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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcaatttgatcatatatatatatatatatatatatataattatccttcaaaacttttctgtgccgaactaattctgtttcattcaaattttgactttcagATAGGTCTATTTGGAATCATTGATTCACACGGAGGACCTTGTGTGGGAAAATATGTGCAACAACACCTTTTTGACAACATTTTGAATGAAGGGGGTGTCC

Basic information

species Physcomitrella patens
transcript PP1S47_179V6.4
intron # 3
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|100419992|gb|BY975923.1|BY975923
EST:     CCATGGAAGACTTTCATGTCGCAGAGTTTCGCAATATCGATGGCGAGGAG                         ATAGGTCTATTTGGAATCATTGATTCACACGGAGGACCTTGTGTGGGAAAA
genomic: CCATGGAAGACTTTCATGTCGCAGAGTTTCGCAATATCGATGGCGAGGAGgtaccaatcc ... tgactttcagATAGGTCTATTTGGAATCATTGATTCACACGGAGGACCTTGTGTGGGAAAA
EST: gi|100452236|gb|CJ975169.1|CJ975169
EST:     CCATGGAAGACTTTCATGTCGCAGAGTTTCGCAATATCGATGGCGAGGAG                         ATAGGTCTATTTGGAATCATTGATTCACACGGAGGACCTTGTGTGGGAAAA
genomic: CCATGGAAGACTTTCATGTCGCAGAGTTTCGCAATATCGATGGCGAGGAGgtaccaatcc ... tgactttcagATAGGTCTATTTGGAATCATTGATTCACACGGAGGACCTTGTGTGGGAAAA
EST: gi|22492172|gb|BU052095.1|BU052095
EST:     CCATGGAAGACTTTCATGTCGCAGAGTTTCGCAATATCGATGGCGAGGAG                         ATAGGTCTATTTGGAATCATTGATTCACACGGAGGACCTTGTGTGGGAAAA
genomic: CCATGGAAGACTTTCATGTCGCAGAGTTTCGCAATATCGATGGCGAGGAGgtaccaatcc ... tgactttcagATAGGTCTATTTGGAATCATTGATTCACACGGAGGACCTTGTGTGGGAAAA

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: 11 (upstream exon), 34 (downstream exon)
Score: 5

GCCCCAAGCCATCTTTGGTTTCTCTCTATTGCAAGGTCTCCGTGGTAATCCCATGGAAGACTTTCATGTCGCAGAGTTTCGCAATATCGATGGCGAGGAGgtaccaatcc ... tgactttcagATAGGTCTATTTGGAATCATTGATTCACACGGAGGACCTTGTGTGGGAAAATATGTGCAACAACACCTTTTTGACAACATTTTGAATGAAGGGGGTGTCC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcaaaacttttctgtgccgaactaattctgtttcattcaaattttgactttcagATAGGTCTATTTGGAATCATTGATTCACACGGAGGACCTTGTGTGGGAAAATATGTGCAACAACACCTTTTTGACAACATTTTGAATGAAGGGGGTGTCC
                                                ctttc  CT-rich tract
                               tttcattcaaatttt  TA-rich tract