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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aggaaggaaagagatcagaaaggtgtgatcgaattcaatttcactagtaagtttttatcacctttgttggagtcggtaaattcatgtctgcgtaattcagGTCGTTGTGCGAGGAGAAATGATTGAATACTACGACGTCTCAGGTTGCTACATCCTTCGTCCATGGTCTTACTCAATCTGGGAATCTATTAAG

Basic information

species Physcomitrella patens
transcript PP1S7_175V6.1
intron # 2
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|100387432|gb|BY988303.1|BY988303
EST:     TTGGTCTTGCTTTTAAGAAGGATGAAAACTTCGGAGAGTGGTATTCAGAT                         GTCGTTGTGCGAGGAGAAATGATTGAATACTACGACGTCTCAGGTTGCTAC
genomic: TTGGTCTTGCTTTTAAGAAGGATGAAAACTTCGGAGAGTGGTATTCAGATgtaagttagc ... cgtaattcagGTCGTTGTGCGAGGAGAAATGATTGAATACTACGACGTCTCAGGTTGCTAC
EST: gi|18344073|gb|BJ176112.1|BJ176112
EST:     TTGGTCTTGCTTTTAAGAAGGATGAAAACTTCGGAGAGTGGTATTCAGAT                         GTCGTTGTGCGAGGAGAAATGATTGAATACTACGACGTCTCAGGTTGCTAC
genomic: TTGGTCTTGCTTTTAAGAAGGATGAAAACTTCGGAGAGTGGTATTCAGATgtaagttagc ... cgtaattcagGTCGTTGTGCGAGGAGAAATGATTGAATACTACGACGTCTCAGGTTGCTAC
EST: gi|18350576|gb|BJ182627.1|BJ182627
EST:     TTGGTCTTGCTTTTAAGAAGGATGAAAACTTCGGAGAGTGGTATTCAGAT                         GTCGTTGTGCGAGGAGAAATGATTGAATACTACGACGTCTCAGGTTGCTAC
genomic: TTGGTCTTGCTTTTAAGAAGGATGAAAACTTCGGAGAGTGGTATTCAGATgtaagttagc ... cgtaattcagGTCGTTGTGCGAGGAGAAATGATTGAATACTACGACGTCTCAGGTTGCTAC
EST: gi|100443225|gb|BY963521.1|BY963521
EST:     TTGGTCTTGCTTTTAAGAAGGATGAAAACTTCGGAGAGTGGTATTCAGAT                         GTCGTTGTGCGAGGAGAAATGATTGAATACTACGACGTCTCAGGTTGCTAC
genomic: TTGGTCTTGCTTTTAAGAAGGATGAAAACTTCGGAGAGTGGTATTCAGATgtaagttagc ... cgtaattcagGTCGTTGTGCGAGGAGAAATGATTGAATACTACGACGTCTCAGGTTGCTAC
EST: gi|18360143|gb|BJ192205.1|BJ192205
EST:     TTGGTCTTGCTTTTAAGAAGGATGAAAACTTCGGAGAGTGGTATTCAGAT                         GTCGTTGTGCGAGGAGAAATGATTGAATACTACGACGTCTCAGGTTGCTAC
genomic: TTGGTCTTGCTTTTAAGAAGGATGAAAACTTCGGAGAGTGGTATTCAGATgtaagttagc ... cgtaattcagGTCGTTGTGCGAGGAGAAATGATTGAATACTACGACGTCTCAGGTTGCTAC
EST: gi|100439329|gb|BY980209.1|BY980209
EST:     TTGGTCTTGCTTTTAAGAAGGATGAAAACTTCGGAGAGTGGTATTCAGAT                         GTCGTTGTGCGAGGAGAAATGATTGAATACTACGACGTCTCAGGTTGCTAC
genomic: TTGGTCTTGCTTTTAAGAAGGATGAAAACTTCGGAGAGTGGTATTCAGATgtaagttagc ... cgtaattcagGTCGTTGTGCGAGGAGAAATGATTGAATACTACGACGTCTCAGGTTGCTAC
EST: gi|100451310|gb|CJ974701.1|CJ974701
EST:     TTGGTCTTGCTTTTAAGAAGGATGAAAACTTCGGAGAGTGGTATTCAGAT                         GTCGTTGTGCGAGGAGAAATGATTGAATACTACGACGTCTCAGGTTGCTAC
