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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cctgatgatttggatctgtgtgtgcttcctttggaaatttttccacgagatttggatgatgcgttaacattcattaaaaattgattttttatttgtaaagAGAGGAGGTTTTTGGTCCTGTAGCACCTCTTATGCGCTTCCAGACGGATGAAGAGGCTATCAAGATGGCAAATGATACTGAATATG

Basic information

species Physcomitrella patens
transcript PP1S279_72V6.2
intron # 16
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|18335538|gb|BJ167558.1|BJ167558
EST:     TATCANCCTACTGTTCTNTGCGGTTGTANCGATGAGATGCTAATATTTAG                         AGAGGAGGTTTTTGGTCCTGTAGCACCTCTTATGCGCTTCCAGACGGATGA
genomic: TATCAACCTACTGTTCTTTGCGGTTGTAACGATGAGATGCTAATATTTAGgtgaggccct ... atttgtaaagAGAGGAGGTTTTTGGTCCTGTAGCACCTCTTATGCGCTTCCAGACGGATGA
EST: gi|162175881|gb|FC351559.1|FC351559
EST:     TATCAACCTACTGTTCTTTGCGGTTGTAACGATGAGATGCTAATATTTAG                         AGAGGAGGTTTTTGGTCCTGTAGCACCTCTTATGCGCTTCCAGACGGATGA
genomic: TATCAACCTACTGTTCTTTGCGGTTGTAACGATGAGATGCTAATATTTAGgtgaggccct ... atttgtaaagAGAGGAGGTTTTTGGTCCTGTAGCACCTCTTATGCGCTTCCAGACGGATGA
EST: gi|162257980|gb|FC433866.1|FC433866
EST:     TATCAACCTACTGTTCTTTGCGGTTGTAACGATGAGATGCTAATATTTAG                         AGAGGAGGTTTTTGGTCCTGTAGCACCTCTTATGCGCTTCCAGACGGATGA
genomic: TATCAACCTACTGTTCTTTGCGGTTGTAACGATGAGATGCTAATATTTAGgtgaggccct ... atttgtaaagAGAGGAGGTTTTTGGTCCTGTAGCACCTCTTATGCGCTTCCAGACGGATGA
EST: gi|162188380|gb|FC364250.1|FC364250
EST:     TATCAACCTACTGTTCTTTGCGGTTGTAACGATGAGATGCTAATATTTAG                         AGAGGAGGTTTTTGGTCCTGTAGCACCTCTTATGCGCTTCCAGACGGATGA
genomic: TATCAACCTACTGTTCTTTGCGGTTGTAACGATGAGATGCTAATATTTAGgtgaggccct ... atttgtaaagAGAGGAGGTTTTTGGTCCTGTAGCACCTCTTATGCGCTTCCAGACGGATGA
EST: gi|67695860|gb|BJ956093.1|BJ956093
EST:     TATCAACCTACTGTTCTTTGCGGTTGTAACGATGAGATGCTAATATTTAG                         AGAGGAGGTTTTTGGTCCTGTAGCACCTCTTATGCGCTTCCAGACGGATGA
genomic: TATCAACCTACTGTTCTTTGCGGTTGTAACGATGAGATGCTAATATTTAGgtgaggccct ... atttgtaaagAGAGGAGGTTTTTGGTCCTGTAGCACCTCTTATGCGCTTCCAGACGGATGA
EST: gi|37848440|gb|BJ606448.1|BJ606448
EST:     TATCAACCTACTGTTCTTTGCGGTTGTAACGATGAGATGCTAATATTTAG                         AGAGGAGGTTTTTGGTCCTGTAGCACCTCTTATGCGCTTCCAGACGGATGA
genomic: TATCAACCTACTGTTCTTTGCGGTTGTAACGATGAGATGCTAATATTTAGgtgaggccct ... atttgtaaagAGAGGAGGTTTTTGGTCCTGTAGCACCTCTTATGCGCTTCCAGACGGATGA
EST: gi|162175611|gb|FC351003.1|FC351003
EST:     TATCAACCTACTGTTCTTTGCGGTTGTAACGATGAGATGCTAATATTTAG                         AGAGGAGGTTTTTGGTCCTGTAGCACCTCTTATGCGCTTCCAGACGGATGA
genomic: TATCAACCTACTGTTCTTTGCGGTTGTAACGATGAGATGCTAATATTTAGgtgaggccct ... atttgtaaagAGAGGAGGTTTTTGGTCCTGTAGCACCTCTTATGCGCTTCCAGACGGATGA
EST: gi|37842855|gb|BJ600863.1|BJ600863
EST:     TATCAACCTACTGTTCTTTGCGGTTGTAACGATGAGATGCTAATATTTAG                         AGAGGAGGTTTTTGGTCCTGTAGCACCTCTTATGCGCTTCCAGACGGATGA
genomic: TATCAACCTACTGTTCTTTGCGGTTGTAACGATGAGATGCTAATATTTAGgtgaggccct ... atttgtaaagAGAGGAGGTTTTTGGTCCTGTAGCACCTCTTATGCGCTTCCAGACGGATGA
EST: gi|37847436|gb|BJ605444.1|BJ605444
EST:     TATCAACCTACTGTTCTTTGCGGTTGTAACGATGAGATGCTAATATTTAG                         AGAGGAGGTTTTTGGTCCTGTAGCACCTCTTATGCGCTTCCAGACGGATGA
genomic: TATCAACCTACTGTTCTTTGCGGTTGTAACGATGAGATGCTAATATTTAGgtgaggccct ... atttgtaaagAGAGGAGGTTTTTGGTCCTGTAGCACCTCTTATGCGCTTCCAGACGGATGA
EST: gi|37838258|gb|BJ596266.1|BJ596266
EST:     TAACGATGAGATGCTAATATTTAG                         AGAGGAGGTTTTTGGTCCTGTAGCACNTCTTATGCGCTTCCAGACGGATGA
genomic: TAACGATGAGATGCTAATATTTAGgtgaggccct ... atttgtaaagAGAGGAGGTTTTTGGTCCTGTAGCACCTCTTATGCGCTTCCAGACGGATGA
EST: gi|208345206|gb|DC925476.1|DC925476
EST:     TATCAACCTACTGTTCTTTGCGGTTGTAACGATGAGATGCTAATATTTAG                         AGAGGAGGTTTTTGGTCCTGTAGCACCTCTTATGCGCTTCCAGACGGATGA
genomic: TATCAACCTACTGTTCTTTGCGGTTGTAACGATGAGATGCTAATATTTAGgtgaggccct ... atttgtaaagAGAGGAGGTTTTTGGTCCTGTAGCACCTCTTATGCGCTTCCAGACGGATGA
EST: gi|37851842|gb|BJ609850.1|BJ609850
EST:     TATCAACCTACTGTTCTTTGCGGTTGTAACGGTGAGATGCTAATATTTAG                         AGAGGAGGTTTTTGGTCCTGTAGCACCTCTTATGCGCTTCCAGACGGATGA
genomic: TATCAACCTACTGTTCTTTGCGGTTGTAACGATGAGATGCTAATATTTAGgtgaggccct ... atttgtaaagAGAGGAGGTTTTTGGTCCTGTAGCACCTCTTATGCGCTTCCAGACGGATGA
EST: gi|162167720|gb|FC344034.1|FC344034
EST:     TATCAACCTACTGTTCTTTGCGGTTGTAACGATGAGATGCTAATATTTAG                         AGAGGAGGTTTTTGGTCCTGTAGCACCTCTTATGCGCTTCCAGACGGATGA
genomic: TATCAACCTACTGTTCTTTGCGGTTGTAACGATGAGATGCTAATATTTAGgtgaggccct ... atttgtaaagAGAGGAGGTTTTTGGTCCTGTAGCACCTCTTATGCGCTTCCAGACGGATGA
EST: gi|37842399|gb|BJ600407.1|BJ600407
EST:     TATCAACCTACTGTTCTTTGCGGTTGTAACGATGAGATGCTAATATTTAG                         AGAGGAGGTTTTTGGTCCTGTAGCACCTCTTATGCGCTTCCAGACGGATGA
genomic: TATCAACCTACTGTTCTTTGCGGTTGTAACGATGAGATGCTAATATTTAGgtgaggccct ... atttgtaaagAGAGGAGGTTTTTGGTCCTGTAGCACCTCTTATGCGCTTCCAGACGGATGA
EST: gi|162175090|gb|FC351158.1|FC351158
