KEGG   PATHWAY: osa03040
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
osa03040

Other DBs
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
  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
  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
  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
  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   
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