KEGG   PATHWAY: pcao03040
Entry
pcao03040                   Pathway                                
Name
Spliceosome - Phalacrocorax carbo (great cormorant)
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
pcao03040  Spliceosome
pcao03040

Other DBs
GO: 0005681
PDB: 5O9Z 5Z56 6FF7 8I0W
Organism
Phalacrocorax carbo (great cormorant) [GN:pcao]
Gene
104039383  SYF2; pre-mRNA-splicing factor SYF2 [KO:K12868]
104039453  CWC25; pre-mRNA-splicing factor CWC25 homolog [KO:K28450]
104039631  BCAS2; pre-mRNA-splicing factor SPF27 [KO:K12861]
104039784  [KO:K03283]
104039822  PLRG1; pleiotropic regulator 1 [KO:K12862]
104040039  EIF4A3; eukaryotic initiation factor 4A-III [KO:K13025] [EC:5.6.2.7]
104040184  TXNL4A; thioredoxin-like protein 4A [KO:K12859]
104040348  [KO:K12877]
104040437  PHF5A; PHD finger-like domain-containing protein 5A [KO:K12834]
104040553  LSM7; U6 snRNA-associated Sm-like protein LSm7 [KO:K12626]
104040578  ALYREF; THO complex subunit 4 [KO:K12881]
104040703  WBP11; LOW QUALITY PROTEIN: WW domain-binding protein 11 [KO:K12866]
104040733  [KO:K12893]
104040772  LSM8; LSM8 homolog, U6 small nuclear RNA associated [KO:K12627]
104040888  [KO:K12896]
104041107  PRPF40A; pre-mRNA-processing factor 40 homolog A [KO:K12821]
104041406  SNRPD3; small nuclear ribonucleoprotein Sm D3 [KO:K11088]
104041522  RBMX; RNA-binding motif protein, X chromosome isoform X1 [KO:K12885]
104041616  LSM6; U6 snRNA-associated Sm-like protein LSm6 [KO:K12625]
104041644  LSM5; U6 snRNA-associated Sm-like protein LSm5 [KO:K12624]
104041878  NCBP1; nuclear cap-binding protein subunit 1 [KO:K12882]
104041924  BUD31; LOW QUALITY PROTEIN: protein BUD31 homolog [KO:K12873]
104041964  TRA2B; transformer-2 protein homolog beta isoform X1 [KO:K12897]
104042386  NHP2L1; NHP2-like protein 1 [KO:K12845]
104042590  SNRPC; U1 small nuclear ribonucleoprotein C [KO:K11095]
104042719  DDX42; ATP-dependent RNA helicase DDX42 [KO:K12835] [EC:5.6.2.7]
104042926  SNW1; SNW domain-containing protein 1 [KO:K06063]
104043068  DHX15; putative pre-mRNA-splicing factor ATP-dependent RNA helicase DHX15 [KO:K12820] [EC:5.6.2.6]
104043208  [KO:K12883]
104043407  CCDC12; coiled-coil domain-containing protein 12 [KO:K12871]
104043863  THOC5; LOW QUALITY PROTEIN: THO complex subunit 5 homolog [KO:K13174]
104043876  USP39; U4/U6.U5 tri-snRNP-associated protein 2 [KO:K12847]
104044010  PRPF18; pre-mRNA-splicing factor 18 [KO:K12817]
104044123  SNRPD1; small nuclear ribonucleoprotein Sm D1 isoform X1 [KO:K11087]
104044203  [KO:K12836]
104044863  DDX5; probable ATP-dependent RNA helicase DDX5 [KO:K12823] [EC:5.6.2.7]
104045090  PRPF3; U4/U6 small nuclear ribonucleoprotein Prp3 [KO:K12843]
104045457  LSM4; U6 snRNA-associated Sm-like protein LSm4 [KO:K12623]
104045773  SRSF5; serine/arginine-rich splicing factor 5 isoform X1 [KO:K12893]
104045950  EFTUD2; 116 kDa U5 small nuclear ribonucleoprotein component isoform X1 [KO:K12852]
104046094  HNRNPA3; heterogeneous nuclear ribonucleoprotein A3 [KO:K12741]
104046285  DDX46; probable ATP-dependent RNA helicase DDX46 [KO:K12811] [EC:5.6.2.7]
104046334  THOC1; THO complex subunit 1 [KO:K12878]
104046394  SF3B3; splicing factor 3B subunit 3 [KO:K12830]
104046584  THOC2; THO complex subunit 2 [KO:K12879]
104046618  RBM17; splicing factor 45 [KO:K12840]
104046626  [KO:K12822]
104046665  [KO:K12890]
104046730  PRPF38B; pre-mRNA-splicing factor 38B [KO:K12850]
104046755  SF3B1; splicing factor 3B subunit 1 [KO:K12828]
104047141  PRPF19; LOW QUALITY PROTEIN: pre-mRNA-processing factor 19 [KO:K10599] [EC:2.3.2.27]
104047623  AQR; intron-binding protein aquarius [KO:K12874]
104047675  CTNNBL1; beta-catenin-like protein 1 [KO:K12864]
104047676  SMNDC1; LOW QUALITY PROTEIN: survival of motor neuron-related-splicing factor 30 [KO:K12839]
104047813  ZMAT2; zinc finger matrin-type protein 2 [KO:K12848]
104048111  [KO:K12662]
104048190  DHX8; ATP-dependent RNA helicase DHX8 [KO:K12818] [EC:5.6.2.6]
104048286  [KO:K12883]
104048356  HNRNPM; heterogeneous nuclear ribonucleoprotein M isoform X1 [KO:K12887]
104048424  CDC5L; cell division cycle 5-like protein [KO:K12860]
104048554  SF3A1; splicing factor 3A subunit 1 [KO:K12825]
104048563  SLU7; pre-mRNA-splicing factor SLU7 [KO:K12819]
104048590  [KO:K12870]
104048894  THOC3; THO complex subunit 3 [KO:K12880]
104049040  SNRPB2; U2 small nuclear ribonucleoprotein B'' [KO:K11094]
104049292  THOC7; THO complex subunit 7 homolog [KO:K13176]
104049447  PPIE; peptidyl-prolyl cis-trans isomerase E [KO:K09564] [EC:5.2.1.8]
104049528  CWC15; LOW QUALITY PROTEIN: spliceosome-associated protein CWC15 homolog [KO:K12863]
104050025  PPIH; peptidyl-prolyl cis-trans isomerase H [KO:K09567] [EC:5.2.1.8]
104050136  TRA2A; transformer-2 protein homolog alpha [KO:K12897]
104050697  HNRNPK; heterogeneous nuclear ribonucleoprotein K isoform X1 [KO:K12886]
104050748  SNRPF; small nuclear ribonucleoprotein F [KO:K11098]
104050859  CRNKL1; crooked neck-like protein 1 [KO:K12869]
104051106  SRSF3; serine/arginine-rich splicing factor 3 [KO:K12892]
104051189  BUD13; BUD13 homolog [KO:K13106]
104051233  SNRPG; small nuclear ribonucleoprotein G [KO:K11099]
104051279  RBM22; pre-mRNA-splicing factor RBM22 [KO:K12872]
104051289  CASC3; protein CASC3 [KO:K14323]
104051376  RBMX2; RNA-binding motif protein, X-linked 2 [KO:K13107]
104051471  SF3A2; splicing factor 3A subunit 2 [KO:K12826]
104051803  SF3B6; splicing factor 3B subunit 6 [KO:K12833]
104052053  DHX38; pre-mRNA-splicing factor ATP-dependent RNA helicase PRP16 [KO:K12815] [EC:5.6.2.6]
104052066  SRSF4; serine/arginine-rich splicing factor 4 [KO:K12893]
104052131  PUF60; poly(U)-binding-splicing factor PUF60 isoform X1 [KO:K12838]
104052375  TCERG1; transcription elongation regulator 1 [KO:K12824]
104052388  LSM3; U6 snRNA-associated Sm-like protein LSm3 [KO:K12622]
104052475  [KO:K28527]
104052619  PRPF6; pre-mRNA-processing factor 6 [KO:K12855]
104052871  SNRNP40; U5 small nuclear ribonucleoprotein 40 kDa protein [KO:K12857]
104052914  SNRPA1; U2 small nuclear ribonucleoprotein A' [KO:K11092]
104053050  SRSF10; serine/arginine-rich splicing factor 10 [KO:K12900]
104053117  PRPF8; pre-mRNA-processing-splicing factor 8 [KO:K12856]
104053293  CHERP; calcium homeostasis endoplasmic reticulum protein [KO:K12841]
104053370  SNIP1; smad nuclear-interacting protein 1 [KO:K13108]
104053509  PRPF38A; pre-mRNA-splicing factor 38A [KO:K12849]
104053661  U2SURP; U2 snRNP-associated SURP motif-containing protein [KO:K12842]
104053731  HNRNPU; heterogeneous nuclear ribonucleoprotein U [KO:K12888]
104053912  CDC40; pre-mRNA-processing factor 17 [KO:K12816]
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
KO pathway
ko03040   

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