EST:     TATCAACCTACTGTTCTTTGCGGTTGTAACGATGAGATGTTAATATTTAG                         AGAGGAGGTTTTTGGTCCGGTAGCACCTCTTATGCGCTTCCAGACGGATGA
genomic: TATCAACCTACTGTTCTTTGCGGTTGTAACGATGAGATGCTAATATTTAGgtgaggccct ... atttgtaaagAGAGGAGGTTTTTGGTCCTGTAGCACCTCTTATGCGCTTCCAGACGGATGA
EST: gi|162170328|gb|FC346525.1|FC346525
EST:     TATCAACCTACTGTTCTTTGCGGTTGTAACGATGAGATGCTAATATTTAG                         AGAGGAGGTTTTTGGTCCTGTAGCACCTCTTATGCGCTTCCAGACGGATGA
genomic: TATCAACCTACTGTTCTTTGCGGTTGTAACGATGAGATGCTAATATTTAGgtgaggccct ... atttgtaaagAGAGGAGGTTTTTGGTCCTGTAGCACCTCTTATGCGCTTCCAGACGGATGA
EST: gi|37841695|gb|BJ599703.1|BJ599703
EST:     TATCAACCTACTGTTCTTTGCGGTTGTAACGATGAGATGCTAATATTTAG                         AGAGGAGGTTTTTGGTCCTGTAGCACCTCTTATGCGCTTCCAGACGGATGA
genomic: TATCAACCTACTGTTCTTTGCGGTTGTAACGATGAGATGCTAATATTTAGgtgaggccct ... atttgtaaagAGAGGAGGTTTTTGGTCCTGTAGCACCTCTTATGCGCTTCCAGACGGATGA
EST: gi|162261210|gb|FC437227.1|FC437227
EST:     TATCAACCTACTGTTCTTTGCGGTTGTAACGATGAGATGCTAATATTTAG                         AGAGGAGGTTTTTGGTCCTGTAGCACCTCTTATGCGCTTCCAGACGGATGA
genomic: TATCAACCTACTGTTCTTTGCGGTTGTAACGATGAGATGCTAATATTTAGgtgaggccct ... atttgtaaagAGAGGAGGTTTTTGGTCCTGTAGCACCTCTTATGCGCTTCCAGACGGATGA
EST: gi|208365822|gb|DC951057.1|DC951057
EST:     TATCAACCTACTGTTCTTTGCGGTTGTAACGATGAGATGCTAATATTTAG                         AGAGGAGGTTTTTGGTCCTGTAGCACCTCTTATGCGCTTCCAGACGGATGA
genomic: TATCAACCTACTGTTCTTTGCGGTTGTAACGATGAGATGCTAATATTTAGgtgaggccct ... atttgtaaagAGAGGAGGTTTTTGGTCCTGTAGCACCTCTTATGCGCTTCCAGACGGATGA
EST: gi|37851044|gb|BJ609052.1|BJ609052
EST:     GTAACGATGAGATGNTAATATTTAG                         AGAGGAGGTTTTTGGTCCTGTAGCACNTCTTATGCGCTTCCAGACGGATGA
genomic: GTAACGATGAGATGCTAATATTTAGgtgaggccct ... atttgtaaagAGAGGAGGTTTTTGGTCCTGTAGCACCTCTTATGCGCTTCCAGACGGATGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgagatttggatgatgcgttaacattcattaaaaattgattttttatttgtaaagAGAGGAGGTTTTTGGTCCTGTAGCACCTCTTATGCGCTTCCAGACGGATGAAGAGGCTATCAAGATGGCAAATGATACTGAATATG
                                       ttttttattt  CT-rich tract
                  ttaacattcattaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cctgatgatttggatctgtgtgtgcttcctttggaaatttttccacgagatttggatgatgcgttaacattcattaaaaattgattttttatttgtaaagAGAGGAGGTTTTTGGTCCTGTAGCACCTCTTATGCGCTTCCAGACGGATGAAGAGGCTATCAAGATGGCAAATGATACTGAATATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG