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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcacgttgaggactggagctgttgggtttttgatgtttgatttttcgcatttctgacgactgagtcgacacagctaagatatgaaacttgctttgcgcagCCTATGCCAGCGGAGCAACTTCAAAAGCTGAAGCATTATAAGGACGTTCTCCACAGAATGATCCCTTATATGAGAGTTCCGAAGGAGCGTATACCAGCTG

Basic information

species Physcomitrella patens
transcript PP1S97_54V6.1
intron # 4
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|18368953|gb|BJ201038.1|BJ201038
EST:     TGAGTAGTATGGTTGAGTTGTATTCGACTCTTACAGCCCGAAGTAACCAG                         CCTATGCCAGCGGAGCAACTTCAAAAGCTGAAGCATTATAAGGACGTTCTC
genomic: TGAGTAGTATGGTTGAGTTGTATTCGACTCTTACAGCCCGAAGTAACCAGgtactactaa ... ctttgcgcagCCTATGCCAGCGGAGCAACTTCAAAAGCTGAAGCATTATAAGGACGTTCTC
EST: gi|18326676|gb|BJ158675.1|BJ158675
EST:     TGAGTAGTATGGTTGAGTTGTATTCGACTCTTACAGCCCGAAGTAACCAG                         CCTATGCCAGCGGAGCAACTTCAAAAGCTGAAGCATTATAAGGACGTTCTC
genomic: TGAGTAGTATGGTTGAGTTGTATTCGACTCTTACAGCCCGAAGTAACCAGgtactactaa ... ctttgcgcagCCTATGCCAGCGGAGCAACTTCAAAAGCTGAAGCATTATAAGGACGTTCTC
EST: gi|18330055|gb|BJ162061.1|BJ162061
EST:     TGAGTAGTATGGTTGAGTTGTATTCGACTCTTACAGCCCGAAGTAACCAG                         CCTATGCCAGCGGAGCAACTTCAAAAGCTGAAGCATTATAAGGACGTTCTC
genomic: TGAGTAGTATGGTTGAGTTGTATTCGACTCTTACAGCCCGAAGTAACCAGgtactactaa ... ctttgcgcagCCTATGCCAGCGGAGCAACTTCAAAAGCTGAAGCATTATAAGGACGTTCTC
EST: gi|18361892|gb|BJ193959.1|BJ193959
EST:     TGAGTAGTATGGTTGAGTTGTATTCGACTCTTACAGCCCGAAGTAACCAG                         CCTATGCCAGCGGAGCAACTTCAAAAGCTGAAGCATTATAAGGACGTTCTC
genomic: TGAGTAGTATGGTTGAGTTGTATTCGACTCTTACAGCCCGAAGTAACCAGgtactactaa ... ctttgcgcagCCTATGCCAGCGGAGCAACTTCAAAAGCTGAAGCATTATAAGGACGTTCTC
EST: gi|37850242|gb|BJ608250.1|BJ608250
EST:     TGAGTAGTATGGTTGAGTTGTATTCGACTCTTACAGCCCGAAGTAACCAG                         CCTATGCCAGCGGAGCAACTTCAAAAGCTGAAGCATTATAAGGACGTTCTC
genomic: TGAGTAGTATGGTTGAGTTGTATTCGACTCTTACAGCCCGAAGTAACCAGgtactactaa ... ctttgcgcagCCTATGCCAGCGGAGCAACTTCAAAAGCTGAAGCATTATAAGGACGTTCTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgcatttctgacgactgagtcgacacagctaagatatgaaacttgctttgcgcagCCTATGCCAGCGGAGCAACTTCAAAAGCTGAAGCATTATAAGGACGTTCTCCACAGAATGATCCCTTATATGAGAGTTCCGAAGGAGCGTATACCAGCTG
     ttctgac  putative branch site (score: 2)
                                         cttgcttt  putative PPT
                             taagatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcacgttgaggactggagctgttgggtttttgatgtttgatttttcgcatttctgacgactgagtcgacacagctaagatatgaaacttgctttgcgcagCCTATGCCAGCGGAGCAACTTCAAAAGCTGAAGCATTATAAGGACGTTCTCCACAGAATGATCCCTTATATGAGAGTTCCGAAGGAGCGTATACCAGCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG