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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgcatgttttaaatcacatattaaatttgcagccaagaattttaggaatccaacagaggctcaaagactatctatactgagaagtttgataaattgcagGGAATGCTTTGTTCTCGTGGAGAACTACTTTTGATGCTAGATTCTGACGGTGCCACTAGGTTTGCAGACTTGAGAAAGTTGGAATTGCAA

Basic information

species Physcomitrella patens
transcript PP1S96_201V6.1
intron # 6
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|208351033|gb|DC910496.1|DC910496
EST:     GAGTTCTTAAGCAAGTAACGAACCAAGGCAAAGGAGCAGCTGTCAGAAAA                         GGAATGCTTTGTTCTCGTGGAGAACTACTTTTGATGCTAGATTCTGACGGT
genomic: GAGTTCTTAAGCAAGTAACGAACCAAGGCAAAGGAGCAGCTGTCAGAAAAgtatgcagtt ... taaattgcagGGAATGCTTTGTTCTCGTGGAGAACTACTTTTGATGCTAGATTCTGACGGT
EST: gi|208399166|gb|DC916549.1|DC916549
EST:     GAGTTCTTAAGCAAGTAACGAACCAAGGCAAAGGAGCAGCTGTCAGAAAA                         GGAATGCTTTGTTCTCGTGGAGAACTACTTTTGATGCTAGATTCTGACGGT
genomic: GAGTTCTTAAGCAAGTAACGAACCAAGGCAAAGGAGCAGCTGTCAGAAAAgtatgcagtt ... taaattgcagGGAATGCTTTGTTCTCGTGGAGAACTACTTTTGATGCTAGATTCTGACGGT
EST: gi|208354666|gb|DC934310.1|DC934310
EST:     GAGTTCTTAAGCAAGTAACGAACCAAGGCAAAGGAGCAGCTGTCAGAAAA                         GGAATGCTTTGTTCTCGTGGAGAACTACTTTTGATGCTAGATTCTGACGGT
genomic: GAGTTCTTAAGCAAGTAACGAACCAAGGCAAAGGAGCAGCTGTCAGAAAAgtatgcagtt ... taaattgcagGGAATGCTTTGTTCTCGTGGAGAACTACTTTTGATGCTAGATTCTGACGGT
EST: gi|208393921|gb|DC946131.1|DC946131
EST:     GAGTTCTTAAGCAAGTAACGAACCAAGGCAAAGGAGCAGCTGTCAGAAAA                         GGAGTGCTTTGTTCTCGTGGAGAACTACTTTTGATGCTAGATTCTGACGGT
genomic: GAGTTCTTAAGCAAGTAACGAACCAAGGCAAAGGAGCAGCTGTCAGAAAAgtatgcagtt ... taaattgcagGGAATGCTTTGTTCTCGTGGAGAACTACTTTTGATGCTAGATTCTGACGGT
EST: gi|100354883|gb|BY983614.1|BY983614
EST:     GAGTTCTTAAGCAAGTAACGAACCAAGGCAAAGGAGCAGCTGTCAGAAAA                         GGAATGCTTTGTTCTCGTGGAGAACTACTTTTGATGCTAGATTCTGACGGT
genomic: GAGTTCTTAAGCAAGTAACGAACCAAGGCAAAGGAGCAGCTGTCAGAAAAgtatgcagtt ... taaattgcagGGAATGCTTTGTTCTCGTGGAGAACTACTTTTGATGCTAGATTCTGACGGT
EST: gi|208374274|gb|DC940659.1|DC940659
EST:     GAGTTCTTAAGCAAGTAACGAACCAAGGCAAAGGAGCAGCTGTCAGAAAA                         GGAATGCTTTGTTCTCGTGGAGAACTACTTTTGATGCTAGATTCTGACGGT
genomic: GAGTTCTTAAGCAAGTAACGAACCAAGGCAAAGGAGCAGCTGTCAGAAAAgtatgcagtt ... taaattgcagGGAATGCTTTGTTCTCGTGGAGAACTACTTTTGATGCTAGATTCTGACGGT
EST: gi|208372484|gb|DC940773.1|DC940773
EST:     GAGTTCTTAAGCAAGTAACGAACCAAGGCAAAGGAGCAGCTGTCAGAAAA                         GGAATGCTTTGTTCTCGTGGAGAACTACTTTTGATGCTAGATTCTGACGGT
genomic: GAGTTCTTAAGCAAGTAACGAACCAAGGCAAAGGAGCAGCTGTCAGAAAAgtatgcagtt ... taaattgcagGGAATGCTTTGTTCTCGTGGAGAACTACTTTTGATGCTAGATTCTGACGGT
EST: gi|208400210|gb|DC908871.1|DC908871
EST:     GAGTTCTTAAGCAAGTAACGAACCAAGGCAAAGGAGCAGCTGTCAGAAAA                         GGAATGCTTTGTTCTCGTGGAGAACTACTTTTGATGCTAGATTCTGACGGT
genomic: GAGTTCTTAAGCAAGTAACGAACCAAGGCAAAGGAGCAGCTGTCAGAAAAgtatgcagtt ... taaattgcagGGAATGCTTTGTTCTCGTGGAGAACTACTTTTGATGCTAGATTCTGACGGT
EST: gi|67694496|gb|BJ954729.1|BJ954729
EST:     GAGTTCTTAAGCAAGTAACGAACCAAGGCAAAGGAGCAGCTGTCAGAAAA                         GGAATGCTTTGTTCTCGTGGAGAACTACTTTTGATGCTAGATTCTGACGGT
genomic: GAGTTCTTAAGCAAGTAACGAACCAAGGCAAAGGAGCAGCTGTCAGAAAAgtatgcagtt ... taaattgcagGGAATGCTTTGTTCTCGTGGAGAACTACTTTTGATGCTAGATTCTGACGGT
EST: gi|208380316|gb|DC922738.1|DC922738
EST:     GAGTTCTTAAGCAAGTAACGAACCAAGGCAAAGGAGCAGCTGTCAGAAAA                         GGAATGCTTTGTTCTCGTGGAGAACTACTTTTGATGCTAGATTCTGACGGT
genomic: GAGTTCTTAAGCAAGTAACGAACCAAGGCAAAGGAGCAGCTGTCAGAAAAgtatgcagtt ... taaattgcagGGAATGCTTTGTTCTCGTGGAGAACTACTTTTGATGCTAGATTCTGACGGT
EST: gi|208396709|gb|DC924321.1|DC924321
EST:     GAGTTCTTAAGCAAGTAACGAACCAAGGCAAAGGAGCAGCTGTCAGAAAA                         GGAATGCTTTGTTCTCGTGGAGAACTACTTTTGATGCTAGATTCTGACGGT
genomic: GAGTTCTTAAGCAAGTAACGAACCAAGGCAAAGGAGCAGCTGTCAGAAAAgtatgcagtt ... taaattgcagGGAATGCTTTGTTCTCGTGGAGAACTACTTTTGATGCTAGATTCTGACGGT
EST: gi|37821806|gb|BJ579872.1|BJ579872
EST:     GAGTTCTTAAGCAAGTAACGAACCAAGGCAAAGGAGCAGCTGTCAGAAAA                         GGAATGCTTTGTTCTCGTGGAGAACTACTTTTGATGCTAGATTCTGACGGT
genomic: GAGTTCTTAAGCAAGTAACGAACCAAGGCAAAGGAGCAGCTGTCAGAAAAgtatgcagtt ... taaattgcagGGAATGCTTTGTTCTCGTGGAGAACTACTTTTGATGCTAGATTCTGACGGT
EST: gi|18342663|gb|BJ174698.1|BJ174698
EST:     GAGTTCTTAAGCAAGTAACGAACCAAGGCAAAGGAGCAGCTGTCAGAAAA                         GGAATGCTTTGT
genomic: GAGTTCTTAAGCAAGTAACGAACCAAGGCAAAGGAGCAGCTGTCAGAAAAgtatgcagtt ... taaattgcagGGAATGCTTTGT
EST: gi|18361295|gb|BJ193361.1|BJ193361
EST:     GAGTTCTTAAGCAAGTAACGAACCAAGGCAAAGGAGCAGCTGTCAGAAAA                         GGAATGCTTTGTTCTCGTGGAGAACTACTTTTGATGCTAGATTCTGACG
genomic: GAGTTCTTAAGCAAGTAACGAACCAAGGCAAAGGAGCAGCTGTCAGAAAAgtatgcagtt ... taaattgcagGGAATGCTTTGTTCTCGTGGAGAACTACTTTTGATGCTAGATTCTGACG
EST: gi|100355017|gb|BY964959.1|BY964959
EST:     GAGTTCTTAAGCAAGTAACGAACCAAGGCAAAGGAGCAGCTGTCAGAAAA                         GGAATGCTTTGTTCTCGTGGAGAACTACTTTTGATGCTAGATTCTGACGGT
genomic: GAGTTCTTAAGCAAGTAACGAACCAAGGCAAAGGAGCAGCTGTCAGAAAAgtatgcagtt ... taaattgcagGGAATGCTTTGTTCTCGTGGAGAACTACTTTTGATGCTAGATTCTGACGGT
EST: gi|208360577|gb|DC930849.1|DC930849
EST:     GAGTTCTTAAGCAAGTAACGAACCAAGGCAAAGGAGCAGCTGTCAGAAAA                         GGAATGCTTTGTTCTCGTGGAGAACTACTTTTGATGCTAGATTCTGACGGT
genomic: GAGTTCTTAAGCAAGTAACGAACCAAGGCAAAGGAGCAGCTGTCAGAAAAgtatgcagtt ... taaattgcagGGAATGCTTTGTTCTCGTGGAGAACTACTTTTGATGCTAGATTCTGACGGT
EST: gi|208354332|gb|DC953780.1|DC953780
EST:     GAGTTCTTAAGCAAGTAACGAACCAAGGCAAAGGAGCAGCTGTCAGAAAA                         GGAATGCTTTGTTCTCGTGGAGAACTACTTTTGATGCTAGATTCTGACGGT
genomic: GAGTTCTTAAGCAAGTAACGAACCAAGGCAAAGGAGCAGCTGTCAGAAAAgtatgcagtt ... taaattgcagGGAATGCTTTGTTCTCGTGGAGAACTACTTTTGATGCTAGATTCTGACGGT
EST: gi|208374496|gb|DC948444.1|DC948444
EST:     GAGTTCTTAAGCAAGTAACGAACCAAGGCAAAGGAGCAGCTGTCAGAAAA                         GGAATGCTTTGTTCTCGTGGAGAACTACTTTTGATGCTAGATTCTGACGGT
genomic: GAGTTCTTAAGCAAGTAACGAACCAAGGCAAAGGAGCAGCTGTCAGAAAAgtatgcagtt ... taaattgcagGGAATGCTTTGTTCTCGTGGAGAACTACTTTTGATGCTAGATTCTGACGGT
EST: gi|100374133|gb|BY985678.1|BY985678
EST:     GAGTTCTTAAGCAAGTAACGAACCAAGGCAAAGGAGCAGCTGTCAGAAAA                         GGAATGCTTTGTTCTCGTGGAGAACTACTTTTGATGCTAGATTCTGACGGT
genomic: GAGTTCTTAAGCAAGTAACGAACCAAGGCAAAGGAGCAGCTGTCAGAAAAgtatgcagtt ... taaattgcagGGAATGCTTTGTTCTCGTGGAGAACTACTTTTGATGCTAGATTCTGACGGT

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-Seq library.


Block sizes: 30 (upstream exon), 12 (downstream exon)
Score: 3

TTTGGAGATTGCATCCGAGTATGTGAAAACCTATGGGATGGATATGATACGAGTTCTTAAGCAAGTAACGAACCAAGGCAAAGGAGCAGCTGTCAGAAAAgtatgcagtt ... taaattgcagGGAATGCTTTGTTCTCGTGGAGAACTACTTTTGATGCTAGATTCTGACGGTGCCACTAGGTTTGCAGACTTGAGAAAGTTGGAATTGCAA































 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggaatccaacagaggctcaaagactatctatactgagaagtttgataaattgcagGGAATGCTTTGTTCTCGTGGAGAACTACTTTTGATGCTAGATTCTGACGGTGCCACTAGGTTTGCAGACTTGAGAAAGTTGGAATTGCAA
                                       gtttgat  putative branch site (score: 3)
                                     aagtttgataaatt  TA-rich tract