ENTRY       sly03040                    Pathway
NAME        Spliceosome - Solanum lycopersicum (tomato)
DESCRIPTION After transcription, eukaryotic mRNA precursors contain protein-coding exons and noncoding introns. In the following splicing, introns are excised and exons are joined by a macromolecular complex, the spliceosome. The standard spliceosome is made up of five small nuclear ribonucleoproteins (snRNPs), U1, U2, U4, U5, and U6 snRNPs, and several spliceosome-associated proteins (SAPs). Spliceosomes are not a simple stable complex, but a dynamic family of particles that assemble on the mRNA precursor and help fold it into a conformation that allows transesterification to proceed. Various spliceosome forms (e.g. A-, B- and C-complexes) have been identified.
CLASS       Genetic Information Processing; Transcription
PATHWAY_MAP sly03040  Spliceosome
DBLINKS     GO: 0005681
ORGANISM    Solanum lycopersicum (tomato) [GN:sly]
GENE        112940205  U1 spliceosomal RNA [KO:K14276]
            112940848  U1 spliceosomal RNA [KO:K14276]
            112941039  U2 spliceosomal RNA [KO:K14277]
            112940206  U2 spliceosomal RNA [KO:K14277]
            112941213  U2 spliceosomal RNA [KO:K14277]
            112940999  U2 spliceosomal RNA [KO:K14277]
            112941765  U2 spliceosomal RNA [KO:K14277]
            112941006  U4 spliceosomal RNA [KO:K14278]
            112941216  U4 spliceosomal RNA [KO:K14278]
            112941215  U4 spliceosomal RNA [KO:K14278]
            112940211  U4 spliceosomal RNA [KO:K14278]
            112941009  U5 spliceosomal RNA [KO:K14279]
            112940773  U5 spliceosomal RNA [KO:K14279]
            112941770  U5 spliceosomal RNA [KO:K14279]
            112940775  U5 spliceosomal RNA [KO:K14279]
            108353825  U6; U6 small nuclear RNA [KO:K14280]
            112939959  U6 spliceosomal RNA [KO:K14280]
            101254580  DEAD-box ATP-dependent RNA helicase 42 [KO:K12811] [EC:3.6.4.13]
            101261336  DEAD-box ATP-dependent RNA helicase 56 isoform X1 [KO:K12812] [EC:3.6.4.13]
            101259772  DEAD-box ATP-dependent RNA helicase 56 isoform X1 [KO:K12812] [EC:3.6.4.13]
            101253458  pre-mRNA-splicing factor ATP-dependent RNA helicase DEAH1 isoform X1 [KO:K12813] [EC:3.6.4.13]
            101265017  pre-mRNA-splicing factor ATP-dependent RNA helicase DEAH1-like isoform X1 [KO:K12813] [EC:3.6.4.13]
            101253638  pre-mRNA-splicing factor ATP-dependent RNA helicase DEAH7 [KO:K12815] [EC:3.6.4.13]
            101259321  LOW QUALITY PROTEIN: pre-mRNA-splicing factor ATP-dependent RNA helicase DEAH7-like [KO:K12815] [EC:3.6.4.13]
            101258325  pre-mRNA-processing factor 17 isoform X1 [KO:K12816]
            101257403  pre-mRNA-splicing factor 18 [KO:K12817]
            101266273  probable pre-mRNA-splicing factor ATP-dependent RNA helicase DEAH5 [KO:K12818] [EC:3.6.4.13]
            101247309  ATP-dependent RNA helicase DEAH12, chloroplastic-like [KO:K12818] [EC:3.6.4.13]
            101265161  pre-mRNA-splicing factor ATP-dependent RNA helicase DEAH10 [KO:K12818] [EC:3.6.4.13]
            101260893  ATP-dependent RNA helicase DEAH11, chloroplastic-like [KO:K12818] [EC:3.6.4.13]
            101264721  probable pre-mRNA-splicing factor ATP-dependent RNA helicase DEAH4 [KO:K12818] [EC:3.6.4.13]
            101267328  probable pre-mRNA-splicing factor ATP-dependent RNA helicase DEAH5 [KO:K12818] [EC:3.6.4.13]
            101252328  pre-mRNA-splicing factor SLU7 [KO:K12819]
            101260949  pre-mRNA-splicing factor SLU7 [KO:K12819]
            101263245  probable pre-mRNA-splicing factor ATP-dependent RNA helicase DEAH2 [KO:K12820] [EC:3.6.4.13]
            101262959  small nuclear ribonucleoprotein-associated proteins B and B'-like [KO:K11086]
            101248611  small nuclear ribonucleoprotein SmD1b [KO:K11087]
            101251485  small nuclear ribonucleoprotein SmD1b [KO:K11087]
            101246377  small nuclear ribonucleoprotein Sm D2 [KO:K11096]
            101250657  small nuclear ribonucleoprotein SmD3b [KO:K11088]
            101256541  small nuclear ribonucleoprotein SmD3b [KO:K11088]
            101247792  small nuclear ribonucleoprotein SmD3b [KO:K11088]
            101258239  small nuclear ribonucleoprotein E [KO:K11097]
            101247333  small nuclear ribonucleoprotein E [KO:K11097]
            101260491  probable small nuclear ribonucleoprotein F [KO:K11098]
            101245652  probable small nuclear ribonucleoprotein G [KO:K11099]
            101264989  probable small nuclear ribonucleoprotein G [KO:K11099]
            101254653  U1 small nuclear ribonucleoprotein 70 kDa isoform X2 [KO:K11093]
            101244611  U1 small nuclear ribonucleoprotein A isoform X2 [KO:K11091]
            101263748  U1 small nuclear ribonucleoprotein C-like isoform X2 [KO:K11095]
            778316  U1 small nuclear ribonucleoprotein C-like [KO:K11095]
            101267083  pre-mRNA-processing protein 40A isoform X2 [KO:K12821]
            101256011  pre-mRNA-processing protein 40A [KO:K12821]
            101253282  RNA-binding protein 25 isoform X1 [KO:K12822]
            101266555  DEAD-box ATP-dependent RNA helicase 46 [KO:K12823] [EC:3.6.4.13]
            101254752  ATP-dependent RNA helicase-like protein DB10 [KO:K12823] [EC:3.6.4.13]
            101265421  DEAD-box ATP-dependent RNA helicase 20 [KO:K12823] [EC:3.6.4.13]
            101258585  DEAD-box ATP-dependent RNA helicase 20 isoform X3 [KO:K12823] [EC:3.6.4.13]
            101248651  ATP-dependent RNA helicase-like protein DB10 [KO:K12823] [EC:3.6.4.13]
            544216  ER68; ethylene-responsive RNA helicase [KO:K12823] [EC:3.6.4.13]
            101250296  pre-mRNA-processing protein 40C isoform X1 [KO:K12824]
            101251999  transcription initiation factor TFIID subunit 15b [KO:K13098]
            101248760  U2 small nuclear ribonucleoprotein A' [KO:K11092]
            101249376  U2 small nuclear ribonucleoprotein B'' [KO:K11094]
            101250651  probable splicing factor 3A subunit 1 [KO:K12825]
            101246043  probable splicing factor 3A subunit 1 [KO:K12825]
            101255621  splicing factor 3A subunit 2 [KO:K12826]
            101254575  splicing factor SF3a60 homolog [KO:K12827]
            101252641  splicing factor 3B subunit 1 [KO:K12828]
            101264481  splicing factor 3B subunit 2 [KO:K12829]
            101261586  splicing factor 3B subunit 2-like [KO:K12829]
            101266504  spliceosome-associated protein 130 A [KO:K12830]
            101261183  pre-mRNA-splicing factor prp12 [KO:K12830]
            101244943  splicing factor 3B subunit 4 [KO:K12831]
            101258326  RNA-binding protein 7 isoform X2 [KO:K12831]
            101244858  uncharacterized protein At4g14342-like isoform X1 [KO:K12832]
            101247946  uncharacterized protein At4g14342 [KO:K12832]
            101267636  RNA recognition motif (RRM) domain-containg protein [KO:K12833]
            101247104  PHD finger-like domain-containing protein 5B [KO:K12834]
            101264757  DEAD-box ATP-dependent RNA helicase 24 [KO:K12835] [EC:3.6.4.13]
            101263952  splicing factor U2af small subunit B [KO:K12836]
            101245917  splicing factor U2af small subunit B [KO:K12836]
            101263485  splicing factor U2af large subunit B isoform X1 [KO:K12837]
            101251944  splicing factor U2af large subunit A isoform X1 [KO:K12837]
            101266099  splicing factor U2af large subunit A isoform X1 [KO:K12837]
            101258490  uncharacterized protein LOC101258490 [KO:K12837]
            101256129  tudor domain-containing protein [KO:K12839]
            101263271  DNA-damage-repair/toleration protein DRT111, chloroplastic [KO:K12840]
            101261199  LOW QUALITY PROTEIN: protein RRC1-like [KO:K12842]
            104649355  sm-like protein LSM2 [KO:K12621]
            101250608  sm-like protein LSM2 [KO:K12621]
            101264277  sm-like protein LSM3A [KO:K12622]
            101255434  probable U6 snRNA-associated Sm-like protein LSm4 [KO:K12623]
            101256523  sm-like protein LSM5 [KO:K12624]
            101268815  sm-like protein LSM36B [KO:K12625]
            101258986  sm-like protein LSM7 isoform X1 [KO:K12626]
            101267415  sm-like protein LSM8 [KO:K12627]
            101255099  protein RDM16 isoform X1 [KO:K12843]
            101258563  protein RDM16-like isoform X1 [KO:K12843]
            101256472  U4/U6 small nuclear ribonucleoprotein PRP4-like protein [KO:K12662]
            101268431  peptidyl-prolyl cis-trans isomerase CYP22 isoform X1 [KO:K09567] [EC:5.2.1.8]
            101261054  U4/U6 small nuclear ribonucleoprotein Prp31 [KO:K12844]
            101243803  U4/U6 small nuclear ribonucleoprotein Prp31 homolog [KO:K12844]
            101244799  NHP2-like protein 1 [KO:K12845]
            101267649  NHP2-like protein 1 [KO:K12845]
            101265655  U4/U6.U5 small nuclear ribonucleoprotein 27 kDa protein [KO:K12846]
            101263781  U4/U6.U5 tri-snRNP-associated protein 2 [KO:K12847]
            101246008  SART-1 family protein DOT2 [KO:K11984]
            101244419  zinc finger matrin-type protein 2 [KO:K12848]
            101263250  pre-mRNA-splicing factor 38 [KO:K12849]
            101266210  pre-mRNA splicing factor SR-like 1 isoform X1 [KO:K12850]
            101252197  110 kDa U5 small nuclear ribonucleoprotein component CLO [KO:K12852]
            101265451  protein STABILIZED1 [KO:K12855]
            101261833  pre-mRNA-processing-splicing factor 8A [KO:K12856]
            101256361  WDR57; WD-repeat protein 57 [KO:K12857]
            101245423  DEAD-box ATP-dependent RNA helicase 21-like [KO:K12858] [EC:3.6.4.13]
            101267079  DEAD-box ATP-dependent RNA helicase 21 [KO:K12858] [EC:3.6.4.13]
            101265686  thioredoxin-like protein YLS8 [KO:K12859]
            101263601  thioredoxin-like protein YLS8 isoform X1 [KO:K12859]
            101263464  pre-mRNA-processing factor 19 [KO:K10599] [EC:2.3.2.27]
            100134885  cdc5; CDC5-like protein [KO:K12860]
