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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taatggccctagaagttcattctgatcagttggatacattattggctttcatcagccatctattgttcaaatattgattttattgagttgtttactgcagATTGTTGCACAATCACAGGCAAGCTGGAAGAAGCTTTTGGTCTTCCTAAAAGAAAACGTTGCTATTCCGTTTCCTGTTTCAAACGGTGATGAGATTGTAC

Basic information

species Physcomitrella patens
transcript PP1S4_328V6.1
intron # 11
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|37852068|gb|BJ610076.1|BJ610076
EST:     GTTATCCATTGCTGTTGCTATATCCGGCTGGCAGGAAGTCAAGTAAACCG                         ATTGTTGCACAATCACAGGCAAGCTGGAAGAAGCTTTTGGTCTTCCTAAAA
genomic: GTTATCCATTGCTGTTGCTATATCCGGCTGGCAGGAAGTCAAGTAAACCGgttcgtataa ... tttactgcagATTGTTGCACAATCACAGGCAAGCTGGAAGAAGCTTTTGGTCTTCCTAAAA
EST: gi|162279238|gb|FC455785.1|FC455785
EST:     GTTATCCATTGCTGTTGCTATATCCGGCTGGCAGGAAGTCAAGTAAACCG                         ATTGTTGCACAATCACAGGCAAGCTGGAAGAAGCTTTTGGTCTTCCTAAAA
genomic: GTTATCCATTGCTGTTGCTATATCCGGCTGGCAGGAAGTCAAGTAAACCGgttcgtataa ... tttactgcagATTGTTGCACAATCACAGGCAAGCTGGAAGAAGCTTTTGGTCTTCCTAAAA
EST: gi|18338484|gb|BJ170508.1|BJ170508
EST:     GTTATCCATTGCTGTTGCTATATCCGGCTGGCAGGAAGTCAAGTAAACCG                         ATTGTTGCACAATCACAGGCAAGCTGGAAGAAGCTTTTGGTCTTCCTAAAA
genomic: GTTATCCATTGCTGTTGCTATATCCGGCTGGCAGGAAGTCAAGTAAACCGgttcgtataa ... tttactgcagATTGTTGCACAATCACAGGCAAGCTGGAAGAAGCTTTTGGTCTTCCTAAAA
EST: gi|37847498|gb|BJ605506.1|BJ605506
EST:     GTTATCCATTGCTGTTGCTATATCCGGCTGGCAGGAAGTCAAGTAAACCG                         ATTGTTGCACAATCACAGGCAAGCTGGAAGAAGCTTTTGGTCTTCCTAAAA
genomic: GTTATCCATTGCTGTTGCTATATCCGGCTGGCAGGAAGTCAAGTAAACCGgttcgtataa ... tttactgcagATTGTTGCACAATCACAGGCAAGCTGGAAGAAGCTTTTGGTCTTCCTAAAA

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: 26 (upstream exon), 35 (downstream exon)
Score: 4

GATGTTCATAGTTATCCATTGCTGTTGCTATATCCGGCTGGCAGGAAGTCAAGTAAACCGgttcgtataa ... tttactgcagATTGTTGCACAATCACAGGCAAGCTGGAAGAAGCTTTTGGTCTTCCTAAAAGAAAACGTTGCTATTCCGTTTCCTGTTTCAAACGGTGATGAGATTGTAC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctttcatcagccatctattgttcaaatattgattttattgagttgtttactgcagATTGTTGCACAATCACAGGCAAGCTGGAAGAAGCTTTTGGTCTTCCTAAAAGAAAACGTTGCTATTCCGTTTCCTGTTTCAAACGGTGATGAGATTGTAC
                          tattgat  putative branch site (score: 4)
 atctattgttcaaata  TA-rich tract