtgtttgtgt gtgtgtatgt gtgctggtga atgtgagtac agggaagcag cggccgccat
 443       121 ttcagggagc ttgtcgacgc tgtcgcaggg gtggatcctg agctgccgaa gccgccgtcc
 444       181 tgctctcccg cgtgggcttc tctaattcca ttgttttttt tagattctct cgggcctagc
 445       241 cgtccttgga acccgatatt cgggctgggc ggttccgcgg cctgggccta ggggcttaac
 446       301 agtagcaaca gaagcggcgg cggcggcagc agcagcagca gcagcagcaa tctcttcccg
 447       361 aacacgagca ccacaggcgc ccgaaggccg gaacaggcgt ttagagaaaa tggcagacga
 448       421 tattgatatt gaagcaatgc ttgaggctcc ttacaagaag gatgagaaca agttgagcag
 449       481 tgccaacggc catgaagaac gtagcaaaaa gaggaaaaaa agcaagagca gaagtcgtag
 450       541 tcatgaacga aagagaagca aaagtaagga acggaagcga agtagagaca gagaaaggaa
 451       601 aaagagcaaa agccgtgaaa gaaagcgaag tagaagcaaa gagaggcgac ggagccgctc
 452       661 aagaagtcga gatcgaagat ttagaggccg ctacagaagt ccttactccg gaccaaaatt
 453       721 taacagtgcc atccgaggaa agattgggtt gcctcatagc atcaaattaa gcagacgacg
 454       781 ttcccgaagc aaaagtccat tcagaaaaga caagagccct gtgagagaac ctattgataa
 455       841 tttaactcct gaggaaagag atgcaaggac agtcttctgt atgcagctgg cggcaagaat
 456       901 tcgaccaagg gatttggaag agtttttctc tacagtagga aaggttcgag atgtgaggat
 457       961 gatttctgac agaaattcaa gacgttccaa aggaattgct tatgtggagt tcgtcgatgt
 458      1021 tagctcagtg cctctagcaa taggattaac tggccaacga gttttaggcg tgccaatcat
 459      1081 agtacaggca tcacaggcag aaaaaaacag agctgcagca atggcaaaca atttacaaaa
 460      1141 gggaagtgct ggacctatga ggctttatgt gggctcatta cacttcaaca taactgaaga
 461      1201 tatgcttcgt gggatctttg agccttttgg aagaattgaa agtatccagc tgatgatgga
 462      1261 cagtgaaact ggtcgatcca agggatatgg atttattaca ttttctgact cagaatgtgc
 463      1321 caaaaaggct ttggaacaac ttaatggatt tgaactagca ggaagaccaa tgaaagttgg
 464      1381 tcatgttact gaacgtactg atgcttcgag tgctagttca tttttggaca gtgatgaact
 465      1441 ggaaaggact ggaattgatt tgggaacaac tggtcgtctt cagttaatgg caagacttgc
 466      1501 agagggtaca ggtttgcaga ttccgccagc agcacagcaa gctctacaga tgagtggctc
 467      1561 tttggcattt ggtgctgtgg cagaattctc ttttgttata gatttgcaaa caagactttc
 468      1621 ccagcagact gaagcttcag ctttagctgc agctgcctct gttcagccac ttgcaacaca
 469      1681 atgtttccaa ctctctaaca tgtttaaccc tcaaacagaa gaagaagttg gatgggatac
 470      1741 cgagattaag gatgatgtga ttgaagaatg taataaacat ggaggagtta ttcatattta
 471      1801 tgttgacaaa aattcagctc agggcaatgt gtatgtgaag tgcccatcaa ttgctgcagc
 472      1861 tattgctgct gtcaatgcat tgcatggcag gtggtttgct ggtaaaatga taacagcagc
 473      1921 atatgtacct cttccaactt accacaacct gtttcctgat tctatgacag caacacagct
 474      1981 actggttcca agtagacgat gaaggaagat atagtccctt atgtatatag ctttttttct
 475      2041 ttcttgagaa ttcatcttga gttatctttt atttagataa aaataaagag gcaaggatct
 476      2101 actgtcattt gtatgcaatt tcctgttacc ttgaaaaaat aaaaatgtta acaggaatgc
 477      2161 agtgtgctca ttctccctaa atagtaaatc ccactgtata caaaactgtt ctcttgttct
 478      2221 gccttttaaa atgttcatgt agaaaattaa tgaactatag gaatagctct aggagaacaa
 479      2281 atgtgctttc tgtaaaaagg cagaccaggg atgtaatgtt tttaatgttt cagaagccta
 480      2341 actttttaca cagtggttac atttcacatt tcactaatgt tgatatttgg ctgatggttg
 481      2401 agcagtttct gaaatacaca tttagtgtat ggaaatacaa gacagctaaa gggctgtttg
 482      2461 gttagcatct catcttgcat tctgatcaat tggcaagaaa gggagatttc aaaattatat
 483      2521 ttcttgatgg tatcttttca attaatgtat ctgtaaaagt ttctttgtaa atactatgtg
 484      2581 ttctggtgtg tcttaaaatt ccaaacaaaa tgatccctgc atttcctgaa gatgtttaaa
 485      2641 cgtgagagtc tggtaggcaa agcagtctga gaaagaaata ggaaatgcag aaataggttt
 486      2701 tgtctggttg catataatct ttgctctttt taagctctgt gagctctgaa atatattttt
 487      2761 gggttacttc agtgtgtttg acaagacagc ttgatatttc tatcaaacaa atgactttca
 488      2821 tattgcaaca atctttgtaa gaaccactca aataaaagtc tcttaaaaag gccaaaaaaa
 489      2881 a
 490
 491
 492     */
 493     private EbiDbEntry() {
 494     }
 495
 496     @Override
 497     public Object clone() throws CloneNotSupportedException {
 498         throw new CloneNotSupportedException();
 499     }
 500
 501     public static SequenceDatabaseEntry createInstanceFromPlainTextForRefSeq( final List<String> lines ) {
 502         final EbiDbEntry e = new EbiDbEntry();
 503         final StringBuilder def = new StringBuilder();
 504         boolean in_def = false;
 505         for( final String line : lines ) {
 506             //  System.out.println( "-" + line );
 507             if ( line.startsWith( "ACCESSION" ) ) {
 508                 e.setPA( SequenceDbWsTools.extractFrom( line, "ACCESSION" ) );
 509                 in_def = false;
 510             }
 511             else if ( line.startsWith( "DEFINITION" ) ) {
 512                 if ( line.indexOf( "[" ) > 0 ) {
 513                     def.append( SequenceDbWsTools.extractFromTo( line, "DEFINITION", "[" ) );
 514                 }
 515                 else if ( line.indexOf( "." ) > 0 ) {
 516                     def.append( SequenceDbWsTools.extractFromTo( line, "DEFINITION", "." ) );
 517                 }
 518                 else {
 519                     def.append( SequenceDbWsTools.extractFrom( line, "DEFINITION" ) );
 520                 }
 521                 in_def = true;
 522             }
 523             else if ( line.startsWith( "SOURCE" ) ) {
 524                 if ( line.indexOf( "(" ) > 0 ) {
 525                     e.setOs( SequenceDbWsTools.extractFromTo( line, "SOURCE", "(" ) );
 526                 }
 527                 else {
 528                     e.setOs( SequenceDbWsTools.extractFrom( line, "SOURCE" ) );
 529                 }
 530                 in_def = false;
 531             }
 532             else if ( line.startsWith( " " ) && in_def ) {
 533                 def.append( " " );
 534                 if ( line.indexOf( "[" ) > 0 ) {
 535                     def.append( SequenceDbWsTools.extractTo( line, "[" ) );
 536                 }
 537                 else if ( line.indexOf( "." ) > 0 ) {
 538                     def.append( SequenceDbWsTools.extractTo( line, "." ) );
 539                 }
 540                 else {
 541                     def.append( line.trim() );
 542                 }
 543             }
 544             else {
 545                 in_def = false;
 546             }
 547         }
 548         if ( def.length() > 0 ) {
 549             e.setDe( def.toString().trim() );
 550         }
 551         return e;
 552     }
 553
 554     public static SequenceDatabaseEntry createInstanceFromPlainText( final List<String> lines ) {
 555         final EbiDbEntry e = new EbiDbEntry();
 556         for( final String line : lines ) {
 557             if ( line.startsWith( "PA" ) ) {
 558                 e.setPA( SequenceDbWsTools.extractFrom( line, "PA" ) );
 559             }
 560             else if ( line.startsWith( "DE" ) ) {
 561                 e.setDe( SequenceDbWsTools.extractFrom( line, "DE" ) );
 562             }
 563             else if ( line.startsWith( "OS" ) ) {
 564                 if ( line.indexOf( "(" ) > 0 ) {
 565                     e.setOs( SequenceDbWsTools.extractFromTo( line, "OS", "(" ) );
 566                 }
 567                 else {
 568                     e.setOs( SequenceDbWsTools.extractFrom( line, "OS" ) );
 569                 }
 570             }
 571             else if ( line.startsWith( "OX" ) ) {
 572                 if ( line.indexOf( "NCBI_TaxID=" ) > 0 ) {
 573                     e.setTaxId( SequenceDbWsTools.extractFromTo( line, "NCBI_TaxID=", ";" ) );
 574                 }
 575             }
 576         }
 577         return e;
 578     }
 579
 580     @Override
 581     public String getAccession() {
 582         return _pa;
 583     }
 584
 585     private void setPA( final String pa ) {
 586         if ( _pa == null ) {
 587             _pa = pa;
 588         }
 589     }
 590
 591     @Override
 592     public String getSequenceName() {
 593         return _de;
 594     }
 595
 596     private void setDe( final String rec_name ) {
 597         if ( _de == null ) {
 598             _de = rec_name;
 599         }
 600     }
 601
 602     @Override
 603     public String getTaxonomyScientificName() {
 604         return _os;
 605     }
 606
 607     private void setOs( final String os ) {
 608         if ( _os == null ) {
 609             _os = os;
 610         }
 611     }
 612
 613     @Override
 614     public String getTaxonomyIdentifier() {
 615         return _tax_id;
 616     }
 617
 618     private void setTaxId( final String tax_id ) {
 619         if ( _tax_id == null ) {
 620             _tax_id = tax_id;
 621         }
 622     }
 623
 624     @Override
 625     public String getSequenceSymbol() {
 626         return _symbol;
 627     }
 628
 629     @Override
 630     public boolean isEmpty() {
 631         return ( ForesterUtil.isEmpty( getAccession() ) && ForesterUtil.isEmpty( getSequenceName() )
 632                 && ForesterUtil.isEmpty( getTaxonomyScientificName() )
 633                 && ForesterUtil.isEmpty( getTaxonomyIdentifier() ) && ForesterUtil.isEmpty( getSequenceSymbol() ) );
 634     }
 635
 636     @Override
 637     public String getProvider() {
 638         return _provider;
 639     }
 640
 641     public void setProvider( final String provider ) {
 642         _provider = provider;
 643     }
 644
 645     @Override
 646     public String getGeneName() {
 647         return null;
 648     }
 649
 650     @Override
 651     public List<GoTerm> getGoTerms() {
 652         return null;
 653     }
 654
 655     @Override
 656     public List<Accession> getCrossReferences() {
 657         return null;
 658     }
 659 }