Lo splicing dell’RNA• definizione• importanza• predizione

Ing Francesco PivaGruppo di biologia computazionale e molecolareDipartimento di Biochimica, Biologia e Genetica

Università Politecnica delle MarcheEdificio Scienze 3, Brecce Bianche, Ancona

f.piva@univpm.it

These are synonymous words, are we sure ?

. . . Ala Val Arg . . .

GCA C G T

GTA C G T

CGA C G TAGA G

GCAGTACGAGCAGTACGCGCAGTACGGGCAGTACGTGCAGTAAGAGCAGTAAGGGCAGTCCGAGCAGTCCGCGCAGTCCGGGCAGTCCGTGCAGTCAGAGCAGTCAGGGCAGTGCGAGCAGTGCGCGCAGTGCGGGCAGTGCGTGCAGTGAGAGCAGTGAGGGCAGTTCGAGCAGTTCGCGCAGTTCGGGCAGTTCGTGCAGTTAGAGCAGTTAGG

GCCGTACGAGCCGTACGCGCCGTACGGGCCGTACGTGCCGTAAGAGCCGTAAGGGCCGTCCGAGCCGTCCGCGCCGTCCGGGCCGTCCGTGCCGTCAGAGCCGTCAGGGCCGTGCGAGCCGTGCGCGCCGTGCGGGCCGTGCGTGCCGTGAGAGCCGTGAGGGCCGTTCGAGCCGTTCGCGCCGTTCGGGCCGTTCGTGCCGTTAGAGCCGTTAGG

GCGGTACGAGCGGTACGCGCGGTACGGGCGGTACGTGCGGTAAGAGCGGTAAGGGCGGTCCGAGCGGTCCGCGCGGTCCGGGCGGTCCGTGCGGTCAGAGCGGTCAGGGCGGTGCGAGCGGTGCGCGCGGTGCGGGCGGTGCGTGCGGTGAGAGCGGTGAGGGCGGTTCGAGCGGTTCGCGCGGTTCGGGCGGTTCGTGCGGTTAGAGCGGTTAGG

GCTGTACGAGCTGTACGCGCTGTACGGGCTGTACGTGCTGTAAGAGCTGTAAGGGCTGTCCGAGCTGTCCGCGCTGTCCGGGCTGTCCGTGCTGTCAGAGCTGTCAGGGCTGTGCGAGCTGTGCGCGCTGTGCGGGCTGTGCGTGCTGTGAGAGCTGTGAGGGCTGTTCGAGCTGTTCGCGCTGTTCGGGCTGTTCGTGCTGTTAGAGCTGTTAGG

