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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaggcttcctcggtattcagacgactctcgtcagcggtttttatggtgatgataattttcttcacatttgtccatcagaaacctatctccaattaatcttatatattgtagctgttaatattttacgactaattctacctacgacaattttttgtaatatcaagtgtaaacgtggtcataaacgcagGTGACTGTAACAGGCGCATCGGATGAAGCTGCAGCCGCAACGGTGGCTCGCTCTGTTGCCGCCTCCTCCTTAACGAAG

Basic information

species Physcomitrella patens
transcript PP1S90_220V6.2
intron # 14
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|162153999|gb|FC330234.1|FC330234
EST:     TAGCTAAGTCAATTGCCTCTGACGGTGAGGGGGCGACGTGTTTAGTCGAG                         GTGACTGTAACAGGCGCATCGGATGAAGCTGCAGCCGCAACGGTGGCTCGC
genomic: TAGCTAAGTCAATTGCCTCTGACGGTGAGGGGGCGACGTGTTTAGTCGAGgtgaggcttc ... ataaacgcagGTGACTGTAACAGGCGCATCGGATGAAGCTGCAGCCGCAACGGTGGCTCGC
EST: gi|162152238|gb|FC328217.1|FC328217
EST:     TAGCTAAGTCAATTGCCTCTGACGGTGAGGGGGCGACGTGTTTAGTCGAG                         GTGACTGTAACAGGCGCATCGGATGAAGCTGCAGCCGCAACGGTGGCTCGC
genomic: TAGCTAAGTCAATTGCCTCTGACGGTGAGGGGGCGACGTGTTTAGTCGAGgtgaggcttc ... ataaacgcagGTGACTGTAACAGGCGCATCGGATGAAGCTGCAGCCGCAACGGTGGCTCGC
EST: gi|208372841|gb|DC956242.1|DC956242
EST:     TAGCTAAGTCAATTGCCTCTGACGGTGAGGGGGCGACGTGTTTAGTCGAG                         GTGACTGTAACAGGCGCATCGGATGAAGCTGCAGCCGCAACGGTGGCTCGC
genomic: TAGCTAAGTCAATTGCCTCTGACGGTGAGGGGGCGACGTGTTTAGTCGAGgtgaggcttc ... ataaacgcagGTGACTGTAACAGGCGCATCGGATGAAGCTGCAGCCGCAACGGTGGCTCGC
EST: gi|18335990|gb|BJ168011.1|BJ168011
EST:     GCTAAGTCAATTGCCTCTGACGGTGAGGGGGCGACGTGTTTAGTCGGG                         GTGACTGTAACAGGCGCATCGGATGAAGCTGCAGCCGCAACGGTGGCTCGC
genomic: GCTAAGTCAATTGCCTCTGACGGTGAGGGGGCGACGTGTTTAGTCGAGgtgaggcttc ... ataaacgcagGTGACTGTAACAGGCGCATCGGATGAAGCTGCAGCCGCAACGGTGGCTCGC
EST: gi|162169774|gb|FC345311.1|FC345311
EST:     TAGCTAAGTCAATTGCCTCTGACGGTGAGGGGGCGACGTGTTTAGTCGAG                         GTGACTGTAACAGGCGCATCGGATGAAGCTGCAGCCGCAACGGTGGCTCGC
genomic: TAGCTAAGTCAATTGCCTCTGACGGTGAGGGGGCGACGTGTTTAGTCGAGgtgaggcttc ... ataaacgcagGTGACTGTAACAGGCGCATCGGATGAAGCTGCAGCCGCAACGGTGGCTCGC
EST: gi|162152239|gb|FC328218.1|FC328218
EST:     TAGCTAAGTCAATTGCCTCTGACGGTGAGGGGGCGACGTGTTTAGTCGAG                         GTGACTGTAACAGGCGCATCGGATGAAGCTGCAGCCGCAACGGTGGCTCGC
genomic: TAGCTAAGTCAATTGCCTCTGACGGTGAGGGGGCGACGTGTTTAGTCGAGgtgaggcttc ... ataaacgcagGTGACTGTAACAGGCGCATCGGATGAAGCTGCAGCCGCAACGGTGGCTCGC
EST: gi|67726457|gb|BJ976716.1|BJ976716
EST:     TAGCTAAGTCAATTGCCTCTGACGGTGAGGGGGCGACGTGTTTAGTCGAG                         GTGACTGTAACAGGCGCATCGGATGAAGCTGCAGCCGCAACGGTGGCTCGC
genomic: TAGCTAAGTCAATTGCCTCTGACGGTGAGGGGGCGACGTGTTTAGTCGAGgtgaggcttc ... ataaacgcagGTGACTGTAACAGGCGCATCGGATGAAGCTGCAGCCGCAACGGTGGCTCGC
EST: gi|67695993|gb|BJ956226.1|BJ956226
EST:     AAGTCAATTGCCTCTGACGGTGAGGGGGCGACGTGTTTAGTCGAG                         GTGACTGTAACAGGCGCATCGGATGAAGCTGCAGCCGCAACGGTGGCTCGC
genomic: AAGTCAATTGCCTCTGACGGTGAGGGGGCGACGTGTTTAGTCGAGgtgaggcttc ... ataaacgcagGTGACTGTAACAGGCGCATCGGATGAAGCTGCAGCCGCAACGGTGGCTCGC
EST: gi|162186917|gb|FC362595.1|FC362595
EST:     TAGCTAAGTCAATTGCCTCTGACGGTGAGGGGGCGACGTGTTTAGTCGAG                         GTGACTGTAACAGGCGCATCGGATGAAGCTGCAGCCGCAACGGTGGCTCGC
genomic: TAGCTAAGTCAATTGCCTCTGACGGTGAGGGGGCGACGTGTTTAGTCGAGgtgaggcttc ... ataaacgcagGTGACTGTAACAGGCGCATCGGATGAAGCTGCAGCCGCAACGGTGGCTCGC
EST: gi|162169775|gb|FC345312.1|FC345312
EST:     TAGCTAAGTCAATTGCCTCTGACGGTGAGGGGGCGACGTGTTTAGTCGAG                         GTGACTGTAACAGGCGCATCGGATGAAGCTGCAGCCGCAACGGTGGCTCGC
genomic: TAGCTAAGTCAATTGCCTCTGACGGTGAGGGGGCGACGTGTTTAGTCGAGgtgaggcttc ... ataaacgcagGTGACTGTAACAGGCGCATCGGATGAAGCTGCAGCCGCAACGGTGGCTCGC
EST: gi|162154000|gb|FC330235.1|FC330235
EST:     TAGCTAAGTCAATTGCCTCTGACGGTGAGGGGGCGACGTGTTTAGTCGAG                         GTGACTGTAACAGGCGCATCGGATGAAGCTGCAGCCGCAACGGTGGCTCGC
genomic: TAGCTAAGTCAATTGCCTCTGACGGTGAGGGGGCGACGTGTTTAGTCGAGgtgaggcttc ... ataaacgcagGTGACTGTAACAGGCGCATCGGATGAAGCTGCAGCCGCAACGGTGGCTCGC
EST: gi|162169382|gb|FC345738.1|FC345738
EST:     TAGCTAAGTCAATTGCCTCTGACGGTGAGGGGGCGACGTGTTTAGTCGAG                         GTGACTGTAACAGGCGCATCGGATGAAGCTGCAGCCGCAACGGTGGCTCGC
genomic: TAGCTAAGTCAATTGCCTCTGACGGTGAGGGGGCGACGTGTTTAGTCGAGgtgaggcttc ... ataaacgcagGTGACTGTAACAGGCGCATCGGATGAAGCTGCAGCCGCAACGGTGGCTCGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctacctacgacaattttttgtaatatcaagtgtaaacgtggtcataaacgcagGTGACTGTAACAGGCGCATCGGATGAAGCTGCAGCCGCAACGGTGGCTCGCTCTGTTGCCGCCTCCTCCTTAACGAAG
             aattttttgtaatatc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgaggcttcctcggtattcagacgactctcgtcagcggtttttatggtgatgataattttcttcacatttgtccatcagaaacctatctccaattaatcttatatattgtagctgttaatattttacgactaattctacctacgacaattttttgtaatatcaagtgtaaacgtggtcataaacgcagGTGACTGTAACAGGCGCATCGGATGAAGCTGCAGCCGCAACGGTGGCTCGCTCTGTTGCCGCCTCCTCCTTAACGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC