KEGG   PATHWAY: xtr03040
Entry
xtr03040                    Pathway                                
Name
Spliceosome - Xenopus tropicalis (tropical clawed frog)
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
xtr03040  Spliceosome
xtr03040

Other DBs
GO: 0005681
Organism
Xenopus tropicalis (tropical clawed frog) [GN:xtr]
Gene
116408489  U1 spliceosomal RNA [KO:K14276]
116408531  U1 spliceosomal RNA [KO:K14276]
116408528  U1 spliceosomal RNA [KO:K14276]
116407300  U2 spliceosomal RNA [KO:K14277]
116407389  U2 spliceosomal RNA [KO:K14277]
116407296  U2 spliceosomal RNA [KO:K14277]
116407269  U2 spliceosomal RNA [KO:K14277]
116407084  U2 spliceosomal RNA [KO:K14277]
116407298  U2 spliceosomal RNA [KO:K14277]
116407270  U2 spliceosomal RNA [KO:K14277]
116407286  U2 spliceosomal RNA [KO:K14277]
116407246  U2 spliceosomal RNA [KO:K14277]
116407363  U2 spliceosomal RNA [KO:K14277]
116407289  U2 spliceosomal RNA [KO:K14277]
116407285  U2 spliceosomal RNA [KO:K14277]
116407247  U2 spliceosomal RNA [KO:K14277]
116407275  U2 spliceosomal RNA [KO:K14277]
116407248  U2 spliceosomal RNA [KO:K14277]
116407341  U2 spliceosomal RNA [KO:K14277]
116408547  U4 spliceosomal RNA [KO:K14278]
116409266  U4 spliceosomal RNA [KO:K14278]
116409267  U4 spliceosomal RNA [KO:K14278]
116409265  U4 spliceosomal RNA [KO:K14278]
116409291  U4 spliceosomal RNA [KO:K14278]
116409278  U4 spliceosomal RNA [KO:K14278]
116409286  U4 spliceosomal RNA [KO:K14278]
116410569  U5 spliceosomal RNA [KO:K14279]
116408095  U6 spliceosomal RNA [KO:K14280]
116408094  U6 spliceosomal RNA [KO:K14280]
100335113  RNA, U6 small nuclear [KO:K14280]
116409348  U6 spliceosomal RNA [KO:K14280]
100145307  ddx46; probable ATP-dependent RNA helicase DDX46 [KO:K12811] [EC:5.6.2.7]
394669  ddx39b; spliceosome RNA helicase DDX39B [KO:K12812] [EC:5.6.2.7]
100127179  dhx16; putative pre-mRNA-splicing factor ATP-dependent RNA helicase DHX16 [KO:K12813] [EC:5.6.2.6]
734019  dhx38; pre-mRNA-splicing factor ATP-dependent RNA helicase PRP16 [KO:K12815] [EC:5.6.2.6]
496947  cdc40; pre-mRNA-processing factor 17 [KO:K12816]
100170196  prpf18; pre-mRNA-splicing factor 18 [KO:K12817]
733563  dhx8; ATP-dependent RNA helicase DHX8 isoform X1 [KO:K12818] [EC:5.6.2.6]
733806  slu7; pre-mRNA-splicing factor SLU7 [KO:K12819]
100216120  dhx15; pre-mRNA-splicing factor ATP-dependent RNA helicase DHX15 [KO:K12820] [EC:5.6.2.6]
407857  snrpb; small nuclear ribonucleoprotein-associated proteins B and B' [KO:K11086]
447999  snrpd1; small nuclear ribonucleoprotein Sm D1 [KO:K11087]
448710  snrpd2; small nuclear ribonucleoprotein Sm D2 [KO:K11096]
549847  snrpd3; small nuclear ribonucleoprotein Sm D3 [KO:K11088]
448738  snrpe; small nuclear ribonucleoprotein E [KO:K11097]
448659  snrpf; small nuclear ribonucleoprotein F [KO:K11098]
100125174  snrpg; small nuclear ribonucleoprotein G [KO:K11099]
493488  snrnp70; U1 small nuclear ribonucleoprotein 70 kDa [KO:K11093]
549538  snrpa; U1 small nuclear ribonucleoprotein A [KO:K11091]
549352  snrpc; U1 small nuclear ribonucleoprotein C [KO:K11095]
100170464  prpf40a; pre-mRNA-processing factor 40 homolog A isoform 1 [KO:K12821]
100493450  prpf40b; pre-mRNA-processing factor 40 homolog B isoform X1 [KO:K12821]
407928  rbm25; RNA-binding protein 25 [KO:K12822]
394837  ddx5; probable ATP-dependent RNA helicase DDX5 [KO:K12823] [EC:5.6.2.7]
100498472  tcerg1; transcription elongation regulator 1 isoform X1 [KO:K12824]
100038234  fus; RNA-binding protein FUS [KO:K13098]
100486145  snrpa1; U2 small nuclear ribonucleoprotein A' [KO:K11092]
496533  snrpb2; U2 small nuclear ribonucleoprotein B'' [KO:K11094]
734097  sf3a1; splicing factor 3A subunit 1 isoform X2 [KO:K12825]
448002  sf3a2; splicing factor 3A subunit 2 [KO:K12826]
549872  sf3a3; splicing factor 3A subunit 3 [KO:K12827]
100127558  sf3b1; splicing factor 3B subunit 1 [KO:K12828]
100170589  sf3b2; splicing factor 3B subunit 2 [KO:K12829]
100101755  sf3b3; splicing factor 3B subunit 3 [KO:K12830]
394721  sf3b4; splicing factor 3B subunit 4 [KO:K12831]
549195  sf3b5; splicing factor 3B subunit 5 [KO:K12832]
550003  sf3b6; splicing factor 3B subunit 6 [KO:K12833]
100170460  phf5a; PHD finger-like domain-containing protein 5A [KO:K12834]
100135374  ddx42; ATP-dependent RNA helicase DDX42 [KO:K12835] [EC:5.6.2.7]
733934  u2af1; U2 small nuclear RNA auxiliary factor 1 [KO:K12836]
549752  u2af2; splicing factor U2AF 65 kDa subunit isoform 2 [KO:K12837]
100145091  puf60; poly(U)-binding-splicing factor PUF60 [KO:K12838]
448621  smndc1; survival of motor neuron-related-splicing factor 30 [KO:K12839]
448396  rbm17; splicing factor 45 [KO:K12840]
496512  cherp; calcium homeostasis endoplasmic reticulum protein [KO:K12841]
100216247  u2surp; U2 snRNP-associated SURP motif-containing protein [KO:K12842]
496684  rp9; retinitis pigmentosa 9 protein [KO:K19604]
549156  lsm2; U6 snRNA-associated Sm-like protein LSm2 [KO:K12621]
100125161  lsm3; U6 snRNA-associated Sm-like protein LSm3 [KO:K12622]
395002  lsm4; U6 snRNA-associated Sm-like protein LSm4 [KO:K12623]
100216118  lsm5; U6 snRNA-associated Sm-like protein LSm5 [KO:K12624]
779701  lsm6; U6 snRNA-associated Sm-like protein LSm6 [KO:K12625]
100127774  lsm7; U6 snRNA-associated Sm-like protein LSm7 [KO:K12626]
100486227  lsm8; LSM8 homolog, U6 small nuclear RNA associated [KO:K12627]
447950  prpf3; U4/U6 small nuclear ribonucleoprotein Prp3 [KO:K12843]
394655  prpf4; U4/U6 small nuclear ribonucleoprotein Prp4 [KO:K12662]
394997  ppih; peptidyl-prolyl cis-trans isomerase H [KO:K09567] [EC:5.2.1.8]
407890  prpf31; U4/U6 small nuclear ribonucleoprotein Prp31 [KO:K12844]
394590  snu13; NHP2-like protein 1 [KO:K12845]
448731  snrnp27; U4/U6.U5 small nuclear ribonucleoprotein 27 kDa protein [KO:K12846]
100495792  usp39; U4/U6.U5 tri-snRNP-associated protein 2 [KO:K12847]
100485596  sart1; U4/U6.U5 tri-snRNP-associated protein 1 [KO:K11984]
448699  zmat2; zinc finger matrin-type protein 2 [KO:K12848]
549894  prpf38a; pre-mRNA-splicing factor 38A [KO:K12849]
100170167  prpf38b; pre-mRNA-splicing factor 38B [KO:K12850]
594937  eftud2; 116 kDa U5 small nuclear ribonucleoprotein component [KO:K12852]
100145098  snrnp200; U5 small nuclear ribonucleoprotein 200 kDa helicase [KO:K12854] [EC:5.6.2.6]
595030  prpf6; pre-mRNA-processing factor 6 [KO:K12855]
100380187  prpf8; pre-mRNA-processing-splicing factor 8 [KO:K12856]
594941  snrnp40; U5 small nuclear ribonucleoprotein 40 kDa protein [KO:K12857]
549967  ddx23; probable ATP-dependent RNA helicase DDX23 [KO:K12858] [EC:5.6.2.7]
549400  txnl4a; thioredoxin-like protein 4A [KO:K12859]
448017  prpf19; pre-mRNA-processing factor 19 [KO:K10599] [EC:2.3.2.27]
493564  cdc5l; cell division cycle 5-like protein [KO:K12860]
394520  bcas2; pre-mRNA-splicing factor SPF27 [KO:K12861]
394977  plrg1; pleiotropic regulator 1 [KO:K12862]
779647  cwc15; protein CWC15 homolog [KO:K12863]
394960  ctnnbl1; beta-catenin-like protein 1 [KO:K12864]
100037899  hsp70; heat shock 70kDa protein [KO:K03283]
779883  hspa1l; heat shock protein family A (Hsp70) member 1 like [KO:K03283]
100496320  hspa8; heat shock cognate 71 kDa protein [KO:K03283]
100485441  hspa1b; LOW QUALITY PROTEIN: heat shock 70 kDa protein [KO:K03283]
100488052  hspa1a; heat shock cognate 71 kDa protein [KO:K03283]
100216040  pqbp1; uncharacterized protein LOC100216040 [KO:K12865]
448171  wbp11; WW domain-binding protein 11 [KO:K12866]
549899  snw1; SNW domain-containing protein 1 [KO:K06063]
100216162  xab2; pre-mRNA-splicing factor SYF1 [KO:K12867]
496706  syf2; pre-mRNA-splicing factor syf2 [KO:K12868]
549649  crnkl1; crooked neck-like protein 1 [KO:K12869]
394618  isy1; ISY1 splicing factor homolog [KO:K12870]
448493  ppil1; peptidyl-prolyl cis-trans isomerase-like 1 [KO:K12733] [EC:5.2.1.8]
100495035  ppie; peptidyl-prolyl cis-trans isomerase E isoform X2 [KO:K09564] [EC:5.2.1.8]
100125177  ccdc12; coiled-coil domain-containing protein 12 [KO:K12871]
394713  rbm22; pre-mRNA-splicing factor RBM22 [KO:K12872]
549113  bud31; protein BUD31 homolog [KO:K12873]
100498148  aqr; RNA helicase aquarius [KO:K12874]
407918  acin1; apoptotic chromatin condensation inducer in the nucleus [KO:K12875]
100135173  eif4a3.1; eukaryotic initiation factor 4A-III [KO:K13025] [EC:5.6.2.7]
733972  rbm8a; RNA-binding protein 8A [KO:K12876]
100038130  magoh; protein mago nashi homolog [KO:K12877]
733546  thoc1; THO complex subunit 1 [KO:K12878]
100145575  thoc2; THO complex subunit 2 [KO:K12879]
100490375  thoc3; THO complex subunit 3 [KO:K12880]
549781  alyref; THO complex subunit 4 [KO:K12881]
448484  ncbp1; nuclear cap-binding protein subunit 1 [KO:K12882]
448671  ncbp2; nuclear cap-binding protein subunit 2 [KO:K12883]
100144993  hnrnpa3; heterogeneous nuclear ribonucleoprotein A3 [KO:K12741]
496507  hnrnpa1; heterogeneous nuclear ribonucleoprotein A1 [KO:K12741]
448664  hnrnpc; heterogeneous nuclear ribonucleoproteins C1/C2 [KO:K12884]
100135403  rbmx; RNA-binding motif protein, X chromosome [KO:K12885]
394952  hnrnpk; heterogeneous nuclear ribonucleoprotein K [KO:K12886]
100489127  hnrnpm; heterogeneous nuclear ribonucleoprotein M isoform X4 [KO:K12887]
100038222  hnrnpu; heterogeneous nuclear ribonucleoprotein U [KO:K12888]
448766  srsf1; serine/arginine-rich splicing factor 1 [KO:K12890]
394953  srsf2; serine/arginine-rich splicing factor 2 [KO:K12891]
448605  srsf3; serine/arginine-rich splicing factor 3 [KO:K12892]
448003  srsf5; serine/arginine-rich splicing factor 5 [KO:K12893]
448104  srsf5a; serine/arginine-rich splicing factor 5 alpha [KO:K12893]
407954  srsf6; arginine/serine-rich splicing factor 4 isoform 1 [KO:K12893]
100038227  srsf4; serine/arginine-rich splicing factor 4 isoform X1 [KO:K12893]
493215  srsf7; serine/arginine-rich splicing factor 7 [KO:K12896]
448015  srsf9; serine/arginine-rich splicing factor 9 [KO:K21123]
448073  tra2a; transformer-2 protein homolog alpha [KO:K12897]
448667  tra2b; transformer-2 protein homolog beta [KO:K12897]
496509  srsf10; serine/arginine-rich splicing factor 10 [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   
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