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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgatgtcgaaaatcgctgtgacatctggctggctattcgggaagaaacattccaggtcaagtccaagtgttcatgaattctgcgcgcatctttcctgcagGTGAAGCGAAAAATTGCTGGTAAAGAAACTCTGAACGAGAATGAATTCGAGGAAGTGACCCAGGGTAATGATGGCGACGTCTCTAGCATTTCGGGATCGG

Basic information

species Physcomitrella patens
transcript PP1S96_235V6.1
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|18357635|gb|BJ189694.1|BJ189694
EST:     CTTTGGAAGAACAGCGCGCTCACTTCAAATCAGATTTCCATAAATTCAAC                         GTGAAGCGAAAAATTGCTGGTAAAGAAACTCTGAACGAGAATGAATTCGAG
genomic: CTTTGGAAGAACAGCGCGCTCACTTCAAATCAGATTTCCATAAATTCAACgtaaattatg ... tttcctgcagGTGAAGCGAAAAATTGCTGGTAAAGAAACTCTGAACGAGAATGAATTCGAG




















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-Seq library.


Block sizes: 35 (upstream exon), 33 (downstream exon)
Score: 11

ATCTTTGTTACAAAGCTGGGCCTGTCATGGCTGTCGTGCTGTCTTTCAATCTTTGGAAGAACAGCGCGCTCACTTCAAATCAGATTTCCATAAATTCAACgtaaattatg ... tttcctgcagGTGAAGCGAAAAATTGCTGGTAAAGAAACTCTGAACGAGAATGAATTCGAGGAAGTGACCCAGGGTAATGATGGCGACGTCTCTAGCATTTCGGGATCGG































 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aacattccaggtcaagtccaagtgttcatgaattctgcgcgcatctttcctgcagGTGAAGCGAAAAATTGCTGGTAAAGAAACTCTGAACGAGAATGAATTCGAGGAAGTGACCCAGGGTAATGATGGCGACGTCTCTAGCATTTCGGGATCGG
                                         catctttcct  CT-rich tract
                           atgaatt  TA-rich tract