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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atgcccatggatgagtttttgttgaatgagtaatttatattcattctacattccattgatctcctctaaatgagatgaaatactctccgctttgttgcagGACATTGAATTCATGGAGAAGAAAATTGACGACTGTGAAAAAGTCTTGAAGCGCAGCAATGCTAAGGAAGCGAAAATGGAATTGGAATGCTGTCAAAAG

Basic information

species Physcomitrella patens
transcript PP1S207_28V6.1
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|18361521|gb|BJ193587.1|BJ193587
EST:     TTGACCCCGTTAGAGATCTGGAAATCATTTCTCAAGAATTGCGTTTAAAG                         GACATTGAATTCATGGAGAAGAAAATTGACGACTGTGAAAAAGTCTTGAAG
genomic: TTGACCCCGTTAGAGATCTGGAAATCATTTCTCAAGAATTGCGTTTAAAGgtaacctctt ... tttgttgcagGACATTGAATTCATGGAGAAGAAAATTGACGACTGTGAAAAAGTCTTGAAG
EST: gi|162272681|gb|FC448307.1|FC448307
EST:     TTGACCCCGTTAGAGATCTGGAAATCATTTCTCAAGAATTGCGTTTAAAG                         GACATTGAATTCATGGAGAAGAAAATTGACGACTGTGAAAAAGTCTTGAAG
genomic: TTGACCCCGTTAGAGATCTGGAAATCATTTCTCAAGAATTGCGTTTAAAGgtaacctctt ... tttgttgcagGACATTGAATTCATGGAGAAGAAAATTGACGACTGTGAAAAAGTCTTGAAG
EST: gi|208383342|gb|DC907517.1|DC907517
EST:     TTGACCCCGTTAGAGATCTGGAAATCATTTCTCAAGAATTGCGTTTAAAG                         GACATTGAATTCATGGAAAAGAAAATTGACGACTGTGAAAAAGTCTTGAAG
genomic: TTGACCCCGTTAGAGATCTGGAAATCATTTCTCAAGAATTGCGTTTAAAGgtaacctctt ... tttgttgcagGACATTGAATTCATGGAGAAGAAAATTGACGACTGTGAAAAAGTCTTGAAG
EST: gi|67573864|gb|BJ946688.1|BJ946688
EST:     TTGACCCCGTTAGAGATCTGGAAATCATTTCTCAAGAATTGCGTTTAAAG                         GACATTGAATTCATGGAGAAGAAAATTGACGACTGTGAAAAAGTCTTGAAG
genomic: TTGACCCCGTTAGAGATCTGGAAATCATTTCTCAAGAATTGCGTTTAAAGgtaacctctt ... tttgttgcagGACATTGAATTCATGGAGAAGAAAATTGACGACTGTGAAAAAGTCTTGAAG
EST: gi|100415938|gb|BY956998.1|BY956998
EST:     TTGACCCCGTTAGAGATCTGGAAATCATTTCTCAGGAATTGCGTTTAAAG                         GACATTGAATCCATGGAGAAGAAAATTGACGACTGTGAAAAAG
genomic: TTGACCCCGTTAGAGATCTGGAAATCATTTCTCAAGAATTGCGTTTAAAGgtaacctctt ... tttgttgcagGACATTGAATTCATGGAGAAGAAAATTGACGACTGTGAAAAAG
EST: gi|208370398|gb|DC931810.1|DC931810
EST:     TTGACCCCGTTAGAGATCTGGAAATCATTTCTCAAGAATTGCGTTTAAAG                         GACATTGGATTCATGGAGAAGAAAATTGACGACTGTGAAAAAGTCTTGAAG
genomic: TTGACCCCGTTAGAGATCTGGAAATCATTTCTCAAGAATTGCGTTTAAAGgtaacctctt ... tttgttgcagGACATTGAATTCATGGAGAAGAAAATTGACGACTGTGAAAAAGTCTTGAAG
EST: gi|208394358|gb|DC904178.1|DC904178
EST:     TTGACCCCGTTAGAGATCTGGAAATCATTTCTCAAGAATTGCGTTTAAAG                         GACATTGAATTCATGGAGAAGAAAATTGACGACTGTGAAAAAGTCTTGAAG
genomic: TTGACCCCGTTAGAGATCTGGAAATCATTTCTCAAGAATTGCGTTTAAAGgtaacctctt ... tttgttgcagGACATTGAATTCATGGAGAAGAAAATTGACGACTGTGAAAAAGTCTTGAAG
EST: gi|100395348|gb|BY953692.1|BY953692
EST:     TTGACCCCGTTAGAGATCTGGAAATCATTTCTCAAGAATTGCGTTTAAAG                         GACATTGAATTCATGGAGAAGAAAATTGACGACTGTGAAAAAGTCTTGAAG
genomic: TTGACCCCGTTAGAGATCTGGAAATCATTTCTCAAGAATTGCGTTTAAAGgtaacctctt ... tttgttgcagGACATTGAATTCATGGAGAAGAAAATTGACGACTGTGAAAAAGTCTTGAAG
EST: gi|162263698|gb|FC439623.1|FC439623
EST:     TTGACCCCGTTAGAGATCTGGAAATCATTTCTCAAGAATTGCGTTTAAAG                         GACATTGAATTCATGGAGAAGAAAATTGACGACTGTGAAAAAGTCTTGAAG
genomic: TTGACCCCGTTAGAGATCTGGAAATCATTTCTCAAGAATTGCGTTTAAAGgtaacctctt ... tttgttgcagGACATTGAATTCATGGAGAAGAAAATTGACGACTGTGAAAAAGTCTTGAAG
EST: gi|18358448|gb|BJ190507.1|BJ190507
EST:     TTGACCCCGTTAGAGATCTGGAAATCATTTCTCAAGAATTGCGTTTAAAG                         GACATTGAATTCATGGAGAAGAAAATTGACGACTGTGAAAAAAGTCTTGAA
genomic: TTGACCCCGTTAGAGATCTGGAAATCATTTCTCAAGAATTGCGTTTAAAGgtaacctctt ... tttgttgcagGACATTGAATTCATGGAGAAGAAAATTGACGACTGTGAAAAA-GTCTTGAA
EST: gi|162202372|gb|FC379991.1|FC379991
EST:     TTGACCCCGTCAGAGATCTGGAAATCATTTCTCAAGAATTGCGTTTAAAG                         GACATTGAATTCATGGAGAAGAAAATTGACGACTGTGAAAAAGTCTTGAAG
genomic: TTGACCCCGTTAGAGATCTGGAAATCATTTCTCAAGAATTGCGTTTAAAGgtaacctctt ... tttgttgcagGACATTGAATTCATGGAGAAGAAAATTGACGACTGTGAAAAAGTCTTGAAG
EST: gi|100387386|gb|BY988257.1|BY988257
EST:     TTGACCCCGTTAGAGATCTGGAAATCATTTCTCAAGAATTGCGTTTGAAG                         GACATTGAATTCATGGAGAAGAAAATTGACGACTGTGAAAAAGTCTTGAAG
genomic: TTGACCCCGTTAGAGATCTGGAAATCATTTCTCAAGAATTGCGTTTAAAGgtaacctctt ... tttgttgcagGACATTGAATTCATGGAGAAGAAAATTGACGACTGTGAAAAAGTCTTGAAG
EST: gi|208399872|gb|DC904954.1|DC904954
EST:     TTGACCCCGTTAGAGATCTGGAAATCATTTCTCAAGAATTGCGTTTAAAG                         GACATTGAATTCATGGAGAAGAAAATTGACGACTGTGAAAAAGTCTTGAAG
genomic: TTGACCCCGTTAGAGATCTGGAAATCATTTCTCAAGAATTGCGTTTAAAGgtaacctctt ... tttgttgcagGACATTGAATTCATGGAGAAGAAAATTGACGACTGTGAAAAAGTCTTGAAG
EST: gi|162264593|gb|FC440889.1|FC440889
EST:     TTGACCCCGTTAGAGATCTGGAAATCATTTCTCAAGAATTGCGTTTAAAG                         GACATTGAATTCATGGAGAAGAAAATTGACGACTGTGAAAAAGTCTTGAAG
genomic: TTGACCCCGTTAGAGATCTGGAAATCATTTCTCAAGAATTGCGTTTAAAGgtaacctctt ... tttgttgcagGACATTGAATTCATGGAGAAGAAAATTGACGACTGTGAAAAAGTCTTGAAG
EST: gi|18361750|gb|BJ193817.1|BJ193817
EST:     TTGACCCCGTTAGAGATCTGGAAATCATTTCTCAAGAATTGCGTTTAAAG                         GACATTGAATTCATGGAGAAGAAAATTGACGA
genomic: TTGACCCCGTTAGAGATCTGGAAATCATTTCTCAAGAATTGCGTTTAAAGgtaacctctt ... tttgttgcagGACATTGAATTCATGGAGAAGAAAATTGACGA
EST: gi|18347703|gb|BJ179750.1|BJ179750
EST:     TTGACCCCGTTAGAGATCTGGAAATCATTTCTCAAGAATTGCGTTTAAAG                         GACATTGAATTCATGGAG
genomic: TTGACCCCGTTAGAGATCTGGAAATCATTTCTCAAGAATTGCGTTTAAAGgtaacctctt ... tttgttgcagGACATTGAATTCATGGAG
EST: gi|208397168|gb|DC911777.1|DC911777
EST:     TTGACCCCGTTAGAGATCTGGAAATCATTTCTCAAGAATTGCGTTTAAAG                         GACATTGAATTCATGGAGAAGAAAATTGACGACTGTGAAAAAGTCTTGAAG
genomic: TTGACCCCGTTAGAGATCTGGAAATCATTTCTCAAGAATTGCGTTTAAAGgtaacctctt ... tttgttgcagGACATTGAATTCATGGAGAAGAAAATTGACGACTGTGAAAAAGTCTTGAAG
EST: gi|100352204|gb|BY983091.1|BY983091
EST:     TTGACCCCGTTAGAGATCTGGAAATCATTTCTCAAGAATTGCGTTTAAAG                         GACATTGAATTCATGCAGAAGAAAATTGACGACTGTTAAAAAGTCTTGAAG
genomic: TTGACCCCGTTAGAGATCTGGAAATCATTTCTCAAGAATTGCGTTTAAAGgtaacctctt ... tttgttgcagGACATTGAATTCATGGAGAAGAAAATTGACGACTGTGAAAAAGTCTTGAAG
EST: gi|208391589|gb|DC933838.1|DC933838
EST:     TTGACCCCGTTAGAGATCTGGAAATCATTTCTCAAGAATTGCGTTTAAAG                         GACATTGAATTCATGGAGAAGAAAATTGACGACTGTGAAAAAGTCTTGAAG
genomic: TTGACCCCGTTAGAGATCTGGAAATCATTTCTCAAGAATTGCGTTTAAAGgtaacctctt ... tttgttgcagGACATTGAATTCATGGAGAAGAAAATTGACGACTGTGAAAAAGTCTTGAAG
EST: gi|162278437|gb|FC454523.1|FC454523
EST:     TTGACCCCGTTAGAGATCTGGAAATCATTTCTCAAGAATTGCGTTTAAAG                         GACATTGAATTCATGGAGAAGAAAATTGACGACTGTGAAAAAGTCTTGAAG
genomic: TTGACCCCGTTAGAGATCTGGAAATCATTTCTCAAGAATTGCGTTTAAAGgtaacctctt ... tttgttgcagGACATTGAATTCATGGAGAAGAAAATTGACGACTGTGAAAAAGTCTTGAAG
EST: gi|18347772|gb|BJ179819.1|BJ179819
EST:     TTGACCCCGTTAGAGATCTGGAAATCATTTCTCAAGAATTGCGTTTAAAG                         GACATTGAATTCATGGAGA
genomic: TTGACCCCGTTAGAGATCTGGAAATCATTTCTCAAGAATTGCGTTTAAAGgtaacctctt ... tttgttgcagGACATTGAATTCATGGAGA
EST: gi|208393061|gb|DC929556.1|DC929556
EST:     TTGACCCCGTTAGAGATCTGGAAATCATTTCTCAAGAATTGCGTTTAAAG                         GACATTGAATTCATGGAGAAGAAAATTGACGACTGTGAAAAAGTCTTGAAG
genomic: TTGACCCCGTTAGAGATCTGGAAATCATTTCTCAAGAATTGCGTTTAAAGgtaacctctt ... tttgttgcagGACATTGAATTCATGGAGAAGAAAATTGACGACTGTGAAAAAGTCTTGAAG
EST: gi|162175835|gb|FC352137.1|FC352137
EST:     TTGACCCCGTCAGAGATCTGGAAATCATTTCTCAAGAATTGCGTTTAAAG                         GACATTGAATTCATGGAGAAGAAAATTGACGACTGTGAAAAAGTCTTGAAG
genomic: TTGACCCCGTTAGAGATCTGGAAATCATTTCTCAAGAATTGCGTTTAAAGgtaacctctt ... tttgttgcagGACATTGAATTCATGGAGAAGAAAATTGACGACTGTGAAAAAGTCTTGAAG
EST: gi|208359117|gb|DC930449.1|DC930449
EST:     TTGACCCCGTTAGAGATCTGGAAATCATTTCTCAAGAATTGCGTTTAAAG                         GACATTGAATTCATGGAGAAGAAAATTGACGACTGTGAAAAAGTCTTGAAG
genomic: TTGACCCCGTTAGAGATCTGGAAATCATTTCTCAAGAATTGCGTTTAAAGgtaacctctt ... tttgttgcagGACATTGAATTCATGGAGAAGAAAATTGACGACTGTGAAAAAGTCTTGAAG
EST: gi|100386335|gb|BY988002.1|BY988002
EST:     TTGACCCCGTTAGAGATCTGGAAATCATTTCTCAAGAATTGCGTTTAAAG                         GACATTGAATTCATGGAGAAGAAAATTGACGACTGTNGAAAA-GTCTTGAA
genomic: TTGACCCCGTTAGAGATCTGGAAATCATTTCTCAAGAATTGCGTTTAAAGgtaacctctt ... tttgttgcagGACATTGAATTCATGGAGAAGAAAATTGACGACTGT-GAAAAAGTCTTGAA

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 33 (upstream exon), 34 (downstream exon)
Score: 11

GGGCTTTTGATGATCCAGAGGTCACACATGTTGAGGATTCAGTTGACCCCGTTAGAGATCTGGAAATCATTTCTCAAGAATTGCGTTTAAAGgtaacctctt ... tttgttgcagGACATTGAATTCATGGAGAAGAAAATTGACGACTGTGAAAAAGTCTTGAAGCGCAGCAATGCTAAGGAAGCGAAAATGGAATTGGAATGCTGTCAAAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctacattccattgatctcctctaaatgagatgaaatactctccgctttgttgcagGACATTGAATTCATGGAGAAGAAAATTGACGACTGTGAAAAAGTCTTGAAGCGCAGCAATGCTAAGGAAGCGAAAATGGAATTGGAATGCTGTCAAAAG
                  ctctaaa  putative branch site (score: 11)
                                     ctctccgctttgtt  putative PPT
                             atgaaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atgcccatggatgagtttttgttgaatgagtaatttatattcattctacattccattgatctcctctaaatgagatgaaatactctccgctttgttgcagGACATTGAATTCATGGAGAAGAAAATTGACGACTGTGAAAAAGTCTTGAAGCGCAGCAATGCTAAGGAAGCGAAAATGGAATTGGAATGCTGTCAAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - -tgttgaa