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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtttttctctcctcgctggatgttaggcataaataaaacctttcggctggtgacttcaacatagtttgtcctcgaatttttcagtcttttcttagacttgtgagggtattgttctcgcttaacacaaaccattcatgctagatcattgacgttgtgatgcgatgtctcttgcagGGGTCCACTTCCTACTAAAGATATTCTTGGACGTTCTGTGTTACGCTACTGGCCACCCGAACGTCTAGGCAGTACAGTTTTTGATACGACTGATCTCTTG

Basic information

species Physcomitrella patens
transcript PP1S9_440V6.1
intron # 3
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|162198997|gb|FC374545.1|FC374545
EST:     GTTTTTGTAATGGGGGATAATAGGAACAACAGTTACGATTCCCACGTCTG                         GGGTCCACTTCCTACTAAAGATATTCTTGGACGTTCTGTGTTACGCTACTG
genomic: GTTTTTGTAATGGGGGATAATAGGAACAACAGTTACGATTCCCACGTCTGgtatgttttt ... tctcttgcagGGGTCCACTTCCTACTAAAGATATTCTTGGACGTTCTGTGTTACGCTACTG
EST: gi|162189174|gb|FC366709.1|FC366709
EST:     GTTTTTGTAATGGGGGATAATAGGAACAACAGTTACGATTCCCACGTCTG                         GGGTCCACTTCCTACTAAAGATATTCTTGGACGTTCTGTGTTACGCTACTG
genomic: GTTTTTGTAATGGGGGATAATAGGAACAACAGTTACGATTCCCACGTCTGgtatgttttt ... tctcttgcagGGGTCCACTTCCTACTAAAGATATTCTTGGACGTTCTGTGTTACGCTACTG
EST: gi|162264038|gb|FC439892.1|FC439892
EST:     GTTTTTGTAATGGGGGATAATAGGAACAACAGTTACGATTCCCACGTCTG                         GGGTCCACTTCCTACTAAAGATATTCTTGGACGTTCTGTGTTACGCTACTG
genomic: GTTTTTGTAATGGGGGATAATAGGAACAACAGTTACGATTCCCACGTCTGgtatgttttt ... tctcttgcagGGGTCCACTTCCTACTAAAGATATTCTTGGACGTTCTGTGTTACGCTACTG
EST: gi|162153130|gb|FC329536.1|FC329536
EST:     GTTTTTGTAATGGGGGATAATAGGAACAACAGTTACGATTCCCACGTCTG                         GGGTCCACTTCCTACTAAAGATATTCTTGGACGTTCTGTGTTACGCTACTG
genomic: GTTTTTGTAATGGGGGATAATAGGAACAACAGTTACGATTCCCACGTCTGgtatgttttt ... tctcttgcagGGGTCCACTTCCTACTAAAGATATTCTTGGACGTTCTGTGTTACGCTACTG
EST: gi|162244931|gb|FC423537.1|FC423537
EST:     GTTTTTGTAATGGGGGATAATAGGAACAACAGTTACGATTCCCACGTCTG                         GGGTCCACTTCCTACTAAAGATATTCTTGGACGTTCTGTGTTACGCTACTG
genomic: GTTTTTGTAATGGGGGATAATAGGAACAACAGTTACGATTCCCACGTCTGgtatgttttt ... tctcttgcagGGGTCCACTTCCTACTAAAGATATTCTTGGACGTTCTGTGTTACGCTACTG
EST: gi|162170912|gb|FC346603.1|FC346603
EST:     GTTTTTGTAATGGGGGATAATAGGAACAACAGTTACGATTCCCACGTCTG                         GGGTCCACTTCCTACTAAAGATATTCTTGGACGTTCTGTGTTACGCTACTG
genomic: GTTTTTGTAATGGGGGATAATAGGAACAACAGTTACGATTCCCACGTCTGgtatgttttt ... tctcttgcagGGGTCCACTTCCTACTAAAGATATTCTTGGACGTTCTGTGTTACGCTACTG
EST: gi|19785708|gb|BQ040373.1|BQ040373
EST:     GTTTTTGTAATGGGGGATAATAGGAACAACAGTTACGATTCCCACGTCTG                         GGGTCCACTTCCTACTAAAGATATTCTTGGACGTTCTGTGTTACGCTACTG
genomic: GTTTTTGTAATGGGGGATAATAGGAACAACAGTTACGATTCCCACGTCTGgtatgttttt ... tctcttgcagGGGTCCACTTCCTACTAAAGATATTCTTGGACGTTCTGTGTTACGCTACTG
EST: gi|162266538|gb|FC441950.1|FC441950
EST:     GTTTTTGTAATGGGGGATAATAGGAACAACAGTTACGATTCCCACGTCTG                         GGGTCCACTTCCTACTAAAGATATTCTTGGACGTTCTGTGTTACGCTACTG
genomic: GTTTTTGTAATGGGGGATAATAGGAACAACAGTTACGATTCCCACGTCTGgtatgttttt ... tctcttgcagGGGTCCACTTCCTACTAAAGATATTCTTGGACGTTCTGTGTTACGCTACTG
EST: gi|162181703|gb|FC358733.1|FC358733
EST:     GTTTTTGTAATGGGGGATAATAGGAACAACAGTTACGATTCCCACGTCTG                         GGGTCCACTTCCTACTAAAGATATTCTTGGACGTTCTGTGTTACGCTACTG
genomic: GTTTTTGTAATGGGGGATAATAGGAACAACAGTTACGATTCCCACGTCTGgtatgttttt ... tctcttgcagGGGTCCACTTCCTACTAAAGATATTCTTGGACGTTCTGTGTTACGCTACTG
EST: gi|162197832|gb|FC373613.1|FC373613
EST:     GTTTTTGTAATGGGGGATAATAGGAACAACAGTTACGATTCCCACGTCTG                         GNGTCCACTTCCTACTAAAGATATTCTTGGACGTTCTGTGTTACGCTACTG
genomic: GTTTTTGTAATGGGGGATAATAGGAACAACAGTTACGATTCCCACGTCTGgtatgttttt ... tctcttgcagGGGTCCACTTCCTACTAAAGATATTCTTGGACGTTCTGTGTTACGCTACTG
EST: gi|22131771|gb|BQ826791.1|BQ826791
EST:     GTTTTTGTAATGGGGGATAATAGGAACAACAGTTACGATTCCCACGTCTG                         GGGTCCACTTCCTACTAAAGATATTCTTGGACGTTCTGTGTTACGCTACTG
genomic: GTTTTTGTAATGGGGGATAATAGGAACAACAGTTACGATTCCCACGTCTGgtatgttttt ... tctcttgcagGGGTCCACTTCCTACTAAAGATATTCTTGGACGTTCTGTGTTACGCTACTG

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: 35 (upstream exon), 33 (downstream exon)
Score: 18

AAAATACCAGAAGATCACGTTTTTGTAATGGGGGATAATAGGAACAACAGTTACGATTCCCACGTCTGgtatgttttt ... tctcttgcagGGGTCCACTTCCTACTAAAGATATTCTTGGACGTTCTGTGTTACGCTACTGGCCACCCGAACGTCTAGGCAGTACAGTTTTTGATACGACTGATCTCTTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taacacaaaccattcatgctagatcattgacgttgtgatgcgatgtctcttgcagGGGTCCACTTCCTACTAAAGATATTCTTGGACGTTCTGTGTTACGCTACTGGCCACCCGAACGTCTAGGCAGTACAGTTTTTGATACGACTGATCTCTTG
                        cattgac  putative branch site (score: 18)
                                           tgtctctt  putative PPT