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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACTGTGGAGGAGCTGTACAAGGTTGCCTCGATTGCTCTGAGCCCCAACGTCACTGGGCAAATAATGgtatgtgttctatgctggctatgaactttatgcaaaatgaagtctagccctcgccctgaactaacatccgcaggagcataatttaggatacggtactgaagtgagtattcgacttgtgtgtgttgtag

Basic information

species Physcomitrella patens
transcript PP1S64_220V6.1
intron # 9
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|162160586|gb|FC336355.1|FC336355
EST:     ACAAGGTTGCCTCGATTGCTCTGAGCCCCAACGTCACTGGGCAAATAATG                         ATGGGTCTGATGGTCAAACCTCCAAGACCAGGCGACGTCTCGTTTCCTCTA
genomic: ACAAGGTTGCCTCGATTGCTCTGAGCCCCAACGTCACTGGGCAAATAATGgtatgtgttc ... tgtgttgtagATGGGTCTGATGGTCAAACCTCCAAGACCAGGCGACGTCTCGTTTCCTCTA
EST: gi|162170440|gb|FC347625.1|FC347625
EST:     ACAAGGTTGCCTCGATTGCTCTGAGCCCCAACGTCACTGGGCAAATAATG                         ATGGGTCTGATGGTCAAACCTCCAAGACCAGGCGACGTCTCGTTTCCTCTA
genomic: ACAAGGTTGCCTCGATTGCTCTGAGCCCCAACGTCACTGGGCAAATAATGgtatgtgttc ... tgtgttgtagATGGGTCTGATGGTCAAACCTCCAAGACCAGGCGACGTCTCGTTTCCTCTA
EST: gi|162166217|gb|FC343434.1|FC343434
EST:     CTGGGCAAATAATG                         ATGGGTCTGATGGTCAAACCTCCAAGACCAGGCGACGTCTCGTTTCCTCTA
genomic: CTGGGCAAATAATGgtatgtgttc ... tgtgttgtagATGGGTCTGATGGTCAAACCTCCAAGACCAGGCGACGTCTCGTTTCCTCTA
EST: gi|162154421|gb|FC330423.1|FC330423
EST:     ACGTCACTGGGCAAATAATG                         ATGGGTCTGATGGTCAAACCTCCAAGACCAGGCGACGTCTCGTTTCCTCTA
genomic: ACGTCACTGGGCAAATAATGgtatgtgttc ... tgtgttgtagATGGGTCTGATGGTCAAACCTCCAAGACCAGGCGACGTCTCGTTTCCTCTA
EST: gi|162156210|gb|FC332585.1|FC332585
EST:     ACAAGGTTGCCTCGATTGCTCTGAGCCCCAACGTCACTGGGCAAATAATG                         ATGGGTCTGATGGTCAAACCTCCAAGACCAGGCGACGTCTCGTTTCCTCTA
genomic: ACAAGGTTGCCTCGATTGCTCTGAGCCCCAACGTCACTGGGCAAATAATGgtatgtgttc ... tgtgttgtagATGGGTCTGATGGTCAAACCTCCAAGACCAGGCGACGTCTCGTTTCCTCTA
EST: gi|162165158|gb|FC341153.1|FC341153
EST:     ACAAGGTTGCCTCGATTGCTCTGAGCCCCAACGTCACTGGGCAAATAATG                         ATGGGTCTGATGGTCAAACCTCCAAGACCAGGCGACGTCTCGTTTCCTCTA
genomic: ACAAGGTTGCCTCGATTGCTCTGAGCCCCAACGTCACTGGGCAAATAATGgtatgtgttc ... tgtgttgtagATGGGTCTGATGGTCAAACCTCCAAGACCAGGCGACGTCTCGTTTCCTCTA
EST: gi|162170441|gb|FC347626.1|FC347626
EST:     ACAAGGTTGCCTCGATTGCTCTGAGCCCCAACGTCACTGGGCAAATAATG                         ATGGGTCTGATGGTCAAACCTCCAAGACCAGGCGACGTCTCGTTTCCTCTA
genomic: ACAAGGTTGCCTCGATTGCTCTGAGCCCCAACGTCACTGGGCAAATAATGgtatgtgttc ... tgtgttgtagATGGGTCTGATGGTCAAACCTCCAAGACCAGGCGACGTCTCGTTTCCTCTA
EST: gi|162191349|gb|FC368145.1|FC368145
EST:     ACAAGGTTGCCTCGATTGCTCTGAGCCCCAACGTCACTGGGCAAATAATG                         ATGGGTCTGATGGTCAAACCTCCCAGACCAGGCGACGTCTCGTTTCCTCTA
genomic: ACAAGGTTGCCTCGATTGCTCTGAGCCCCAACGTCACTGGGCAAATAATGgtatgtgttc ... tgtgttgtagATGGGTCTGATGGTCAAACCTCCAAGACCAGGCGACGTCTCGTTTCCTCTA
EST: gi|162182492|gb|FC357467.1|FC357467
EST:     GCTCTGAGCCCCAACGTCACTGGGCAAATAATG                         ATGGGTCTGATGGTCAAACCTCCAAGACCAGGCGACGTCTCGTTTCCTCTA
genomic: GCTCTGAGCCCCAACGTCACTGGGCAAATAATGgtatgtgttc ... tgtgttgtagATGGGTCTGATGGTCAAACCTCCAAGACCAGGCGACGTCTCGTTTCCTCTA
EST: gi|162246304|gb|FC421049.1|FC421049
EST:     ACAAGGTTGCCTCGATTGCTCTGAGCCCCAACGTCACTGGGCAAATAATG                         ATGGGTCTGATGGTCAAACCTCCAA
genomic: ACAAGGTTGCCTCGATTGCTCTGAGCCCCAACGTCACTGGGCAAATAATGgtatgtgttc ... tgtgttgtagATGGGTCTGATGGTCAAACCTCCAA
EST: gi|161978655|gb|EE296353.1|EE296353
EST:     CAAGGTTGCCTCGTATTGCTCTGAGCCCCAACGTCACTGGGCAAATAATG                         ATGGGTCTGATGGTCAAACCTCCAAGACCAGGCGACGTCTCGNTTTCCTCT
genomic: CAAGGTTGCCTCG-ATTGCTCTGAGCCCCAACGTCACTGGGCAAATAATGgtatgtgttc ... tgtgttgtagATGGGTCTGATGGTCAAACCTCCAAGACCAGGCGACGTCTCG-TTTCCTCT
EST: gi|162244637|gb|FC424604.1|FC424604
EST:     ACAAGGTTGCCTCGATTGCTCTGAGCCCCAACGTCACTGGGCAAATAATG                         ATGGGTCTGATGGTCAAACCTCCAAGACCAGGCGACGTCTCGTTTCCTCTA
genomic: ACAAGGTTGCCTCGATTGCTCTGAGCCCCAACGTCACTGGGCAAATAATGgtatgtgttc ... tgtgttgtagATGGGTCTGATGGTCAAACCTCCAAGACCAGGCGACGTCTCGTTTCCTCTA
EST: gi|162188744|gb|FC364030.1|FC364030
EST:     ACAAGGTTGCCTCGATTGCTCTGAGCCCCAACGTCACTGGGCAAATAATG                         ATGGGTCTGATGGTCAAACCTCCAAGACCAGGCGACGTCTCGTTTCCTCTA
genomic: ACAAGGTTGCCTCGATTGCTCTGAGCCCCAACGTCACTGGGCAAATAATGgtatgtgttc ... tgtgttgtagATGGGTCTGATGGTCAAACCTCCAAGACCAGGCGACGTCTCGTTTCCTCTA

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: 33 (upstream exon), 35 (downstream exon)
Score: 28

ACTGTGGAGGAGCTGTACAAGGTTGCCTCGATTGCTCTGAGCCCCAACGTCACTGGGCAAATAATGgtatgtgttc ... tgtgttgtagATGGGTCTGATGGTCAAACCTCCAAGACCAGGCGACGTCTCGTTTCCTCTATACGCTGCAGAGAG




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