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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTCCCATGGGGCACATTTTGTACGATGAGGTGATGAAGTACAATCCGAAGAATCCCTACTGGTTTAACAGGGACCGCTTCGTGTTGTCTGCTGGCCACGgtgagcaattgcggctaatatcatttcattcatgatctgggatctgaattaatcactgctatttcaaatttgaatgtcgctagccgcatgtgaaaattgaaggaacccaattgaactctcaatgccgtagatttgtcactgactgacaatgcgtattggcccggcag

Basic information

species Physcomitrella patens
transcript PP1S120_164V6.1
intron # 1
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|18373902|gb|BJ205480.1|BJ205480
EST:     GAATCCCTACTGGTTTAACAGGGACCGCTTCGTGTTGTCTGCTGGCCACG                         GATGCATGCTCCAGTACGCTCTCCTCCACCTCGCTGGGTACGA
genomic: GAATCCCTACTGGTTTAACAGGGACCGCTTCGTGTTGTCTGCTGGCCACGgtgagcaatt ... ggcccggcagGATGCATGCTCCAGTACGCTCTCCTCCACCTCGCTGGGTACGA
EST: gi|18332293|gb|BJ164306.1|BJ164306
EST:     GAATCCCTACTGGTTTAACAGGGACCGCTTCGTGTTGTCTGCTGGCCACG                         GATGCATGCTCCAGTACGCTCTCCTCCACCTCGCTGGGTA
genomic: GAATCCCTACTGGTTTAACAGGGACCGCTTCGTGTTGTCTGCTGGCCACGgtgagcaatt ... ggcccggcagGATGCATGCTCCAGTACGCTCTCCTCCACCTCGCTGGGTA
EST: gi|18324787|gb|BJ156782.1|BJ156782
EST:     GAATCCCTACTGGTTTAACAGGGACCGCTTCGTGTTGTCTGCTGGCCACG                         GATGCATGCTCCAGTACGCTCTCCTCCACCTCGCTGGGTACGACAGTGTTC
genomic: GAATCCCTACTGGTTTAACAGGGACCGCTTCGTGTTGTCTGCTGGCCACGgtgagcaatt ... ggcccggcagGATGCATGCTCCAGTACGCTCTCCTCCACCTCGCTGGGTACGACAGTGTTC
EST: gi|100433314|gb|BY960543.1|BY960543
EST:     GAATCCCTACTGGTTTAACAGGGACCGCTTCGTGTTGTCTGCTGGGCACG                         GATGCATGCTCCAGTACGCTCTCCTCCACCTCGCTGGGTACGACAGTGTTC
genomic: GAATCCCTACTGGTTTAACAGGGACCGCTTCGTGTTGTCTGCTGGCCACGgtgagcaatt ... ggcccggcagGATGCATGCTCCAGTACGCTCTCCTCCACCTCGCTGGGTACGACAGTGTTC
EST: gi|100448433|gb|CJ972732.1|CJ972732
EST:     GAATCCCTACTGGTTTAACAGGGACCGCTTCGTGTTGTCTGCTGGCCACG                         GATGCATGCTCCAGTACGCTCTCCTCCACCTCGCTGGGTACGACAGTGTTC
genomic: GAATCCCTACTGGTTTAACAGGGACCGCTTCGTGTTGTCTGCTGGCCACGgtgagcaatt ... ggcccggcagGATGCATGCTCCAGTACGCTCTCCTCCACCTCGCTGGGTACGACAGTGTTC
EST: gi|100446557|gb|CJ970856.1|CJ970856
EST:     GAATCCCTACTGGTTTAACAGGGACCGCTTCGTGTTGTCTGCTGGCCACG                         GATGCATGCTCCAGTACGCTCTCCTCCACCTCGCTGGGTACGACAGTGTTC
genomic: GAATCCCTACTGGTTTAACAGGGACCGCTTCGTGTTGTCTGCTGGCCACGgtgagcaatt ... ggcccggcagGATGCATGCTCCAGTACGCTCTCCTCCACCTCGCTGGGTACGACAGTGTTC
EST: gi|100442191|gb|BY963084.1|BY963084
EST:     GAATCCCTACTGGTTTAACAGGGACCGCTTCGTGTTGTCTGCTGGCCACG                         GATGCATGCTCCAGTACGCTCTCCTCCACCTCGCTGGGTACGACAGTGTTC
genomic: GAATCCCTACTGGTTTAACAGGGACCGCTTCGTGTTGTCTGCTGGCCACGgtgagcaatt ... ggcccggcagGATGCATGCTCCAGTACGCTCTCCTCCACCTCGCTGGGTACGACAGTGTTC
EST: gi|18368720|gb|BJ200805.1|BJ200805
EST:     GAATCCCTACTGGTTTAACAGGGACCGCTTCGTGTTGTCTGCTGGCCACG                         GATGCATGCTCCAGTACGCTCTCCTCCACCTCGCTGGGTACGACAGTGTTC
genomic: GAATCCCTACTGGTTTAACAGGGACCGCTTCGTGTTGTCTGCTGGCCACGgtgagcaatt ... ggcccggcagGATGCATGCTCCAGTACGCTCTCCTCCACCTCGCTGGGTACGACAGTGTTC
EST: gi|100404862|gb|BY991318.1|BY991318
EST:     GAATCCCTACTGGTTTAACAGGGACCGCTTCGTGTTGTCTGCTGGCCACG                         GATGCATGCTCCAGTACGCTCTCCTCCACCTCGCTGGGTACGACAGTGTTC
genomic: GAATCCCTACTGGTTTAACAGGGACCGCTTCGTGTTGTCTGCTGGCCACGgtgagcaatt ... ggcccggcagGATGCATGCTCCAGTACGCTCTCCTCCACCTCGCTGGGTACGACAGTGTTC
EST: gi|100443241|gb|BY963537.1|BY963537
EST:     GAATCCCTACTGGTTTAACAGGGACCGCTTCGTGTTGTCTGCTGGCCACG                         GATGCATGCTCCAGTACGCTCTCCTCCACCTCGCTGGGTACGACAGTGTTC
genomic: GAATCCCTACTGGTTTAACAGGGACCGCTTCGTGTTGTCTGCTGGCCACGgtgagcaatt ... ggcccggcagGATGCATGCTCCAGTACGCTCTCCTCCACCTCGCTGGGTACGACAGTGTTC
EST: gi|18359609|gb|BJ191670.1|BJ191670
EST:     GAATCCCTACTGGTTTAACAGGGACCGCTTCGTGTTGTCTGCTGGCCACG                         GATGCATGCTCCANTACGCTCTCCTCCACCTNGCTGGG
genomic: GAATCCCTACTGGTTTAACAGGGACCGCTTCGTGTTGTCTGCTGGCCACGgtgagcaatt ... ggcccggcagGATGCATGCTCCAGTACGCTCTCCTCCACCTCGCTGGG
EST: gi|18364366|gb|BJ196439.1|BJ196439
EST:     GAATCCCTACTGGTTTAACAGGGACCGCTTCGTGTTGTCTGCTGGCCACG                         GATGCATGCTCCAGTACGCTCTCCTCCACCTCGCTGGGTACGACAGTGTTC
genomic: GAATCCCTACTGGTTTAACAGGGACCGCTTCGTGTTGTCTGCTGGCCACGgtgagcaatt ... ggcccggcagGATGCATGCTCCAGTACGCTCTCCTCCACCTCGCTGGGTACGACAGTGTTC

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: 32 (upstream exon), 35 (downstream exon)
Score: 78

GCTCCCATGGGGCACATTTTGTACGATGAGGTGATGAAGTACAATCCGAAGAATCCCTACTGGTTTAACAGGGACCGCTTCGTGTTGTCTGCTGGCCACGgtgagcaatt ... ggcccggcagGATGCATGCTCCAGTACGCTCTCCTCCACCTCGCTGGGTACGACAGTGTTCAG




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