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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattaccctcaccttcacgcaatccttgaccactcctctgcgttggctgcttcttgactaggttccttgataattagggttcgctttgcagATCACTGAGGTGGATAGGCTGATGGAGATTATCCGGCAAGGAGCGCAGGAGGAGGCATTGGTTCTCTATACGCTCGCCGACCCACAAATGGCAGAGGCTG

Basic information

species Physcomitrella patens
transcript PP1S123_99V6.1
intron # 1
splice site 3'
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|100389507|gb|BY988985.1|BY988985
EST:     ATTGTTTGGTGGATCGAGCATGCTCTGTGAATACTCATCTCTTCTCTCAG                         ATCACTGAGGTGGATAGGCTGATGGAGATTATCCGGCAAGGAGCGCAGGAG
genomic: ATTGTTTGGTGGATCGAGCATGCTCTGTGAATACTCATCTCTTCTCTCAGgtattaccct ... cgctttgcagATCACTGAGGTGGATAGGCTGATGGAGATTATCCGGCAAGGAGCGCAGGAG
EST: gi|208399111|gb|DC904520.1|DC904520
EST:     ATTGTTTGGTGGATCGAGCATGCTCTGTGAATACTCATCTCTTCTCTCAG                         ATCACTGAGGTGGATAGGCTGATGGAGATTATCCGGCGAGGAGCGCAGGAG
genomic: ATTGTTTGGTGGATCGAGCATGCTCTGTGAATACTCATCTCTTCTCTCAGgtattaccct ... cgctttgcagATCACTGAGGTGGATAGGCTGATGGAGATTATCCGGCAAGGAGCGCAGGAG
EST: gi|208368590|gb|DC936029.1|DC936029
EST:     ATTGTTTGGTGGATCGAGCATGCTCTGTGAATACTCATCTCTTCTCTCAG                         ATCACTGAGGTGGATAGGCTGATGGAGATTATCCGGCAAGGAGCGCAGGAG
genomic: ATTGTTTGGTGGATCGAGCATGCTCTGTGAATACTCATCTCTTCTCTCAGgtattaccct ... cgctttgcagATCACTGAGGTGGATAGGCTGATGGAGATTATCCGGCAAGGAGCGCAGGAG

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), 35 (downstream exon)
Score: 16

TGGGTGGACCTTGGAGCATGCCGCACAAGCAGCCTTGGGGCAGTTCGAGCATTGTTTGGTGGATCGAGCATGCTCTGTGAATACTCATCTCTTCTCTCAGgtattaccct ... cgctttgcagATCACTGAGGTGGATAGGCTGATGGAGATTATCCGGCAAGGAGCGCAGGAGGAGGCATTGGTTCTCTATACGCTCGCCGACCCACAAATGGCAGAGGCTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctgcgttggctgcttcttgactaggttccttgataattagggttcgctttgcagATCACTGAGGTGGATAGGCTGATGGAGATTATCCGGCAAGGAGCGCAGGAGGAGGCATTGGTTCTCTATACGCTCGCCGACCCACAAATGGCAGAGGCTG
                                           ttcgcttt  CT-rich tract
                              ttgataatta  TA-rich tract