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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcataatgtatgcattgaagaacgacttcaacggatatccaacactatgatcgtggccgtggattcactaactcggaaaaaatgaatctgtactgttcagGGAGGACTGGCACCTGGAGGGTTCAATTTTGACGCAAAACT

Basic information

species Physcomitrella patens
transcript PP1S180_53V6.2
intron # 17
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|162265050|gb|FC440929.1|FC440929
EST:     TCACCGATGTCAGTGAGGCAACTCTGATCATGCTCTCTGTGATAAAGAAT                         GGAGGACTGGCACCTGGAGGGTTCAATTTTGACGCAAAACT
genomic: TCACCGATGTCAGTGAGGCAACTCTGATCATGCTCTCTGTGATAAAGAATgtgagggacc ... tactgttcagGGAGGACTGGCACCTGGAGGGTTCAATTTTGACGCAAAACT
EST: gi|162265051|gb|FC440930.1|FC440930
EST:     TCACCGATGTCAGTGAGGCAACTCTGATCATGCTCTCTGTGATAAAGAAT                         GGAGGACTGGCACCTGGAGGGTTCAATTTTGACGCAAAACT
genomic: TCACCGATGTCAGTGAGGCAACTCTGATCATGCTCTCTGTGATAAAGAATgtgagggacc ... tactgttcagGGAGGACTGGCACCTGGAGGGTTCAATTTTGACGCAAAACT
EST: gi|208383274|gb|DC928260.1|DC928260
EST:     TCACCGATGTCAGTGAGGCAACTCTGATCATGCTCTCTGTGATAAAGAAT                         GGAGGACTGGCACCTGGAGGGTTCAATTTTGACGCAAAACT
genomic: TCACCGATGTCAGTGAGGCAACTCTGATCATGCTCTCTGTGATAAAGAATgtgagggacc ... tactgttcagGGAGGACTGGCACCTGGAGGGTTCAATTTTGACGCAAAACT
EST: gi|37850897|gb|BJ608905.1|BJ608905
EST:     TCACCGATGTCAGTGAGGCAACTCTGATCATGCTCTCTGTGATAAAGAAT                         GGAGGACTGGCACCTGGAGGGTTCAATTTTGACGCAAAACT
genomic: TCACCGATGTCAGTGAGGCAACTCTGATCATGCTCTCTGTGATAAAGAATgtgagggacc ... tactgttcagGGAGGACTGGCACCTGGAGGGTTCAATTTTGACGCAAAACT
EST: gi|18332905|gb|BJ164918.1|BJ164918
EST:     TCACCGATGTCAGTGAGGCAACTCTGATCATGCTCTCTGTGATAAAGAAT                         GGAGGACTGGCACCTGGAGGGTTCAATTTTGACGCAAAACT
genomic: TCACCGATGTCAGTGAGGCAACTCTGATCATGCTCTCTGTGATAAAGAATgtgagggacc ... tactgttcagGGAGGACTGGCACCTGGAGGGTTCAATTTTGACGCAAAACT
EST: gi|162172551|gb|FC348596.1|FC348596
EST:     TCACCGATGTCAGTGAGGCAACTCTGATCATGCTCTCTGTGATAAAGAAT                         GGAGGACTGGCACCTGGAGGGTTCAATTTTGACGCAAAACT
genomic: TCACCGATGTCAGTGAGGCAACTCTGATCATGCTCTCTGTGATAAAGAATgtgagggacc ... tactgttcagGGAGGACTGGCACCTGGAGGGTTCAATTTTGACGCAAAACT
EST: gi|208370481|gb|DC952184.1|DC952184
EST:     TCACCGATGTCAGTGAGGCAACTCTGATCATGCTCTCTGTGATAAAGAAT                         GGAGGACTGGCACCTGGAGGGTTCAATTTTGACGCAAAACT
genomic: TCACCGATGTCAGTGAGGCAACTCTGATCATGCTCTCTGTGATAAAGAATgtgagggacc ... tactgttcagGGAGGACTGGCACCTGGAGGGTTCAATTTTGACGCAAAACT
EST: gi|37838406|gb|BJ596414.1|BJ596414
EST:     TCACCGATGTCAGTGAGGCAACTCTGATCATGCTCTCTGTGGTAAAGAAT                         GGAGGACTGGCACCTGGAGGGTTCAATTTTGACGCAAAACT
genomic: TCACCGATGTCAGTGAGGCAACTCTGATCATGCTCTCTGTGATAAAGAATgtgagggacc ... tactgttcagGGAGGACTGGCACCTGGAGGGTTCAATTTTGACGCAAAACT
EST: gi|67570917|gb|BJ943741.1|BJ943741
EST:     TCACCGATGTCAGTGAGGCAACTCTGATCATGCTCTCTGTGATAAAGAAT                         GGAGGACTGGCACCTGGAGGGTTCAATTTTGACGCAAAACT
genomic: TCACCGATGTCAGTGAGGCAACTCTGATCATGCTCTCTGTGATAAAGAATgtgagggacc ... tactgttcagGGAGGACTGGCACCTGGAGGGTTCAATTTTGACGCAAAACT
EST: gi|67694219|gb|BJ954452.1|BJ954452
EST:     TCACCGATGTCAGTGAGGCAACTCTGATCATGCTCTCTGTGATAAAGAAT                         GGAGGACTGGCACCTGGAGGGTTCAATTTTGACGCAAAACT
genomic: TCACCGATGTCAGTGAGGCAACTCTGATCATGCTCTCTGTGATAAAGAATgtgagggacc ... tactgttcagGGAGGACTGGCACCTGGAGGGTTCAATTTTGACGCAAAACT
EST: gi|37839393|gb|BJ597401.1|BJ597401
EST:     TCACCGATGTCAGTGAGGCAACTCTGATCATGCTCTCTGTGATAAAGAAT                         GGAGGACTGGCACCTGGAGGGTTCAATTTTGACGCAAAACT
genomic: TCACCGATGTCAGTGAGGCAACTCTGATCATGCTCTCTGTGATAAAGAATgtgagggacc ... tactgttcagGGAGGACTGGCACCTGGAGGGTTCAATTTTGACGCAAAACT
EST: gi|208359219|gb|DC954156.1|DC954156
EST:     TCACCGATGTCAGTGAGGCAACTCTGATCATGCTCTCTGTGATAAAGAAT                         GGAGGACTGGCACCTGGAGGGTTCAATTTTGACGCAAAACT
genomic: TCACCGATGTCAGTGAGGCAACTCTGATCATGCTCTCTGTGATAAAGAATgtgagggacc ... tactgttcagGGAGGACTGGCACCTGGAGGGTTCAATTTTGACGCAAAACT
EST: gi|37852526|gb|BJ610534.1|BJ610534
EST:     TCACCGATGTCAGTGAGGCAACTCTGATCATGCTCTCTGTGATAAAGAAT                         GGAGGACTGGCACCTGGAGGGTTCAATTTTGACGCAAAACT
genomic: TCACCGATGTCAGTGAGGCAACTCTGATCATGCTCTCTGTGATAAAGAATgtgagggacc ... tactgttcagGGAGGACTGGCACCTGGAGGGTTCAATTTTGACGCAAAACT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatgatcgtggccgtggattcactaactcggaaaaaatgaatctgtactgttcagGGAGGACTGGCACCTGGAGGGTTCAATTTTGACGCAAAACT
                    cactaac  putative branch site (score: 1)
                               aaaaaatgaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcataatgtatgcattgaagaacgacttcaacggatatccaacactatgatcgtggccgtggattcactaactcggaaaaaatgaatctgtactgttcagGGAGGACTGGCACCTGGAGGGTTCAATTTTGACGCAAAACT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG