ENTRY       osa03040                    Pathway
NAME        Spliceosome - Oryza sativa japonica (Japanese rice) (RefSeq)
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 osa03040  Spliceosome
DBLINKS     GO: 0005681
ORGANISM    Oryza sativa japonica (Japanese rice) (RefSeq) [GN:osa]
GENE        4344716  DEAD-box ATP-dependent RNA helicase 42 [KO:K12811] [EC:3.6.4.13]
            4326193  DEAD-box ATP-dependent RNA helicase 15 isoform X1 [KO:K12812] [EC:3.6.4.13]
            4326192  DEAD-box ATP-dependent RNA helicase 56 isoform X1 [KO:K12812] [EC:3.6.4.13]
            4338675  pre-mRNA-splicing factor ATP-dependent RNA helicase DEAH1 [KO:K12813] [EC:3.6.4.13]
            4345304  pre-mRNA-splicing factor ATP-dependent RNA helicase DEAH1 [KO:K12813] [EC:3.6.4.13]
            9268581  pre-mRNA-splicing factor ATP-dependent RNA helicase DEAH1 [KO:K12813] [EC:3.6.4.13]
            4343339  pre-mRNA-splicing factor ATP-dependent RNA helicase DEAH7 [KO:K12815] [EC:3.6.4.13]
            4333045  pre-mRNA-processing factor 17 [KO:K12816]
            4343671  pre-mRNA-splicing factor 18 [KO:K12817]
            4333826  pre-mRNA-splicing factor 18 isoform X1 [KO:K12817]
            4329095  probable pre-mRNA-splicing factor ATP-dependent RNA helicase DEAH5 [KO:K12818] [EC:3.6.4.13]
            4340375  pre-mRNA-splicing factor ATP-dependent RNA helicase DEAH10 [KO:K12818] [EC:3.6.4.13]
            4350353  probable pre-mRNA-splicing factor ATP-dependent RNA helicase DEAH4 [KO:K12818] [EC:3.6.4.13]
            4343939  ATP-dependent RNA helicase DEAH11, chloroplastic isoform X1 [KO:K12818] [EC:3.6.4.13]
            9267698  probable pre-mRNA-splicing factor ATP-dependent RNA helicase DEAH5 [KO:K12818] [EC:3.6.4.13]
            4344572  pre-mRNA-splicing factor SLU7 [KO:K12819]
            4332645  probable pre-mRNA-splicing factor ATP-dependent RNA helicase DEAH3 isoform X1 [KO:K12820] [EC:3.6.4.13]
            9270807  small nuclear ribonucleoprotein-associated protein N [KO:K11086]
            4329810  small nuclear ribonucleoprotein Sm D1 [KO:K11087]
            4336118  small nuclear ribonucleoprotein Sm D1 [KO:K11087]
            4338385  small nuclear ribonucleoprotein Sm D2 isoform X1 [KO:K11096]
            4324004  probable small nuclear ribonucleoprotein Sm D2 [KO:K11096]
            4327991  small nuclear ribonucleoprotein SmD3b [KO:K11088]
            4332206  small nuclear ribonucleoprotein SmD3b [KO:K11088]
            4328158  small nuclear ribonucleoprotein E [KO:K11097]
            4344666  small nuclear ribonucleoprotein E [KO:K11097]
            4328484  probable small nuclear ribonucleoprotein F [KO:K11098]
            4351052  probable small nuclear ribonucleoprotein F [KO:K11098]
            4333092  probable small nuclear ribonucleoprotein G [KO:K11099]
            4343870  probable small nuclear ribonucleoprotein G [KO:K11099]
            4347985  U1 small nuclear ribonucleoprotein 70 kDa [KO:K11093]
            4337846  U1 small nuclear ribonucleoprotein A [KO:K11091]
            4328958  U1 small nuclear ribonucleoprotein C-1 [KO:K11095]
            4327802  pre-mRNA-processing protein 40A isoform X1 [KO:K12821]
            4345578  RNA-binding protein 25 isoform X1 [KO:K12822]
            4326190  DEAD-box ATP-dependent RNA helicase 40 isoform X1 [KO:K12823] [EC:3.6.4.13]
            4351155  DEAD-box ATP-dependent RNA helicase 40 isoform X1 [KO:K12823] [EC:3.6.4.13]
            4327645  DEAD-box ATP-dependent RNA helicase 14 isoform X2 [KO:K12823] [EC:3.6.4.13]
            9271802  DEAD-box ATP-dependent RNA helicase 30 [KO:K12823] [EC:3.6.4.13]
            9268869  DEAD-box ATP-dependent RNA helicase 20 [KO:K12823] [EC:3.6.4.13]
            4348939  pre-mRNA-processing protein 40C isoform X1 [KO:K12824]
            4324412  transcription initiation factor TFIID subunit 15b isoform X1 [KO:K13098]
            4328823  U2 small nuclear ribonucleoprotein A' [KO:K11092]
            4332557  U2 small nuclear ribonucleoprotein B'' isoform X1 [KO:K11094]
            4328860  probable splicing factor 3A subunit 1 [KO:K12825]
            4332334  splicing factor 3A subunit 2 [KO:K12826]
            4333915  splicing factor 3A subunit 3 [KO:K12827]
            4328284  splicing factor 3B subunit 1 isoform X1 [KO:K12828]
            9272713  LOW QUALITY PROTEIN: splicing factor 3B subunit 1 [KO:K12828]
            4331222  splicing factor 3B subunit 2 [KO:K12829]
            4328237  splicing factor 3B subunit 3 [KO:K12830]
            4342674  splicing factor 3B subunit 3 isoform X1 [KO:K12830]
            4348798  splicing factor 3B subunit 4 [KO:K12831]
            4338860  splicing factor 3B subunit 4 [KO:K12831]
            4325082  splicing factor 3B subunit 4 isoform X1 [KO:K12831]
            4345702  uncharacterized protein At4g14342 [KO:K12832]
            9272211  uncharacterized protein At4g14342 [KO:K12832]
            4334543  splicing factor 3B subunit 6-like protein [KO:K12833]
            4337303  PHD finger-like domain-containing protein 5B [KO:K12834]
            4338563  PHD finger-like domain-containing protein 5B [KO:K12834]
            107277487  PHD finger-like domain-containing protein 5B [KO:K12834]
            4332617  DEAD-box ATP-dependent RNA helicase 24 [KO:K12835] [EC:3.6.4.13]
            4339621  splicing factor U2af small subunit B [KO:K12836]
            9268567  splicing factor U2af small subunit A [KO:K12836]
            4350981  splicing factor U2af large subunit A [KO:K12837]
            4325413  uncharacterized protein LOC4325413 [KO:K12837]
            4331556  splicing factor U2af large subunit B-like isoform X1 [KO:K12837]
            4351124  splicing factor U2af large subunit B isoform X2 [KO:K12837]
            4344474  survival of motor neuron-related-splicing factor 30 isoform X1 [KO:K12839]
            4323935  DNA-damage-repair/toleration protein DRT111, chloroplastic [KO:K12840]
            4328504  U2 snRNP-associated SURP motif-containing protein isoform X1 [KO:K12842]
            4344686  sm-like protein LSM2 [KO:K12621]
            4325074  sm-like protein LSM3A [KO:K12622]
            4326227  probable U6 snRNA-associated Sm-like protein LSm4 [KO:K12623]
            4338670  sm-like protein LSM5 [KO:K12624]
            4329449  U6 snRNA-associated Sm-like protein LSm6 [KO:K12625]
            4335668  U6 snRNA-associated Sm-like protein LSm6 [KO:K12625]
            4344803  sm-like protein LSM7 [KO:K12626]
            4339810  sm-like protein LSM8 [KO:K12627]
            4346506  U4/U6 small nuclear ribonucleoprotein Prp3 isoform X1 [KO:K12843]
            4332861  U4/U6 small nuclear ribonucleoprotein PRP4-like protein [KO:K12662]
            107275966  U4/U6 small nuclear ribonucleoprotein PRP4-like protein [KO:K12662]
            4334542  peptidyl-prolyl cis-trans isomerase CYP22 [KO:K09567] [EC:5.2.1.8]
            4336619  U4/U6 small nuclear ribonucleoprotein Prp31 isoform X1 [KO:K12844]
            4342372  U4/U6 small nuclear ribonucleoprotein Prp31 [KO:K12844]
            4330613  U4/U6 small nuclear ribonucleoprotein Prp31 [KO:K12844]
            4332209  NHP2-like protein 1 [KO:K12845]
            4348007  13 kDa ribonucleoprotein-associated protein [KO:K12845]
            4329300  U4/U6.U5 small nuclear ribonucleoprotein 27 kDa protein [KO:K12846]
            4347019  U4/U6.U5 tri-snRNP-associated protein 2 [KO:K12847]
            4329455  SART-1 family protein DOT2 isoform X1 [KO:K11984]
            4334674  zinc finger matrin-type protein 2 [KO:K12848]
            4346374  pre-mRNA-splicing factor 38 [KO:K12849]
            4337972  pre-mRNA-splicing factor 38B [KO:K12850]
            107281411  pre-mRNA-splicing factor 38B-like [KO:K12850]
            4341492  116 kDa U5 small nuclear ribonucleoprotein component [KO:K12852]
            4328024  DExH-box ATP-dependent RNA helicase DExH12 [KO:K12854] [EC:3.6.4.13]
            107276130  LOW QUALITY PROTEIN: DExH-box ATP-dependent RNA helicase DExH12-like [KO:K12854] [EC:3.6.4.13]
            4349020  protein STABILIZED1 [KO:K12855]
            9270118  LOW QUALITY PROTEIN: protein STABILIZED1 [KO:K12855]
            4337900  pre-mRNA-processing-splicing factor 8 [KO:K12856]
            4340248  pre-mRNA-processing-splicing factor 8 [KO:K12856]
            4341706  U5 small nuclear ribonucleoprotein 40 kDa protein [KO:K12857]
            4333866  DEAD-box ATP-dependent RNA helicase 21 [KO:K12858] [EC:3.6.4.13]
            4348949  thioredoxin-like protein YLS8 [KO:K12859]
            9268087  thioredoxin-like protein YLS8 [KO:K12859]
            4348844  pre-mRNA-processing factor 19 [KO:K10599] [EC:2.3.2.27]
            4335542  cell division cycle 5-like protein [KO:K12860]
            9272163  pre-mRNA-splicing factor SPF27 homolog [KO:K12861]
            4332781  protein pleiotropic regulatory locus 1 [KO:K12862]
            4339866  protein CWC15 homolog [KO:K12863]
            4331250  beta-catenin-like protein 1 [KO:K12864]
            4339012  probable mediator of RNA polymerase II transcription subunit 37c [KO:K03283]
            4351208  heat shock cognate 70 kDa protein 2 [KO:K03283]
            4351875  stromal 70 kDa heat shock-related protein, chloroplastic [KO:K03283]
            4327388  probable mediator of RNA polymerase II transcription subunit 37c [KO:K03283]
            4332413  heat shock cognate 70 kDa protein 2 [KO:K03283]
            4332420  heat shock cognate 70 kDa protein [KO:K03283]
            4334598  heat shock cognate 70 kDa protein 2 [KO:K03283]
            4332416  heat shock cognate 70 kDa protein [KO:K03283]
            9271426  heat shock cognate 70 kDa protein [KO:K03283]
            4349971  heat shock cognate 70 kDa protein [KO:K03283]
            4349972  heat shock cognate 70 kDa protein [KO:K03283]
            4338354  stromal 70 kDa heat shock-related protein, chloroplastic [KO:K03283]
            107275844  heat shock cognate 70 kDa protein-like [KO:K03283]
            107279546  heat shock cognate 70 kDa protein-like [KO:K03283]
            4324332  uncharacterized protein LOC4324332 [KO:K12865]
            4330796  SNW/SKI-interacting protein [KO:K06063]
            107275655  SNW/SKI-interacting protein-like [KO:K06063]
            4344088  pre-mRNA-splicing factor SYF1 [KO:K12867]
            4342038  pre-mRNA-splicing factor syf2 [KO:K12868]
            4338298  crooked neck-like protein 1 isoform X1 [KO:K12869]
            4348330  crooked neck-like protein 1 [KO:K12869]
            4329902  pre-mRNA-splicing factor ISY1 homolog [KO:K12870]
            4346316  peptidyl-prolyl cis-trans isomerase CYP18-2 [KO:K12733] [EC:5.2.1.8]
            4342149  coiled-coil domain-containing protein 12 [KO:K12871]
            4340263  zinc finger CCCH domain-containing protein 40 [KO:K12872]
            4342926  zinc finger CCCH domain-containing protein 49 [KO:K12872]
            4338942  protein BUD31 homolog 2 [KO:K12873]
            4337198  protein BUD31 homolog 1 [KO:K12873]
            4324760  protein BUD31 homolog 1 [KO:K12873]
            4351510  protein BUD31 homolog 3 [KO:K12873]
            4332999  intron-binding protein aquarius [KO:K12874]
            4343967  protein starmaker isoform X1 [KO:K12875]
            4332988  apoptotic chromatin condensation inducer in the nucleus [KO:K12875]
            4326580  DEAD-box ATP-dependent RNA helicase 2 [KO:K13025] [EC:3.6.4.13]
            4333273  DEAD-box ATP-dependent RNA helicase 34 [KO:K13025] [EC:3.6.4.13]
            4337757  RNA-binding protein 8A [KO:K12876]
            4334528  RNA-binding protein 8A [KO:K12876]
            4351998  protein mago nashi homolog [KO:K12877]
            4344462  protein mago nashi homolog isoform X2 [KO:K12877]
            4331353  THO complex subunit 1 [KO:K12878]
            4324336  THO complex subunit 2 isoform X1 [KO:K12879]
            4346657  THO complex subunit 3 [KO:K12880]
            4332426  THO complex subunit 4A [KO:K12881]
            4349526  THO complex subunit 4A isoform X1 [KO:K12881]
            4342793  THO complex subunit 4A isoform X1 [KO:K12881]
            4340675  THO complex subunit 4D [KO:K12881]
            4345621  THO complex subunit 4D isoform X1 [KO:K12881]
            4351236  THO complex subunit 4A isoform X1 [KO:K12881]
            4332822  LOW QUALITY PROTEIN: nuclear cap-binding protein subunit 1-like [KO:K12882]
            4329963  nuclear cap-binding protein subunit 2 [KO:K12883]
            4328758  glycine-rich RNA-binding protein 3, mitochondrial [KO:K12741]
            4343831  glycine-rich RNA-binding protein 2, mitochondrial [KO:K12741]
            4352279  glycine-rich RNA-binding protein blt801 [KO:K12741]
            4348309  glycine-rich RNA-binding protein 10 [KO:K12741]
            4337147  UBP1-associated protein 2B [KO:K12741]
            4326641  UBP1-associated protein 2C [KO:K12741]
            4329903  UBP1-associated protein 2B [KO:K12741]
            4326212  UBP1-associated protein 2A [KO:K12741]
            4345254  heterogeneous nuclear ribonucleoprotein 1 [KO:K12741]
            4341330  heterogeneous nuclear ribonucleoprotein 1 [KO:K12741]
            4345910  heterogeneous nuclear ribonucleoprotein A0 [KO:K12741]
            4344256  serine/arginine-rich-splicing factor SR34 isoform X1 [KO:K12890]
            4332806  serine/arginine-rich-splicing factor SR34 [KO:K12890]
            4338552  serine/arginine-rich-splicing factor SR34 [KO:K12890]
            4345884  serine/arginine-rich splicing factor SC35 [KO:K12891]
            4343955  serine/arginine-rich splicing factor SC35 isoform X1 [KO:K12891]
            4333005  serine/arginine-rich splicing factor SC35 isoform X1 [KO:K12891]
            4328133  serine/arginine-rich splicing factor RS41 isoform X1 [KO:K12893]
            4334964  serine/arginine-rich splicing factor RS31 isoform X1 [KO:K12893]
            4324080  serine/arginine-rich splicing factor RS2Z32 [KO:K12896]
            4337644  serine/arginine-rich splicing factor RS2Z33 [KO:K12896]
            4332476  serine/arginine-rich splicing factor RS2Z32 [KO:K12896]
            4337897  serine/arginine-rich splicing factor RS2Z32 [KO:K12896]
            4329951  serine/arginine-rich splicing factor RSZ23 isoform X2 [KO:K12896]
            4330968  serine/arginine-rich splicing factor RSZ21 isoform X1 [KO:K12896]
            4340353  serine/arginine-rich splicing factor RSZ21A [KO:K12896]
            4345455  serine/arginine-rich splicing factor SR45a [KO:K12897]
            4342102  serine/arginine-rich splicing factor SR45a [KO:K12897]
            4332903  serine/arginine-rich SC35-like splicing factor SCL28 [KO:K12900]
            4344009  serine/arginine-rich SC35-like splicing factor SCL33 isoform X1 [KO:K12900]
            9268085  serine/arginine-rich SC35-like splicing factor SCL33 isoform X1 [KO:K12900]
            4352590  serine/arginine-rich SC35-like splicing factor SCL30 [KO:K12900]
            4328900  serine/arginine-rich SC35-like splicing factor SCL30 [KO:K12900]
            4351215  serine/arginine-rich SC35-like splicing factor SCL30A isoform X1 [KO:K12900]
            107275752  serine/arginine-rich SC35-like splicing factor SCL30 [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
///
