ESE/ESS:	Display All	Do not display those located at splice junctions
Gene status:	All Known	Novel
Transcript status:	All Known	Novel
Number of nucleotides surrounding the exon
Both 5' and 3' introns (max: 1000):
Or
5' intron (max: 1000):
3' intron (max: 1000):

Splice site matrices

• HSF matrices - Calculation is performed using a new matrix. For more information, please contact us
• MaxEnt - Read article by Yeo G and Burge CB. Yeo G and Burge CB. Maximum Entropy Modeling of Short Sequence Motifs with Applications to RNA Splicing Signals. Journal of Computational Biology. March 1, 2004, 11

  Define thresholds for MaxEnt

  5' site
  3' site

• NNSplice
  Reese MG, Eeckman, FH, Kulp, D, Haussler, D, 1997. Improved Splice Site Detection in Genie. J Comp Biol 4(3), 311-23.

  Define thresholds for NNSplice

  5' site
  3' site

Branch point matrices

• Branch Point sequence
  Calculation is performed using a new matrix. For more information, please contact us

Enhancer-only matrices

• ESE Finder matrices for SRp40, SC35, SF2/ASF and SRp55 proteins
  Cartegni L., Wang J., Zhu Z., Zhang M. Q., Krainer A. R.; 2003. ESEfinder: a web resource to identify exonic splicing enhancers, Nucleic Acid Research, 2003, Vol. 31, No.13 3568-3571.

  Define thresholds for ESE Finder

  	HSF scale	ESE Finder scale
  ESE Finder - SF2/ASF
  ESE Finder - SF2/ASF (IgM - BRCA1)
  ESE Finder - SC35
  ESE Finder - SRp40
  ESE Finder - SRp55

• RESCUE ESE hexamers
  Fairbrother WG, Yeh RF, Sharp PA, Burge CB. Predictive identification of exonic splicing enhancers in human genes. Science. 2002 Aug 9;297(5583):1007-13.
• ESE matrices for Tra2-β and 9G8 - Experimental
  Calculation is performed using new matrices. For more information, please contact us

  Define thresholds for Tra2-β and 9G8

  9G8
  Tra2 - β

Silencer-only matrices

• Silencer motifs from Sironi et al.
  Sironi M, Menozzi G, Riva L, Cagliani R, Comi GP, Bresolin N, Giorda R, Pozzoli U. Silencer elements as possible inhibitors of pseudoexon splicing. Nucleic Acids Res. 2004 Mar 19;32(5):1783-91.

  Define thresholds for Sironi motifs

  Sironi Motif 1 - CTAGAGGT
  Sironi Motif 2 - [T/G]G[T/A]GGGG
  Sironi Motif 3 - TCTCCCAA

• ESS decamers from Wang et al.
  Wang Z, Rolish ME, Yeo G, Tung V, Mawson M, Burge CB. Systematic identification and analysis of exonic splicing silencers. Cell. 2004 Dec 17;119(6):831-45.
• hnRNP matrix for hnRNP A1 - Experimental
  Calculation is performed using a new matrix. For more information, please contact us

  Define threshold for hnRNP A1

  hnRNP A1

Enhancer and silencer matrices

• PESE and PESS Octamers
  Zhang XH, Chasin LA. Computational definition of sequence motifs governing constitutive exon splicing. Genes Dev. 2004 Jun 1;18(11):1241-50.
• Exonic Splicing Regulatory Sequences from Goren et al.
  Goren A, Ram O, Amit M, Keren H, Lev-Maor G, Vig I, Pupko T, Ast G. Comparative analysis identifies exonic splicing regulatory sequences - the complex definition of enhancers and silencers. Molecular cell. 2006, June 23; 22, 769-781
• EIEs and IIEs Hexamers from Zhang et al.
  Zhang C, Li W-H, Krainer A R, Zhang M Q. RNA landscape of evolution for optimal exon and intron discrimination. Proceedings of the National Academy of Science of the USA. 2008, April 7