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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGGACAAGGTTGCAGCAACGAGAGTTATGAATGAGAAGAATGCCGAACTTAAAGGGCGGGGAGTTCAGgtaacctaatgctgtgaagcagcacatggtgttgccgttgctgcatatccctcaggaagctgcatcaaagagttcatacatacactaaattaggctcctt...

Basic information

species Physcomitrella patens
transcript PP1S100_30V6.1
intron # 12
splice site 5'
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|162161220|gb|FC337283.1|FC337283
EST:     CGAGAGTTATGAATGAGAAGAATGCCGAACTTAAAGGGCGGGGAGTTCAG                         GCATACATTATTCAAGGGAAGGAACCCACTCAGTTCCTGGCGCTGTTCAAA
genomic: CGAGAGTTATGAATGAGAAGAATGCCGAACTTAAAGGGCGGGGAGTTCAGgtaacctaat ... ttcatgacagGCATACATTATTCAAGGGAAGGAACCCACTCAGTTCCTGGCGCTGTTCAA-
EST: gi|162256364|gb|FC432374.1|FC432374
EST:     CGAGAGTTATGAATGAGAAGAATGCCGAACTTAAAGGGCGGGGAGTTCAG                         GCATACATTATTCAAGGGAAGGAACCCACTCAGTTCCTGGCGCTGTTCAAA
genomic: CGAGAGTTATGAATGAGAAGAATGCCGAACTTAAAGGGCGGGGAGTTCAGgtaacctaat ... ttcatgacagGCATACATTATTCAAGGGAAGGAACCCACTCAGTTCCTGGCGCTGTTC-AA
EST: gi|100393142|gb|BY989764.1|BY989764
EST:     ATGAGAAGAATGCCGAACTTAAAGGGCGGGGAGTTCAG                         GCATACATTATTCAAGGGAAGGAACCCACTCAGTTCCTGGCGCTGTTCAAA
genomic: ATGAGAAGAATGCCGAACTTAAAGGGCGGGGAGTTCAGgtaacctaat ... ttcatgacagGCATACATTATTCAAGGGAAGGAACCCACTCAGTTCCTGGCGCTGTTC-AA
EST: gi|162185667|gb|FC362054.1|FC362054
EST:     CGAGAGTTATGAATGAGAAGAATGCCGAACTTAAAGGGCGGGGAGTTCAG                         GCATACATTATTCAAGGGAAGGAACCCACTCAGTTCCTGGCGCTGTTCAAA
genomic: CGAGAGTTATGAATGAGAAGAATGCCGAACTTAAAGGGCGGGGAGTTCAGgtaacctaat ... ttcatgacagGCATACATTATTCAAGGGAAGGAACCCACTCAGTTCCTGGCGCTGTTC-AA
EST: gi|162180210|gb|FC355527.1|FC355527
EST:     CGAGAGTTATGAATGAGAAGAATGCCGAACTTAAAGGGCGGGGAGTTCAG                         GCATACATTATTCAAGGGAAGGAACCCACTCAGTTCCTGGCGCTGTTCAAA
genomic: CGAGAGTTATGAATGAGAAGAATGCCGAACTTAAAGGGCGGGGAGTTCAGgtaacctaat ... ttcatgacagGCATACATTATTCAAGGGAAGGAACCCACTCAGTTCCTGGCGCTGTTC-AA
EST: gi|162222679|gb|FC397491.1|FC397491
EST:     CGAGAGTTATGAATGAGAAGAATGCCGAACTTAAAGGGCGGGGAGTTCAG                         GCATACATTATTCAAGGGAAGGAACCCACTCAGTTCCTGGCGCTGTTCAAA
genomic: CGAGAGTTATGAATGAGAAGAATGCCGAACTTAAAGGGCGGGGAGTTCAGgtaacctaat ... ttcatgacagGCATACATTATTCAAGGGAAGGAACCCACTCAGTTCCTGGCGCTGTTC-AA
EST: gi|162255247|gb|FC431557.1|FC431557
EST:     CGAGAGTTATGAATGAGAAGAATGCCGAACTTAAAGGGCGGGGAGTTCAG                         GCATACATTATTCAAGGGAAGGAACCCACTCAGTTCCTGGCGCTGTTCAAA
genomic: CGAGAGTTATGAATGAGAAGAATGCCGAACTTAAAGGGCGGGGAGTTCAGgtaacctaat ... ttcatgacagGCATACATTATTCAAGGGAAGGAACCCACTCAGTTCCTGGCGCTGTTCAA-
EST: gi|162199756|gb|FC375829.1|FC375829
EST:     CGAGAGTTATGAATGAGAAGAATGCCGAACTTAAAGGGCGGGGAGTTCAG                         GCATACATTATTCAAGGGAAGGAACCCACTCAGTTCCTGGCGCTGTTCAAA
genomic: CGAGAGTTATGAATGAGAAGAATGCCGAACTTAAAGGGCGGGGAGTTCAGgtaacctaat ... ttcatgacagGCATACATTATTCAAGGGAAGGAACCCACTCAGTTCCTGGCGCTGTTC-AA

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), 30 (downstream exon)
Score: 9

GAGGACAAGGTTGCAGCAACGAGAGTTATGAATGAGAAGAATGCCGAACTTAAAGGGCGGGGAGTTCAGgtaacctaat ... ttcatgacagGCATACATTATTCAAGGGAAGGAACCCACTCAGTTCCTGGCGCTGTTCAATGC




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