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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagctattgcgcttgatgatctgaagctagttttactaatgtctaaacattttcattgttatacttatctaaaacaacgctcttcatggtgcacattgttcaatgactgttagttttgttctagcactcaaagctttctttgttttacagGGTTGGATGATGGGAGAAACTCTGCTTAGTCCCGGAGATTCAAGACTTTGTGATTGACAATTTTGTAGAACAGTACTTTTTACCTCATTGATTCACAGCT

Basic information

species Physcomitrella patens
transcript PP1S53_92V6.2
intron # 11
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|162271773|gb|FC448906.1|FC448906
EST:     AGCTCACTCATGATTTGTACGACTCCTTCAAAGAAGAGGCGAAGTCCCAG                         GGTTGGATGATGGGAGAAACTCTGCTTAGTCCCGGAGATTCAAGACTTTGT
genomic: AGCTCACTCATGATTTGTACGACTCCTTCAAAGAAGAGGCGAAGTCCCAGgtgagctatt ... tgttttacagGGTTGGATGATGGGAGAAACTCTGCTTAGTCCCGGAGATTCAAGACTTTGT
EST: gi|7648047|gb|AW739030.1|AW739030
EST:     AGCTCACTCATGATTTGTACGACTCCTTCAAAGAAGAGGCGAAGTCCCAG                         GGTTGGATGATGGGAGAAACTCTGCTTAGTCCCGGAGATTCAAGACTTTGT
genomic: AGCTCACTCATGATTTGTACGACTCCTTCAAAGAAGAGGCGAAGTCCCAGgtgagctatt ... tgttttacagGGTTGGATGATGGGAGAAACTCTGCTTAGTCCCGGAGATTCAAGACTTTGT
EST: gi|162241338|gb|FC416969.1|FC416969
EST:     AGCTCACTCATGATTTGTACGACTCCTTCAAAGAAGAGGCGAAGTCCCAG                         GGTTGGATGATGGGAGAAACTCTGCTTAGTCCCGGAGATTCAAGACTTTGT
genomic: AGCTCACTCATGATTTGTACGACTCCTTCAAAGAAGAGGCGAAGTCCCAGgtgagctatt ... tgttttacagGGTTGGATGATGGGAGAAACTCTGCTTAGTCCCGGAGATTCAAGACTTTGT
EST: gi|162159654|gb|FC336040.1|FC336040
EST:     AGCTCACTCATGATTTGTACGACTCCTTCAAAGAAGAGGCGAAGTCCCAG                         GGTTGGATGATGGGAGAAACTCTGCTTAGTCCCGGAGATTCAAGACTTTGT
genomic: AGCTCACTCATGATTTGTACGACTCCTTCAAAGAAGAGGCGAAGTCCCAGgtgagctatt ... tgttttacagGGTTGGATGATGGGAGAAACTCTGCTTAGTCCCGGAGATTCAAGACTTTGT
EST: gi|37827926|gb|BJ585938.1|BJ585938
EST:     AGCTCACTCATGATTTGTACGACTCCTTCAAAGAAGAGGCGAAGTCCCAG                         GGTTGGATGATGGGAGAAACTCTGCTTAGTCCCGGAGATTCAAGACTTTGT
genomic: AGCTCACTCATGATTTGTACGACTCCTTCAAAGAAGAGGCGAAGTCCCAGgtgagctatt ... tgttttacagGGTTGGATGATGGGAGAAACTCTGCTTAGTCCCGGAGATTCAAGACTTTGT
EST: gi|162271772|gb|FC448905.1|FC448905
EST:     AGCTCACTCATGATTTGTACGACTCCTTCAAAGAAGAGGCGAAGTCCCAG                         GGTTGGATGATGGGAGAAACTCTGCTTAGTCCCGGAGATTCAAGACTTTGT
genomic: AGCTCACTCATGATTTGTACGACTCCTTCAAAGAAGAGGCGAAGTCCCAGgtgagctatt ... tgttttacagGGTTGGATGATGGGAGAAACTCTGCTTAGTCCCGGAGATTCAAGACTTTGT

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: 34 (upstream exon), 35 (downstream exon)
Score: 27

AAGCACACTTATTACCAGCAACGTTGGGGCTATCGTGGAAGAGAGCACTAAGCTCACTCATGATTTGTACGACTCCTTCAAAGAAGAGGCGAAGTCCCAGgtgagctatt ... tgttttacagGGTTGGATGATGGGAGAAACTCTGCTTAGTCCCGGAGATTCAAGACTTTGTGATTGACAATTTTGTAGAACAGTACTTTTTACCTCATTGATTCACAGCT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgttcaatgactgttagttttgttctagcactcaaagctttctttgttttacagGGTTGGATGATGGGAGAAACTCTGCTTAGTCCCGGAGATTCAAGACTTTGTGATTGACAATTTTGTAGAACAGTACTTTTTACCTCATTGATTCACAGCT
                                      ctttctttgttttac  CT-rich tract
                                           tttgtttta  TA-rich tract