4 * 4 * 6 = 96Three AAs specified by 96 synonymous words

ATGTAAACGTATATCGTGACAGTGGTCTGTTAGTATTCCTTTAGTCATGGTTT

ATGTAAACTGGTCTGTTATCATGGTTT

Genomic DNA

mRNA

attggaaaccgaaacccgttggtcacctctgcaatagccctccctccctcacttctacaattttgtgacagtggtcttgttttctgcattctctgcttcacgtgcttgttttgttggagcgcgtttgcatgctgctttaaattctgaaatattaaaaaaatttcgaagtttttcagcacatgggatgggagttttgaatttcaattttttaaaaacatttttctgtgattagtgccgtcgtggcacggctgttagccgcctatccggtttattcgatactttGTGAGTTTTTTGTAACTTTATGGTCGTCGAAATGGGAAAACTTGGCCACCAATATAAGTTTGGAAAACAATTTCCTAAAAATAAAATAATTGAACTTTTCCGATGAATAAAAAAATCGATCAGATATTCTGGAAAAAAAATCGATAAATTAATCGATTTTCTTGGAAAATACATCGAAAAATTGAGAAAAATAGAAAAATGAATGTTTTTCGATTACCGATTTATTGATTTTTCGTGAAAACTGAGTTCAGATAATTTTAAAAGCAATGTTTTTCATTTTTCAAATCAGAATCACTATAGTTTTGAAAAATCAATAATTAATTTATTGATTTTTCAATATAATTTTTTGGAAAAAATAGAAAAATCCCTTTCTAAAAGTTTTAAATTTCCAAGAAAAATTCATTTTCAAAATCACCAACGCGCTCTATAGAGTAGTCGATGAAAATCTCCGTTAAGGGTGCATGGGCAAAACGCGCTCGAACGACAATTGTTATTGTATGTTTGGTCTTGCAACGAAAAGTTTGAAAAATTGAAAAAAAGTTGTGTCTGATACATTTTTTTTTGGCATTTTCTGCTATTTTACACCAGAAAAAATTTAATAAACATAAAAAATCGAAATTTTTCAAGTTGGACAATTTTCAGtgagcatcttatccatcctagttctcagttcaggacttgtgcacattcgtttagagccagatattcgcaaagccttttcaccggatgattcagatgctggataGTAAGTGACTACTGACCTTGAAGCCTCCTTCCTCCACCAGTCAGAAATAACACGTTTTTTCGCAATGTTTTTCTTTTTCTAATTCGATTTCCCTTTCTCCCTTTCTTATTGTGATTTGGTCAATGTTTGGTTGACTGGGAAGAAAATTGAATTTTTTTGGAATTCCACTTGAAGTTAAAAAACCCAAAATAAATATTTGATCAAAAATAAATAAGAAAAAAAAGAAAACTTTAAAGCAAATGAAAATTTCGTTCGTAACTATTTTGTTAATTTTTTTAAAACTCCTATTTTAAATATATGCTTTTTGCGGAAATTTCTATAAATTTTTTTACATTTTTCAGtgaaacccgtgtctggctggaatactacggactcgacatctatccggaacgagcattctgtatttttaccgccaagcgcgaaaattccagtattctccaggaaggcgcactggcagacGTAAGTTGATTCTCCGTCACGCCCACTTTTCTGGCGGGAATTTAAAAAATTTCAGatttatactgtggacaatcgactatcggcggcagttggctaccaagatggggatggacgaaaaaattgcgatccactctgcgacttgaacagcccctttcacttgttagcgGTAGGTGGTGGTCTAGGGTGTCATTTTTCGATTTTTTCAATTATTCGATGTTTTTAGTGAAAATCGAAAAATCTAAAAATTGAAAATCGAAAAATGAAAGAAACATTGTTTTTTGGGGACCAAACATCTTAATGAATTTAACAACAGGGAAAACTGAACAGAAACCTGGACGGTCTTATCCCATTTATCTATATTCTTAAAATGAATGATGGAGAAAAAAGTTAAAATAAAAACATTATCAGCTTTTTGTAAGTTTTTCTCAAAAATTGTTCGATTTTTCGATTTTCTAAAAAGTCGAAAAACCGAAACCCTTGGTGGTGGTGGTGGTGGACTAGAAAACTCTTCAACGACCACATGGCAATTTTCAGaatttgacgcggagaaacaatggtaccacaagtgtattcacctatccggatatgccatatagcggactggatattttcctgggacttcacttgagtaatgcggattttggtaagattttttttgaaatgttaaatgaaaagttgaaaaatagtttttatgatttagccactttccagttaaaatttcatttttttaactataaaaagttctggaaaaatg

Struttura tipica dei geni umani

esoni introni

esone1 introne1 esone2 introne2 esone3

esone1

esone1

introne1

esone2

esone2

introne2

esone3

esone3

SPLICING

eliminazione introni

unione esoni

GT GTAG AG

Lo splicing avviene in tutto il trascritto, anche nelle zone non codificanti

R = G, AY = T, C

R C ORI

O

HO RII+

=

R C ORII

O

HO RI+

Meccanismo di splicingestere alcool

due legami fosfoesterici

U2AF

U2AF

U2AFU2AF

arly

U2AF si lega al tratto pirimidinico a valle del sito di ramificazione

snRNP U2 si lega al sito di ramificazione (richiesta idrolisi ATP)

Arg-Ser

le prot SR connettono U2Af con snRNP U1

si legano insieme

snRNP U5 si lega al 5’ss, snRNP U6 si lega a snRNP U2

snRNP U1 è rilasciato, snRNP U5 si sposta dall’esone all’introne, snRNP U6 si lega al 5’ss

snRNP U4 è rilasciato (richiesta idrolisi ATP), snRNP U6 e U2 catalizzano la

transesterificazione, snRNP U5 si lega al 3’ss, il 5’ ss è tagliato e si forma il

cappio

il 3’ss è tagliato e gli esoni vengono saldati insieme, il cappio verrà deramificato

introne (5’ss)

Sm protein

snRNP U1

C5

G16

RBD: RNA binding domain

si appaia al sito di ramificazione

Sm protein

snRNP U2si appaiano con snRNA U6

U5

U17

3 541 2

1 2 3 5Muscolo cardiaco

1 43 5Muscolo uterino

Lo splicing è tessuto specifico

Esempio di alternative splicing di un gene umano

Alternative splicing tessuto specifico

Tutti i modi di fare splicing alternativo

Alcuni genomi virali subiscono splicing all’interno della cellula ospite

equine infectious anemia virus (EIAV)

AIM:

SPLICING PREDICTION TOOL

pre mRNAsequence

mRNAstructure

attggaaaccgaaacccgttggtcacctctgcaatagccctccctccctcacttctacaattttgtgacagtggtcttgttttctgcattctctgcttcacgtgcttgttttgttggagcgcgtttgcatgctgctttaaattctgaaatattaaaaaaatttcgaagtttttcagcacatgggatgggagttttgaatttcaattttttaaaaacatttttctgtgattagtgccgtcgtggcacggctgttagccgcctatccggtttattcgatactttGTGAGTTTTTTGTAACTTTATGGTCGTCGAAATGGGAAAACTTGGCCACCAATATAAGTTTGGAAAACAATTTCCTAAAAATAAAATAATTGAACTTTTCCGATGAATAAAAAAATCGATCAGATATTCTGGAAAAAAAATCGATAAATTAATCGATTTTCTTGGAAAATACATCGAAAAATTGAGAAAAATAGAAAAATGAATGTTTTTCGATTACCGATTTATTGATTTTTCGTGAAAACTGAGTTCAGATAATTTTAAAAGCAATGTTTTTCATTTTTCAAATCAGAATCACTATAGTTTTGAAAAATCAATAATTAATTTATTGATTTTTCAATATAATTTTTTGGAAAAAATAGAAAAATCCCTTTCTAAAAGTTTTAAATTTCCAAGAAAAATTCATTTTCAAAATCACCAACGCGCTCTATAGAGTAGTCGATGAAAATCTCCGTTAAGGGTGCATGGGCAAAACGCGCTCGAACGACAATTGTTATTGTATGTTTGGTCTTGCAACGAAAAGTTTGAAAAATTGAAAAAAAGTTGTGTCTGATACATTTTTTTTTGGCATTTTCTGCTATTTTACACCAGAAAAAATTTAATAAACATAAAAAATCGAAATTTTTCAAGTTGGACAATTTTCAGtgagcatcttatccatcctagttctcagttcaggacttgtgcacattcgtttagagccagatattcgcaaagccttttcaccggatgattcagatgctggataGTAAGTGACTACTGACCTTGAAGCCTCCTTCCTCCACCAGTCAGAAATAACACGTTTTTTCGCAATGTTTTTCTTTTTCTAATTCGATTTCCCTTTCTCCCTTTCTTATTGTGATTTGGTCAATGTTTGGTTGACTGGGAAGAAAATTGAATTTTTTTGGAATTCCACTTGAAGTTAAAAAACCCAAAATAAATATTTGATCAAAAATAAATAAGAAAAAAAAGAAAACTTTAAAGCAAATGAAAATTTCGTTCGTAACTATTTTGTTAATTTTTTTAAAACTCCTATTTTAAATATATGCTTTTTGCGGAAATTTCTATAAATTTTTTTACATTTTTCAGtgaaacccgtgtctggctggaatactacggactcgacatctatccggaacgagcattctgtatttttaccgccaagcgcgaaaattccagtattctccaggaaggcgcactggcagacGTAAGTTGATTCTCCGTCACGCCCACTTTTCTGGCGGGAATTTAAAAAATTTCAGatttatactgtggacaatcgactatcggcggcagttggctaccaagatggggatggacgaaaaaattgcgatccactctgcgacttgaacagcccctttcacttgttagcgGTAGGTGGTGGTCTAGGGTGTCATTTTTCGATTTTTTCAATTATTCGATGTTTTTAGTGAAAATCGAAAAATCTAAAAATTGAAAATCGAAAAATGAAAGAAACATTGTTTTTTGGGGACCAAACATCTTAATGAATTTAACAACAGGGAAAACTGAACAGAAACCTGGACGGTCTTATCCCATTTATCTATATTCTTAAAATGAATGATGGAGAAAAAAGTTAAAATAAAAACATTATCAGCTTTTTGTAAGTTTTTCTCAAAAATTGTTCGATTTTTCGATTTTCTAAAAAGTCGAAAAACCGAAACCCTTGGTGGTGGTGGTGGTGGACTAGAAAACTCTTCAACGACCACATGGCAATTTTCAGaatttgacgcggagaaacaatggtaccacaagtgtattcacctatccggatatgccatatagcggactggatattttcctgggacttcacttgagtaatgcggattttggtaagattttttttgaaatgttaaatgaaaagttgaaaaatagtttttatgatttagccactttccagttaaaatttcatttttttaactataaaaagttctggaaaaatg

