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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTTGCACTTCTTGGACACATTGATGAGAAGATAATTGACATGTACGACATGTATGAGCCAGTCAATGATCCCTCACTCGACAACTGCTTCATTTCTAAGgtatcaactattcatcatttatttgtgaatatgactcagcttgtctagtaggctacttctcaatttggatactctttgtgtcaccctagaaggtatgata...

Basic information

species Physcomitrella patens
transcript PP1S20_16V6.1
intron # 11
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|67699368|gb|BJ959601.1|BJ959601
EST:     TGTATGAGCCAGTCAATGATCCCTCACTCGACAACTGCTTCATTTCTAAG                         AGCTACGATCCTACTACCCACTTTGAGACGACAGTTCAAGATGTACTTTCA
genomic: TGTATGAGCCAGTCAATGATCCCTCACTCGACAACTGCTTCATTTCTAAGgtatcaacta ... tgtgttacagAGCTACGATCCTACTACCCACTTTGAGACGACAGTTCAAGATGTACTTTCA
EST: gi|67694426|gb|BJ954659.1|BJ954659
EST:     TGTATGAGCCAGTCAATGATCCCTCACTCGACAACTGCTTCATTTCTAAG                         AGCTACGATCCTACTACCCACTTTGAGACGACAGTTCAAGATGTACTTTCA
genomic: TGTATGAGCCAGTCAATGATCCCTCACTCGACAACTGCTTCATTTCTAAGgtatcaacta ... tgtgttacagAGCTACGATCCTACTACCCACTTTGAGACGACAGTTCAAGATGTACTTTCA
EST: gi|37851885|gb|BJ609893.1|BJ609893
EST:     TGTATGAGCCAGTCAATGATCCCTCACTCGACAACTGCTTCATTTCTAAG                         AGCTACGATCCTACTACCCACTTTGAGACGACAGTTCAAGATGTACTTTCA
genomic: TGTATGAGCCAGTCAATGATCCCTCACTCGACAACTGCTTCATTTCTAAGgtatcaacta ... tgtgttacagAGCTACGATCCTACTACCCACTTTGAGACGACAGTTCAAGATGTACTTTCA
EST: gi|208363930|gb|DC947202.1|DC947202
EST:     TGTATGAGCCAGTCAATGATCCCTCACTCGACAACTGCTTCATTTCTAAG                         AGCTACGATCCTACTACCCACTTTGAGACGACAGTTCAAGATGTACTTTCA
genomic: TGTATGAGCCAGTCAATGATCCCTCACTCGACAACTGCTTCATTTCTAAGgtatcaacta ... tgtgttacagAGCTACGATCCTACTACCCACTTTGAGACGACAGTTCAAGATGTACTTTCA
EST: gi|18333101|gb|BJ165115.1|BJ165115
EST:     TGTATGAGCCAGTCAATGATCCCTCACTCGACAACTGCTTCATTTCTAAG                         AGCTACGATCCTACTACCCACTTTGAGACGACAGTTCAAGATGTACTTTCA
genomic: TGTATGAGCCAGTCAATGATCCCTCACTCGACAACTGCTTCATTTCTAAGgtatcaacta ... tgtgttacagAGCTACGATCCTACTACCCACTTTGAGACGACAGTTCAAGATGTACTTTCA
EST: gi|162196486|gb|FC375439.1|FC375439
EST:     TGTATGAGCCAGTCAATGATCCCTCACTCGACAACTGCTTCATTTCTAAG                         AGCTACGATCCTACTACCCACTTTGAGACGACAGTTCAAGATGTACTTTCA
genomic: TGTATGAGCCAGTCAATGATCCCTCACTCGACAACTGCTTCATTTCTAAGgtatcaacta ... tgtgttacagAGCTACGATCCTACTACCCACTTTGAGACGACAGTTCAAGATGTACTTTCA
EST: gi|162180983|gb|FC358637.1|FC358637
EST:     TGTATGAGCCAGTCAATGATCCCTCACTCGACAACTGCTTCATTTCTAAG                         AGCTACGATCCTACTACCCACTTTGAGACGACAGTTCAAGATGTACTTTCA
genomic: TGTATGAGCCAGTCAATGATCCCTCACTCGACAACTGCTTCATTTCTAAGgtatcaacta ... tgtgttacagAGCTACGATCCTACTACCCACTTTGAGACGACAGTTCAAGATGTACTTTCA
EST: gi|37827350|gb|BJ585362.1|BJ585362
EST:     TGTATGAGCCAGTCAATGATCCCTCACTCGACAACTGCTTCATTTCTAAG                         AGCTACGATCCTACTACCCACTTTGAGACGACAGTTCAAGATGTACTTTCA
genomic: TGTATGAGCCAGTCAATGATCCCTCACTCGACAACTGCTTCATTTCTAAGgtatcaacta ... tgtgttacagAGCTACGATCCTACTACCCACTTTGAGACGACAGTTCAAGATGTACTTTCA
EST: gi|37844517|gb|BJ602525.1|BJ602525
EST:     TGTATGAGCCAGTCAATGATCCCTCACTCGACAACTGCTTCATTTCTAAG                         AGCTACGATCCTACTACCCACTTTGAGACGACAGTTCAAGATGTACTTTCA
genomic: TGTATGAGCCAGTCAATGATCCCTCACTCGACAACTGCTTCATTTCTAAGgtatcaacta ... tgtgttacagAGCTACGATCCTACTACCCACTTTGAGACGACAGTTCAAGATGTACTTTCA
EST: gi|162229880|gb|FC404333.1|FC404333
EST:     TGTATGAGCCAGTCAATGATCCCTCACTCGACAACTGCTTCATTTCTAAG                         AGCTACGATCCTACTACCCACTTTGAGACGACAGTTCAAGATGTACTTTCA
genomic: TGTATGAGCCAGTCAATGATCCCTCACTCGACAACTGCTTCATTTCTAAGgtatcaacta ... tgtgttacagAGCTACGATCCTACTACCCACTTTGAGACGACAGTTCAAGATGTACTTTCA
EST: gi|37836338|gb|BJ594346.1|BJ594346
EST:     TGTATGAGCCAGTCAATGATCCCTCACTCGACAACTGCTTCATTTCTAAG                         AGCTACGATCCTACTACCCACTTTGAGACGACAGTTCAAGATGTACTTTCA
genomic: TGTATGAGCCAGTCAATGATCCCTCACTCGACAACTGCTTCATTTCTAAGgtatcaacta ... tgtgttacagAGCTACGATCCTACTACCCACTTTGAGACGACAGTTCAAGATGTACTTTCA
EST: gi|162166682|gb|FC342651.1|FC342651
EST:     TGTATGAGCCAGTCAATGATCCCTCACTCGACAACTGCTTCATTTCTAAG                         AGCTACGATCCTACTACCCACTTTGAGACGACAGTTCAAGATGTACTTTCA
genomic: TGTATGAGCCAGTCAATGATCCCTCACTCGACAACTGCTTCATTTCTAAGgtatcaacta ... tgtgttacagAGCTACGATCCTACTACCCACTTTGAGACGACAGTTCAAGATGTACTTTCA
EST: gi|208374624|gb|DC948624.1|DC948624
EST:     TGTATGAGCCAGTCAATGATCCCTCACTCGACAACTGCTTCATTTCTAAG                         AGCTACGATCCTACTACCCACTTTGAGACGACAGTTCAAGATGTACTTTCA
genomic: TGTATGAGCCAGTCAATGATCCCTCACTCGACAACTGCTTCATTTCTAAGgtatcaacta ... tgtgttacagAGCTACGATCCTACTACCCACTTTGAGACGACAGTTCAAGATGTACTTTCA
EST: gi|18341638|gb|BJ173673.1|BJ173673
EST:     TGTATGAGCCAGTCAATGATCCCTCACTCGACAACTGCTTCATTTCTAAG                         AGCTACGATCCTACTACCCACTTTGAGACGACAGTTCAAGATGTACTTTCA
genomic: TGTATGAGCCAGTCAATGATCCCTCACTCGACAACTGCTTCATTTCTAAGgtatcaacta ... tgtgttacagAGCTACGATCCTACTACCCACTTTGAGACGACAGTTCAAGATGTACTTTCA

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: 26 (upstream exon), 34 (downstream exon)
Score: 6

GCTTGCACTTCTTGGACACATTGATGAGAAGATAATTGACATGTACGACATGTATGAGCCAGTCAATGATCCCTCACTCGACAACTGCTTCATTTCTAAGgtatcaacta ... tgtgttacagAGCTACGATCCTACTACCCACTTTGAGACGACAGTTCAAGATGTACTTTCAATGTATACAAAAATTACTGGCAAG




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