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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCGGCGTTGATGATCCATCGAAGGTTCAAACTCTACTTTTTAGTGCAACTCTGCCCACGTGGGTTCAACAGgtatagttcattcaatatctttaccgcatcttttcttttcaactttgatttacgaagtgcataaaggcgcatgtgttatgcgaattttcactgattcact...

Basic information

species Physcomitrella patens
transcript PP1S40_169V6.1
intron # 5
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|162183859|gb|FC360165.1|FC360165
EST:     AGGTTCAAACTCTACTTTTTAGTGCAACTCTGCCCACGTGGGTTCAACAG                         ATTGCCCGTAAGTTTTTGAAGCCTGAGAGGAGAACTGTTGACTTGGTTGGT
genomic: AGGTTCAAACTCTACTTTTTAGTGCAACTCTGCCCACGTGGGTTCAACAGgtatagttca ... gtgaatgcagATTGCCCGTAAGTTTTTGAAGCCTGAGAGGAGAACTGTTGACTTGGTTGGT
EST: gi|162199364|gb|FC374030.1|FC374030
EST:     AGGTTCAAACTCTACTTTTTAGTGCAACTCTGCCCACGTGGGTTCAACAG                         ATTGCCCGTAAGTTTTTGAAGCCTGAGAGGAGAACTGTTGACTTGGTTGGT
genomic: AGGTTCAAACTCTACTTTTTAGTGCAACTCTGCCCACGTGGGTTCAACAGgtatagttca ... gtgaatgcagATTGCCCGTAAGTTTTTGAAGCCTGAGAGGAGAACTGTTGACTTGGTTGGT
EST: gi|100392613|gb|BY971797.1|BY971797
EST:     AGGTTCAAACTCTACTTTTTAGTGCAACTCTGCCCACGTGGGTTCAACAG                         ATTGCCCGTAAGTTTTTGAAGCCTGAGAGGAGAACTGTTGACTTGGTTGGT
genomic: AGGTTCAAACTCTACTTTTTAGTGCAACTCTGCCCACGTGGGTTCAACAGgtatagttca ... gtgaatgcagATTGCCCGTAAGTTTTTGAAGCCTGAGAGGAGAACTGTTGACTTGGTTGGT
EST: gi|162165912|gb|FC341262.1|FC341262
EST:     AGGTTCAAACTCTACTTTTTAGTGCAACTCTGCCCACGTGGGTTCAACAG                         ATTGCCCGTAAGTTTTTGAAGCCTGAGAGGAGAACTGTTGACTTGGTTGGT
genomic: AGGTTCAAACTCTACTTTTTAGTGCAACTCTGCCCACGTGGGTTCAACAGgtatagttca ... gtgaatgcagATTGCCCGTAAGTTTTTGAAGCCTGAGAGGAGAACTGTTGACTTGGTTGGT
EST: gi|162166233|gb|FC342631.1|FC342631
EST:     AGGTTCAAACTCTACTTTTTAGTGCAACTCTGCCCACGTGGGTTCAACAG                         ATTGCCCGTAAGTTTTTGAAGCCTGAGAGGAGAACTGTTGACTTGGTTGGT
genomic: AGGTTCAAACTCTACTTTTTAGTGCAACTCTGCCCACGTGGGTTCAACAGgtatagttca ... gtgaatgcagATTGCCCGTAAGTTTTTGAAGCCTGAGAGGAGAACTGTTGACTTGGTTGGT
EST: gi|162201473|gb|FC377407.1|FC377407
EST:     AGGTTCAAACTCTACTTTTTAGTGCAACTCTGCCCACGTGGGTTCAACAG                         ATTGCCCGTAAGTTTTTGAAGCCTGAGAGGAGAACTGTTGACTTGGTTGGT
genomic: AGGTTCAAACTCTACTTTTTAGTGCAACTCTGCCCACGTGGGTTCAACAGgtatagttca ... gtgaatgcagATTGCCCGTAAGTTTTTGAAGCCTGAGAGGAGAACTGTTGACTTGGTTGGT
EST: gi|162167302|gb|FC342290.1|FC342290
EST:     AGGTTCAAACTCTACTTTTTAGTGCAACTCTGCCCACGTGGGTTCAACAG                         ATTGCCCGTAAGTTTTTGAAGCCTGAGAGGAGAACTGTTGACTTGGTTGGT
genomic: AGGTTCAAACTCTACTTTTTAGTGCAACTCTGCCCACGTGGGTTCAACAGgtatagttca ... gtgaatgcagATTGCCCGTAAGTTTTTGAAGCCTGAGAGGAGAACTGTTGACTTGGTTGGT
EST: gi|162163230|gb|FC339348.1|FC339348
EST:     AGGTTCAAACTCTACTTTTTAGTGCAACTCTGCCCACGTGGGTTCAACAG                         ATTGCCCGTAAGTTTTTGAAGCCTGAGAGGAGAACTGTTGACTTGGTTGGT
genomic: AGGTTCAAACTCTACTTTTTAGTGCAACTCTGCCCACGTGGGTTCAACAGgtatagttca ... gtgaatgcagATTGCCCGTAAGTTTTTGAAGCCTGAGAGGAGAACTGTTGACTTGGTTGGT
EST: gi|162168031|gb|FC344345.1|FC344345
EST:     GCAACTCTGCCCACGTGGGTTCAACAG                         ATTGCCCGTAAGTTTTTGAAGCCTGAGAGGAGAACTGTTGACTTGGTTGGT
genomic: GCAACTCTGCCCACGTGGGTTCAACAGgtatagttca ... gtgaatgcagATTGCCCGTAAGTTTTTGAAGCCTGAGAGGAGAACTGTTGACTTGGTTGGT

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: 35 (upstream exon), 34 (downstream exon)
Score: 36

GCGGCGTTGATGATCCATCGAAGGTTCAAACTCTACTTTTTAGTGCAACTCTGCCCACGTGGGTTCAACAGgtatagttca ... gtgaatgcagATTGCCCGTAAGTTTTTGAAGCCTGAGAGGAGAACTGTTGACTTGGTTGGTGATGAGAAGATGAAGGCTAGCAACAATGTGAAGCACTTGTTGCTTCCAG




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