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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgttttgatagtaatgcaagggttaagtgcgtctgatttcatttattgcctcatacctcagcataaaacttttgaattttggactggatacgcttttcagGGCGGCAAAATTTTGACTGGTGGCTCTGTGATTGATCGTGATGGCAACTTTGTCGAACCGACTGTAGTCGAGATATCACATGATGCAGAAATTGTGAGGG

Basic information

species Physcomitrella patens
transcript PP1S237_29V6.1
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|162268956|gb|FC445760.1|FC445760
EST:     AGCACTCTAAGGCATGCTTCGAAGAGGGTATTAAGAAAATCAAGGCTCAG                         GGCGGCAAAATTTTGACTGGTGGCTCTGTGATTGATCGTGATGGCAACTTT
genomic: AGCACTCTAAGGCATGCTTCGAAGAGGGTATTAAGAAAATCAAGGCTCAGgcaatgattc ... cgcttttcagGGCGGCAAAATTTTGACTGGTGGCTCTGTGATTGATCGTGATGGCAACTTT
EST: gi|162180806|gb|FC358307.1|FC358307
EST:     AAGAGGGTATTAAGAAAATCAAGGCTCAG                         GGCGGCAAAATTTTGACTGGTGGCTCTGTGATTGATCGTGATGGCAACTTT
genomic: AAGAGGGTATTAAGAAAATCAAGGCTCAGgcaatgattc ... cgcttttcagGGCGGCAAAATTTTGACTGGTGGCTCTGTGATTGATCGTGATGGCAACTTT
EST: gi|162153738|gb|FC329141.1|FC329141
EST:     AGCACTCTAAGGCATGCTTCGAAGAGGGTATTAAGAAAATCAAGGCTCAG                         GGCGGCAAAATTTTGACTGGTGGCTCTGTGATTGATCGTGATGGCAACTTT
genomic: AGCACTCTAAGGCATGCTTCGAAGAGGGTATTAAGAAAATCAAGGCTCAGgcaatgattc ... cgcttttcagGGCGGCAAAATTTTGACTGGTGGCTCTGTGATTGATCGTGATGGCAACTTT
EST: gi|162268955|gb|FC445759.1|FC445759
EST:     AGCACTCTAAGGCATGCTTCGAAGAGGGTATTAAGAAAATCAAGGCTCAG                         GGCGGCAAAATTTTGACTGGTGGCTCTGTGATTGATCGTGATGGCAACTTT
genomic: AGCACTCTAAGGCATGCTTCGAAGAGGGTATTAAGAAAATCAAGGCTCAGgcaatgattc ... cgcttttcagGGCGGCAAAATTTTGACTGGTGGCTCTGTGATTGATCGTGATGGCAACTTT

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: 30 (upstream exon), 33 (downstream exon)
Score: 13

AACTGGAAATGCAGTAGATGAAACCACATTGTGTGGACCCCTTCATTCCAAGCACTCTAAGGCATGCTTCGAAGAGGGTATTAAGAAAATCAAGGCTCAGgcaatgattc ... cgcttttcagGGCGGCAAAATTTTGACTGGTGGCTCTGTGATTGATCGTGATGGCAACTTTGTCGAACCGACTGTAGTCGAGATATCACATGATGCAGAAATTGTGAGGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgcctcatacctcagcataaaacttttgaattttggactggatacgcttttcagGGCGGCAAAATTTTGACTGGTGGCTCTGTGATTGATCGTGATGGCAACTTTGTCGAACCGACTGTAGTCGAGATATCACATGATGCAGAAATTGTGAGGG
                                             cgcttttc  CT-rich tract
                 ataaaacttttgaatt  TA-rich tract