KEGG   PATHWAY: ko03040
Entry
ko03040                     Pathway                                
Name
Spliceosome
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
ko03040  Spliceosome
ko03040

Other DBs
GO: 0005681
PDB: 5O9Z 5Z56 6FF7 8I0W
Orthology
K03283  HSPA1_6_8; heat shock 70kDa protein 1/6/8
K06063  SNW1, SKIIP, SKIP; SNW domain-containing protein 1
K09564  PPIE; peptidyl-prolyl isomerase E (cyclophilin E) [EC:5.2.1.8]
K09567  PPIH, CYPH; peptidyl-prolyl isomerase H (cyclophilin H) [EC:5.2.1.8]
K10599  PRPF19, PRP19; pre-mRNA-processing factor 19 [EC:2.3.2.27]
K11086  SNRPB, SMB; small nuclear ribonucleoprotein B and B'
K11087  SNRPD1, SMD1; small nuclear ribonucleoprotein D1
K11088  SNRPD3, SMD3; small nuclear ribonucleoprotein D3
K11091  SNRPA; U1 small nuclear ribonucleoprotein A
K11092  SNRPA1; U2 small nuclear ribonucleoprotein A'
K11093  SNRP70; U1 small nuclear ribonucleoprotein 70kDa
K11094  SNRPB2; U2 small nuclear ribonucleoprotein B''
K11095  SNRPC; U1 small nuclear ribonucleoprotein C
K11096  SNRPD2, SMD2; small nuclear ribonucleoprotein D2
K11097  SNRPE, SME; small nuclear ribonucleoprotein E
K11098  SNRPF, SMF; small nuclear ribonucleoprotein F
K11099  SNRPG, SMG; small nuclear ribonucleoprotein G
K11984  SART1, HAF, SNU66; U4/U6.U5 tri-snRNP-associated protein 1
K12621  LSM2; U6 snRNA-associated Sm-like protein LSm2
K12622  LSM3; U6 snRNA-associated Sm-like protein LSm3
K12623  LSM4; U6 snRNA-associated Sm-like protein LSm4
K12624  LSM5; U6 snRNA-associated Sm-like protein LSm5
K12625  LSM6; U6 snRNA-associated Sm-like protein LSm6
K12626  LSM7; U6 snRNA-associated Sm-like protein LSm7
K12627  LSM8; U6 snRNA-associated Sm-like protein LSm8
K12662  PRPF4, PRP4; U4/U6 small nuclear ribonucleoprotein PRP4
K12733  PPIL1; peptidyl-prolyl cis-trans isomerase-like 1 [EC:5.2.1.8]
K12741  HNRNPA1_3; heterogeneous nuclear ribonucleoprotein A1/A3
K12811  DDX46, PRP5; ATP-dependent RNA helicase DDX46/PRP5 [EC:5.6.2.7]
K12812  DDX39B, UAP56, SUB2; ATP-dependent RNA helicase UAP56/SUB2 [EC:5.6.2.7]
K12813  DHX16; pre-mRNA-splicing factor ATP-dependent RNA helicase DHX16 [EC:5.6.2.6]
K12814  PRP2; pre-mRNA-splicing factor ATP-dependent RNA helicase-like protein PRP2 [EC:5.6.2.6]
K12815  DHX38, PRP16; pre-mRNA-splicing factor ATP-dependent RNA helicase DHX38/PRP16 [EC:5.6.2.6]
K12816  CDC40, PRP17; pre-mRNA-processing factor 17
K12817  PRPF18, PRP18; pre-mRNA-splicing factor 18
K12818  DHX8, PRP22; ATP-dependent RNA helicase DHX8/PRP22 [EC:5.6.2.6]
K12819  SLU7; pre-mRNA-processing factor SLU7
K12820  DHX15, PRP43; pre-mRNA-splicing factor ATP-dependent RNA helicase DHX15/PRP43 [EC:5.6.2.6]
K12821  PRPF40, PRP40; pre-mRNA-processing factor 40
K12822  RBM25, S164; RNA-binding protein 25
K12823  DDX5, DBP2; ATP-dependent RNA helicase DDX5/DBP2 [EC:5.6.2.7]
K12824  TCERG1, CA150; transcription elongation regulator 1
K12825  SF3A1, SAP114; splicing factor 3A subunit 1
K12826  SF3A2, SAP62; splicing factor 3A subunit 2
K12827  SF3A3, SAP61, PRP9; splicing factor 3A subunit 3
K12828  SF3B1, SAP155; splicing factor 3B subunit 1
K12829  SF3B2, SAP145, CUS1; splicing factor 3B subunit 2
K12830  SF3B3, SAP130, RSE1; splicing factor 3B subunit 3
K12831  SF3B4, SAP49; splicing factor 3B subunit 4
K12832  SF3B5, SF3B10; splicing factor 3B subunit 5
K12833  SF3B14; pre-mRNA branch site protein p14
K12834  PHF5A; PHD finger-like domain-containing protein 5A
K12835  DDX42, SF3B125; ATP-dependent RNA helicase DDX42 [EC:5.6.2.7]
K12836  U2AF1; splicing factor U2AF 35 kDa subunit
K12837  U2AF2; splicing factor U2AF 65 kDa subunit
K12838  PUF60; poly(U)-binding-splicing factor PUF60
K12839  SMNDC1, SPF30; survival of motor neuron-related-splicing factor 30
K12840  RBM17, SPF45; splicing factor 45
K12841  CHERP; calcium homeostasis endoplasmic reticulum protein
K12842  SR140; U2-associated protein SR140
K12843  PRPF3, PRP3; U4/U6 small nuclear ribonucleoprotein PRP3
K12844  PRPF31; U4/U6 small nuclear ribonucleoprotein PRP31
K12845  SNU13, NHP2L; U4/U6 small nuclear ribonucleoprotein SNU13
K12846  SNRNP27; U4/U6.U5 tri-snRNP-associated protein 3
K12847  USP39, SAD1; U4/U6.U5 tri-snRNP-associated protein 2
K12848  SNU23; U4/U6.U5 tri-snRNP component SNU23
K12849  PRPF38A; pre-mRNA-splicing factor 38A
K12850  PRPF38B; pre-mRNA-splicing factor 38B
K12851  PRP38; pre-mRNA-splicing factor 38
K12852  EFTUD2; 116 kDa U5 small nuclear ribonucleoprotein component
K12853  SNU114; 114 kDa U5 small nuclear ribonucleoprotein component
K12854  SNRNP200, BRR2; pre-mRNA-splicing helicase BRR2 [EC:5.6.2.6]
K12855  PRPF6, PRP6; pre-mRNA-processing factor 6
K12856  PRPF8, PRP8; pre-mRNA-processing factor 8
K12857  SNRNP40, PRP8BP; Prp8 binding protein
K12858  DDX23, PRP28; ATP-dependent RNA helicase DDX23/PRP28 [EC:5.6.2.7]
K12859  TXNL4A, DIB1; U5 snRNP protein, DIM1 family
K12860  CDC5L, CDC5, CEF1; pre-mRNA-splicing factor CDC5/CEF1
K12861  BCAS2; pre-mRNA-splicing factor SPF27
K12862  PLRG1, PRL1, PRP46; pleiotropic regulator 1
K12863  CWC15; protein CWC15
K12864  CTNNBL1; beta-catenin-like protein 1
K12865  PQBP1, NPW38; polyglutamine-binding protein 1
K12866  WBP11, NPWBP; WW domain-binding protein 11
K12867  SYF1, XAB2; pre-mRNA-splicing factor SYF1
K12868  SYF2; pre-mRNA-splicing factor SYF2
K12869  CRN, CRNKL1, CLF1, SYF3; crooked neck
K12870  ISY1; pre-mRNA-splicing factor ISY1
K12871  CCDC12; coiled-coil domain-containing protein 12
K12872  RBM22, SLT11; pre-mRNA-splicing factor RBM22/SLT11
K12873  BUD31, G10; bud site selection protein 31
K12874  AQR; intron-binding protein aquarius
K12875  ACIN1, ACINUS; apoptotic chromatin condensation inducer in the nucleus
K12876  RBM8A, Y14; RNA-binding protein 8A
K12877  MAGOH; protein mago nashi
K12878  THOC1; THO complex subunit 1
K12879  THOC2; THO complex subunit 2
K12880  THOC3; THO complex subunit 3
K12881  THOC4, ALYREF; THO complex subunit 4
K12882  NCBP1, CBP80; nuclear cap-binding protein subunit 1
K12883  NCBP2, CBP20; nuclear cap-binding protein subunit 2
K12884  HNRNPC; heterogeneous nuclear ribonucleoprotein C1/C2
K12885  RBMX, HNRNPG; heterogeneous nuclear ribonucleoprotein G
K12886  HNRNPK; heterogeneous nuclear ribonucleoprotein K
K12887  HNRNPM; heterogeneous nuclear ribonucleoprotein M
K12888  HNRNPU; heterogeneous nuclear ribonucleoprotein U
K12889  PCBP1; poly(rC)-binding protein 1
K12890  SRSF1, SFRS1, ASF, SF2; serine/arginine-rich splicing factor 1
K12891  SRSF2_8, SFRS2A_B; serine/arginine-rich splicing factor 2/8
K12892  SRSF3, SFRS3; serine/arginine-rich splicing factor 3
K12893  SRSF4_5_6, SFRS4_5_6; serine/arginine-rich splicing factor 4/5/6
K12896  SRSF7, SFRS7; serine/arginine-rich splicing factor 7
K12897  TRA2; transformer-2 protein
K12900  SRSF10, FUSIP1; serine/arginine-rich splicing factor 10
K13025  EIF4A3, FAL1; ATP-dependent RNA helicase [EC:5.6.2.7]
K13095  SF1; splicing factor 1
K13098  TLS, FUS; RNA-binding protein FUS
K13101  GPKOW; G patch domain and KOW motifs-containing protein
K13106  BUD13, CWC26; pre-mRNA-splicing factor CWC26
K13107  RBMX2, IST3; RNA-binding motif protein, X-linked 2
K13108  SNIP1; smad nuclear-interacting protein 1
K13174  THOC5; THO complex subunit 5
K13175  THOC6; THO complex subunit 6
K13176  THOC7; THO complex subunit 7
K14276  U1snRNA; U1 spliceosomal RNA
K14277  U2snRNA; U2 spliceosomal RNA
K14278  U4snRNA; U4 spliceosomal RNA
K14279  U5snRNA; U5 spliceosomal RNA
K14280  U6snRNA; U6 spliceosomal RNA
K14323  CASC3, MLN51; protein CASC3
K19604  RP9, PAP-1; retinitis pigmentosa 9 protein
K21123  SRSF9, SFRS9; serine/arginine-rich splicing factor 9
K28450  CWC25; pre-mRNA-splicing factor CWC25
K28512  SPP2; pre-mRNA-splicing factor SPP2
K28527  YJU2; splicing factor YJU2
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
Reference
PMID:28781166
  Authors
Bertram K, Agafonov DE, Dybkov O, Haselbach D, Leelaram MN, Will CL, Urlaub H, Kastner B, Luhrmann R, Stark H
  Title
Cryo-EM Structure of a Pre-catalytic Human Spliceosome Primed for Activation.
  Journal
Cell 170:701-713.e11 (2017)
DOI:10.1016/j.cell.2017.07.011
Reference
PMID:29360106
  Authors
Zhang X, Yan C, Zhan X, Li L, Lei J, Shi Y
  Title
Structure of the human activated spliceosome in three conformational states.
  Journal
Cell Res 28:307-322 (2018)
DOI:10.1038/cr.2018.14
Reference
PMID:29361316
  Authors
Haselbach D, Komarov I, Agafonov DE, Hartmuth K, Graf B, Dybkov O, Urlaub H, Kastner B, Luhrmann R, Stark H
  Title
Structure and Conformational Dynamics of the Human Spliceosomal B(act) Complex.
  Journal
Cell 172:454-464.e11 (2018)
DOI:10.1016/j.cell.2018.01.010
Reference
PMID:39068178
  Authors
Zhan X, Lu Y, Shi Y
  Title
Molecular basis for the activation of human spliceosome.
  Journal
Nat Commun 15:6348 (2024)
DOI:10.1038/s41467-024-50785-0

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