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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TAGGCTGGCCAGACATGCGGCTTCCCATCCTGTACACCATGTCGTGGCCAGAGCGCATTTCCTGTTCAGAGAAGACCTGGCCTCGTCTGGACTTTTTCAAgtaagtttatgtatcttattctgatattctacgggtgaagttttccacgcactgcttcaatcgtagagtgaatattttttgttctgctgtttgaattaac...

Basic information

species Physcomitrella patens
transcript PP1S62_157V6.2
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|162156415|gb|FC332647.1|FC332647
EST:     GAGCGCATTTCCTGTTCAGAGAAGACCTGGCCTCGTCTGGACTTTTTCAA                         AATGGGAAATCTTACTTTCATGAAGCCCGACCACGCAAAATATCCCTCTAT
genomic: GAGCGCATTTCCTGTTCAGAGAAGACCTGGCCTCGTCTGGACTTTTTCAAgtaagtttat ... ttgtgagtagAATGGGAAATCTTACTTTCATGAAGCCCGACCACGCAAAATATCCCTCTAT
EST: gi|37826113|gb|BJ584125.1|BJ584125
EST:     GAGCGCATTTCCTGTTCAGAGAAGACCTGGCCTCGTCTGGACTTTTTCAA                         AATGGGAAATCTTACTTTCATGAAGCCCGACCACGCAAAATATCCCTCTAT
genomic: GAGCGCATTTCCTGTTCAGAGAAGACCTGGCCTCGTCTGGACTTTTTCAAgtaagtttat ... ttgtgagtagAATGGGAAATCTTACTTTCATGAAGCCCGACCACGCAAAATATCCCTCTAT
EST: gi|18336329|gb|BJ168351.1|BJ168351
EST:     TGGACTTTTTCAA                         AATGGGAAATCTTACTTTCATGAAGCCCGACCACGCAAAATATCCCTCTAT
genomic: TGGACTTTTTCAAgtaagtttat ... ttgtgagtagAATGGGAAATCTTACTTTCATGAAGCCCGACCACGCAAAATATCCCTCTAT
EST: gi|162203496|gb|FC380412.1|FC380412
EST:     GAGCGCATTTCCTGTTCAGAGAAGACCTGGCCTCGTCTGGACTTTTTCAA                         AATGGGAAATCTTACTTTCATGAAGCCCGACCACGCAAAATATCCCTCTAT
genomic: GAGCGCATTTCCTGTTCAGAGAAGACCTGGCCTCGTCTGGACTTTTTCAAgtaagtttat ... ttgtgagtagAATGGGAAATCTTACTTTCATGAAGCCCGACCACGCAAAATATCCCTCTAT
EST: gi|162272850|gb|FC448006.1|FC448006
EST:     GAGCGCATTTCCTGTTCAGAGAAGACCTGGCCTCGTCTGGACTTTTTCAA                         AATGGGAAATCTTACTTTCATGAAGCCCGACCACGCAAAATATCCCTCTAT
genomic: GAGCGCATTTCCTGTTCAGAGAAGACCTGGCCTCGTCTGGACTTTTTCAAgtaagtttat ... ttgtgagtagAATGGGAAATCTTACTTTCATGAAGCCCGACCACGCAAAATATCCCTCTAT
EST: gi|162185513|gb|FC361237.1|FC361237
EST:     GAGCGCATTTCCTGTTCAGAGAAGACCTGGCCTCGTCTGGACTTTTTCAA                         AATGGGAAATCTTACTTTCATGAAGCCCGACCACGCAAAATATCCCTCTAT
genomic: GAGCGCATTTCCTGTTCAGAGAAGACCTGGCCTCGTCTGGACTTTTTCAAgtaagtttat ... ttgtgagtagAATGGGAAATCTTACTTTCATGAAGCCCGACCACGCAAAATATCCCTCTAT
EST: gi|162203495|gb|FC380411.1|FC380411
EST:     GTCTGGACTTTTTCAA                         AATGGGAAATCTTACTTTCATGAAGCCCGACCACGCAAAATATCCCTCTAT
genomic: GTCTGGACTTTTTCAAgtaagtttat ... ttgtgagtagAATGGGAAATCTTACTTTCATGAAGCCCGACCACGCAAAATATCCCTCTAT
EST: gi|208382561|gb|DC919771.1|DC919771
EST:     GAGCGCATTTCCTGTTCAGAGAAGACCTGGCCTCGTCTGGAC-TTTTCAA                         AATGGGAAATCTTACTTTCATGAAGCCCGACCACGCAAAATATCCCTCTAT
genomic: GAGCGCATTTCCTGTTCAGAGAAGACCTGGCCTCGTCTGGACTTTTTCAAgtaagtttat ... ttgtgagtagAATGGGAAATCTTACTTTCATGAAGCCCGACCACGCAAAATATCCCTCTAT
EST: gi|162179791|gb|FC356382.1|FC356382
EST:     GAGCGCATTTCCTGTTCAGAGAAGACCTGGCCTCGTCTGGACTTTTTCAA                         AATGGGAAATCTTACTTTCATGAAGCCCGACCACGCAAAATATCCCTCTAT
genomic: GAGCGCATTTCCTGTTCAGAGAAGACCTGGCCTCGTCTGGACTTTTTCAAgtaagtttat ... ttgtgagtagAATGGGAAATCTTACTTTCATGAAGCCCGACCACGCAAAATATCCCTCTAT

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: 35 (upstream exon), 34 (downstream exon)
Score: 24

TAGGCTGGCCAGACATGCGGCTTCCCATCCTGTACACCATGTCGTGGCCAGAGCGCATTTCCTGTTCAGAGAAGACCTGGCCTCGTCTGGACTTTTTCAAgtaagtttat ... ttgtgagtagAATGGGAAATCTTACTTTCATGAAGCCCGACCACGCAAAATATCCCTCTATGGCACTCTCTTACAGCGCTGGTCGAGCTGGTGGAACGATGACTGGTGTA




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