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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAACGTCGTTCGCCATTCAATATGGCACTGGGTCCATGGAAGGTTTCTTGAGCCAAGACGACGTTACTCTTGGTGACCTCACAGTGAAATGGCAGgtgaatttggaagaatgattcgcaaaagagggttttgacctggttttcaccgttaaacaataatgcaggagcttatctgatctgtctatacatcattttcagcagtttgtagctcgaggaatacctgatttcgtagtaccttttgcag

Basic information

species Physcomitrella patens
transcript PP1S113_31V6.1
intron # 3
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|67709650|gb|BJ965466.1|BJ965466
EST:     TCTTGGGCCAAGACGACGTTACTCTTGGTGACCTCACAGTGAAATGGCAG                         GTCTTTGCTGAACCTACGAANGAGCCTGGTGTCACATTTGTCTCAGCCAAG
genomic: TCTTGAGCCAAGACGACGTTACTCTTGGTGACCTCACAGTGAAATGGCAGgtgaatttgg ... ccttttgcagGTCTTTGCTGAAGCTACGAAGGAGCCTGGTGTCACATTTGTCTCAGCCAAG
EST: gi|208370860|gb|DC936898.1|DC936898
EST:     TCTTGAGCCAAGACGACGTTACTCTTGGTGACCTCACAGTGAAATGGCAG                         GTCTTTGCTGAAGCTACGAAGGAGCCTGGTGTCACATTTGTCTCAGCCAAG
genomic: TCTTGAGCCAAGACGACGTTACTCTTGGTGACCTCACAGTGAAATGGCAGgtgaatttgg ... ccttttgcagGTCTTTGCTGAAGCTACGAAGGAGCCTGGTGTCACATTTGTCTCAGCCAAG
EST: gi|67717411|gb|BJ967670.1|BJ967670
EST:     TCTTGAGCCAAGACGACGTTACTCTTGGTGACCTCACAGTGAAATGGCAG                         GTCTTTGCTGAAGCTACNAAGGAGCCTGGTGTCACATTTGTCTCANCCAAG
genomic: TCTTGAGCCAAGACGACGTTACTCTTGGTGACCTCACAGTGAAATGGCAGgtgaatttgg ... ccttttgcagGTCTTTGCTGAAGCTACGAAGGAGCCTGGTGTCACATTTGTCTCAGCCAAG
EST: gi|162235503|gb|FC411833.1|FC411833
EST:     TCTTGAGCCAAGACGACGTTACTCTTGGTGACCTCACAGTGAAATGGCAG                         GTCTTTGCTGAAGCTACGAAGGAGCCTGGTGTCACATTTGTCTCAGCCAAG
genomic: TCTTGAGCCAAGACGACGTTACTCTTGGTGACCTCACAGTGAAATGGCAGgtgaatttgg ... ccttttgcagGTCTTTGCTGAAGCTACGAAGGAGCCTGGTGTCACATTTGTCTCAGCCAAG
EST: gi|208378113|gb|DC902586.1|DC902586
EST:     TCTTGAGCCAAGACGACGTTACTCTTGGTGACCTCACAGTGAAATGGCAG                         GTCTTTGCCGAAGCTACGAANGAGCCTGGTGTCACATTTGTCTCAGCCAAG
genomic: TCTTGAGCCAAGACGACGTTACTCTTGGTGACCTCACAGTGAAATGGCAGgtgaatttgg ... ccttttgcagGTCTTTGCTGAAGCTACGAAGGAGCCTGGTGTCACATTTGTCTCAGCCAAG
EST: gi|100415055|gb|BY975143.1|BY975143
EST:     TCTTGAGCCAAGACGACGTTACTCTTGGTGACCTCACAGTGAAATGGCAG                         GTCTTTGCTGAAGCTACGAAGGAGCCTGGTGGCACATTTGTCTCACCCAAG
genomic: TCTTGAGCCAAGACGACGTTACTCTTGGTGACCTCACAGTGAAATGGCAGgtgaatttgg ... ccttttgcagGTCTTTGCTGAAGCTACGAAGGAGCCTGGTGTCACATTTGTCTCAGCCAAG
EST: gi|162151133|gb|FC327652.1|FC327652
EST:     TCTTGAGCCAAGACGACGTTACTCTTGGTGACCTCACAGTGAAATGGCAG                         GTCTTTGCTGAAGCTACGAAGGAGCCTGGTGTCACATTTGTCTCAGCCAAG
genomic: TCTTGAGCCAAGACGACGTTACTCTTGGTGACCTCACAGTGAAATGGCAGgtgaatttgg ... ccttttgcagGTCTTTGCTGAAGCTACGAAGGAGCCTGGTGTCACATTTGTCTCAGCCAAG

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: 23 (upstream exon), 35 (downstream exon)
Score: 3

GAACGTCGTTCGCCATTCAATATGGCACTGGGTCCATGGAAGGTTTCTTGAGCCAAGACGACGTTACTCTTGGTGACCTCACAGTGAAATGGCAGgtgaatttgg ... ccttttgcagGTCTTTGCTGAAGCTACGAAGGAGCCTGGTGTCACATTTGTCTCAGCCAAGTTTGATGGCATTCTCGGCCTTGGCTTCAAGGAGATTTCCGTTGATCGAG




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