            101253172  pre-mRNA-splicing factor SPF27 homolog [KO:K12861]
            101250160  protein pleiotropic regulatory locus 1 [KO:K12862]
            101265967  protein CWC15 homolog [KO:K12863]
            101245968  protein CWC15 homolog A isoform X1 [KO:K12863]
            101263564  beta-catenin-like protein 1 [KO:K12864]
            101265681  stromal 70 kDa heat shock-related protein, chloroplastic [KO:K03283]
            100134914  HSP70; heat shock protein 70 [KO:K03283]
            100736433  Hsc70.1; heat shock cognate 70 kDa protein 1 [KO:K03283]
            101055596  hsc70.3; heat shock protein 70-3 [KO:K03283]
            101247772  Hsc70.2; heat shock cognate 70 kDa protein 2 [KO:K03283]
            101248309  heat shock 70 kDa protein-like [KO:K03283]
            101247151  heat shock cognate 70 kDa protein 2-like [KO:K03283]
            101254866  heat shock cognate 70 kDa protein 2-like [KO:K03283]
            101255164  heat shock cognate 70 kDa protein [KO:K03283]
            101255185  heat shock 70 kDa protein 5 [KO:K03283]
            101257622  uncharacterized protein LOC101257622 [KO:K12865]
            101256945  SNW/SKI-interacting protein A [KO:K06063]
            101262885  SNW/SKI-interacting protein-like [KO:K06063]
            101268140  pre-mRNA-splicing factor SYF1 [KO:K12867]
            101245103  pre-mRNA-splicing factor syf2 [KO:K12868]
            101250425  pre-mRNA-splicing factor SYF2-like [KO:K12868]
            101263580  crooked neck-like protein 1 [KO:K12869]
            101245441  crooked neck-like protein 1 [KO:K12869]
            101257538  LOW QUALITY PROTEIN: crooked neck-like protein 1 [KO:K12869]
            101262521  pre-mRNA-splicing factor ISY1 homolog [KO:K12870]
            101245283  peptidyl-prolyl cis-trans isomerase CYP18-2 [KO:K12733] [EC:5.2.1.8]
            101249091  coiled-coil domain-containing protein 12 isoform X2 [KO:K12871]
            101253177  zinc finger CCCH domain-containing protein 49-like [KO:K12872]
            101262575  Zinc finger transcription factor 61 [KO:K12872]
            101264965  protein BUD31 homolog 2 [KO:K12873]
            101250862  protein BUD31 homolog 1 [KO:K12873]
            101244224  RNA helicase aquarius [KO:K12874]
            101245055  apoptotic chromatin condensation inducer in the nucleus [KO:K12875]
            101256152  eukaryotic initiation factor 4A-3 [KO:K13025] [EC:3.6.4.13]
            101248886  RNA-binding protein 8A-like [KO:K12876]
            101268456  protein mago nashi homolog [KO:K12877]
            101245499  THO complex subunit 1 isoform X3 [KO:K12878]
            101261518  THO complex subunit 2 [KO:K12879]
            101265940  THO complex subunit 3 [KO:K12880]
            101268859  THO complex subunit 4D-like isoform X2 [KO:K12881]
            101256343  THO complex subunit 4D [KO:K12881]
            101262878  THO complex subunit 4A [KO:K12881]
            101266904  RNA-binding (RRM/RBD/RNP motifs) family protein [KO:K12881]
            101249122  nuclear cap-binding protein subunit 1 [KO:K12882]
            101268545  nuclear cap-binding protein subunit 2 [KO:K12883]
            101249605  glycine-rich RNA-binding protein 4, mitochondrial [KO:K12741]
            101261381  glycine-rich RNA-binding protein 3, mitochondrial [KO:K12741]