aatttctAGgccgccgatcctaaaAGTgcaccatttcgcAGaAGTacGTacAGTttcccatctatccctAGTgGTcttGTtttctgcattctctgcttcacGTgcttGTtttGTtggAGcgcGTttgcatgctgctttaaattctgaaatattaaaaaaatttcgaAGTttttcAGcacatgggatgggAGTtttgaatttcaattttttaaaaacatttttctGTgattAGTgccGTcGTggcacggctGTtAGccgcctatccgGTttattcgatactttGTGAGTTTTTTGTAACTTTATGGTCGTCGAAATGGGAAAACTTGGCCACCAATATAAGTTTGGAAAACAATTTCCTAAAAATAAAATAATTGAACTTTTCCGATGAATAAAAAAATCGATCAGATATTCTGGAAAAAAAATCGATAAATTAATCGATTTTCTTGGAAAATACATCGAAAAATTGAGAAAAATAGAAAAATGAATGTTTTTCGATTACCGATTTATTGATTTTTCGTGAAAACTGAGTTCAGATAATTTTAAAAGCAATGTTTTTCATTTTTCAAATCAGAATCACTATAGTTTTGAAAAATCAATAATTAATTTATTGATTTTTCAATATAATTTTTTGGAAAAAATAGAAAAATCCCTTTCTAAAAGTTTTAAATTTCCAAGAAAAATTCATTTTCAAAATCACCAACGCGCTCTATAGAGTAGTCGATGAAAATCTCCGTTAAGGGTGCATGGGCAAAACGCGCTCGAACGACAATTGTTATTGTATGTTTGGTCTTGCAACGAAAAGTTTGAAAAATTGAAAAAAAGTTGTGTCTGATACATTTTTTTTTGGCATTTTCTGCTATTTTACACCAGAAAAAATTTAATAAACATAAAAAATCGAAATTTTTCAAGTTGGACAATTTTCAGtgAGcatcttatccatcctAGTtctcAGTtcAGgacttGTgcacattcGTttAGAGccAGatattcgcaaAGccttttcaccggatgattcAGatgctggatAGTAAGTGACTACTGACCTTGAAGCCTCCTTCCTCCACCAGTCAGAAATAACACGTTTTTTCGCAATGTTTTTCTTTTTCTAATTCGATTTCCCTTTCTCCCTTTCTTATTGTGATTTGGTCAATGTTTGGTTGACTGGGAAGAAAATTGAATTTTTTTGGAATTCCACTTGAAGTTAAAAAACCCAAAATAAATATTTGATCAAAAATAAATAAGAAAAAAAAGAAAACTTTAAAGCAAATGAAAATTTCGTTCGTAACTATTTTGTTAATTTTTTTAAAACTCCTATTTTAAATATATGCTTTTTGCGGAAATTTCTATAAATTTTTTTACATTTTTCAGTgaaacccGTGTctggctggaatactacggactcgacatctatccggaacgAGcattctGTatttttaccgccaAGcgcgaaaattccAGTattctccAGgaAGgcgcactggcAGacGTAAGTTGATTCTCCGTCACGCCCACTTTTCTGGCGGGAATTTAAAAAATTTCAGatttatactGTggacaatcgactatcggcggcAGTtggctaccaAGatggggatggacgaaaaaattgcgatccactctgcgacttgaacAGcccctttcacttGTtAGcgGTAGGTGGTGGTCTAGGGTGTCATTTTTCGATTTTTTCAATTATTCGATGTTTTTAGTGAAAATCGAAAAATCTAAAAATTGAAAATCGAAAAATGAAAGAAACATTGTTTTTTGGGGACCAAACATCTTAATGAATTTAACAACAGGGAAAACTGAACAGAAACCTGGACGGTCTTATCCCATTTATCTATATTCTTAAAATGAATGATGGAGAAAAAAGTTAAAATAAAAACATTATCAGCTTTTTGTAAGTTTTTCTCAAAAATTGTTCGATTTTTCGATTTTCTAAAAAGTCGAAAAACCGAAACCCTTGGTGGTGGTGGTGGTGGACTAGAAAACTCTTCAACGACCACATGGCAATTTTCAGaatttgacgcggAGaaacaatgGTaccacaAGTGTattcacctatccggatatgccatatAGcggactggatattttcctgggacttcacttgAGTaatgcggattttgGTaAGattttttttgaaatGTtaaatgaaaAGTtgaaaaatAGTttttatgatttAGccactttccAGTtaaaatttcatttttttaactataaaaAGTtctggaaaaatG

Segnali per il riconoscimento degli introni

Motivi conservati

I segnali dei siti di splicing sono ben conservati tra le specieprobabilmente la comparsa del meccanismo di splicing è molto antica

5’splice sites

Binding of DAZAP1 and hnRNPA1/A2 to an Exonic Splicing Silencer in a Natural BRCA1 Exon 18 MutantGoina E, Skoko N, Pagani F. Mol Cell Biol 2008; 28: 3850–3860

One point mutation at a time

BRCA1 exon 18

17 18 19

17 19

20%

80%17 18 19

100%

Two point mutations at a time

BRCA1 exon 18

Binding of DAZAP1 and hnRNPA1/A2 to an Exonic Splicing Silencer in a Natural BRCA1 Exon 18 MutantGoina E, Skoko N, Pagani F. Mol Cell Biol 2008; 28: 3850–3860

Complete exon 18 skipping Decreased efficiency

WT 5’-ACAGTTGTTGGCGGTTG-3’TACCACCC TTATTGGTTC AA CCGC G G T

0102030405060708090

100

G T G A G T C T C G C A C A C A C C T T C A G T T C T

WT 144A145C 146A 147G 148T 149T150G 151T 153G 154G 155C 156G 157G

ex9 +ex9 -

% e

xon

9 in

clus

ion

Effect of variations in CFTR exon 9

Pagani, F., Buratti, E., Stuani, C., and Baralle, F. E. (2003) J Biol Chem Pagani, F., Stuani, C., Zuccato, E., Kornblihtt, A. R., and Baralle, F. E. (2003) J Biol Chem

A

pathological

path

olog

ical

path

olog

ical

An additional exonic constraints: the splicing code

The genetic code is degenerate, but it is not all rodustness

. . . Ala Val Arg . . .

GCA C G T

GTA C G T

CGA C G TAGA G

GCAGTACGAGCAGTACGCGCAGTACGGGCAGTACGTGCAGTAAGAGCAGTAAGGGCAGTCCGAGCAGTCCGCGCAGTCCGGGCAGTCCGTGCAGTCAGAGCAGTCAGGGCAGTGCGAGCAGTGCGCGCAGTGCGGGCAGTGCGTGCAGTGAGAGCAGTGAGGGCAGTTCGAGCAGTTCGCGCAGTTCGGGCAGTTCGTGCAGTTAGAGCAGTTAGG

GCCGTACGAGCCGTACGCGCCGTACGGGCCGTACGTGCCGTAAGAGCCGTAAGGGCCGTCCGAGCCGTCCGCGCCGTCCGGGCCGTCCGTGCCGTCAGAGCCGTCAGGGCCGTGCGAGCCGTGCGCGCCGTGCGGGCCGTGCGTGCCGTGAGAGCCGTGAGGGCCGTTCGAGCCGTTCGCGCCGTTCGGGCCGTTCGTGCCGTTAGAGCCGTTAGG

GCGGTACGAGCGGTACGCGCGGTACGGGCGGTACGTGCGGTAAGAGCGGTAAGGGCGGTCCGAGCGGTCCGCGCGGTCCGGGCGGTCCGTGCGGTCAGAGCGGTCAGGGCGGTGCGAGCGGTGCGCGCGGTGCGGGCGGTGCGTGCGGTGAGAGCGGTGAGGGCGGTTCGAGCGGTTCGCGCGGTTCGGGCGGTTCGTGCGGTTAGAGCGGTTAGG

GCTGTACGAGCTGTACGCGCTGTACGGGCTGTACGTGCTGTAAGAGCTGTAAGGGCTGTCCGAGCTGTCCGCGCTGTCCGGGCTGTCCGTGCTGTCAGAGCTGTCAGGGCTGTGCGAGCTGTGCGCGCTGTGCGGGCTGTGCGTGCTGTGAGAGCTGTGAGGGCTGTTCGAGCTGTTCGCGCTGTTCGGGCTGTTCGTGCTGTTAGAGCTGTTAGG

4 * 4 * 6 = 96Three AAs specified by 96 synonymous words

exon31cryptic exonNF1 gene

A>G

ttttatagTGAGAATA

WT MUT

Raponi M, Upadhyaya M, Baralle D.Functional splicing assay shows a pathogenic intronic mutation in neurofibromatosis type 1 (NF1) due to intronic sequence exonization.Hum Mutat. 2006; 27(3):294-295.

La mutazione attiva un esone criptico (in rosso)

TAGgtaataTAGgtggga

TAGataata CAGgtattgCAAgtattg

CAAgtaagcCAAgtaagg

Raponi M, Upadhyaya M, Baralle D.Functional splicing assay shows a pathogenic intronic mutation in neurofibromatosis type 1 (NF1) due to intronic sequence exonization.Hum Mutat. 2006;27(3):294-295.

exon31cryptic exonNF1 gene

Disruption of 5’ss restores normal splicing

La seq 2 ha un sito di splicing in 5’ più debole della seq 1. La seq 3 non ha il sito.

ATM gene structure

20 21

M WT del mut

20 21

20 21

mutations

results

A new type of mutation causes a splicing defect in ATMPagani F, Buratti E, Stuani C, Bendix R, Dörk T, Baralle FENature Genetics 2002, 30: 426-429

20 21

WT: GGCCAGGTAAGTGATA

DEL: GGCCAG____GTGATAMUT: GGCCAGGTCTGTGATA

exonic splicing enhancer ESE

exonic splicing silencer ESS

intronic splicing enhancer ISE

intronic splicing silencer ISS

Many elements regulate the splicing process

A compact formalism, but…

scorematrix

Experimental assessed binding sites

ACGT

Gconsensus sequence

AGGAGTCGGCGT

unzip

AGGAGTCGTAGGCGT

Compression and reconstruction of motifs

zip

Intron definition / exon definition

Modello di exonic splicing enhancer mediato da proteine SR

Modello di exonic splicing silencer

elements promoting exons

elements promoting introns

ESE, ISS: esone

ESS, ISE: introne

9G8, CUG-BP1, DAZAP1, ETR-3, Fox-1, Fox-2, FMRP, hnRNP A0, hnRNP A1, hnRNP A2/B1, hnRNP C, hnRNP C1, hnRNP C2, hnRNP D, hnRNP D0, hnRNP DL, hnRNP E1, hnRNP E2, hnRNP F, hnRNP G, hnRNP H1, hnRNP H2, hnRNP I (PTB), hnRNP J, hnRNP K, hnRNP L, hnRNP LL, hnRNP M, hnRNP P (TLS), hnRNP Q, hnRNP U, HTra2alpha, HTra2beta1, HuB, HuD, HuR, KSRP, MBNL1, Nova-1, Nova-2, nPTB, PSF, RBM4, RBM25, Sam68, SAP155, SC35, SF1, SF2/ASF, SLM-1, SLM-2, SRp20, SRp30c, SRp38, SRp40, SRp54, SRp55, SRp75, TDP43, TIA-1, TIAL1, YB-1, ZRANB2 …

PROTEINS REGULATING SPLICING STORED IN SPLICEAID

SEQUENCESPLICEAID COMPETING TOOLS

EXPERIMENTALLY ASSESSED BINDING ESE Finder Rescue ESE Splicing

Rainbow ACAAC YB-1 no binding no ESE SRp40

GAAGAAGAHTra2A, HTra2B1, SF2/ASF, SC35, SRp40, SRp55, SRp75

no binding 3 ESE Tra2B

CUGGCGUCGUCGC no binding SF2/ASF, SRp55 2 ESE SRp40, SRp55

UGACUG hnRNP A1 no binding no ESE SRp40, SRp55

UUUUAGACAA

hnRNP C1, Sam68, hnRNP A1, hnRNP D, hnRNP E1, hnRNP E2, SRp38

no binding 1 ESE

hnRNP A2/B1, hnRNP C1/C2, hnRNP E1/E2, SRp40, SRp55, U2AF65

UGUGUGUGUGUGUGUGUG CUG-BP1, ETR-3, TDP43 SRp55 no ESE hnRNP U

Some comparisons among literature data (SpliceAid) and prediction tools

Pan troglodytesaverage nucleotide divergence of just 1.2%

Suggested papers

Nature reviews. Genetics. 2002; 3(4): 285-298Listening to silence and understanding nonsense: exonic mutations that affect splicing.Cartegni L, Chew SL, Krainer AR.PMID: 11967553

Nature reviews. Genetics. 2007; 8(10): 749-761. Splicing in disease: disruption of the splicing code and the decoding machinery.Wang GS, Cooper TA.PMID: 17726481