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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTACTGGCAGGAAGTCTCAGCGGGTCCAAACAATGCCTTTCTGCTGTGCGAGCTCTGCACAATATTCTCGGAGGTGTTGTAGACCCAgtaagtgttcgtatctcttctcactcgaagaacggttctgctgtatttatgtgatggctgtggattgtgcgaacaggctgtacctggctacgcagtgaaa...

Basic information

species Physcomitrella patens
transcript PP1S49_246V6.1
intron # 7
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|162198912|gb|FC372939.1|FC372939
EST:     TTTCTGCTGTGCGAGCTCTGCACAATATTCTCGGAGGTGTTGTAGACCCA                         AATGCTGCATACCTAATTTTGCGTGGATTGAAGACTTTAGATCTTCGAGTC
genomic: TTTCTGCTGTGCGAGCTCTGCACAATATTCTCGGAGGTGTTGTAGACCCAgtaagtgttc ... tttggaacagAATGCTGCATACCTAATTTTGCGTGGATTGAAGACTTTAGATCTTCGAGTC
EST: gi|162198913|gb|FC372940.1|FC372940
EST:     TTTCTGCTGTGCGAGCTCTGCACAATATTCTCGGAGGTGTTGTAGACCCA                         AATGCTGCATACCTAATTTTGCGTGGATTGAAGACTTTAGATCTTCGAGTC
genomic: TTTCTGCTGTGCGAGCTCTGCACAATATTCTCGGAGGTGTTGTAGACCCAgtaagtgttc ... tttggaacagAATGCTGCATACCTAATTTTGCGTGGATTGAAGACTTTAGATCTTCGAGTC
EST: gi|162164565|gb|FC341860.1|FC341860
EST:     TTTCTGCTGTGCGAGCTCTGCACAATATTCTCGGAGGTGTTGTAGACCCA                         AATGCTGCATACCTAATTTTGCGTGGATTGAAGACTTTAGATCTTCGAGTC
genomic: TTTCTGCTGTGCGAGCTCTGCACAATATTCTCGGAGGTGTTGTAGACCCAgtaagtgttc ... tttggaacagAATGCTGCATACCTAATTTTGCGTGGATTGAAGACTTTAGATCTTCGAGTC
EST: gi|162165089|gb|FC341630.1|FC341630
EST:     GCTGTGCGAGCTCTGCACAATATTCTCGGAGGTGTTGTAGACCCA                         AATGCTGCATACCTAATTTTGCGTGGATTGAAGACTTTAGATCTTCGAGTC
genomic: GCTGTGCGAGCTCTGCACAATATTCTCGGAGGTGTTGTAGACCCAgtaagtgttc ... tttggaacagAATGCTGCATACCTAATTTTGCGTGGATTGAAGACTTTAGATCTTCGAGTC
EST: gi|162156222|gb|FC332597.1|FC332597
EST:     TTTCTGCTGTGCGAGCTCTGCACAATATTCTCGGAGGTGTTGTAGACCCA                         AATGCTGCATACCTAATTTTGCGTGGATTGAAGACTTTAGATCTTCGAGTC
genomic: TTTCTGCTGTGCGAGCTCTGCACAATATTCTCGGAGGTGTTGTAGACCCAgtaagtgttc ... tttggaacagAATGCTGCATACCTAATTTTGCGTGGATTGAAGACTTTAGATCTTCGAGTC
EST: gi|162156221|gb|FC332596.1|FC332596
EST:     AGGTGTTGTAGACCCA                         AATGCTGCATACCTAATTTTGCGTGGATTGAAGACTTTAGATCTTCGAGTC
genomic: AGGTGTTGTAGACCCAgtaagtgttc ... tttggaacagAATGCTGCATACCTAATTTTGCGTGGATTGAAGACTTTAGATCTTCGAGTC
EST: gi|37848198|gb|BJ606206.1|BJ606206
EST:     TTTCTGCTGTGCGAGCTCTGCACAATATTCTCGGAGGTGTTGTAGACCCA                         AATGCTGCATACCTAATTTTGCGTGGATTGAAGACTTTAGATCTTCGAGTC
genomic: TTTCTGCTGTGCGAGCTCTGCACAATATTCTCGGAGGTGTTGTAGACCCAgtaagtgttc ... tttggaacagAATGCTGCATACCTAATTTTGCGTGGATTGAAGACTTTAGATCTTCGAGTC
EST: gi|67701447|gb|BJ961680.1|BJ961680
EST:     TTCTCGGAGGTGTTGTAGACCCA                         AATGCTGCATACCTAATTTTGCGTGGATTGAAGACTTTAGATCTTCGAGTC
genomic: TTCTCGGAGGTGTTGTAGACCCAgtaagtgttc ... tttggaacagAATGCTGCATACCTAATTTTGCGTGGATTGAAGACTTTAGATCTTCGAGTC

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: 21 (upstream exon), 15 (downstream exon)
Score: 1

GTACTGGCAGGAAGTCTCAGCGGGTCCAAACAATGCCTTTCTGCTGTGCGAGCTCTGCACAATATTCTCGGAGGTGTTGTAGACCCAgtaagtgttc ... tttggaacagAATGCTGCATACCTAATTTTGCGTGGATTGAAGACTTTAGATCTTCGAGTCAAGCAACAGAACAAAACAGCATATTTGCTAGCACAGAATCTAGAAGCTC




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