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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtagcaaataaaattgcacttgattcaatgccgccatgctttgtatatctgttttaatttgtattattcatgatcgtctctatgatgtggtcaattgcagGTGATGGTGGTGAGGAACTTGACAAAGCTGCTTACGCTGATGGAAATCAAAGGCGTATCACTGCCAACACCAAATGGAGTGAAGTGCAG

Basic information

species Physcomitrella patens
transcript PP1S58_197V6.1
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|208382909|gb|DC928334.1|DC928334
EST:     GGACTTCAACTGTTATATCAAATGCAACTTCATTATTTATGTTCCCCCAA                         GTGATGGTGGTGAGGAACTTGACAAAGCTGCTTACGCTGATGGAAATCAAA
genomic: GGACTTCAACTGTTATATCAAATGCAACTTCATTATTTATGTTCCCCCAAgtaagcccgc ... tcaattgcagGTGATGGTGGTGAGGAACTTGACAAAGCTGCTTACGCTGATGGAAATCAAA
EST: gi|67726513|gb|BJ976772.1|BJ976772
EST:     GGACTTCAACTGTTATATCAAATGCAACTTCATTATTTATGTTCCCCCAA                         GTGATGGTGGTGAGGAACTTGACAAAGCTGCTTACGCTGATGGAAATCAAA
genomic: GGACTTCAACTGTTATATCAAATGCAACTTCATTATTTATGTTCCCCCAAgtaagcccgc ... tcaattgcagGTGATGGTGGTGAGGAACTTGACAAAGCTGCTTACGCTGATGGAAATCAAA
EST: gi|6167306|gb|AW145570.1|AW145570
EST:     GGACTTCAACTGTTATATCAAATGCAACTTCATTATTTATGTTCCCCCAA                         GTGATGGTGGGTGAGGAACTTGACAAAGCTGCTTACGCTGATGGAAATCAA
genomic: GGACTTCAACTGTTATATCAAATGCAACTTCATTATTTATGTTCCCCCAAgtaagcccgc ... tcaattgcagGTGATGGTGG-TGAGGAACTTGACAAAGCTGCTTACGCTGATGGAAATCAA
EST: gi|37823222|gb|BJ581288.1|BJ581288
EST:     TATATCAAATGCAACTTCATTATTTATGTTCCCCCAA                         GTGATGGTGGTGAGGAACTTGACAAAGCTGCTTACGCTGATGGAAATCAAA
genomic: TATATCAAATGCAACTTCATTATTTATGTTCCCCCAAgtaagcccgc ... tcaattgcagGTGATGGTGGTGAGGAACTTGACAAAGCTGCTTACGCTGATGGAAATCAAA
EST: gi|37836886|gb|BJ594894.1|BJ594894
EST:     TATATCAAATGCAACTTCATTATTTATGTTCCCCCAA                         GTGATGGTGGTGAGGAACTTGACAAAGCTGCTTACGCTGATGGAAATCAAA
genomic: TATATCAAATGCAACTTCATTATTTATGTTCCCCCAAgtaagcccgc ... tcaattgcagGTGATGGTGGTGAGGAACTTGACAAAGCTGCTTACGCTGATGGAAATCAAA
EST: gi|208370963|gb|DC944338.1|DC944338
EST:     GGACTTCAACTGTTATATCAAATGCAACTTCATTATTTATGTTCCCCCAA                         GTGATGGTGGTGAGGAACTTGACAAAGCTGCTTACGCTGATGGAAATCAAA
genomic: GGACTTCAACTGTTATATCAAATGCAACTTCATTATTTATGTTCCCCCAAgtaagcccgc ... tcaattgcagGTGATGGTGGTGAGGAACTTGACAAAGCTGCTTACGCTGATGGAAATCAAA
EST: gi|162176258|gb|FC352715.1|FC352715
EST:     GGACTTCAACTGTTATATCAAATGCAACTTCATTATTTATGTTCCCCCAA                         GTGATGGTGGTGAGGAACTTGACAAAGCTGCTTACGCTGATGGAAATCAAA
genomic: GGACTTCAACTGTTATATCAAATGCAACTTCATTATTTATGTTCCCCCAAgtaagcccgc ... tcaattgcagGTGATGGTGGTGAGGAACTTGACAAAGCTGCTTACGCTGATGGAAATCAAA
EST: gi|37842901|gb|BJ600909.1|BJ600909
EST:     GGACTTCAACTGTTATATCAAATGCAACTTCATTATTTATGTTCCCCCAA                         GTGATGGTGGTGAGGAACTTGACAAAGCTGCTTACGCTGATGGAAATCAAA
genomic: GGACTTCAACTGTTATATCAAATGCAACTTCATTATTTATGTTCCCCCAAgtaagcccgc ... tcaattgcagGTGATGGTGGTGAGGAACTTGACAAAGCTGCTTACGCTGATGGAAATCAAA
EST: gi|162155578|gb|FC331529.1|FC331529
EST:     GGACTTCAACTGTTATATCAAATGCAACTTCATTATTTATGTTCCCCCAA                         GTGATGGTGGTGAGGAACTTGACAAAGCTGCTTACGCTGATGGAAATCAAA
genomic: GGACTTCAACTGTTATATCAAATGCAACTTCATTATTTATGTTCCCCCAAgtaagcccgc ... tcaattgcagGTGATGGTGGTGAGGAACTTGACAAAGCTGCTTACGCTGATGGAAATCAAA
EST: gi|37821349|gb|BJ579415.1|BJ579415
EST:     GGACTTCAACTGTTATATCAAATGCAACTTCATTATTTATGTTCCCCCAA                         GTGATGGTGGTGAGGAACTTGACAAAGCTGCTTACGCTGATGGAAATCAAA
genomic: GGACTTCAACTGTTATATCAAATGCAACTTCATTATTTATGTTCCCCCAAgtaagcccgc ... tcaattgcagGTGATGGTGGTGAGGAACTTGACAAAGCTGCTTACGCTGATGGAAATCAAA

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: 26 (upstream exon), 32 (downstream exon)
Score: 2

ACTCATCGCATCAAGAAGTTTGTACTTCATACCAATTTTCCAGGTCACACGGACTTCAACTGTTATATCAAATGCAACTTCATTATTTATGTTCCCCCAAgtaagcccgc ... tcaattgcagGTGATGGTGGTGAGGAACTTGACAAAGCTGCTTACGCTGATGGAAATCAAAGGCGTATCACTGCCAACACCAAATGGAGTGAAGTGCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatctgttttaatttgtattattcatgatcgtctctatgatgtggtcaattgcagGTGATGGTGGTGAGGAACTTGACAAAGCTGCTTACGCTGATGGAAATCAAAGGCGTATCACTGCCAACACCAAATGGAGTGAAGTGCAG
      ttttaat  putative branch site (score: 2)
      ttttaatttgtattat  TA-rich tract