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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgccattcccaagcaagctgcagtaaacagcttggattcttcggaaagaattgtacattgggaaatttgtgtgttcctaacttagctctattctatgcagGAGTATATATTTTGCGCATGGATGGGCGAGCACTTCAGATGATGGCGAGCGTCAATCTTGAAACCTTTAGAAGGAATCCTTCTGCAATAATCAACCTCAA

Basic information

species Physcomitrella patens
transcript PP1S155_48V6.1
intron # 1
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|18327794|gb|BJ159798.1|BJ159798
EST:     CAGCACTGCTTGCATCGGCTCCCCATTCAGCAGATTTTCGTACTGGCCAT                         GAGTATATATTTTGCGCATGGATGGGCGAGCACTTCAGATGATGGCGAGCG
genomic: CAGCACTGCTTGCATCGGCTCCCCATTCAGCAGATTTTCGTACTGGCCATgtgagtgata ... ttctatgcagGAGTATATATTTTGCGCATGGATGGGCGAGCACTTCAGATGATGGCGAGCG
EST: gi|18351842|gb|BJ183894.1|BJ183894
EST:     CAGCACTGCTTGCATCGGCTCCCCATTCAGCAGATTTTCGTACTGGCCAT                         GAGTATATATTTTGCGCATGGATGGGCGAGCACTTCAGATGATGGCGAGCG
genomic: CAGCACTGCTTGCATCGGCTCCCCATTCAGCAGATTTTCGTACTGGCCATgtgagtgata ... ttctatgcagGAGTATATATTTTGCGCATGGATGGGCGAGCACTTCAGATGATGGCGAGCG
EST: gi|100438125|gb|BY961666.1|BY961666
EST:     CAGCACTGCTTGCATCGGCTCCCCATTCAGCAGATTTTCGTACTGGCCAT                         GAGTATATATTTTGCGCATGGATGGGCGAGCACTTCAGATGATGGCGAGCG
genomic: CAGCACTGCTTGCATCGGCTCCCCATTCAGCAGATTTTCGTACTGGCCATgtgagtgata ... ttctatgcagGAGTATATATTTTGCGCATGGATGGGCGAGCACTTCAGATGATGGCGAGCG
EST: gi|18331809|gb|BJ163820.1|BJ163820
EST:     CAGCACTGCTTGCATCGGCTCCCCATTCAGCAGATTTTCGTACTGGCCAT                         GAGTATATATTTTGCGCATGGATGGGCGAGCACTTCAGATGATGGCGAGCG
genomic: CAGCACTGCTTGCATCGGCTCCCCATTCAGCAGATTTTCGTACTGGCCATgtgagtgata ... ttctatgcagGAGTATATATTTTGCGCATGGATGGGCGAGCACTTCAGATGATGGCGAGCG
EST: gi|18344946|gb|BJ176987.1|BJ176987
EST:     CAGCACTGCTTGCATCGGCTCCCCATTCAGCAGATTTTCGTACTGGCCAT                         GAGTATATATTTTGCGCATGGATGGGCGAGCACTTCAGATGATGGCGAGCG
genomic: CAGCACTGCTTGCATCGGCTCCCCATTCAGCAGATTTTCGTACTGGCCATgtgagtgata ... ttctatgcagGAGTATATATTTTGCGCATGGATGGGCGAGCACTTCAGATGATGGCGAGCG
EST: gi|18357132|gb|BJ189191.1|BJ189191
EST:     CAGCACTGCTTGCATCGGCTCCCCATTCAGCAGATTTTCGTACTGGCCAT                         GAGTATATATTTTGCGCATGGATGGGCGAGCACTTCAGATGATGGCGAGCG
genomic: CAGCACTGCTTGCATCGGCTCCCCATTCAGCAGATTTTCGTACTGGCCATgtgagtgata ... ttctatgcagGAGTATATATTTTGCGCATGGATGGGCGAGCACTTCAGATGATGGCGAGCG
EST: gi|67575712|gb|BJ948536.1|BJ948536
EST:     TTTCGTACTGGCCAT                         GAGTATATATTTTGCGCATGGATGGGCGAGCACTTCAGATGATGGCGAGCG
genomic: TTTCGTACTGGCCATgtgagtgata ... ttctatgcagGAGTATATATTTTGCGCATGGATGGGCGAGCACTTCAGATGATGGCGAGCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagaattgtacattgggaaatttgtgtgttcctaacttagctctattctatgcagGAGTATATATTTTGCGCATGGATGGGCGAGCACTTCAGATGATGGCGAGCGTCAATCTTGAAACCTTTAGAAGGAATCCTTCTGCAATAATCAACCTCAA
                             tcctaac  putative branch site (score: 1)
                                        ctctattct  putative PPT
                 aaatttgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgccattcccaagcaagctgcagtaaacagcttggattcttcggaaagaattgtacattgggaaatttgtgtgttcctaacttagctctattctatgcagGAGTATATATTTTGCGCATGGATGGGCGAGCACTTCAGATGATGGCGAGCGTCAATCTTGAAACCTTTAGAAGGAATCCTTCTGCAATAATCAACCTCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - -agctgca