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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atatagaacaatcttgagaaggtagaagagcgctttccttctttgtgaaggacctttgatttttgcatcatctcctgacatacatagcaattctttgcagAGTATCGAACTGTGTCAGGTGTGGCAGGACCTCTTGTCATTTTAGAGAAAGTCAAG

Basic information

species Physcomitrella patens
transcript PP1S100_117V6.2
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|18342277|gb|BJ174312.1|BJ174312
EST:     GCCCTTGAGCAATTCTATTACAATGGGTTACGAGTGTCAACCACTGCTTG                         AGTATCGAACTGTGTCAGGTGTGGCAGGACCTCTTGTCATTTTAGAGAAAG
genomic: GCCCTTGAGCAATTCTATTACAATGGGTTACGAGTGTCAACCACTGCTTGgtatgttact ... ttctttgcagAGTATCGAACTGTGTCAGGTGTGGCAGGACCTCTTGTCATTTTAGAGAAAG
EST: gi|18368349|gb|BJ200434.1|BJ200434
EST:     GCCCTTGAGCAATTCTATTACAATGGGTTACGAGTGTCAACCACTGCTTG                         AGTATCGAACTGTGTCAGGTGTGGCAGGACCTCTTGTCATTTTAGAGAAAG
genomic: GCCCTTGAGCAATTCTATTACAATGGGTTACGAGTGTCAACCACTGCTTGgtatgttact ... ttctttgcagAGTATCGAACTGTGTCAGGTGTGGCAGGACCTCTTGTCATTTTAGAGAAAG
EST: gi|162221566|gb|FC397583.1|FC397583
EST:     GCCCTTGAGCAATTCTATTACAATGGGTTACGAGTGTCAACCACTGCTTG                         AGTATCGAACTGTGTCAGGTGTGGCAGGACCTCTTGTCATTTTAGAGAAAG
genomic: GCCCTTGAGCAATTCTATTACAATGGGTTACGAGTGTCAACCACTGCTTGgtatgttact ... ttctttgcagAGTATCGAACTGTGTCAGGTGTGGCAGGACCTCTTGTCATTTTAGAGAAAG
EST: gi|100425066|gb|BY976955.1|BY976955
EST:     GCCCTTGAGCAATTCTATTACAATGGGTTACGAGTGTCAACCACTGCTTG                         AGTATCGAACTGTGTCAGGTGTGGCAGGACCTCTTGTCATTTTAGAGAAAG
genomic: GCCCTTGAGCAATTCTATTACAATGGGTTACGAGTGTCAACCACTGCTTGgtatgttact ... ttctttgcagAGTATCGAACTGTGTCAGGTGTGGCAGGACCTCTTGTCATTTTAGAGAAAG
EST: gi|100441292|gb|BY962581.1|BY962581
EST:     GCCCTTGAGCAATTCTATTACAATGGGTTACGAGTGTCAACCACTGCTTG                         AGTATCGAACTGTGTCAGGTGTGGCAGGACCTCTTGTCATTTTAGAGAAAG
genomic: GCCCTTGAGCAATTCTATTACAATGGGTTACGAGTGTCAACCACTGCTTGgtatgttact ... ttctttgcagAGTATCGAACTGTGTCAGGTGTGGCAGGACCTCTTGTCATTTTAGAGAAAG
EST: gi|208357262|gb|DC910659.1|DC910659
EST:     GCCCTTGAGCAATTCTATTACAATGGGTTACGAGTGTCAACCACTGCTTG                         AGTATCGAACTGTGTCAGGTGTGGCAGGACCTCTTGTCATTTTAGAGAAAG
genomic: GCCCTTGAGCAATTCTATTACAATGGGTTACGAGTGTCAACCACTGCTTGgtatgttact ... ttctttgcagAGTATCGAACTGTGTCAGGTGTGGCAGGACCTCTTGTCATTTTAGAGAAAG
EST: gi|100392297|gb|BY953293.1|BY953293
EST:     GCCCTTGAGCAATTCTATTACAATGGGTTACGAGTGTCAACCACTGCTTG                         AGTATCGAACTGTGTCAGGTGTGGCAGGACCTCTTGTCATTTTAGAGAAAG
genomic: GCCCTTGAGCAATTCTATTACAATGGGTTACGAGTGTCAACCACTGCTTGgtatgttact ... ttctttgcagAGTATCGAACTGTGTCAGGTGTGGCAGGACCTCTTGTCATTTTAGAGAAAG
EST: gi|67574817|gb|BJ947641.1|BJ947641
EST:     GCCCTTGAGCAATTCTATTACAATGGGTTACGAGTGTCAACCACTGCTTG                         AGTATCGAACTGTGTCAGGTGTGGCAGGACCTCTTGTCATTTTAGAGAAAG
genomic: GCCCTTGAGCAATTCTATTACAATGGGTTACGAGTGTCAACCACTGCTTGgtatgttact ... ttctttgcagAGTATCGAACTGTGTCAGGTGTGGCAGGACCTCTTGTCATTTTAGAGAAAG
EST: gi|162278567|gb|FC454029.1|FC454029
EST:     GCCCTTGAGCAATTCTATTACAATGGGTTACGAGTGTCAACCACTGCTTG                         AGTATCGAACTGTGTCAGGTGTGGCAGGACCTCTTGTCATTTTAGAGAAAG
genomic: GCCCTTGAGCAATTCTATTACAATGGGTTACGAGTGTCAACCACTGCTTGgtatgttact ... ttctttgcagAGTATCGAACTGTGTCAGGTGTGGCAGGACCTCTTGTCATTTTAGAGAAAG
EST: gi|18357729|gb|BJ189788.1|BJ189788
EST:     GCCCTTGAGCAATTCTATTACAATGGGTTACGAGTGTCAACCACTGCTTG                         AGTATCGAACTGTGTCAGGTGTGGCAGGACCTCTTGTCATTTTAGAGAAAG
genomic: GCCCTTGAGCAATTCTATTACAATGGGTTACGAGTGTCAACCACTGCTTGgtatgttact ... ttctttgcagAGTATCGAACTGTGTCAGGTGTGGCAGGACCTCTTGTCATTTTAGAGAAAG
EST: gi|100360601|gb|BY984200.1|BY984200
EST:     GCCCTTGAGCAATTCTATTACAATGGGTTACGAGTGTCAACCACTGCTTG                         AGTATCGAACTGTGTCAGGTGTGGCAGGACCTCTTGTCATTTTAGAGAAAG
genomic: GCCCTTGAGCAATTCTATTACAATGGGTTACGAGTGTCAACCACTGCTTGgtatgttact ... ttctttgcagAGTATCGAACTGTGTCAGGTGTGGCAGGACCTCTTGTCATTTTAGAGAAAG
EST: gi|100432786|gb|BY978739.1|BY978739
EST:     GCCCTTGAGCAATTCTATTACAATGGGTTACGAGTGTCAACCACTGCTTG                         AGTATCGAACTGTGTCAGGTGTGGCAGGACCTCTTGTCATTTTAGAGAAAG
genomic: GCCCTTGAGCAATTCTATTACAATGGGTTACGAGTGTCAACCACTGCTTGgtatgttact ... ttctttgcagAGTATCGAACTGTGTCAGGTGTGGCAGGACCTCTTGTCATTTTAGAGAAAG
EST: gi|100437022|gb|BY979644.1|BY979644
EST:     GCCCTTGAGCAATTCTATTACAATGGGTTACGAGTGTCAACCACTGCTTG                         AGTATCGAACTGTGTCAGGTGTGGCAGGACCTCTTGTCATTTTAGAGAAAG
genomic: GCCCTTGAGCAATTCTATTACAATGGGTTACGAGTGTCAACCACTGCTTGgtatgttact ... ttctttgcagAGTATCGAACTGTGTCAGGTGTGGCAGGACCTCTTGTCATTTTAGAGAAAG
EST: gi|100397347|gb|BY972453.1|BY972453
EST:     GCCCTTGAGCAATTCTATTACAATGGGTTACGAGTGTCAACCACTGCTTG                         AGTATCGAACTGTGTCAGGTGTGGCAGGACCTCTTGTCATTTTAGAGAAAG
genomic: GCCCTTGAGCAATTCTATTACAATGGGTTACGAGTGTCAACCACTGCTTGgtatgttact ... ttctttgcagAGTATCGAACTGTGTCAGGTGTGGCAGGACCTCTTGTCATTTTAGAGAAAG

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: 29 (upstream exon), 34 (downstream exon)
Score: 9

CTTCCTCTTTGGGAGCCCTTGAGCAATTCTATTACAATGGGTTACGAGTGTCAACCACTGCTTGgtatgttact ... ttctttgcagAGTATCGAACTGTGTCAGGTGTGGCAGGACCTCTTGTCATTTTAGAGAAAGTCAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgaaggacctttgatttttgcatcatctcctgacatacatagcaattctttgcagAGTATCGAACTGTGTCAGGTGTGGCAGGACCTCTTGTCATTTTAGAGAAAGTCAAG
                           tcctgac  putative branch site (score: 9)
                                             ttctttgc  putative PPT
         tttgattttt  TA-rich tract