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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagggcctgcagcaatgccttctgcgtccgcctaacctttcctgccattctggacttgccaataggatctcaagagcttgaaacctggatgctttcatttttgaagtcttcgctgtgagaggttgtgaataggataaacgctgtacaaaaaggttttgctgacatatggtcttgccacttatcagGATTTTTCGATAAACTAGCATTTTGGAACAGACATTCACATGACCAACTTTCCTTGCCTATAGCTATATGCATAGGTGAGGTGGCAATTCATTCCATGCA

Basic information

species Physcomitrella patens
transcript PP1S288_43V6.1
intron # 6
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|37839819|gb|BJ597827.1|BJ597827
EST:     TGAGGACGGAATTGCTCTGAACGTGGTGCAACTCACGAGAGGAACTCTAG                         GATTTTTCGATAAACTAGCATTTTGGAACAGACATTCACATGACCAACTTT
genomic: TGAGGACGGAATTGCTCTGAACGTGGTGCAACTCACGAGAGGAACTCTAGgtagggcctg ... cacttatcagGATTTTTCGATAAACTAGCATTTTGGAACAGACATTCACATGACCAACTTT
EST: gi|37848187|gb|BJ606195.1|BJ606195
EST:     TGAGGACGGAATTGCTCTGAACGTGGTGCAACTCACGAGAGGAACTCTAG                         GATTTTTCGATAAACTAGCATTTTGGAACAGACATTCACATGACCAACTTT
genomic: TGAGGACGGAATTGCTCTGAACGTGGTGCAACTCACGAGAGGAACTCTAGgtagggcctg ... cacttatcagGATTTTTCGATAAACTAGCATTTTGGAACAGACATTCACATGACCAACTTT
EST: gi|37850119|gb|BJ608127.1|BJ608127
EST:     TGAGGACGGAATTGCTCTGAACGTGGTGCAACTCACGAGAGGAACTCTAG                         GATTTTTCGATAAACTAGCATTTTGGAACAGACATTCACATGACCAACTTT
genomic: TGAGGACGGAATTGCTCTGAACGTGGTGCAACTCACGAGAGGAACTCTAGgtagggcctg ... cacttatcagGATTTTTCGATAAACTAGCATTTTGGAACAGACATTCACATGACCAACTTT

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: 5

CAATCAGAAGGTCAAACTGCTGGTGGTTGTGCGTGTTGACAACCTGTGGGTGAGGACGGAATTGCTCTGAACGTGGTGCAACTCACGAGAGGAACTCTAGgtagggcctg ... cacttatcagGATTTTTCGATAAACTAGCATTTTGGAACAGACATTCACATGACCAACTTTCCTTGCCTATAGCTATATGCATAGGTGAGGTGGCAATTCATTCCATGCA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aggataaacgctgtacaaaaaggttttgctgacatatggtcttgccacttatcagGATTTTTCGATAAACTAGCATTTTGGAACAGACATTCACATGACCAACTTTCCTTGCCTATAGCTATATGCATAGGTGAGGTGGCAATTCATTCCATGCA
                          tgctgac  putative branch site (score: 5)
                                       tcttgcc  putative PPT
             tacaaaaa  TA-rich tract