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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...actttccgaattttattgaagtgatttttctgacaattataactggccaattgattctagtacaatagcttacattgttcattccattttcatgtacaagATTACTGCAGCAGATTACATTCTGAAGGCAGGAGTGTCCAACTTCAGAAATGCCTGGGAGTCTTTGGACTCAGAGTCGGAACGTGTTGATGAGTACAGTC

Basic information

species Physcomitrella patens
transcript PP1S15_298V6.2
intron # 15
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|162170614|gb|FC347110.1|FC347110
EST:     ATGCTGACGAAGATGGATACGAAGATGAATATCAACTTGAAGATTTGGAG                         ATTACTGCAGCAGATTACATTCTGAAGGCAGGAGTGTCCAACTTCAGAAAT
genomic: ATGCTGACGAAGATGGATACGAAGATGAATATCAACTTGAAGATTTGGAGgtgggcttat ... catgtacaagATTACTGCAGCAGATTACATTCTGAAGGCAGGAGTGTCCAACTTCAGAAAT
EST: gi|162150206|gb|FC326291.1|FC326291
EST:     ATGCTGACGAAGATGGATACGAAGATGAATATCAACTTGAAGATTTGGAG                         ATTACTGCAGCAGATTACATTCTGAAGGCAGGAGTGTCCAACTTCAGAAAT
genomic: ATGCTGACGAAGATGGATACGAAGATGAATATCAACTTGAAGATTTGGAGgtgggcttat ... catgtacaagATTACTGCAGCAGATTACATTCTGAAGGCAGGAGTGTCCAACTTCAGAAAT
EST: gi|37853045|gb|BJ611053.1|BJ611053
EST:     ATGCTGACGAAGATGGATACGAAGATGAATATCAACTTGAAGATTTGGAG                         ATTACTGCAGCAGATTACATTCTGAAGGCAGGAGTGTCCAACTTCAGAAAT
genomic: ATGCTGACGAAGATGGATACGAAGATGAATATCAACTTGAAGATTTGGAGgtgggcttat ... catgtacaagATTACTGCAGCAGATTACATTCTGAAGGCAGGAGTGTCCAACTTCAGAAAT
EST: gi|162270703|gb|FC446316.1|FC446316
EST:     ATGCTGACGAAGATGGATACGAAGATGAATATCAACTTGAAGATTTGGAG                         ATTACTGCAGCAGATTACATTCTGAAGGCAGGAGTGTCCAACTTCAGAAAT
genomic: ATGCTGACGAAGATGGATACGAAGATGAATATCAACTTGAAGATTTGGAGgtgggcttat ... catgtacaagATTACTGCAGCAGATTACATTCTGAAGGCAGGAGTGTCCAACTTCAGAAAT
EST: gi|37839057|gb|BJ597065.1|BJ597065
EST:     ATGCTGACGAAGATGGATACGAAGATGAATATCAACTTGAAGATTNGGAG                         ATTACTGCAGCAGATTACATTCTGAAGGCAGGAGTGTCCAACTTCAGAAAT
genomic: ATGCTGACGAAGATGGATACGAAGATGAATATCAACTTGAAGATTTGGAGgtgggcttat ... catgtacaagATTACTGCAGCAGATTACATTCTGAAGGCAGGAGTGTCCAACTTCAGAAAT
EST: gi|37840740|gb|BJ598748.1|BJ598748
EST:     ATGCTGACGAAGATGGATACGAAGATGAATATCAACTNGAAGATTNGGAG                         ATTACTGCAGCAGATTACATTCTGAAGGCAGGAGTGTCCAACTTCAGAAAT
genomic: ATGCTGACGAAGATGGATACGAAGATGAATATCAACTTGAAGATTTGGAGgtgggcttat ... catgtacaagATTACTGCAGCAGATTACATTCTGAAGGCAGGAGTGTCCAACTTCAGAAAT
EST: gi|162161341|gb|FC336767.1|FC336767
EST:     AGATGAATATCAACTTGAAGATTTGGAG                         ATTACTGCAGCAGATTACATTCTGAAGGCAGGAGTGTCCAACTTCAGAAAT
genomic: AGATGAATATCAACTTGAAGATTTGGAGgtgggcttat ... catgtacaagATTACTGCAGCAGATTACATTCTGAAGGCAGGAGTGTCCAACTTCAGAAAT
EST: gi|162151628|gb|FC327757.1|FC327757
EST:     AAGATTTGGAG                         ATTACTGCAGCAGATTACATTCTGAAGGCAGGAGTGTCCAACTTCAGAAAT
genomic: AAGATTTGGAGgtgggcttat ... catgtacaagATTACTGCAGCAGATTACATTCTGAAGGCAGGAGTGTCCAACTTCAGAAAT
EST: gi|162151226|gb|FC327186.1|FC327186
EST:     ATGCTGACGAAGATGGATACGAAGATGAATATCAACTTGAAGATTTGGAG                         ATTACTGCAGCAGATTACATTCTGAAGGCAGGAGTGTCCAACTTCAGAAAT
genomic: ATGCTGACGAAGATGGATACGAAGATGAATATCAACTTGAAGATTTGGAGgtgggcttat ... catgtacaagATTACTGCAGCAGATTACATTCTGAAGGCAGGAGTGTCCAACTTCAGAAAT
EST: gi|37842472|gb|BJ600480.1|BJ600480
EST:     ATGCTGACGAAGATGGATACGAAGATGAATATCAACTTGAAGATTTGGAG                         ATTACTGCAGCAGATTACATTNTGAAGGCAGGAGTGTCCAACTTCAGAAAT
genomic: ATGCTGACGAAGATGGATACGAAGATGAATATCAACTTGAAGATTTGGAGgtgggcttat ... catgtacaagATTACTGCAGCAGATTACATTCTGAAGGCAGGAGTGTCCAACTTCAGAAAT

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), 35 (downstream exon)
Score: 9

GTGGATCCCAGCACAGGTGATGCTGACGAAGATGGATACGAAGATGAATATCAACTTGAAGATTTGGAGgtgggcttat ... catgtacaagATTACTGCAGCAGATTACATTCTGAAGGCAGGAGTGTCCAACTTCAGAAATGCCTGGGAGTCTTTGGACTCAGAGTCGGAACGTGTTGATGAGTACAGTC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gccaattgattctagtacaatagcttacattgttcattccattttcatgtacaagATTACTGCAGCAGATTACATTCTGAAGGCAGGAGTGTCCAACTTCAGAAATGCCTGGGAGTCTTTGGACTCAGAGTCGGAACGTGTTGATGAGTACAGTC
                     agcttac  putative branch site (score: 9)
                                ttcattccattttc  putative PPT
                                        attttcat  TA-rich tract