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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttcatctccttgtgatagtgattgcatattctttgaattggatattatagttacatgttaggaagttgattcagccctggaaacggatgggtgtctgcagTGTTGAAGTCACGTTGATTCGACAAGCGCATGAGATGGGTTTCTTGACTACCCCGTATGCTTTTAACTCACAAGAATCGCACGCCATGGCGATGGCCGGA

Basic information

species Physcomitrella patens
transcript PP1S9_334V6.1
intron # 8
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|37844563|gb|BJ602571.1|BJ602571
EST:     ATTGATGGCAATTTCCGGCAAAATCTGGAGGAAACGGGCATGGGCTATGG                         TGTTGAAGTCACGTTGATTCGACAAGCGCATGAGATGGGTTTCTTGACTAC
genomic: ATTGATGGCAATTTCCGGCAAAATCTGGAGGAAACGGGCATGGGCTATGGgtaaatcggt ... gtgtctgcagTGTTGAAGTCACGTTGATTCGACAAGCGCATGAGATGGGTTTCTTGACTAC
EST: gi|37844514|gb|BJ602522.1|BJ602522
EST:     ATTGATGGCAATTTCCGGCAAAATCTGGAGGAAACGGGCATGGGCTATGG                         TGTTGAAGTCACGTTGATTCGACAAGCGCATGAGATGGGTTTCTTGACTAC
genomic: ATTGATGGCAATTTCCGGCAAAATCTGGAGGAAACGGGCATGGGCTATGGgtaaatcggt ... gtgtctgcagTGTTGAAGTCACGTTGATTCGACAAGCGCATGAGATGGGTTTCTTGACTAC
EST: gi|37842335|gb|BJ600343.1|BJ600343
EST:     ATTGATGGCAATTTCCGGCAAAATCTGGAGGAAACGGGCATGGGCTATGG                         TGTTGAAGTCACGTTGATTCGACAAGCGCATGAGATGGGTTTCTTGACTAC
genomic: ATTGATGGCAATTTCCGGCAAAATCTGGAGGAAACGGGCATGGGCTATGGgtaaatcggt ... gtgtctgcagTGTTGAAGTCACGTTGATTCGACAAGCGCATGAGATGGGTTTCTTGACTAC
EST: gi|37838990|gb|BJ596998.1|BJ596998
EST:     ATTGATGGCAATTTCCGGCAAAATCTGGAGGAAACGGGCATGGGCTATGG                         TGTTGAAGTCACGTTGATTCGACAAGCGCATGAGATGGGTTTCTTGACTAC
genomic: ATTGATGGCAATTTCCGGCAAAATCTGGAGGAAACGGGCATGGGCTATGGgtaaatcggt ... gtgtctgcagTGTTGAAGTCACGTTGATTCGACAAGCGCATGAGATGGGTTTCTTGACTAC
EST: gi|37845029|gb|BJ603037.1|BJ603037
EST:     ATTGATGGCAATTTCCGGCAAAATCTGGAGGAAACGGGCATGGGCTATGG                         TGTTGAAGTCACGTTGATTCGACAAGCGCATGAGATGGGTTTCTTGACTAC
genomic: ATTGATGGCAATTTCCGGCAAAATCTGGAGGAAACGGGCATGGGCTATGGgtaaatcggt ... gtgtctgcagTGTTGAAGTCACGTTGATTCGACAAGCGCATGAGATGGGTTTCTTGACTAC
EST: gi|162175714|gb|FC351301.1|FC351301
EST:     ATTGATGGCAATTTCCGGCAAAATCTGGAGGAAACGGGCATGGGCTATGG                         TGTTGAAGTCACGTTGATTCGACAAGCGCATGAGATGGGTTTCTTGACTAC
genomic: ATTGATGGCAATTTCCGGCAAAATCTGGAGGAAACGGGCATGGGCTATGGgtaaatcggt ... gtgtctgcagTGTTGAAGTCACGTTGATTCGACAAGCGCATGAGATGGGTTTCTTGACTAC
EST: gi|37834878|gb|BJ592890.1|BJ592890
EST:     ATTGATGGCAATTTCCGGCAAAATCTGGAGGAAACGGGCATGGGCTATGG                         TGTTGAAGTCACGTTGATTCGACAAGCGCATGAGATGGGTTTCTTGACTAC
genomic: ATTGATGGCAATTTCCGGCAAAATCTGGAGGAAACGGGCATGGGCTATGGgtaaatcggt ... gtgtctgcagTGTTGAAGTCACGTTGATTCGACAAGCGCATGAGATGGGTTTCTTGACTAC
EST: gi|162226926|gb|FC403114.1|FC403114
EST:     ATTGATGGCAATTTCCGGCAAAATCTGGAGGAAACGGGCATGGGCTATGG                         TGTTGAAGTCACGTTGATTCGACAAGCGCATGAGATGGGTTTCTTGACTAC
genomic: ATTGATGGCAATTTCCGGCAAAATCTGGAGGAAACGGGCATGGGCTATGGgtaaatcggt ... gtgtctgcagTGTTGAAGTCACGTTGATTCGACAAGCGCATGAGATGGGTTTCTTGACTAC
EST: gi|162246378|gb|FC421071.1|FC421071
EST:     AAACGGGCATGGGCTATGG                         TGTTGAAGTCACGTTGATTCGACAAGCGCATGAGATGGGTTTCTTGACTAC
genomic: AAACGGGCATGGGCTATGGgtaaatcggt ... gtgtctgcagTGTTGAAGTCACGTTGATTCGACAAGCGCATGAGATGGGTTTCTTGACTAC
EST: gi|18334199|gb|BJ166215.1|BJ166215
EST:     ATTGATGGCAATTTCCGGCAAAATCTGGAGGAAACGGGCATGGGCTATGG                         TGTTGAAGTCACGTTGATTCGACAAGCGCATGAGATGGGTTTCTTGACTAC
genomic: ATTGATGGCAATTTCCGGCAAAATCTGGAGGAAACGGGCATGGGCTATGGgtaaatcggt ... gtgtctgcagTGTTGAAGTCACGTTGATTCGACAAGCGCATGAGATGGGTTTCTTGACTAC
EST: gi|37839750|gb|BJ597758.1|BJ597758
EST:     ATTGATGGCAATTTCCGGCAAAATCTGGAGGAAACGGGCATGGGCTATGG                         TGTTGAAGTCACGTTGATTCGACAAGCGCATGAGATGGGTTTCTTGACTAC
genomic: ATTGATGGCAATTTCCGGCAAAATCTGGAGGAAACGGGCATGGGCTATGGgtaaatcggt ... gtgtctgcagTGTTGAAGTCACGTTGATTCGACAAGCGCATGAGATGGGTTTCTTGACTAC
EST: gi|37850404|gb|BJ608412.1|BJ608412
EST:     ATTGATGGCAATTTCCGGCAAAATCTGGAGGAAACGGGCATGGGCTATGG                         TGTTGAAGTCACGTTGATTCGACAAGCGCATGAGATGGGTTTCTTGACTAC
genomic: ATTGATGGCAATTTCCGGCAAAATCTGGAGGAAACGGGCATGGGCTATGGgtaaatcggt ... gtgtctgcagTGTTGAAGTCACGTTGATTCGACAAGCGCATGAGATGGGTTTCTTGACTAC
EST: gi|162184283|gb|FC360511.1|FC360511
EST:     ATTGATGGCAATNTCCGGCAAAATCTGGAGGAAACGGGCATGGGCTATGG                         TGTTGAAGTCACGTTGATTCGACAAGCGCATGAGATGGGTTTCTTGACTAC
genomic: ATTGATGGCAATTTCCGGCAAAATCTGGAGGAAACGGGCATGGGCTATGGgtaaatcggt ... gtgtctgcagTGTTGAAGTCACGTTGATTCGACAAGCGCATGAGATGGGTTTCTTGACTAC

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: 34 (upstream exon), 31 (downstream exon)
Score: 27

TGGAGCGATTGGGCTTTGACGGTATTCAAAACTTTCCCACAGTTGGCCTTATTGATGGCAATTTCCGGCAAAATCTGGAGGAAACGGGCATGGGCTATGGgtaaatcggt ... gtgtctgcagTGTTGAAGTCACGTTGATTCGACAAGCGCATGAGATGGGTTTCTTGACTACCCCGTATGCTTTTAACTCACAAGAATCGCACGCCATGGCGATGGCCGGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatagttacatgttaggaagttgattcagccctggaaacggatgggtgtctgcagTGTTGAAGTCACGTTGATTCGACAAGCGCATGAGATGGGTTTCTTGACTACCCCGTATGCTTTTAACTCACAAGAATCGCACGCCATGGCGATGGCCGGA
                  agttgat  putative branch site (score: 27)