            101263390  heterogeneous nuclear ribonucleoprotein 1-like [KO:K12741]
            101258549  UBP1-associated protein 2B-like [KO:K12741]
            101254436  glycine-rich RNA-binding protein 2, mitochondrial [KO:K12741]
            101259385  UBP1-associated protein 2A-like [KO:K12741]
            101259124  UBP1-associated protein 2C-like [KO:K12741]
            101255522  UBP1-associated protein 2A [KO:K12741]
            101261559  UBP1-associated protein 2C [KO:K12741]
            101263479  heterogeneous nuclear ribonucleoprotein 1 [KO:K12741]
            104648075  heterogeneous nuclear ribonucleoprotein 1 isoform X2 [KO:K12741]
            101265253  heterogeneous nuclear ribonucleoprotein 1 [KO:K12741]
            101257012  serine/arginine-rich splicing factor SR30 isoform X1 [KO:K12890]
            101247256  serine/arginine-rich-splicing factor SR34 [KO:K12890]
            101247702  serine/arginine-rich splicing factor SR34A [KO:K12890]
            101257670  serine/arginine-rich splicing factor SR34B [KO:K12890]
            101257217  serine/arginine-rich splicing factor SC35 isoform X2 [KO:K12891]
            101251771  serine/arginine-rich splicing factor SC35 isoform X1 [KO:K12891]
            101258786  serine/arginine-rich splicing factor RS31 isoform X1 [KO:K12893]
            101263057  serine/arginine-rich splicing factor RS41 isoform X2 [KO:K12893]
            101264097  serine/arginine-rich splicing factor RS31 isoform X1 [KO:K12893]
            101266564  serine/arginine-rich splicing factor RS31 isoform X1 [KO:K12893]
            101246991  serine/arginine-rich splicing factor RS31 isoform X1 [KO:K12893]
            101253688  serine/arginine-rich splicing factor RS2Z32 isoform X1 [KO:K12896]
            101266446  serine/arginine-rich splicing factor RS2Z33 isoform X1 [KO:K12896]
            101248804  uncharacterized protein LOC101248804 isoform X3 [KO:K12896]
            101266050  serine/arginine-rich splicing factor RSZ22 [KO:K12896]
            101255764  serine/arginine-rich splicing factor SR45a [KO:K12897]
            101246587  serine/arginine-rich splicing factor SR45a [KO:K12897]
            101246661  serine/arginine-rich SC35-like splicing factor SCL28 [KO:K12900]
            101259473  serine/arginine-rich SC35-like splicing factor SCL33 [KO:K12900]
REFERENCE   PMID:19239890
  AUTHORS   Wahl MC, Will CL, Luhrmann R
  TITLE     The spliceosome: design principles of a dynamic RNP machine.
  JOURNAL   Cell 136:701-18 (2009)
            DOI:10.1016/j.cell.2009.02.009
REFERENCE   PMID:10978320
  AUTHORS   Morris DP, Greenleaf AL
  TITLE     The splicing factor, Prp40, binds the phosphorylated carboxyl-terminal domain of RNA polymerase II.
  JOURNAL   J Biol Chem 275:39935-43 (2000)
            DOI:10.1074/jbc.M004118200
REFERENCE   PMID:17537823
  AUTHORS   Chen YI, Moore RE, Ge HY, Young MK, Lee TD, Stevens SW
  TITLE     Proteomic analysis of in vivo-assembled pre-mRNA splicing complexes expands the catalog of participating factors.
  JOURNAL   Nucleic Acids Res 35:3928-44 (2007)
            DOI:10.1093/nar/gkm347
REFERENCE   PMID:19733268
  AUTHORS   Ritchie DB, Schellenberg MJ, MacMillan AM
  TITLE     Spliceosome structure: piece by piece.
  JOURNAL   Biochim Biophys Acta 1789:624-33 (2009)
            DOI:10.1016/j.bbagrm.2009.08.010
KO_PATHWAY  ko03040
///
