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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agaaatatgtaaatattaacatgtttttgttcattcatctgtattgaaatacagtttgcaaggttcttgactgagaaggcttgtggctagggtgttgcagTGCTCGACAGTACGAGGCAGAGATTGAGGACTCTTTAGCTTCACAGAAGAAGCCTGATACATTTAACGAGGTTCTGCGAAGTCTCGTGGATTGGCTCATT

Basic information

species Physcomitrella patens
transcript PP1S51_320V6.1
intron # 5
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|208391479|gb|DC937627.1|DC937627
EST:     AACTGGTTTATTCAAGAGAAAAGCTGCAAGATTCTGACCCTGATTATTAG                         TGCTCGACAGTACGAGGCAGAGATTGAGGACTCTTTAGCTTCACAGAAGAA
genomic: AACTGGTTTATTCAAGAGAAAAGCTGCAAGATTCTGACCCTGATTATTAGgtaggttttg ... ggtgttgcagTGCTCGACAGTACGAGGCAGAGATTGAGGACTCTTTAGCTTCACAGAAGAA
EST: gi|100396694|gb|BY953780.1|BY953780
EST:     AACTGGTTTATTCAAGAGAAAAGCTGCAAGATTCTGACCCTGATTATTAG                         TGCTCGACAGTACGAGGCAGAGATTGAGGACTCTTTAGCTTCACAGAAGAA
genomic: AACTGGTTTATTCAAGAGAAAAGCTGCAAGATTCTGACCCTGATTATTAGgtaggttttg ... ggtgttgcagTGCTCGACAGTACGAGGCAGAGATTGAGGACTCTTTAGCTTCACAGAAGAA
EST: gi|100434945|gb|BY960883.1|BY960883
EST:     AACTGGTTTATTCAAGAGAAAAGCTGCAAGATTCTGACCCTGATTATTAG                         TGCTCGACAGTACGAGGCAGAGATTGAGGACTCTTTAGCTTCACAGAAGAA
genomic: AACTGGTTTATTCAAGAGAAAAGCTGCAAGATTCTGACCCTGATTATTAGgtaggttttg ... ggtgttgcagTGCTCGACAGTACGAGGCAGAGATTGAGGACTCTTTAGCTTCACAGAAGAA
EST: gi|162201234|gb|FC378469.1|FC378469
EST:     AACTGGTTTATTCAAGAGAAAAGCTGCAAGATTCTGACCCTGATTATTAG                         TGCTCGACAGTACGAGGCAGAGGTTGAGGACTCTTTAGCTTCACAGAAGAA
genomic: AACTGGTTTATTCAAGAGAAAAGCTGCAAGATTCTGACCCTGATTATTAGgtaggttttg ... ggtgttgcagTGCTCGACAGTACGAGGCAGAGATTGAGGACTCTTTAGCTTCACAGAAGAA
EST: gi|100448937|gb|CJ973236.1|CJ973236
EST:     AACTGGTTTATTCAAGAGAAAAGCTGCAAGATTCTGACCCTGATTATTAG                         TGCTCGACAGTACGAGGCAGAGATTGANGACTCTTTAGCTTCACAGAAGAA
genomic: AACTGGTTTATTCAAGAGAAAAGCTGCAAGATTCTGACCCTGATTATTAGgtaggttttg ... ggtgttgcagTGCTCGACAGTACGAGGCAGAGATTGAGGACTCTTTAGCTTCACAGAAGAA
EST: gi|100411612|gb|BY992251.1|BY992251
EST:     AACTGGTTTATTCAAGAGAAAAGCTGCAAGATTCTGACCCTGATTATTAG                         TGCTCGACAGTACGAGGCAGAGATTGAGGACTCTTTAGCTTCACAGAAGAA
genomic: AACTGGTTTATTCAAGAGAAAAGCTGCAAGATTCTGACCCTGATTATTAGgtaggttttg ... ggtgttgcagTGCTCGACAGTACGAGGCAGAGATTGAGGACTCTTTAGCTTCACAGAAGAA
EST: gi|162194589|gb|FC369980.1|FC369980
EST:     AACTGGTTTATTCAAGAGAAAAGCTGCAAGATTCTGACCCTGATTATTAG                         TGCTCGACAGTACGAGGCAGAGGTTGAGGACTCTTTAGCTTCACAGAAGAA
genomic: AACTGGTTTATTCAAGAGAAAAGCTGCAAGATTCTGACCCTGATTATTAGgtaggttttg ... ggtgttgcagTGCTCGACAGTACGAGGCAGAGATTGAGGACTCTTTAGCTTCACAGAAGAA

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: 27 (upstream exon), 29 (downstream exon)
Score: 2

GTTGCTGTCAAAGAAGAACTGGTTTATTCAAGAGAAAAGCTGCAAGATTCTGACCCTGATTATTAGgtaggttttg ... ggtgttgcagTGCTCGACAGTACGAGGCAGAGATTGAGGACTCTTTAGCTTCACAGAAGAAGCCTGATACATTTAACGAGGTTCTGCGAAGTCTCGTGGATTGGCTCATT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaaatacagtttgcaaggttcttgactgagaaggcttgtggctagggtgttgcagTGCTCGACAGTACGAGGCAGAGATTGAGGACTCTTTAGCTTCACAGAAGAAGCCTGATACATTTAACGAGGTTCTGCGAAGTCTCGTGGATTGGCTCATT
                   tcttgac  putative branch site (score: 2)