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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAGTTCTCTCTGCCTTCGTTGGTCTCGGCTCATGCTTCCTCCATAGCCCGGAGCACCGCTTCCGTCGTCCTTCCGGAAACACGTCTTCTTATTATTACAGgtatgctgttgcttccattcccgagtaggcgcttcgttgggagaggaagtgagtgagtgagtgattgatttacacgtagacgacgagatgaggctttttg...

Basic information

species Physcomitrella patens
transcript PP1S102_139V6.1
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|18367387|gb|BJ199470.1|BJ199470
EST:     GAGCACCGCTTCCGTCGTCCTTCCGGAAACACGTCTTCTTATTATTACAG                         AAGGGGGAGGAAGCACACGGGCTCATAATGATTAAGCTATTCAGTGTGAAG
genomic: GAGCACCGCTTCCGTCGTCCTTCCGGAAACACGTCTTCTTATTATTACAGgtatgctgtt ... tttttcacagAAGGGGGAGGAAGCACACGGGCTCATAATGATTAAGCTATTCAGTGTGAAG
EST: gi|162223007|gb|FC399638.1|FC399638
EST:     GAGCACCGCTTCCGTCGTCCTTCCGGAAACACGTCTTCTTATTATTACAG                         AAGGGGGAGGAAGCACACGGGCTCATAATGATTAAGCTATTCAGTGTGAAG
genomic: GAGCACCGCTTCCGTCGTCCTTCCGGAAACACGTCTTCTTATTATTACAGgtatgctgtt ... tttttcacagAAGGGGGAGGAAGCACACGGGCTCATAATGATTAAGCTATTCAGTGTGAAG
EST: gi|18346051|gb|BJ178094.1|BJ178094
EST:     GAGCACCGCTTCCGTCGTCCTTCCGGAAACACGTCTTCTTATTATTACAG                         AAGGGGGAGGAAGCACACGGGCTCATAATGATTAAGCTATTCAGTGTGAAG
genomic: GAGCACCGCTTCCGTCGTCCTTCCGGAAACACGTCTTCTTATTATTACAGgtatgctgtt ... tttttcacagAAGGGGGAGGAAGCACACGGGCTCATAATGATTAAGCTATTCAGTGTGAAG
EST: gi|208381403|gb|DC927839.1|DC927839
EST:     GAGCACCGCTTCCGTCGTCCTTCCGGAAACACGTCTTCTTATTATTACAG                         AAGGGGGAGGAAGCACACGGGCTCATAATGATTAAGCTATTCAGTGTGAAG
genomic: GAGCACCGCTTCCGTCGTCCTTCCGGAAACACGTCTTCTTATTATTACAGgtatgctgtt ... tttttcacagAAGGGGGAGGAAGCACACGGGCTCATAATGATTAAGCTATTCAGTGTGAAG
EST: gi|162275673|gb|FC451662.1|FC451662
EST:     GAGCACCGCTTCCGTCGTCCTTCCGGAAACACGTCTTCTTATTATTACAG                         AAGGGGGAGGAAGCACACGGGCTCATAATGATTAAGCTATTCAGTGTGAAG
genomic: GAGCACCGCTTCCGTCGTCCTTCCGGAAACACGTCTTCTTATTATTACAGgtatgctgtt ... tttttcacagAAGGGGGAGGAAGCACACGGGCTCATAATGATTAAGCTATTCAGTGTGAAG
EST: gi|208353937|gb|DC914091.1|DC914091
EST:     GAGCACCGCTTCCGTCGTCCTTCCGGAAACACGTCTTCTTATTATTACAG                         AAGGGGGAGGAAGCACACGGGCTCATAATGATTAAGCTATTCAGTGTGAAG
genomic: GAGCACCGCTTCCGTCGTCCTTCCGGAAACACGTCTTCTTATTATTACAGgtatgctgtt ... tttttcacagAAGGGGGAGGAAGCACACGGGCTCATAATGATTAAGCTATTCAGTGTGAAG

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: 29 (upstream exon), 34 (downstream exon)
Score: 16

CAGTTCTCTCTGCCTTCGTTGGTCTCGGCTCATGCTTCCTCCATAGCCCGGAGCACCGCTTCCGTCGTCCTTCCGGAAACACGTCTTCTTATTATTACAGgtatgctgtt ... tttttcacagAAGGGGGAGGAAGCACACGGGCTCATAATGATTAAGCTATTCAGTGTGAAGCAGAAGCAAAGAGAGGATGCTCTGAACAACAATGGCCGTCCCATCAAGA




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