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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctgttaatccgtgcttgctttgctttctttcatttctaaacttgtttgcggggaggtctgtttgccagacgatgtgctcattgtctatgttgcttgtatggttccagGAATGGACACGAGAAGAGAAGAACAAGTGCCTCAAAGAGACGGAGAATTCTTTCAAATACTCTGGTAAGATCTTGCGTTTGATCGCCACTTCGAAATGAA

Basic information

species Physcomitrella patens
transcript PP1S47_217V6.1
intron # 4
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|208365090|gb|DC947326.1|DC947326
EST:     TCTCTCAGCTCCTGGGAGCAGTTAAGGAAAATCTTAACAAAGTTGCAGAG                         GAATGGACACGAGAAGAGAAGAACAAGTGCCTCAAAGAGACGGAGAATTCT
genomic: TCTCTCAGCTCCTGGGAGCAGTTAAGGAAAATCTTAACAAAGTTGCAGAGgtctgttaat ... atggttccagGAATGGACACGAGAAGAGAAGAACAAGTGCCTCAAAGAGACGGAGAATTCT
EST: gi|162249998|gb|FC427099.1|FC427099
EST:     CTCAGCTCCTGGGAGCAGTTAAGGAAAATCTTAACAAAGTTGCAGAG                         GAATGGACACGAGAAGAGAAGAACAAGTGCCTCAAAGAGACGGAGAATTCT
genomic: CTCAGCTCCTGGGAGCAGTTAAGGAAAATCTTAACAAAGTTGCAGAGgtctgttaat ... atggttccagGAATGGACACGAGAAGAGAAGAACAAGTGCCTCAAAGAGACGGAGAATTCT
EST: gi|162260449|gb|FC435062.1|FC435062
EST:     TCTCTCAGCTCCTGGGAGCAGTTAAGGAAAATCTTAACAAAGTTGCAGAG                         GAATGGACACGAGAAGAGAAGAACAAGTGCCTCAAAGAGACGGAGAATTCT
genomic: TCTCTCAGCTCCTGGGAGCAGTTAAGGAAAATCTTAACAAAGTTGCAGAGgtctgttaat ... atggttccagGAATGGACACGAGAAGAGAAGAACAAGTGCCTCAAAGAGACGGAGAATTCT
EST: gi|162269610|gb|FC445569.1|FC445569
EST:     TCTCTCAGCTCCTGGGAGCAGTTAAGGAAAATCTTAACAAAGTTGCAGAG                         GAATGGACACGAGAAGAGAAGAACAAGTGCCTCAAAGAGACGGAGAATTCT
genomic: TCTCTCAGCTCCTGGGAGCAGTTAAGGAAAATCTTAACAAAGTTGCAGAGgtctgttaat ... atggttccagGAATGGACACGAGAAGAGAAGAACAAGTGCCTCAAAGAGACGGAGAATTCT
EST: gi|162269919|gb|FC445930.1|FC445930
EST:     TCTCTCAGCTCCTGGGAGCAGTTAAGGAAAATCTTAACAAAGTTGCAGAG                         GAATGGACACGAGAAGAGAAGAACAAGTGCCTCANAGAGACGGAGAAATCT
genomic: TCTCTCAGCTCCTGGGAGCAGTTAAGGAAAATCTTAACAAAGTTGCAGAGgtctgttaat ... atggttccagGAATGGACACGAGAAGAGAAGAACAAGTGCCTCAAAGAGACGGAGAATTCT
EST: gi|208367180|gb|DC947858.1|DC947858
EST:     TCTCTCAGCTCCTGGGAGCAGTTAAGGAAAATCTTAACAAAGTTGCAGAG                         GAATGGACACGAGAAGAGAAGAACAAGTGCCTCAAAGAGACGGAGAATTCT
genomic: TCTCTCAGCTCCTGGGAGCAGTTAAGGAAAATCTTAACAAAGTTGCAGAGgtctgttaat ... atggttccagGAATGGACACGAGAAGAGAAGAACAAGTGCCTCAAAGAGACGGAGAATTCT
EST: gi|67693892|gb|BJ954125.1|BJ954125
EST:     TCTCTCAGCTCCTGGGAGCAGTTAAGGAAAATCTTAACAAAGTTGCAGAG                         GAATGGACACGAGAAGAGAAGAACAAGTGCCTCAAAGAGACGGAGAATTCT
genomic: TCTCTCAGCTCCTGGGAGCAGTTAAGGAAAATCTTAACAAAGTTGCAGAGgtctgttaat ... atggttccagGAATGGACACGAGAAGAGAAGAACAAGTGCCTCAAAGAGACGGAGAATTCT

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), 35 (downstream exon)
Score: 54

GATGATTTTGGATGGTAGGGAGTTGGAGTTTTATAAGTGGGATGGAGAGCTCTCTCAGCTCCTGGGAGCAGTTAAGGAAAATCTTAACAAAGTTGCAGAGgtctgttaat ... atggttccagGAATGGACACGAGAAGAGAAGAACAAGTGCCTCAAAGAGACGGAGAATTCTTTCAAATACTCTGGTAAGATCTTGCGTTTGATCGCCACTTCGAAATGAA




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