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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtataaactcattcatacaacttgccagttttcccacttcatctaatagaaagtcatttctaacagaccctttttgcagATTTAACGGTACTGCACCAGAGCCCCGCAAGGGTGTTCGTGGTGGGCATATTCCTGGCAGCAAGTGTGTACCATTCACTGAG

Basic information

species Physcomitrella patens
transcript PP1S78_4V6.2
intron # 8
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|67725353|gb|BJ975612.1|BJ975612
EST:     AACCTTGAAGAGAAGAAGTTCCAAGTTATCGATGCACGCGGCAAGGCTAG                         ATTTAACGGTACTGCACCAGAGCCCCGCAAGGGTGTTCGTGGTGGGCATAT
genomic: AACCTTGAAGAGAAGAAGTTCCAAGTTATCGATGCACGCGGCAAGGCTAGgtataaactc ... ctttttgcagATTTAACGGTACTGCACCAGAGCCCCGCAAGGGTGTTCGTGGTGGGCATAT
EST: gi|162277312|gb|FC453118.1|FC453118
EST:     AACCTTGAAGAGAAGAAGTTCCAAGTTATCGATGCACGCGGCAAGGCTAG                         ATTTAACGGTACTGCACCAGAGCCCCGCAAGGGTGTTCGTGGTGGGCATAT
genomic: AACCTTGAAGAGAAGAAGTTCCAAGTTATCGATGCACGCGGCAAGGCTAGgtataaactc ... ctttttgcagATTTAACGGTACTGCACCAGAGCCCCGCAAGGGTGTTCGTGGTGGGCATAT
EST: gi|162268668|gb|FC445165.1|FC445165
EST:     AACCTTGAAGAGAAGAAGTTCCAAGTTATCGATGCACGCGGCAAGGCTAG                         ATTTAACGGTACTGCACCAGAGCCCCGCAAGGGTGTTCGTGGTGGGCATAT
genomic: AACCTTGAAGAGAAGAAGTTCCAAGTTATCGATGCACGCGGCAAGGCTAGgtataaactc ... ctttttgcagATTTAACGGTACTGCACCAGAGCCCCGCAAGGGTGTTCGTGGTGGGCATAT
EST: gi|162268669|gb|FC445166.1|FC445166
EST:     AACCTTGAAGAGAAGAAGTTCCAAGTTATCGATGCACGCGGCAAGGCTAG                         ATTTAACGGTACTGCACCAGAGCCCCGTCA-GGGTGTTCGTGGTGGGCATA
genomic: AACCTTGAAGAGAAGAAGTTCCAAGTTATCGATGCACGCGGCAAGGCTAGgtataaactc ... ctttttgcagATTTAACGGTACTGCACCAGAGCCCCG-CAAGGGTGTTCGTGGTGGGCATA
EST: gi|18334696|gb|BJ166713.1|BJ166713
EST:     AACCTTGAAGAGAAGAAGTTCCAAGTTATCGATGCACGCGGCAAGGCTAG                         ATTTAACGGTACTGCACCAGAGCCCCGCAAGGGTGTTCGTGGTGGGCATAT
genomic: AACCTTGAAGAGAAGAAGTTCCAAGTTATCGATGCACGCGGCAAGGCTAGgtataaactc ... ctttttgcagATTTAACGGTACTGCACCAGAGCCCCGCAAGGGTGTTCGTGGTGGGCATAT
EST: gi|67695705|gb|BJ955938.1|BJ955938
EST:     AACCTTGAAGAGAAGAAGTTCCAAGTTATCGATGCACGCGGCAAGGCTAG                         ATTTAACGGTACTGCACCAGAGCCCCGCAAGGGTGTTCGTGGTGGGCATAT
genomic: AACCTTGAAGAGAAGAAGTTCCAAGTTATCGATGCACGCGGCAAGGCTAGgtataaactc ... ctttttgcagATTTAACGGTACTGCACCAGAGCCCCGCAAGGGTGTTCGTGGTGGGCATAT
EST: gi|37852646|gb|BJ610654.1|BJ610654
EST:     AACCTTGAAGAGAAGAAGTTCCAAGTTATCGATGCACGCGGCAAGGCTAG                         ATTTAACGGTACTGCACCAGAGCCCCGCAAGGGTGTTCGTGGTGGGCATAT
genomic: AACCTTGAAGAGAAGAAGTTCCAAGTTATCGATGCACGCGGCAAGGCTAGgtataaactc ... ctttttgcagATTTAACGGTACTGCACCAGAGCCCCGCAAGGGTGTTCGTGGTGGGCATAT
EST: gi|67726274|gb|BJ976533.1|BJ976533
EST:     AACCTTGAAGAGAAGAAGTTCCAAGTTATCGATGCACGCGGCAAGGCTAG                         ATTTAACGGTACTGCACCAGAGCCCCGCAAGGGTGTTCGTGGTGGGCATAT
genomic: AACCTTGAAGAGAAGAAGTTCCAAGTTATCGATGCACGCGGCAAGGCTAGgtataaactc ... ctttttgcagATTTAACGGTACTGCACCAGAGCCCCGCAAGGGTGTTCGTGGTGGGCATAT
EST: gi|67508643|gb|BJ941504.1|BJ941504
EST:     AACCTTGAAGAGAAGAAGTTCCAAGTTATCGATGCACGCGGCAAGGCTAG                         ATTTAACGGTACTGCACCAGAGCCCCGCAAGGGTGTTCGTGGTGGGCATAT
genomic: AACCTTGAAGAGAAGAAGTTCCAAGTTATCGATGCACGCGGCAAGGCTAGgtataaactc ... ctttttgcagATTTAACGGTACTGCACCAGAGCCCCGCAAGGGTGTTCGTGGTGGGCATAT
EST: gi|67725181|gb|BJ975440.1|BJ975440
EST:     AACCTTGAAGAGAAGAAGTTCCAAGTTATCGATGCACGCGGCAAGGCTAG                         ATTTAACGGTACTGCACCAGAGCCCCGCAAGGGTGTTCGTGGTGGGCATAT
genomic: AACCTTGAAGAGAAGAAGTTCCAAGTTATCGATGCACGCGGCAAGGCTAGgtataaactc ... ctttttgcagATTTAACGGTACTGCACCAGAGCCCCGCAAGGGTGTTCGTGGTGGGCATAT
EST: gi|67724933|gb|BJ975192.1|BJ975192
EST:     AACCTTGAAGAGAAGAAGTTCCAAGTTATCGATGCACGCGGCAAGGCTAG                         ATTTAACGGTACTGCACCAGAGCCCCGCAAGGGTGTTCGTGGTGGGCATAT
genomic: AACCTTGAAGAGAAGAAGTTCCAAGTTATCGATGCACGCGGCAAGGCTAGgtataaactc ... ctttttgcagATTTAACGGTACTGCACCAGAGCCCCGCAAGGGTGTTCGTGGTGGGCATAT
EST: gi|67695360|gb|BJ955593.1|BJ955593
EST:     AACCTTGAAGAGAAGAAGTTCCAAGTTATCGATGCACGCGGCAAGGCTAG                         ATTTAACGGTACTGCACCAGAGCCCCGCAAGGGTGTTCGTGGTGGGCATAT
genomic: AACCTTGAAGAGAAGAAGTTCCAAGTTATCGATGCACGCGGCAAGGCTAGgtataaactc ... ctttttgcagATTTAACGGTACTGCACCAGAGCCCCGCAAGGGTGTTCGTGGTGGGCATAT
EST: gi|18335656|gb|BJ167676.1|BJ167676
EST:     AACCTTGAAGAGAAGAAGTTCCAAGTTATCGATGCACGCGGCAAGGCTAG                         ATTTAACGGTACTGCACCAGAGCCCCGCAAGGGTGTTCGTGGTGGGCATAT
genomic: AACCTTGAAGAGAAGAAGTTCCAAGTTATCGATGCACGCGGCAAGGCTAGgtataaactc ... ctttttgcagATTTAACGGTACTGCACCAGAGCCCCGCAAGGGTGTTCGTGGTGGGCATAT
EST: gi|67572332|gb|BJ945156.1|BJ945156
EST:     AACCTTGAAGAGAAGAAGTTCCAAGTTATCGATGCACGCGGCAAGGCTAG                         ATTTAACGGTACTGCACCAGAGCCCCGCAAGGGTGTTCGTGGTGGGCATAT
genomic: AACCTTGAAGAGAAGAAGTTCCAAGTTATCGATGCACGCGGCAAGGCTAGgtataaactc ... ctttttgcagATTTAACGGTACTGCACCAGAGCCCCGCAAGGGTGTTCGTGGTGGGCATAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccagttttcccacttcatctaatagaaagtcatttctaacagaccctttttgcagATTTAACGGTACTGCACCAGAGCCCCGCAAGGGTGTTCGTGGTGGGCATATTCCTGGCAGCAAGTGTGTACCATTCACTGAG
                                 ttctaac  putative branch site (score: 1)
                                           ccctttttgc  putative PPT
                   taatagaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtataaactcattcatacaacttgccagttttcccacttcatctaatagaaagtcatttctaacagaccctttttgcagATTTAACGGTACTGCACCAGAGCCCCGCAAGGGTGTTCGTGGTGGGCATATTCCTGGCAGCAAGTGTGTACCATTCACTGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG