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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtggggtgactctggaagtctctcccctttaaccgcagatggcgtcgacattctgaacctgtttttttaatgcacatatcagaatgttcaagtctttgatgatattcctctgtcctcctttttattaagttctgaacagatcgaaaatttcctgaacggttttgccaatttttgcagTTGGAGACTTTCAAACGGACACTTATGCAATCCCTTCAGGAAGAAGACGATAAGCACGGC

Basic information

species Physcomitrella patens
transcript PP1S460_21V6.2
intron # 2
splice site 3'
intron type U2

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|208344571|gb|DC909130.1|DC909130
EST:     AGAATTCGCTGGCTCTTCANGTGAAAAAGTTAATGCGGGATGTTGCAAAG                         TTGGAGACTTTCAA-CGGACACTTATGCA
genomic: AGAATTCGCTGGCTCTTCAAGTGAAAAAGTTAATGCGGGATGTTGCAAAGgtggggtgac ... atttttgcagTTGGAGACTTTCAAACGGACACTTATGCA
EST: gi|162186580|gb|FC363344.1|FC363344
EST:     AGAATTCGCTGGCTCTTCAAGTGAAAAAGTTAATGCGGGATGTTGCAAAG                         TTGGAGACTTTCAAACGGACACTTATGCAATCCCTTCAGGAAGAAGACGAT
genomic: AGAATTCGCTGGCTCTTCAAGTGAAAAAGTTAATGCGGGATGTTGCAAAGgtggggtgac ... atttttgcagTTGGAGACTTTCAAACGGACACTTATGCAATCCCTTCAGGAAGAAGACGAT
EST: gi|162172964|gb|FC347874.1|FC347874
EST:     AGAATTCGCTGGCTCTTCAAGTGAAAAAGTTAATGCGGGATGTTGCAAAG                         TTGGAGACTTTCAAACGGACACTTATGCAATCCCTTCAGGAAGAAGACGAT
genomic: AGAATTCGCTGGCTCTTCAAGTGAAAAAGTTAATGCGGGATGTTGCAAAGgtggggtgac ... atttttgcagTTGGAGACTTTCAAACGGACACTTATGCAATCCCTTCAGGAAGAAGACGAT
EST: gi|162200373|gb|FC376372.1|FC376372
EST:     AGAATTCGCTGGCTCTTCAAGTGAAAAAGTTAATGCGGGATGTTGCAAAG                         TTGGAGACTTTCAAACGGACACTTATGCAATCCCTTCAGGAAGAAGACGAT
genomic: AGAATTCGCTGGCTCTTCAAGTGAAAAAGTTAATGCGGGATGTTGCAAAGgtggggtgac ... atttttgcagTTGGAGACTTTCAAACGGACACTTATGCAATCCCTTCAGGAAGAAGACGAT
EST: gi|67568939|gb|BJ941763.1|BJ941763
EST:     AGAATTCGCTGGCTCTTCAAGTGAAAAAGTTAATGCGGGATGTTGCAAAG                         TTGGAGACTTTCAAACGGACACTTATGCAATCCCTTCAGGAAGAAGACGAT
genomic: AGAATTCGCTGGCTCTTCAAGTGAAAAAGTTAATGCGGGATGTTGCAAAGgtggggtgac ... atttttgcagTTGGAGACTTTCAAACGGACACTTATGCAATCCCTTCAGGAAGAAGACGAT
EST: gi|67573087|gb|BJ945911.1|BJ945911
EST:     AGAATTCGCTGGCTCTTCAAGTGAAAAAGTTAATGCGGGATGTTGCAAAG                         TTGGAGACTTTCAAACGGACACTTATGCAATCCCTTCAG
genomic: AGAATTCGCTGGCTCTTCAAGTGAAAAAGTTAATGCGGGATGTTGCAAAGgtggggtgac ... atttttgcagTTGGAGACTTTCAAACGGACACTTATGCAATCCCTTCAG
EST: gi|162280234|gb|FC456251.1|FC456251
EST:     AGAATTCGCTGGCTCTTCAAGTGAAAAAGTTAATGCGGGATGTTGCAAAG                         TTGGAGACTTTCAAACGGACACTTATGCAATCCCTTCAGGAAGAAGACGAT
genomic: AGAATTCGCTGGCTCTTCAAGTGAAAAAGTTAATGCGGGATGTTGCAAAGgtggggtgac ... atttttgcagTTGGAGACTTTCAAACGGACACTTATGCAATCCCTTCAGGAAGAAGACGAT
EST: gi|162181414|gb|FC357118.1|FC357118
EST:     AGAATTCGCTGGCTCTTCAAGTGAAAAAGTTAATGCGGGATGTTGCAAAG                         TTGGAGACTTTCAAACGGACACTTATGCAATCCCTTCAGGAAGAAGACGAT
genomic: AGAATTCGCTGGCTCTTCAAGTGAAAAAGTTAATGCGGGATGTTGCAAAGgtggggtgac ... atttttgcagTTGGAGACTTTCAAACGGACACTTATGCAATCCCTTCAGGAAGAAGACGAT
EST: gi|100387746|gb|BY951746.1|BY951746
EST:     AGAATTCGCTGGCTCTTCAAGTGAAAAAGTTAATGCGGGATGTTGCAAAG                         TTGGAGACTTTCAAACGGACACTTATGCAATCCCTTCAGGAAGAAGACGAT
genomic: AGAATTCGCTGGCTCTTCAAGTGAAAAAGTTAATGCGGGATGTTGCAAAGgtggggtgac ... atttttgcagTTGGAGACTTTCAAACGGACACTTATGCAATCCCTTCAGGAAGAAGACGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattaagttctgaacagatcgaaaatttcctgaacggttttgccaatttttgcagTTGGAGACTTTCAAACGGACACTTATGCAATCCCTTCAGGAAGAAGACGATAAGCACGGC
                                              tttttgc  CT-rich tract
                     aaaattt  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtggggtgactctggaagtctctcccctttaaccgcagatggcgtcgacattctgaacctgtttttttaatgcacatatcagaatgttcaagtctttgatgatattcctctgtcctcctttttattaagttctgaacagatcgaaaatttcctgaacggttttgccaatttttgcagTTGGAGACTTTCAAACGGACACTTATGCAATCCCTTCAGGAAGAAGACGATAAGCACGGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG