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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cacacacacacactatatatatatatatatatatatatatatatatatacgtaattgaagtgaagtaatcatgagacttaatattttcttttcttaacagAGGAGGAAGGTGCGCGAAGCTTTGGCATATCGGACTAGACCTACAAGATTATGGGATTTGTATACTTTTTCAGACGCTTACCCCTCTAGCGGGGACCCAC

Basic information

species Physcomitrella patens
transcript PP1S71_215V6.1
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|208372505|gb|DC940780.1|DC940780
EST:     GGAAGGATTTACGAACTATTACTTTTGGTTTTTTGCCTCACACTAAGCAG                         AGGAGGAAGGTGCGCGAAGCTTTGGCATATCGGACTAGACCTACAAGATTA
genomic: GGAAGGATTTACGAACTATTACTTTTGGTTTTTTGCCTCACACTAAGCAGgtaaatatct ... ttcttaacagAGGAGGAAGGTGCGCGAAGCTTTGGCATATCGGACTAGACCTACAAGATTA
EST: gi|18350469|gb|BJ182520.1|BJ182520
EST:     GGAAGGATTTACGAACTATTACTTTTGGTTTTTTGCCTCACACTAAGCAG                         AGGAGGAAGGTGCGCGAAGCTTTGGCATATCGGACTAGACCTACAAGATTA
genomic: GGAAGGATTTACGAACTATTACTTTTGGTTTTTTGCCTCACACTAAGCAGgtaaatatct ... ttcttaacagAGGAGGAAGGTGCGCGAAGCTTTGGCATATCGGACTAGACCTACAAGATTA

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: 20 (upstream exon), 35 (downstream exon)
Score: 3

GGAAGGATTTACGAACTATTACTTTTGGTTTTTTGCCTCACACTAAGCAGgtaaatatct ... ttcttaacagAGGAGGAAGGTGCGCGAAGCTTTGGCATATCGGACTAGACCTACAAGATTATGGGATTTGTATACTTTTTCAGACGCTTACCCCTCTAGCGGGGACCCAC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatacgtaattgaagtgaagtaatcatgagacttaatattttcttttcttaacagAGGAGGAAGGTGCGCGAAGCTTTGGCATATCGGACTAGACCTACAAGATTATGGGATTTGTATACTTTTTCAGACGCTTACCCCTCTAGCGGGGACCCAC
                              acttaat  putative branch site (score: 3)
                                    tattttcttttctt  CT-rich tract
                              acttaatattttcttt  TA-rich tract