genomic: TTGGTCTTGCTTTTAAGAAGGATGAAAACTTCGGAGAGTGGTATTCAGATgtaagttagc ... cgtaattcagGTCGTTGTGCGAGGAGAAATGATTGAATACTACGACGTCTCAGGTTGCTAC
EST: gi|18349320|gb|BJ181369.1|BJ181369
EST:     TTGGTCTTGCTTTTAAGAAGGATGAAAACTTCGGAGAGTGGTATTCAGAT                         GTCGTTGTGCGAGGAGAAATGATTGAATACTACGACGTCTCAGGTTGCTAC
genomic: TTGGTCTTGCTTTTAAGAAGGATGAAAACTTCGGAGAGTGGTATTCAGATgtaagttagc ... cgtaattcagGTCGTTGTGCGAGGAGAAATGATTGAATACTACGACGTCTCAGGTTGCTAC
EST: gi|100389088|gb|BY952292.1|BY952292
EST:     TTGGTCTTGCTTTTAAGAAGGATGAAAACTTCGGAGAGTGGTATTCAGAT                         GTCGTTGTGCGAGGAGAAATGATTGAATACTACGACGTCTCAGGTTGCTAC
genomic: TTGGTCTTGCTTTTAAGAAGGATGAAAACTTCGGAGAGTGGTATTCAGATgtaagttagc ... cgtaattcagGTCGTTGTGCGAGGAGAAATGATTGAATACTACGACGTCTCAGGTTGCTAC
EST: gi|18364143|gb|BJ196216.1|BJ196216
EST:     TTGGTCTTGCTTTTAAGAAGGATGAAAACTTCGGAGAGTGGTATTCAGAT                         GTCGTTGTGCGAGGAGAAATGATTGAATACTACGACGTCTCAGGTTGCTAC
genomic: TTGGTCTTGCTTTTAAGAAGGATGAAAACTTCGGAGAGTGGTATTCAGATgtaagttagc ... cgtaattcagGTCGTTGTGCGAGGAGAAATGATTGAATACTACGACGTCTCAGGTTGCTAC
EST: gi|18348271|gb|BJ180318.1|BJ180318
EST:     TTGGTCTTGCTTTTAAGAAGGATGAAAACTTCGGAGAGTGGTATTCAGAT                         GTCGTTGTGCGAGGAGAAATGATTGAATACTACGACGTCTCAGGTTGCTAC
genomic: TTGGTCTTGCTTTTAAGAAGGATGAAAACTTCGGAGAGTGGTATTCAGATgtaagttagc ... cgtaattcagGTCGTTGTGCGAGGAGAAATGATTGAATACTACGACGTCTCAGGTTGCTAC
EST: gi|162237815|gb|FC413924.1|FC413924
EST:     TTGGTCTTGCTTTTAAGAAGGATGAAAACTTCGGAGAGTGGTATTCAGAT                         GTCGTTGTGCGAGGAGAAATGATTGAATACTACGACGTCTCAGGTTGCTAC
genomic: TTGGTCTTGCTTTTAAGAAGGATGAAAACTTCGGAGAGTGGTATTCAGATgtaagttagc ... cgtaattcagGTCGTTGTGCGAGGAGAAATGATTGAATACTACGACGTCTCAGGTTGCTAC
EST: gi|100370301|gb|BY985342.1|BY985342
EST:     TTGGTCTTGCTTTTAAGAAGGATGAAAACTTCGGAGAGTGGTATTCAGAT                         GTCGTTGTGCGAGGAGAAATGATTGAATACTACGACGTCTCAGGTTGCTAC
genomic: TTGGTCTTGCTTTTAAGAAGGATGAAAACTTCGGAGAGTGGTATTCAGATgtaagttagc ... cgtaattcagGTCGTTGTGCGAGGAGAAATGATTGAATACTACGACGTCTCAGGTTGCTAC

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: 25 (upstream exon), 23 (downstream exon)
Score: 15

CCAAGAAGGAGGTGAAGAAGGAATCGGGACTTGGTCTTGCTTTTAAGAAGGATGAAAACTTCGGAGAGTGGTATTCAGATgtaagttagc ... cgtaattcagGTCGTTGTGCGAGGAGAAATGATTGAATACTACGACGTCTCAGGTTGCTACATCCTTCGTCCATGGTCTTACTCAATCTGGGAATCTATTAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtaagtttttatcacctttgttggagtcggtaaattcatgtctgcgtaattcagGTCGTTGTGCGAGGAGAAATGATTGAATACTACGACGTCTCAGGTTGCTACATCCTTCGTCCATGGTCTTACTCAATCTGGGAATCTATTAAG
      tttttatca  TA-rich tract