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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAGGTCTGCAATGGGATTTCAAATCATGACAATGTCCATACCAAGACTGCTGAGGTTGCTGTACCCGTCACTCATCCGTCTTGATGAGTACCTTTTGCAGgtgattatctggcttagctttggtgtcccagtgatgacttgcatcatgttctgcaactcggtgtatggctaccattttcatgtgttgattggaagtagtg...

Basic information

species Physcomitrella patens
transcript PP1S570_1V6.1
intron # 12
splice site 5'
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|37826251|gb|BJ584263.1|BJ584263
EST:     GAGGTTGCTGTACCCGTCACTCCATCCGTCTTGATGAGTACCTTTTGCAG                         GACTCGAGAGGTGATGGTCCTGCGGGATTGCCTGCTCCTTTGGTTCTTTCT
genomic: GAGGTTGCTGTACCCGTCACT-CATCCGTCTTGATGAGTACCTTTTGCAGgtgattatct ... ttgtctgcagGACTCGAGAGGTGATGGTCCTGCGGGATTGCCTGCTCCTTTGGTTCTTTCT
EST: gi|37839397|gb|BJ597405.1|BJ597405
EST:     TGAGGTTGCTGTACCCGTCACTCATCCGTCTTGATGAGTACCTTTTGCAG                         GACTCGAGAGGTGATGGTCCTGCGGGATTGCCTGCTCCTTTGGTTCTTTCT
genomic: TGAGGTTGCTGTACCCGTCACTCATCCGTCTTGATGAGTACCTTTTGCAGgtgattatct ... ttgtctgcagGACTCGAGAGGTGATGGTCCTGCGGGATTGCCTGCTCCTTTGGTTCTTTCT
EST: gi|37830212|gb|BJ588224.1|BJ588224
EST:     TGAGGTTGCTGTACCCGTCACTCATCCGTCTTGATGAGTACCTTTTGCAG                         GACTCGAGAGGTGATGGTCCTGCGGGATTGCCTGCTCCTTTGGTTCTTTCT
genomic: TGAGGTTGCTGTACCCGTCACTCATCCGTCTTGATGAGTACCTTTTGCAGgtgattatct ... ttgtctgcagGACTCGAGAGGTGATGGTCCTGCGGGATTGCCTGCTCCTTTGGTTCTTTCT
EST: gi|37851486|gb|BJ609494.1|BJ609494
EST:     TGAGGTTGCTGTACCCGTCACTCATCCGTCTTGATGAGTACCTTTTGCAG                         GACTCGAGAGGTGATGGTCCTGCGGGATTGCCTGCTCCTTTGGTTCTTTCT
genomic: TGAGGTTGCTGTACCCGTCACTCATCCGTCTTGATGAGTACCTTTTGCAGgtgattatct ... ttgtctgcagGACTCGAGAGGTGATGGTCCTGCGGGATTGCCTGCTCCTTTGGTTCTTTCT
EST: gi|162151695|gb|FC327824.1|FC327824
EST:     TGAGGTTGCTGTACCCGTCACTCATCCGTCTTGATGAGTACCTTTTGCAG                         GACTCGAGAGGTGATGGTCCTGCGGGATTGCCTGCTCCTTTGGTTCTTTCT
genomic: TGAGGTTGCTGTACCCGTCACTCATCCGTCTTGATGAGTACCTTTTGCAGgtgattatct ... ttgtctgcagGACTCGAGAGGTGATGGTCCTGCGGGATTGCCTGCTCCTTTGGTTCTTTCT
EST: gi|37829499|gb|BJ587511.1|BJ587511
EST:     TGAGGTTGCTGTACCCGTCACTCATCCGTCTTGATGAGTACCTTTTGCAG                         GACTCGAGAGGTGATGGTCCTGCGGGATTGCCTGCTCCTTTGGTTCTTTCT
genomic: TGAGGTTGCTGTACCCGTCACTCATCCGTCTTGATGAGTACCTTTTGCAGgtgattatct ... ttgtctgcagGACTCGAGAGGTGATGGTCCTGCGGGATTGCCTGCTCCTTTGGTTCTTTCT
EST: gi|162155670|gb|FC331283.1|FC331283
EST:     GAGGTTGCTGTACCCGTCACTCATCCGTC-TGNATGAGTACCTTNTGCAG                         GACTCGAGAGGTGATGGTCCTGCGGGATTGCCTGCTCCTTTGGTTCTTTCT
genomic: GAGGTTGCTGTACCCGTCACTCATCCGTCTTG-ATGAGTACCTTTTGCAGgtgattatct ... ttgtctgcagGACTCGAGAGGTGATGGTCCTGCGGGATTGCCTGCTCCTTTGGTTCTTTCT
EST: gi|37827853|gb|BJ585865.1|BJ585865
EST:     GAGGTTGGCTGTACCCGTCACTCATCCGTCTTGATGAGTACCTTTTGCAG                         GACTCGAGAGGTGATGGTCCTGCGGGATTGCCTGCTCCTTTGGTTCTTTCT
genomic: GAGGTT-GCTGTACCCGTCACTCATCCGTCTTGATGAGTACCTTTTGCAGgtgattatct ... ttgtctgcagGACTCGAGAGGTGATGGTCCTGCGGGATTGCCTGCTCCTTTGGTTCTTTCT

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: 9 (upstream exon), 33 (downstream exon)
Score: 2

AAGGTCTGCAATGGGATTTCAAATCATGACAATGTCCATACCAAGACTGCTGAGGTTGCTGTACCCGTCACTCATCCGTCTTGATGAGTACCTTTTGCAGgtgattatct ... ttgtctgcagGACTCGAGAGGTGATGGTCCTGCGGGATTGCCTGCTCCTTTGGTTCTTTCTTCAGAACAGCTTGACCCGCGCGGAGCATTTTTATTAAATGATGGGTTAT




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