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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTGTATCAAGTAGCAAGTGTCAAGCAGGAGTGGAATACCATTAAAGTTTTCCCTGATCTTTCTGGGACAGgtgatgactcttcttgttttgatgcttattgtgaccaacttgatttactgtttagagaccatgggatgactttagttcagatttgtaatttcttgcagcg...

Basic information

species Physcomitrella patens
transcript PP1S14_250V6.2
intron # 17
splice site 5'
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|67725231|gb|BJ975490.1|BJ975490
EST:     CAAGCAGGAGTGGAATACCATTAAAGTTTTCCCTGATCCTTCTGGGACAG                         GCAAAGTGACGTCAGTCCGATTTGGTCCAGATGCGTCGTATTTGGCAGTTG
genomic: CAAGCAGGAGTGGAATACCATTAAAGTTTTCCCTGATCTTTCTGGGACAGgtgatgactc ... tgcatgacagGCAAAGTGACGTCAGTCCGATTTGGTCCAGATGCGTCGTATTTGGCAGTTG
EST: gi|162238755|gb|FC419053.1|FC419053
EST:     CAAGCAGGAGTGGAATACCATTAAAGTTTTCCCTGATCTTTCTGGGACAG                         GCAAAGTGACGTCAGTCCGATTTGGTCCAGATGCGTCGTATTTGGCAGTTG
genomic: CAAGCAGGAGTGGAATACCATTAAAGTTTTCCCTGATCTTTCTGGGACAGgtgatgactc ... tgcatgacagGCAAAGTGACGTCAGTCCGATTTGGTCCAGATGCGTCGTATTTGGCAGTTG
EST: gi|37822061|gb|BJ580127.1|BJ580127
EST:     CAAGCAGGAGTGGAATACCATTAAAGTTTTCCCTGATCTTTCTGGGACAG                         GCAAAGTGACGTCAGTCCGATTTGGTCCAGATGCGTCGTATTTGGCAGTTG
genomic: CAAGCAGGAGTGGAATACCATTAAAGTTTTCCCTGATCTTTCTGGGACAGgtgatgactc ... tgcatgacagGCAAAGTGACGTCAGTCCGATTTGGTCCAGATGCGTCGTATTTGGCAGTTG
EST: gi|6102231|gb|AW126701.1|AW126701
EST:     CAAGCAGGAGTGGAATACCATTAAAGTTTTCCCTGATCTTTCTGGGACAG                         GCAAAGTGACGTCAGTCCGATTTGGTCCAGATGCGTCGTATTTGGCAGTTG
genomic: CAAGCAGGAGTGGAATACCATTAAAGTTTTCCCTGATCTTTCTGGGACAGgtgatgactc ... tgcatgacagGCAAAGTGACGTCAGTCCGATTTGGTCCAGATGCGTCGTATTTGGCAGTTG
EST: gi|19787424|gb|BQ040623.1|BQ040623
EST:     CAAGCAGGAGTGGAATACCATTAAAGTTTTCCCTGATCTTTCTGGGACAG                         GCAAAGTGACGTCAGTCCGATTTGGTCCAGATGCGTCGTATTTGGCAGTTG
genomic: CAAGCAGGAGTGGAATACCATTAAAGTTTTCCCTGATCTTTCTGGGACAGgtgatgactc ... tgcatgacagGCAAAGTGACGTCAGTCCGATTTGGTCCAGATGCGTCGTATTTGGCAGTTG
EST: gi|18340446|gb|BJ172474.1|BJ172474
EST:     CAAGCAGGAGTGGAATACCATTAAAGTTTTCCCTGATCTTTCTGGGACAG                         GCAAAGTGACGTCAGTCCGATTTGGTCCAGATGCGTCGTATTTGGCAGTTG
genomic: CAAGCAGGAGTGGAATACCATTAAAGTTTTCCCTGATCTTTCTGGGACAGgtgatgactc ... tgcatgacagGCAAAGTGACGTCAGTCCGATTTGGTCCAGATGCGTCGTATTTGGCAGTTG
EST: gi|67726008|gb|BJ976267.1|BJ976267
EST:     CAAGCAGGAGTGGAATACCATTAAAGTTTTCCCTGATCCTTCTGGGACAG                         GCAAAGTGACGTCAGTCCGATTTGGTCCAGATGCGTCGTATTTGGCAGTTG
genomic: CAAGCAGGAGTGGAATACCATTAAAGTTTTCCCTGATCTTTCTGGGACAGgtgatgactc ... tgcatgacagGCAAAGTGACGTCAGTCCGATTTGGTCCAGATGCGTCGTATTTGGCAGTTG
EST: gi|162167817|gb|FC344547.1|FC344547
EST:     CAAGCAGGAGTGGAATACCATTAAAGTTTTCCCTGATCTTTCTGGGACAG                         GCAAAGTGACGTCAGTCCGATTTGGTCCAGATGCGTCGTATTTGGCAGTTG
genomic: CAAGCAGGAGTGGAATACCATTAAAGTTTTCCCTGATCTTTCTGGGACAGgtgatgactc ... tgcatgacagGCAAAGTGACGTCAGTCCGATTTGGTCCAGATGCGTCGTATTTGGCAGTTG
EST: gi|37852835|gb|BJ610843.1|BJ610843
EST:     CAAGCAGGAGTGGAATACCATTAAAGTTTTCCCTGATCTTTCTGGGACAG                         GCAAAGTGACGTCAGTCCGATTTGGTCCAGATGCGTCGTATTTGGCAGTTG
genomic: CAAGCAGGAGTGGAATACCATTAAAGTTTTCCCTGATCTTTCTGGGACAGgtgatgactc ... tgcatgacagGCAAAGTGACGTCAGTCCGATTTGGTCCAGATGCGTCGTATTTGGCAGTTG
EST: gi|162257669|gb|FC433596.1|FC433596
EST:     CAAGCAGGAGTGGAATACCATTAAAGTTTTCCCTGATCTTTCTGGGACAG                         GCAAAGTGACGTCAGTCCGATTTGGTCCAGATGCGTCGTATTTGGCAGTTG
genomic: CAAGCAGGAGTGGAATACCATTAAAGTTTTCCCTGATCTTTCTGGGACAGgtgatgactc ... tgcatgacagGCAAAGTGACGTCAGTCCGATTTGGTCCAGATGCGTCGTATTTGGCAGTTG
EST: gi|37830480|gb|BJ588492.1|BJ588492
EST:     CAAGCAGGAGTGGAATACCATTAAAGTTTTCCCTGATCTTTCTGGGACAG                         GCAAAGTGACGTCAGTCCGATTTGGTCCAGATGCGTCGTATTTGGCAGTTG
genomic: CAAGCAGGAGTGGAATACCATTAAAGTTTTCCCTGATCTTTCTGGGACAGgtgatgactc ... tgcatgacagGCAAAGTGACGTCAGTCCGATTTGGTCCAGATGCGTCGTATTTGGCAGTTG
EST: gi|162182528|gb|FC357503.1|FC357503
EST:     CAAGCAGGAGTGGAATACCATTAAAGTTTTCCCTGATCTTTCTGGGACAG                         GCAAAGTGACGTCAGTCCGATTTGGTCCAGATGCGTCGTATTTGGCAGTTG
genomic: CAAGCAGGAGTGGAATACCATTAAAGTTTTCCCTGATCTTTCTGGGACAGgtgatgactc ... tgcatgacagGCAAAGTGACGTCAGTCCGATTTGGTCCAGATGCGTCGTATTTGGCAGTTG

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: 22 (upstream exon), 31 (downstream exon)
Score: 3

GTTGTATCAAGTAGCAAGTGTCAAGCAGGAGTGGAATACCATTAAAGTTTTCCCTGATCTTTCTGGGACAGgtgatgactc ... tgcatgacagGCAAAGTGACGTCAGTCCGATTTGGTCCAGATGCGTCGTATTTGGCAGTTGGCAGCAGCGACCGTAACCTGCGTATTTTTGGTGCTCCTACGGCTACTTC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTGTATCAAGTAGCAAGTGTCAAGCAGGAGTGGAATACCATTAAAGTTTTCCCTGATCTTTCTGGGACAGgtgatgactcttcttgttttgatgcttattgtgaccaacttgatttactgtttagagaccatgggatgactttagttcagatttgtaatttcttgcagcg

- - - - - - - - - - - - - -  AGTGGA