KEGG   PATHWAY: char03040
Entry
char03040                   Pathway                                
Name
Spliceosome - Clupea harengus (Atlantic herring)
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
char03040  Spliceosome
char03040

Other DBs
GO: 0005681
Organism
Clupea harengus (Atlantic herring) [GN:char]
Gene
105888575  sf3b5; splicing factor 3B subunit 5 [KO:K12832]
105888632  [KO:K12882]
105888837  [KO:K12818] [EC:5.6.2.6]
105888846  phf5a; PHD finger-like domain-containing protein 5A [KO:K12834]
105889115  dhx38; pre-mRNA-splicing factor ATP-dependent RNA helicase PRP16 [KO:K12815] [EC:5.6.2.6]
105889118  snrpd3l; small nuclear ribonucleoprotein D3 polypeptide, like [KO:K11088]
105889195  ppil1; peptidyl-prolyl cis-trans isomerase-like 1 [KO:K12733] [EC:5.2.1.8]
105889354  puf60b; poly(U)-binding-splicing factor PUF60-B isoform X3 [KO:K12838]
105889369  [KO:K12842]
105889520  [KO:K12884]
105889660  snw1; SNW domain-containing protein 1 isoform X1 [KO:K06063]
105889755  bcas2; pre-mRNA-splicing factor SPF27 [KO:K12861]
105890007  snrnp27; U4/U6.U5 small nuclear ribonucleoprotein 27 kDa protein [KO:K12846]
105890272  [KO:K12857]
105890375  hnrpkl; heterogeneous nuclear ribonucleoprotein K, like isoform X1 [KO:K12886]
105890784  eftud2; 116 kDa U5 small nuclear ribonucleoprotein component [KO:K12852]
105890989  srsf5a; serine and arginine rich splicing factor 5a [KO:K12893]
105891552  eif4a3; eukaryotic initiation factor 4A-III [KO:K13025] [EC:5.6.2.7]
105891816  rbm8a; RNA-binding protein 8A isoform X1 [KO:K12876]
105891918  [KO:K12823] [EC:5.6.2.7]
105892047  sf3b4; splicing factor 3B subunit 4 [KO:K12831]
105893642  [KO:K12872]
105893649  pqbp1; polyglutamine-binding protein 1 [KO:K12865]
105894322  ctnnbl1; beta-catenin-like protein 1 [KO:K12864]
105894366  usp39; U4/U6.U5 tri-snRNP-associated protein 2 [KO:K12847]
105894375  hnrnpk; heterogeneous nuclear ribonucleoprotein K [KO:K12886]
105894449  sf3b6; splicing factor 3B subunit 6 [KO:K12833]
105894461  hnrnpub; heterogeneous nuclear ribonucleoprotein Ub [KO:K12888]
105894580  snrnp200; U5 small nuclear ribonucleoprotein 200 kDa helicase isoform X1 [KO:K12854] [EC:5.6.2.6]
105894993  u2af2a; U2 small nuclear RNA auxiliary factor 2a isoform X1 [KO:K12837]
105895503  [KO:K12848]
105895517  syf2; pre-mRNA-splicing factor syf2 [KO:K12868]
105895946  snrpe; small nuclear ribonucleoprotein E [KO:K11097]
105896004  hnrnpc; heterogeneous nuclear ribonucleoproteins C1/C2 isoform X1 [KO:K12884]
105896247  ddx46; probable ATP-dependent RNA helicase DDX46 [KO:K12811] [EC:5.6.2.7]
105896343  [KO:K03283]
105896574  aqr; RNA helicase aquarius isoform X1 [KO:K12874]
105896931  rbm25a; RNA-binding protein 25 isoform X1 [KO:K12822]
105897057  ppie; peptidyl-prolyl cis-trans isomerase E [KO:K09564] [EC:5.2.1.8]
105897077  crnkl1; crooked neck-like protein 1 [KO:K12869]
105897347  hspa1b; LOW QUALITY PROTEIN: heat shock 70 kDa protein-like [KO:K03283]
105897413  [KO:K12881]
105897510  lsm8; LSM8 homolog, U6 small nuclear RNA associated [KO:K12627]
105897866  snrpc; U1 small nuclear ribonucleoprotein C isoform X1 [KO:K11095]
105897871  lsm3; snRNA-associated Sm-like protein LSm3 [KO:K12622]
105897907  srsf3b; serine/arginine-rich splicing factor 3b [KO:K12892]
105897946  snrpb; small nuclear ribonucleoprotein-associated proteins B and B' [KO:K11086]
105898210  prpf8; pre-mRNA-processing-splicing factor 8 [KO:K12856]
105898357  rbm17; splicing factor 45 [KO:K12840]
105898430  [KO:K12824]
105898626  snrnp70; U1 small nuclear ribonucleoprotein 70 kDa [KO:K11093]
105898811  [KO:K12866]
105898812  ddx42; ATP-dependent RNA helicase DDX42 [KO:K12835] [EC:5.6.2.7]
105899127  puf60a; poly(U)-binding-splicing factor PUF60a isoform X1 [KO:K12838]
105899334  ccdc12; coiled-coil domain-containing protein 12 [KO:K12871]
105899381  sf3b1; splicing factor 3B subunit 1 isoform X1 [KO:K12828]
105899442  srsf5b; serine and arginine rich splicing factor 5b [KO:K12893]
105899507  [KO:K12890]
105899509  snrpd2; small nuclear ribonucleoprotein Sm D2 [KO:K11096]
105900160  [KO:K12893]
105900217  [KO:K12823] [EC:5.6.2.7]
105900363  [KO:K03283]
105900380  [KO:K03283]
105900589  thoc1; THO complex subunit 1 [KO:K12878]
105900886  lsm4; U6 snRNA-associated Sm-like protein LSm4 [KO:K12623]
105900893  magoh; protein mago nashi homolog [KO:K12877]
105900966  hnrnpm; heterogeneous nuclear ribonucleoprotein M [KO:K12887]
105900975  lsm7; U6 snRNA-associated Sm-like protein LSm7 [KO:K12626]
105900990  [KO:K12841]
105901301  srsf2a; serine and arginine rich splicing factor 2a [KO:K12891]
105901576  snrpb2; U2 small nuclear ribonucleoprotein B'' [KO:K11094]
105901706  prpf31; U4/U6 small nuclear ribonucleoprotein Prp31 [KO:K12844]
105902007  rp9; retinitis pigmentosa 9 protein [KO:K19604]
105902020  u2af2b; U2 small nuclear RNA auxiliary factor 2b isoform X1 [KO:K12837]
105902682  prpf40a; pre-mRNA-processing factor 40 homolog A isoform X1 [KO:K12821]
105902952  sf3b2; splicing factor 3B subunit 2 [KO:K12829]
105903264  snrpg; small nuclear ribonucleoprotein G [KO:K11099]
105903534  lsm6; U6 snRNA-associated Sm-like protein LSm6 [KO:K12625]
105903668  snrpd1; small nuclear ribonucleoprotein Sm D1 [KO:K11087]
105903704  srsf4; serine/arginine-rich splicing factor 4 isoform X1 [KO:K12893]
105903721  sf3a3; LOW QUALITY PROTEIN: splicing factor 3A subunit 3 [KO:K12827]
105903789  hspa8b; heat shock protein family A (Hsp70) member 8b [KO:K03283]
105904036  plrg1; pleiotropic regulator 1 [KO:K12862]
105904505  sf3b3; splicing factor 3B subunit 3 [KO:K12830]
105904611  rbm22; pre-mRNA-splicing factor RBM22 [KO:K12872]
105904710  ddx39b; LOW QUALITY PROTEIN: DEAD (Asp-Glu-Ala-Asp) box polypeptide 39B [KO:K12812] [EC:5.6.2.7]
105904970  [KO:K12881]
105905021  taf15; TATA-binding protein-associated factor 2N isoform X1 [KO:K13098]
105905238  lsm5; U6 snRNA-associated Sm-like protein LSm5 [KO:K12624]
105905715  xab2; pre-mRNA-splicing factor SYF1 [KO:K12867]
105905798  [KO:K12896]
105905815  [KO:K03283]
105906251  thoc3; THO complex subunit 3 [KO:K12880]
105906344  tra2a; transformer-2 protein homolog alpha isoform X3 [KO:K12897]
105906367  hsc70; heat shock cognate 71 kDa protein [KO:K03283]
105906396  dhx16; pre-mRNA-splicing factor ATP-dependent RNA helicase DHX16 [KO:K12813] [EC:5.6.2.6]
105906562  snrpa1; U2 small nuclear ribonucleoprotein A' [KO:K11092]
105907057  sf3a2; splicing factor 3A subunit 2 [KO:K12826]
105907072  prpf38b; pre-mRNA-splicing factor 38B [KO:K12850]
105907114  cwc15; protein CWC15 homolog [KO:K12863]
105907309  rbm25b; RNA-binding protein 25b isoform X1 [KO:K12822]
105907333  cdc40; pre-mRNA-processing factor 17 [KO:K12816]
105907836  snrpa; U1 small nuclear ribonucleoprotein A [KO:K11091]
105908031  hnrnpa3; heterogeneous nuclear ribonucleoprotein A3 [KO:K12741]
105908147  hnrnpa1a; heterogeneous nuclear ribonucleoprotein A1a isoform X1 [KO:K12741]
105908668  tra2b; transformer-2 protein homolog beta isoform X1 [KO:K12897]
105908686  u2af1; splicing factor U2AF 35 kDa subunit isoform X6 [KO:K12836]
105908765  prpf19; pre-mRNA-processing factor 19 [KO:K10599] [EC:2.3.2.27]
105908811  prpf18; pre-mRNA-splicing factor 18 isoform X1 [KO:K12817]
105909468  cdc5l; cell division cycle 5-like protein [KO:K12860]
105909857  isy1; pre-mRNA-splicing factor ISY1 homolog [KO:K12870]
105909895  srsf6b; serine and arginine rich splicing factor 6b [KO:K12893]
105910057  [KO:K11087]
105910272  txnl4a; thioredoxin-like protein 4A [KO:K12859]
105910273  [KO:K12859]
105910579  smndc1; survival of motor neuron-related-splicing factor 30 [KO:K12839]
105910602  sf3a1; splicing factor 3A subunit 1 [KO:K12825]
105910941  [KO:K12837]
105911206  hnrnpua; heterogeneous nuclear ribonucleoprotein U [KO:K12888]
105911358  snrpd3; small nuclear ribonucleoprotein Sm D3 [KO:K11088]
105911887  srsf9; serine/arginine-rich splicing factor 9 [KO:K21123]
105912006  thoc2; THO complex subunit 2 isoform X1 [KO:K12879]
105912443  dhx15; pre-mRNA-splicing factor ATP-dependent RNA helicase DHX15 isoform X1 [KO:K12820] [EC:5.6.2.6]
105912461  rbmx; RNA-binding motif protein, X chromosome isoform X1 [KO:K12885]
105912484  zgc:163098; U2 snRNP-associated SURP motif-containing protein isoform X3 [KO:K12842]
105912746  ddx23; probable ATP-dependent RNA helicase DDX23 [KO:K12858] [EC:5.6.2.7]
105912748  prpf6; pre-mRNA-processing factor 6 [KO:K12855]
105912760  snrpf; small nuclear ribonucleoprotein F [KO:K11098]
105912950  ncbp2; nuclear cap-binding protein subunit 2 [KO:K12883]
105913000  prpf3; U4/U6 small nuclear ribonucleoprotein Prp3 isoform X1 [KO:K12843]
105913085  slu7; pre-mRNA-splicing factor SLU7 isoform X1 [KO:K12819]
105913183  prpf38a; pre-mRNA-splicing factor 38A [KO:K12849]
105913342  sart1; U4/U6.U5 tri-snRNP-associated protein 1 [KO:K11984]
116218026  [KO:K14276]
116218275  [KO:K14280]
116218288  [KO:K14276]
116218716  alyref; THO complex subunit 4 [KO:K12881]
116218802  [KO:K12818] [EC:5.6.2.6]
116218848  [KO:K14279]
116218849  [KO:K14279]
116218850  [KO:K14279]
116218851  [KO:K14279]
116218856  [KO:K14279]
116218857  [KO:K14279]
116219665  [KO:K14277]
116219676  [KO:K14277]
116219683  [KO:K14277]
116219684  [KO:K14277]
116219685  [KO:K14277]
116219755  [KO:K03283]
116220072  [KO:K14278]
116220073  [KO:K14278]
116220074  [KO:K14278]
116220075  [KO:K14278]
116220876  [KO:K14276]
116220877  [KO:K14276]
116220878  [KO:K14276]
116220879  [KO:K14276]
116220880  [KO:K14277]
116220881  [KO:K14277]
116220882  [KO:K14277]
116220883  [KO:K14277]
116220896  [KO:K14276]
116220908  [KO:K14276]
116220913  [KO:K14276]
116221221  [KO:K14277]
116221618  [KO:K14277]
116221622  [KO:K14279]
116221623  [KO:K14279]
116221624  [KO:K14279]
116221954  [KO:K14277]
116221965  [KO:K14276]
116221970  [KO:K14276]
116221971  [KO:K14277]
116221972  [KO:K14277]
116222562  [KO:K14276]
116222576  [KO:K14276]
116222577  [KO:K14276]
116222578  [KO:K14276]
116223015  [KO:K14276]
116223026  [KO:K14277]
116223038  [KO:K14277]
116223039  [KO:K14277]
116223347  [KO:K14277]
116223348  [KO:K14278]
116223952  [KO:K14280]
116223961  [KO:K14280]
116224221  [KO:K14276]
116224222  [KO:K14276]
116224223  [KO:K14276]
116224224  [KO:K14276]
116224226  [KO:K14277]
116224227  [KO:K14277]
116224228  [KO:K14277]
116224229  [KO:K14277]
116224232  [KO:K14278]
116224233  [KO:K14278]
116224234  [KO:K14278]
116224243  [KO:K14278]
116224246  [KO:K14278]
116224249  [KO:K14279]
116224250  [KO:K14279]
116224251  [KO:K14279]
116224252  [KO:K14279]
116224253  [KO:K14279]
116224254  [KO:K14279]
116224255  [KO:K14279]
116224256  [KO:K14279]
116224257  [KO:K14279]
116224258  [KO:K14279]
116224259  [KO:K14279]
116224262  [KO:K14276]
116224494  [KO:K14279]
116224602  [KO:K12848]
116225108  [KO:K14279]
116225132  [KO:K14276]
116225133  [KO:K14277]
122128875  [KO:K12823] [EC:5.6.2.7]
122129070  srsf7a; serine and arginine rich splicing factor 7a isoform X1 [KO:K12896]
122129269  bud31; protein BUD31 homolog [KO:K12873]
122129337  [KO:K14276]
122129347  [KO:K14280]
122129538  prpf4; U4/U6 small nuclear ribonucleoprotein Prp4 [KO:K12662]
122129890  [KO:K12892]
122129903  [KO:K14280]
122130087  [KO:K12845]
122130097  [KO:K14280]
122130243  [KO:K14280]
122130379  [KO:K14280]
122130395  [KO:K14280]
122130451  [KO:K14276]
122130452  [KO:K14279]
122130453  [KO:K14279]
122130454  [KO:K14279]
122130455  [KO:K14276]
122130456  [KO:K14276]
122130457  [KO:K14276]
122130458  [KO:K14279]
122130636  ppih; LOW QUALITY PROTEIN: peptidyl-prolyl cis-trans isomerase H [KO:K09567] [EC:5.2.1.8]
122130643  [KO:K14279]
122130644  [KO:K14280]
122130645  [KO:K14280]
122130646  [KO:K14280]
122130814  smx5; smx5 [KO:K12621]
122131074  [KO:K09567] [EC:5.2.1.8]
122131075  [KO:K14277]
122131233  snrnp40; U5 small nuclear ribonucleoprotein 40 kDa protein [KO:K12857]
122131719  [KO:K12836]
122131896  [KO:K12900]
122132112  [KO:K12845]
122132126  hnrnpa1b; heterogeneous nuclear ribonucleoprotein A1b isoform X1 [KO:K12741]
122132193  [KO:K12897]
122133557  [KO:K14280]
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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