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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgattcttgcttgaaccgtaatgtagttccatctgcagtgataatcgttttaattttattttaaagctataggtttctcacctttgctatgttttctcagGTCGTCGCCAATCAGGTGATATTGGGTCCTATTGTTATCACACTTGTCTTCGCATGGAACAAACTTTGGGAAGGCCGTCTTGAGCAGCTTCCTACCCTCT

Basic information

species Physcomitrella patens
transcript PP1S94_157V6.1
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|208392132|gb|DC949564.1|DC949564
EST:     TTCTTGATCACTTCATGCCAGTCAAGAATTTGACAAATCTCTCACTCAAG                         GTCGTCGCCAATCAGGTGATATTGGGTCCTATTGTTATCACACTTGTCTTC
genomic: TTCTTGATCACTTCATGCCAGTCAAGAATTTGACAAATCTCTCACTCAAGgttttttttc ... gttttctcagGTCGTCGCCAATCAGGTGATATTGGGTCCTATTGTTATCACACTTGTCTTC
EST: gi|208389112|gb|DC945688.1|DC945688
EST:     TTCTTGATCACTTCATGCCAGTCAAGAATTTGGCAAATCTCTCACTCAAG                         GTCGTCGCCAATCAGGTGATATTGGGTCCTATTGTTATCACACTTGTCTTC
genomic: TTCTTGATCACTTCATGCCAGTCAAGAATTTGACAAATCTCTCACTCAAGgttttttttc ... gttttctcagGTCGTCGCCAATCAGGTGATATTGGGTCCTATTGTTATCACACTTGTCTTC
EST: gi|208367534|gb|DC943937.1|DC943937
EST:     TTCTTGATCACTTCATGCCAGTCAAGAATTTGACAAATCTCTCACTCAAG                         GTCGTCGCCAATCAGGTGATATTGGGTCCTATTGTTATCACACTTGTCTTC
genomic: TTCTTGATCACTTCATGCCAGTCAAGAATTTGACAAATCTCTCACTCAAGgttttttttc ... gttttctcagGTCGTCGCCAATCAGGTGATATTGGGTCCTATTGTTATCACACTTGTCTTC
EST: gi|162250631|gb|FC428222.1|FC428222
EST:     TTCTTGACCACTTCATGCCAGTCAAGAATTTGACAAATCTCTCACTCAAG                         GTCGTCGCCAATCAGGTGATATTGGGTCCTATTGTTATCACACTTGTCTTC
genomic: TTCTTGATCACTTCATGCCAGTCAAGAATTTGACAAATCTCTCACTCAAGgttttttttc ... gttttctcagGTCGTCGCCAATCAGGTGATATTGGGTCCTATTGTTATCACACTTGTCTTC
EST: gi|208378723|gb|DC914697.1|DC914697
EST:     TTCTTGATCACTTCATGCCAGTCAAGAATTTGACAAATCTCTCACTCAAG                         GTCGTCGCCAATCAGGTGATATTGGGTCCTATTGTTATCACACTTGTCTTC
genomic: TTCTTGATCACTTCATGCCAGTCAAGAATTTGACAAATCTCTCACTCAAGgttttttttc ... gttttctcagGTCGTCGCCAATCAGGTGATATTGGGTCCTATTGTTATCACACTTGTCTTC
EST: gi|67695308|gb|BJ955541.1|BJ955541
EST:     TTCTTGATCACTTCATGCCAGTCAAGAATTTGACAAATCTCTCACTCAAG                         GTCGTCGCCAATCAGGTGATATTGGGTCCTATTGTTATCACACTTGTCTTC
genomic: TTCTTGATCACTTCATGCCAGTCAAGAATTTGACAAATCTCTCACTCAAGgttttttttc ... gttttctcagGTCGTCGCCAATCAGGTGATATTGGGTCCTATTGTTATCACACTTGTCTTC
EST: gi|208381786|gb|DC928449.1|DC928449
EST:     TTCTTGATCACTTCATGCCAGTCAAGAATTTGACAAATCTCTCACTCAAG                         GTCGTCGCCAATCAGGTGATATTGGGTCCTATTGTTATCACACTTGTCTTC
genomic: TTCTTGATCACTTCATGCCAGTCAAGAATTTGACAAATCTCTCACTCAAGgttttttttc ... gttttctcagGTCGTCGCCAATCAGGTGATATTGGGTCCTATTGTTATCACACTTGTCTTC
EST: gi|208394106|gb|DC957187.1|DC957187
EST:     TTCTTGATCACTTCATGCCAGTCAAGAATTTGACAAATCTCTCACTCAAG                         GTCGTCGCCAATCAGGTGATATTGGGTCCTATTGTTATCACACTTGTCTTC
genomic: TTCTTGATCACTTCATGCCAGTCAAGAATTTGACAAATCTCTCACTCAAGgttttttttc ... gttttctcagGTCGTCGCCAATCAGGTGATATTGGGTCCTATTGTTATCACACTTGTCTTC
EST: gi|162250632|gb|FC428223.1|FC428223
EST:     TTCTTGACCACTTCATGCCAGTCAAGAATTTGACAAATCTCTCACTCAAG                         GTCGTCGCCAATCAGGTGATATTGGGTCCTATTGTTATCACACTTGTCTTC
genomic: TTCTTGATCACTTCATGCCAGTCAAGAATTTGACAAATCTCTCACTCAAGgttttttttc ... gttttctcagGTCGTCGCCAATCAGGTGATATTGGGTCCTATTGTTATCACACTTGTCTTC
EST: gi|208365240|gb|DC931178.1|DC931178
EST:     TTCTTGATCACTTCATGCCAGTCAAGAATTTGGCAAATCTCTCACTCAAG                         GTCGTCGCCAATCAGGTGATATTGGGTCCTATTGTTATCACACTTGTCTTC
genomic: TTCTTGATCACTTCATGCCAGTCAAGAATTTGACAAATCTCTCACTCAAGgttttttttc ... gttttctcagGTCGTCGCCAATCAGGTGATATTGGGTCCTATTGTTATCACACTTGTCTTC
EST: gi|67699886|gb|BJ960119.1|BJ960119
EST:     TTCTTGATCACTTCATGCCAGTCAAGAATTTGACAAATCTCTCACTCAAG                         GTCGTCGCCAATCAGGTGATATTGGGTCCTATTGTTATCACACTTGTCTTC
genomic: TTCTTGATCACTTCATGCCAGTCAAGAATTTGACAAATCTCTCACTCAAGgttttttttc ... gttttctcagGTCGTCGCCAATCAGGTGATATTGGGTCCTATTGTTATCACACTTGTCTTC
EST: gi|208361882|gb|DC953932.1|DC953932
EST:     TTCTTGATCACTTCATGCCAGTCAAGAATTTGACAAATCTCTCACTCAAG                         GTCGTCGCCAATCAGGTGATATTGGGTCCTATTGTTATCACACTTGTCTTC
genomic: TTCTTGATCACTTCATGCCAGTCAAGAATTTGACAAATCTCTCACTCAAGgttttttttc ... gttttctcagGTCGTCGCCAATCAGGTGATATTGGGTCCTATTGTTATCACACTTGTCTTC
EST: gi|208377816|gb|DC940928.1|DC940928
EST:     TTCTTGATCACTTCATGCCAGTCAAGAATTTGACAAATCTCTCACTCAAG                         GTCGTCGCCAATCAGGTGATATTGGGTCCTATTGTTATCACACTTGTCTTC
genomic: TTCTTGATCACTTCATGCCAGTCAAGAATTTGACAAATCTCTCACTCAAGgttttttttc ... gttttctcagGTCGTCGCCAATCAGGTGATATTGGGTCCTATTGTTATCACACTTGTCTTC
EST: gi|162183967|gb|FC359337.1|FC359337
EST:     TTCTTGACCACTTCATGCCAGTCAAGAATTTGACAAATCTCTCACTCAAG                         GTCGTCGCCAATCAGGTGATATTGGGTCCTATTGTTATCACACTTGTCTTC
genomic: TTCTTGATCACTTCATGCCAGTCAAGAATTTGACAAATCTCTCACTCAAGgttttttttc ... gttttctcagGTCGTCGCCAATCAGGTGATATTGGGTCCTATTGTTATCACACTTGTCTTC
EST: gi|67571942|gb|BJ944766.1|BJ944766
EST:     TTCTTGATCACTTCATGCCAGTCAAGAATTTGACAAATCTCTCACTCAAG                         GTCGTCGCCAATCAGGTGATATTGGGTCCTATTGTTATCACACTTGTCTTC
genomic: TTCTTGATCACTTCATGCCAGTCAAGAATTTGACAAATCTCTCACTCAAGgttttttttc ... gttttctcagGTCGTCGCCAATCAGGTGATATTGGGTCCTATTGTTATCACACTTGTCTTC
EST: gi|208365662|gb|DC935759.1|DC935759
EST:     TTCTTGATCACTTCATGCCAGTCAAGAATTTGACAAATCTCTCACTCAAG                         GTCGTCGCCAATCAGGTGATATTGGGTCCTATTGTTATCACACTTGTCTTC
genomic: TTCTTGATCACTTCATGCCAGTCAAGAATTTGACAAATCTCTCACTCAAGgttttttttc ... gttttctcagGTCGTCGCCAATCAGGTGATATTGGGTCCTATTGTTATCACACTTGTCTTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgttttaattttattttaaagctataggtttctcacctttgctatgttttctcagGTCGTCGCCAATCAGGTGATATTGGGTCCTATTGTTATCACACTTGTCTTCGCATGGAACAAACTTTGGGAAGGCCGTCTTGAGCAGCTTCCTACCCTCT
                             ttctcac  putative branch site (score: 2)
                                            tgttttctc  putative PPT
     taattttattttaaag  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgattcttgcttgaaccgtaatgtagttccatctgcagtgataatcgttttaattttattttaaagctataggtttctcacctttgctatgttttctcagGTCGTCGCCAATCAGGTGATATTGGGTCCTATTGTTATCACACTTGTCTTCGCATGGAACAAACTTTGGGAAGGCCGTCTTGAGCAGCTTCCTACCCTCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT