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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgagaacaacttccacgctgtgatgacgtttgttttgtttttatttttttatttaatctttttaatgtaaaaaattacgacttcgtgtaaatcgacgcagAAAAAGATACCAGGAGTTAAATCAGCTATTTCAAGAGCAAGTGGTGCCAAAGCTGACATTCACCTGGATGCTGGCGACAAAATCTGCTTCGGCAACCTGT

Basic information

species Physcomitrella patens
transcript PP1S99_229V6.2
intron # 3
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|208359919|gb|DC934892.1|DC934892
EST:     TGAACACCCATGTACACGCAGATCATGTCACCGGCACTGGTCTTCTCNNN                         NNNNNGATACCAGGAGTTAAATCAGCTATTTCAAGAGCAAGTGGTGCCAAA
genomic: TGAACACCCATGTACACGCAGATCATGTCACCGGCACTGGTCTTCTCAAAgtacgctatt ... atcgacgcagAAAAAGATACCAGGAGTTAAATCAGCTATTTCAAGAGCAAGTGGTGCCAAA
EST: gi|208384928|gb|DC903435.1|DC903435
EST:     TGAACACCCATGTACACGCAGATCATGTCACCGGCACTGGTCTTCTCNNN                         NNNNNGATACCAGGAGTTAAATCAGCTATTTCAAGAGCAAGTGGTGCCAAA
genomic: TGAACACCCATGTACACGCAGATCATGTCACCGGCACTGGTCTTCTCAAAgtacgctatt ... atcgacgcagAAAAAGATACCAGGAGTTAAATCAGCTATTTCAAGAGCAAGTGGTGCCAAA
EST: gi|208362752|gb|DC950552.1|DC950552
EST:     TGAACACCCATGTACACGCAGATCATGTCACCGGCACTGGTCTTCTCNNN                         NNNNNGATACCAGGAGTTAAATCAGCTATTTCAAGAGCAAGTGGTGCCAAA
genomic: TGAACACCCATGTACACGCAGATCATGTCACCGGCACTGGTCTTCTCAAAgtacgctatt ... atcgacgcagAAAAAGATACCAGGAGTTAAATCAGCTATTTCAAGAGCAAGTGGTGCCAAA
EST: gi|100389518|gb|BY988996.1|BY988996
EST:     TGAACACCCATGTACACGCAGATCATGTCACCGGCACTGGTCTTCTCNNN                         NNNNNGATACCAGGAGTTAAATCAGCTATTTCAAGAGCAAGTGGTGCCAAA
genomic: TGAACACCCATGTACACGCAGATCATGTCACCGGCACTGGTCTTCTCAAAgtacgctatt ... atcgacgcagAAAAAGATACCAGGAGTTAAATCAGCTATTTCAAGAGCAAGTGGTGCCAAA
EST: gi|100428897|gb|BY959488.1|BY959488
EST:     GAACACCCATGTACACGCAAGATCATGTCACCGGCACTGGTCTTCTCNNN                         NNNNNGATACCAGGAGTTAAATCAGCTATTTCAAGAGCAAGTG-TGCCAAA
genomic: GAACACCCATGTACACGCA-GATCATGTCACCGGCACTGGTCTTCTCAAAgtacgctatt ... atcgacgcagAAAAAGATACCAGGAGTTAAATCAGCTATTTCAAGAGCAAGTGGTGCCAAA
EST: gi|100400342|gb|BY954429.1|BY954429
EST:     TGAACACCCATGTACACGCAGATCATGTCACCGGCACTGGTCTTCTCNNN                         NNNNNGATACCAGGAGTTAAATCAGCTATTTCAAGAGCAAGTGGTGCCAAA
genomic: TGAACACCCATGTACACGCAGATCATGTCACCGGCACTGGTCTTCTCAAAgtacgctatt ... atcgacgcagAAAAAGATACCAGGAGTTAAATCAGCTATTTCAAGAGCAAGTGGTGCCAAA
EST: gi|100430949|gb|BY959951.1|BY959951
EST:     TGAACACCCATGTACACGCAGATCATGTCACCGGCACTGGTCTTCTCNNN                         NNNNNGATAACAGGAGTTAAATCAGCTATTTCCAGAGCAAGTGGTGCCAAA
genomic: TGAACACCCATGTACACGCAGATCATGTCACCGGCACTGGTCTTCTCAAAgtacgctatt ... atcgacgcagAAAAAGATACCAGGAGTTAAATCAGCTATTTCAAGAGCAAGTGGTGCCAAA
EST: gi|100422429|gb|BY976369.1|BY976369
EST:     TGAACACCCATGTACACGCAGATCATGTCACCGGCACTGGTCTTCTCNNN                         NNNNNGATACCAGGAGTTAAATCAGCTATTTCAAGAGCAAGTGGTGCCAAA
genomic: TGAACACCCATGTACACGCAGATCATGTCACCGGCACTGGTCTTCTCAAAgtacgctatt ... atcgacgcagAAAAAGATACCAGGAGTTAAATCAGCTATTTCAAGAGCAAGTGGTGCCAAA
EST: gi|18360987|gb|BJ193051.1|BJ193051
EST:     TGAACACCCATGTACACGCAGATCATGTCACCGGCACTGGTCTTCTCNNN                         NNNNNGATACCAGGAGTTAAATCAGCTATTTCAAGAGCAAGTGGTGCCAAA
genomic: TGAACACCCATGTACACGCAGATCATGTCACCGGCACTGGTCTTCTCAAAgtacgctatt ... atcgacgcagAAAAAGATACCAGGAGTTAAATCAGCTATTTCAAGAGCAAGTGGTGCCAAA
EST: gi|100411668|gb|BY992279.1|BY992279
EST:     TGAACACCCATGTACACGCAGATCATGTCACCGGCACTGGTCTTCTCNNN                         NNNNNGATACCAGGAGTTAAATCAGCTATTTCAAGAGCAAGTGGTGCCAAA
genomic: TGAACACCCATGTACACGCAGATCATGTCACCGGCACTGGTCTTCTCAAAgtacgctatt ... atcgacgcagAAAAAGATACCAGGAGTTAAATCAGCTATTTCAAGAGCAAGTGGTGCCAAA
EST: gi|162166628|gb|FC343520.1|FC343520
EST:     TGAACACCCATGTACACGCAGATCATGTCACCGGCACTGGTCTTCTCNNN                         NNNNNGATACCAGGAGTTAAATCAGCTATTTCAAGAGCAAGTGGTGCCAAA
genomic: TGAACACCCATGTACACGCAGATCATGTCACCGGCACTGGTCTTCTCAAAgtacgctatt ... atcgacgcagAAAAAGATACCAGGAGTTAAATCAGCTATTTCAAGAGCAAGTGGTGCCAAA
EST: gi|18364447|gb|BJ196520.1|BJ196520
EST:     TGAACACCCATGTACACGCAGATCATGTCACCGGCACTGGTCTTCTCNNN                         NNNNNGATACCAGGAGTTAAATCAGCTATTTCAAGAGCAAGTGGTGCCAAA
genomic: TGAACACCCATGTACACGCAGATCATGTCACCGGCACTGGTCTTCTCAAAgtacgctatt ... atcgacgcagAAAAAGATACCAGGAGTTAAATCAGCTATTTCAAGAGCAAGTGGTGCCAAA
EST: gi|162229838|gb|FC404291.1|FC404291
EST:     TGAACACCCATGTACACGCAGATCATGTCACCGGCACTGGTCTTCTCNNN                         NNNNNGATACCAGGAGTTAAATCAGCTATTTCAAGAGCAAGTGGTGCCAAA
genomic: TGAACACCCATGTACACGCAGATCATGTCACCGGCACTGGTCTTCTCAAAgtacgctatt ... atcgacgcagAAAAAGATACCAGGAGTTAAATCAGCTATTTCAAGAGCAAGTGGTGCCAAA
EST: gi|208358441|gb|DC930573.1|DC930573
EST:     TGAACACCCATGTACACGCAGATCATGTCACCGGCACTGGTCTTCTCNNN                         NNNNNGATACCAGGAGTTAAATCAGCTATTTCAAGAGCAAGTGGTGCCAAA
genomic: TGAACACCCATGTACACGCAGATCATGTCACCGGCACTGGTCTTCTCAAAgtacgctatt ... atcgacgcagAAAAAGATACCAGGAGTTAAATCAGCTATTTCAAGAGCAAGTGGTGCCAAA
EST: gi|208392227|gb|DC929488.1|DC929488
EST:     TGAACACCCATGTACACGCAGATCATGTCACCGGCACTGGTCTTCTCNNN                         NNNNNGATACCAGGAGTTAAATCAGCTATTTCAAGAGCAAGTGGTGCCAAA
genomic: TGAACACCCATGTACACGCAGATCATGTCACCGGCACTGGTCTTCTCAAAgtacgctatt ... atcgacgcagAAAAAGATACCAGGAGTTAAATCAGCTATTTCAAGAGCAAGTGGTGCCAAA
EST: gi|162167044|gb|FC342506.1|FC342506
EST:     TGAACACCCATGTACACGCAGATCATGTCACCGGCACTGGTCTTCTCNNN                         NNNNNGATACCAGGAGTTAAATCAGCTATTTCAAGAGCAAGTGGTGCCAAA
genomic: TGAACACCCATGTACACGCAGATCATGTCACCGGCACTGGTCTTCTCAAAgtacgctatt ... atcgacgcagAAAAAGATACCAGGAGTTAAATCAGCTATTTCAAGAGCAAGTGGTGCCAAA
EST: gi|100355071|gb|BY964986.1|BY964986
EST:     TGAACACCCATGTACACGCAGATCATGTCACCGGCACTGGTCTTCTCNAA                         AAAA-GATACCAGGAGTTAAATCAGCTATTTCAAGAGCAAGTGGTGCCAAA
genomic: TGAACACCCATGTACACGCAGATCATGTCACCGGCACTGGTCTTCTCAAAgtacgctatt ... atcgacgcagAAAAAGATACCAGGAGTTAAATCAGCTATTTCAAGAGCAAGTGGTGCCAAA
EST: gi|100372654|gb|BY948639.1|BY948639
EST:     TGAACACCCATGTACACGCAGATCATGTCACCGGCACTGGTCTTCTCNNN                         NNNNNGATACCAGGAGTTAAATCAGCTATTTCAAGAGCAAGTGGTGCCAAA
genomic: TGAACACCCATGTACACGCAGATCATGTCACCGGCACTGGTCTTCTCAAAgtacgctatt ... atcgacgcagAAAAAGATACCAGGAGTTAAATCAGCTATTTCAAGAGCAAGTGGTGCCAAA
EST: gi|100391246|gb|BY971560.1|BY971560
EST:     TGAACACCCATGTACACGCAGATCATGTCACCGGCACTGGTCTTCTCNNN                         NNNNNGATACCAGGAGTTAAATCAGCTATTTCAAGAGCAAGTGGTGCCAAA
genomic: TGAACACCCATGTACACGCAGATCATGTCACCGGCACTGGTCTTCTCAAAgtacgctatt ... atcgacgcagAAAAAGATACCAGGAGTTAAATCAGCTATTTCAAGAGCAAGTGGTGCCAAA
EST: gi|208390552|gb|DC937484.1|DC937484
EST:     TGAACACCCATGTACACGCAGATCATGTCACCGGCACTGGTCTTCTCNNN                         NNNNNGATACCAGGAGTTAAATCAGCTATTTCAAGAGCAAGTGGTGCCAAA
genomic: TGAACACCCATGTACACGCAGATCATGTCACCGGCACTGGTCTTCTCAAAgtacgctatt ... atcgacgcagAAAAAGATACCAGGAGTTAAATCAGCTATTTCAAGAGCAAGTGGTGCCAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttttatttaatctttttaatgtaaaaaattacgacttcgtgtaaatcgacgcagAAAAAGATACCAGGAGTTAAATCAGCTATTTCAAGAGCAAGTGGTGCCAAAGCTGACATTCACCTGGATGCTGGCGACAAAATCTGCTTCGGCAACCTGT
              ttttaat  putative branch site (score: 3)
     atttaatctttttaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgagaacaacttccacgctgtgatgacgtttgttttgtttttatttttttatttaatctttttaatgtaaaaaattacgacttcgtgtaaatcgacgcagAAAAAGATACCAGGAGTTAAATCAGCTATTTCAAGAGCAAGTGGTGCCAAAGCTGACATTCACCTGGATGCTGGCGACAAAATCTGCTTCGGCAACCTGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG