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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtaggttttatcgagcatcttagtgaaattttcacaattcaactatttttagttgttacagtcgatcttatttgcaaatgctcttttttcttgtaacagAAAGTCCTAATGGAGCTAGAAGCTGATCCTAAACTTGTATACCACTGCGGGCTTACCTCACGACGTTTGCCT

Basic information

species Physcomitrella patens
transcript PP1S82_30V6.1
intron # 7
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|18334747|gb|BJ166764.1|BJ166764
EST:     ATCTTATAAATCGTGCTTTGAAAGGTCCTTTGGCACCTGCGCAGCAAAAG                         AAAGTCCTAATGGAGCTAGAAGCTGATCCTAAACTTGTATACCACTGCGGG
genomic: ATCTTATAAATCGTGCTTTGAAAGGTCCTTTGGCACCTGCGCAGCAAAAGgtcctttttc ... cttgtaacagAAAGTCCTAATGGAGCTAGAAGCTGATCCTAAACTTGTATACCACTGCGGG
EST: gi|37822015|gb|BJ580081.1|BJ580081
EST:     ATCTTATAAATCGTGCTTTGAAAGGTCCTTTGGCACCTGCGCAGCAAAAG                         AAAGTCCTAATGGAGCTAGAAGCTGATCCTAAACTTGTATACCACTGCGGG
genomic: ATCTTATAAATCGTGCTTTGAAAGGTCCTTTGGCACCTGCGCAGCAAAAGgtcctttttc ... cttgtaacagAAAGTCCTAATGGAGCTAGAAGCTGATCCTAAACTTGTATACCACTGCGGG
EST: gi|162165273|gb|FC341931.1|FC341931
EST:     ATCTTATAAATCGTGCTTTGAAAGGTCCTTTGGCACCTGCGCAGCAAAAG                         AAAGTCCTAATGGAGCTAGAAGCTGATCCTAAACTTGTATACCACTGCGGG
genomic: ATCTTATAAATCGTGCTTTGAAAGGTCCTTTGGCACCTGCGCAGCAAAAGgtcctttttc ... cttgtaacagAAAGTCCTAATGGAGCTAGAAGCTGATCCTAAACTTGTATACCACTGCGGG
EST: gi|208360796|gb|DC946492.1|DC946492
EST:     ATCTTATAAATCGTGCTTTGAAAGGTCCTTTGGCACCTGCGCGGCAAAAG                         AAAGTCCTAATGGAGCTAGAAGCTGATCCTAAACTTGTATACCACTGCGGG
genomic: ATCTTATAAATCGTGCTTTGAAAGGTCCTTTGGCACCTGCGCAGCAAAAGgtcctttttc ... cttgtaacagAAAGTCCTAATGGAGCTAGAAGCTGATCCTAAACTTGTATACCACTGCGGG
EST: gi|162165272|gb|FC341930.1|FC341930
EST:     ATCTTATAAATCGTGCTTTGAAAGGTCCTTTGGCACCTGCGCAGCAAAAG                         AAAGTCCTAATGGAGCTAGAAGCTGATCCTAAACTTGTATACCACTGCGGG
genomic: ATCTTATAAATCGTGCTTTGAAAGGTCCTTTGGCACCTGCGCAGCAAAAGgtcctttttc ... cttgtaacagAAAGTCCTAATGGAGCTAGAAGCTGATCCTAAACTTGTATACCACTGCGGG
EST: gi|162228505|gb|FC404129.1|FC404129
EST:     ATCTTATAAATCGTGCTTTGAAAGGTCCTTTGGCACCTGCGCAGCAAAAG                         AAAGTCCTAATGGAGCTAGAAGCTGATCCTAAACTTGTATACCACTGCGGG
genomic: ATCTTATAAATCGTGCTTTGAAAGGTCCTTTGGCACCTGCGCAGCAAAAGgtcctttttc ... cttgtaacagAAAGTCCTAATGGAGCTAGAAGCTGATCCTAAACTTGTATACCACTGCGGG
EST: gi|18339762|gb|BJ171789.1|BJ171789
EST:     ATCTTATAAATCGTGCTTTGAAAGGTCCTTTGGCACCTGCGCAGCAAAAG                         AAAGTCCTAATGGAGCTAGAAGCTGATCCTAAACTTGTATACCACTGCGGG
genomic: ATCTTATAAATCGTGCTTTGAAAGGTCCTTTGGCACCTGCGCAGCAAAAGgtcctttttc ... cttgtaacagAAAGTCCTAATGGAGCTAGAAGCTGATCCTAAACTTGTATACCACTGCGGG

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: 20 (upstream exon), 16 (downstream exon)
Score: 1

GTGGGATTATGGGATGTGTGCCGATACCAGCCGTGATGCTGCTATCCGAGATCTTATAAATCGTGCTTTGAAAGGTCCTTTGGCACCTGCGCAGCAAAAGgtcctttttc ... cttgtaacagAAAGTCCTAATGGAGCTAGAAGCTGATCCTAAACTTGTATACCACTGCGGGCTTACCTCACGACGTTTGCCT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttttagttgttacagtcgatcttatttgcaaatgctcttttttcttgtaacagAAAGTCCTAATGGAGCTAGAAGCTGATCCTAAACTTGTATACCACTGCGGGCTTACCTCACGACGTTTGCCT
                                  tgctcttttttcttgt  CT-rich tract
                    atcttattt  TA-rich tract