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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgttcagagggaagcgtgtttgtgttgttttgtggtttgagaatgatggctggcatctctatggcattgattttctaaagaaaaccgcgatcatttgcagGAGTTGAGGTCCTTCCGAAATCTACGATTTGCAGGAAGATCGAGTAGTGTAGTTGAGTTTTAATCACAGGAAAACTGCGTGAAAGATTGGGAGCGGGTCC

Basic information

species Physcomitrella patens
transcript PP1S55_31V6.1
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|18329538|gb|BJ161544.1|BJ161544
EST:     TTCGATCATCGCTACCGCGCCGCACAGGTGCTGCTATTGCAG                         GAGTTGAGGTCCTTCCGAAATCTACGATTTGCAGGAAGATCGAGTAGTGTA
genomic: TTCGATCATCGCTACCGCGCCGCACAGGTGCTGCTATTGCAGgttccaatgt ... tcatttgcagGAGTTGAGGTCCTTCCGAAATCTACGATTTGCAGGAAGATCGAGTAGTGTA
EST: gi|162159727|gb|FC336113.1|FC336113
EST:     ATCGCTACCGCGCTGCACAGGTGCTGCTATTGCAG                         GAGTTGAGGTCCTTCCGAAATCTACGATTTGCAGGAAGATCGAGTAGTGTA
genomic: ATCGCTACCGCGCCGCACAGGTGCTGCTATTGCAGgttccaatgt ... tcatttgcagGAGTTGAGGTCCTTCCGAAATCTACGATTTGCAGGAAGATCGAGTAGTGTA
EST: gi|18364593|gb|BJ196666.1|BJ196666
EST:     TTCGATCATCGCTACCGCGCCGCACAGGTGCTGCTATTGCAG                         GAGTTGAGGTCCTTCCGAAATCTACGATTTGCAGGAAGATCGAGTAGTGTA
genomic: TTCGATCATCGCTACCGCGCCGCACAGGTGCTGCTATTGCAGgttccaatgt ... tcatttgcagGAGTTGAGGTCCTTCCGAAATCTACGATTTGCAGGAAGATCGAGTAGTGTA
EST: gi|100425663|gb|BY958708.1|BY958708
EST:     AGTATTCGATCATCGCTACCGCGCCGCACAGGTGCTGCTATTGCAG                         GAGTTGAGGTCCTTCCGAAATCTACGATTTGCAGGAAGATCGAGTAGTGTA
genomic: AGTATTCGATCATCGCTACCGCGCCGCACAGGTGCTGCTATTGCAGgttccaatgt ... tcatttgcagGAGTTGAGGTCCTTCCGAAATCTACGATTTGCAGGAAGATCGAGTAGTGTA

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), 35 (downstream exon)
Score: 27

GCAGTATTCGATCATCGCTACCGCGCCGCACAGGTGCTGCTATTGCAGgttccaatgt ... tcatttgcagGAGTTGAGGTCCTTCCGAAATCTACGATTTGCAGGAAGATCGAGTAGTGTAGTTGAGTTTTAATCACAGGAAAACTGCGTGAAAGATTGGGAGCGGGTCC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atggctggcatctctatggcattgattttctaaagaaaaccgcgatcatttgcagGAGTTGAGGTCCTTCCGAAATCTACGATTTGCAGGAAGATCGAGTAGTGTAGTTGAGTTTTAATCACAGGAAAACTGCGTGAAAGATTGGGAGCGGGTCC
                           ttctaaa  putative branch site (score: 27)
                        attttctaaagaaaa  TA-rich tract