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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTCCCAATATTTCCTGTTACGGGAGATTACTGGGTAATGAAGCTTGATGAGAATTATCAGTGGGCCCTAATAGGCCAACCCTCCAGAAGATATCTCTGGgtacgttaatcgcgattccttattttttcacacccttctcctcaggacatcaaatgctgtgaattgttctttaggaaaaaataggtcaatgatttacgca...

Basic information

species Physcomitrella patens
transcript PP1S464_11V6.2
intron # 2
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|22491848|gb|BU051771.1|BU051771
EST:     AGAATTATCAGTGGGCCCTAATAGGCCAACCCTCCAGAAGATATCTCTGG                         GTTTTATCTCGGACGCCAGAGCTCAGCGACGAAATTT
genomic: AGAATTATCAGTGGGCCCTAATAGGCCAACCCTCCAGAAGATATCTCTGGgtacgttaat ... ggatcttcagGTTTTATCTCGGACGCCAGAGCTCAGCGACGAAATTT
EST: gi|162261651|gb|FC438084.1|FC438084
EST:     AGAATTATCAGTGGGCCCTAATAGGCCAACCCTCCAGAAGATATCTCTGG                         GTTTTATCTCGGACGCCAGAGCTCAGCGACGAAATTTACAATCAACTTCTG
genomic: AGAATTATCAGTGGGCCCTAATAGGCCAACCCTCCAGAAGATATCTCTGGgtacgttaat ... ggatcttcagGTTTTATCTCGGACGCCAGAGCTCAGCGACGAAATTTACAATCAACTTCTG
EST: gi|162270639|gb|FC446564.1|FC446564
EST:     AGAATTATCAGTGGGCCCTAATAGGCCAACCCTCCAGAAGATATCTCTGG                         GTTTTATCTCGGACGCCAGAGCTCAGCGACGAAATTTACAATCAACTTCTG
genomic: AGAATTATCAGTGGGCCCTAATAGGCCAACCCTCCAGAAGATATCTCTGGgtacgttaat ... ggatcttcagGTTTTATCTCGGACGCCAGAGCTCAGCGACGAAATTTACAATCAACTTCTG
EST: gi|162261650|gb|FC438083.1|FC438083
EST:     AGAATTATCAGTGGGCCCTAATAGGCCAACCCTCCAGAAGATATCTCTGG                         GTTTTATCTCGGACGCCAGAGCTCAGCGACGAAATTTACAATCAACTTCTG
genomic: AGAATTATCAGTGGGCCCTAATAGGCCAACCCTCCAGAAGATATCTCTGGgtacgttaat ... ggatcttcagGTTTTATCTCGGACGCCAGAGCTCAGCGACGAAATTTACAATCAACTTCTG
EST: gi|22133095|gb|BQ827542.1|BQ827542
EST:     AGAATTATCAGTGGGCCCTAATAGGCCAACCCTCCAGAAGATATCTCTGG                         GTTTTATCTCGGACGCCAGAGCTCAGCGACGAAATTTACAATCAACTTCTG
genomic: AGAATTATCAGTGGGCCCTAATAGGCCAACCCTCCAGAAGATATCTCTGGgtacgttaat ... ggatcttcagGTTTTATCTCGGACGCCAGAGCTCAGCGACGAAATTTACAATCAACTTCTG
EST: gi|22132588|gb|BQ827241.1|BQ827241
EST:     AGAATTATCAGTGGGCCCTAATAGGCCAACCCTCCAGAAGATATCTCTGG                         GTTTTATCTCGGACGCCAGAGCTCAGCGACGAAATTTACAATCAACTTCTG
genomic: AGAATTATCAGTGGGCCCTAATAGGCCAACCCTCCAGAAGATATCTCTGGgtacgttaat ... ggatcttcagGTTTTATCTCGGACGCCAGAGCTCAGCGACGAAATTTACAATCAACTTCTG
EST: gi|162261421|gb|FC438257.1|FC438257
EST:     AGAATTATCAGTGGGCCCTAATAGGCCAACCCTCCAGAAGATATCTCTGG                         GTTTTATCTCGGACGCCAGAGCTCAGCGACGAAATTTACAATCAACTTCTG
genomic: AGAATTATCAGTGGGCCCTAATAGGCCAACCCTCCAGAAGATATCTCTGGgtacgttaat ... ggatcttcagGTTTTATCTCGGACGCCAGAGCTCAGCGACGAAATTTACAATCAACTTCTG
EST: gi|162261420|gb|FC438256.1|FC438256
EST:     AGAATTATCAGTGGGCCCTAATAGGCCAACCCTCCAGAAGATATCTCTGG                         GTTTTATCTCGGACGCCAGAGCTCAGCGACGAAATTTACAATCAACTTCTG
genomic: AGAATTATCAGTGGGCCCTAATAGGCCAACCCTCCAGAAGATATCTCTGGgtacgttaat ... ggatcttcagGTTTTATCTCGGACGCCAGAGCTCAGCGACGAAATTTACAATCAACTTCTG
EST: gi|18332696|gb|BJ164709.1|BJ164709
EST:     AGAATTATCAGTGGGCCCTAATAGGCCAACCCTCCAGAAGATATCTCTGG                         GTTTTATCTCGGACGCCAGAGCTCAGCGACGAAATTTACAATCAACTTCTG
genomic: AGAATTATCAGTGGGCCCTAATAGGCCAACCCTCCAGAAGATATCTCTGGgtacgttaat ... ggatcttcagGTTTTATCTCGGACGCCAGAGCTCAGCGACGAAATTTACAATCAACTTCTG
EST: gi|67692117|gb|BJ952350.1|BJ952350
EST:     AGAATTATCAGTGGGCCCTAATAGGCCAACCCTCCAGAAGATATCTCTGG                         GTTTTATCTCGGACGCCAGAGCTCAGCGACGAAATTTACAATCAACTTCTG
genomic: AGAATTATCAGTGGGCCCTAATAGGCCAACCCTCCAGAAGATATCTCTGGgtacgttaat ... ggatcttcagGTTTTATCTCGGACGCCAGAGCTCAGCGACGAAATTTACAATCAACTTCTG
EST: gi|67568909|gb|BJ941733.1|BJ941733
EST:     AGAATTATCAGTGGGCCCTAATAGGCCAACCCTCCAGAAGATATCTCTGG                         GTTTTATCTCGGACGCCAGAGCTCAGCGACGAAATTTACAATCAACTTCTG
genomic: AGAATTATCAGTGGGCCCTAATAGGCCAACCCTCCAGAAGATATCTCTGGgtacgttaat ... ggatcttcagGTTTTATCTCGGACGCCAGAGCTCAGCGACGAAATTTACAATCAACTTCTG
EST: gi|162263496|gb|FC439434.1|FC439434
EST:     AGAATTATCAGTGGGCCCTAATAGGCCAACCCTCCAGAAGATATCTCTGG                         GTTTTATCTCGGACGCCAGAGCTCAGCGACGAAATTTACAATCAACTTCTG
genomic: AGAATTATCAGTGGGCCCTAATAGGCCAACCCTCCAGAAGATATCTCTGGgtacgttaat ... ggatcttcagGTTTTATCTCGGACGCCAGAGCTCAGCGACGAAATTTACAATCAACTTCTG
EST: gi|22491918|gb|BU051841.1|BU051841
EST:     AGAATTATCAGTGGGCCCTAATAGGCCAACCCTCCAGAAGATATCTCTGG                         GTTTTATCTCGGACGCCAGAGCTCAGCGACGAAATTTACAATCAACTTCTG
genomic: AGAATTATCAGTGGGCCCTAATAGGCCAACCCTCCAGAAGATATCTCTGGgtacgttaat ... ggatcttcagGTTTTATCTCGGACGCCAGAGCTCAGCGACGAAATTTACAATCAACTTCTG

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-Seq library.


Block sizes: 8 (upstream exon), 33 (downstream exon)
Score: 3

CTTCCCAATATTTCCTGTTACGGGAGATTACTGGGTAATGAAGCTTGATGAGAATTATCAGTGGGCCCTAATAGGCCAACCCTCCAGAAGATATCTCTGGgtacgttaat ... ggatcttcagGTTTTATCTCGGACGCCAGAGCTCAGCGACGAAATTTACAATCAACTTCTGGAGCATGCAACTAACGAAGGTTACGATGTTAGCAAGTTACATAAAACGC