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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTCCTGTTCGCTGTTATGTTTGGTGATTGGGGGCACGGTATTTGCCTACTTTTGGGGGCGCTTTATTTAGTGTTGAATGAGAAAAAACTTGGAAAACAGgtacatttctggagcatggaagagtcttttgaacagttgattcttgtggttttgtagaagtttgtgtgcgcttacagcatgagcactgtagttcaaaactatcgccggaactggagattcgtttcaagtcgtatggttaaactaatattgtgacattgttgcag

Basic information

species Physcomitrella patens
transcript PP1S6_159V6.1
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S6_159V6.1 (Physcomitrella patens), 5'ss of exon 10
lower sequence: AT4G39080.1 (Arabidopsis thaliana), 5'ss of exon 11
CTTCCTGTTCGCTGTTATGTTTGGTGATTGGGGGCACGGTATTTGCCTACTTTTGGGGGCGCTTTATTTAGTGTTGAATGAGAAAAAACTTGGAAAACAGgta-catttctggagcatggaagagtcttttgaacagttgattcttgtggttttgtagaagtttgtgtgcgcttacagcatgagcactgtagttcaaaactatcgccggaactggagattcgtttcaagtcgtatggttaaactaatattgtgacattgttgcag
|||||| ||||||||||||||||||||||||||||| || || ||| | ||  | |   |  | || ||  | ||||| || || |||||||  |  ||||||  | | ||  | |   || |   |||  ||   ||| |  |  | | ||     ||| | ||| | |     ||| |   ||  | || || |   || |       ||                                                     
CTTCCTTTTCGCTGTTATGTTTGGTGATTGGGGGCATGGAATATGCATTCTGCTTGCAACTATGTACTTGATATTGAAAGAAAAGAAACTTGCCAGCCAGgtaataatactccaact--gatgtcacttacgagt-gttaacacgcgagatt-----gaaatctgtct-catcagcagaacttgc-ttataatttag--ctgtttgttttac-----------------------------------------------------

upper sequence: PP1S6_159V6.1 (Physcomitrella patens), 5'ss of exon 10
lower sequence: AT2G21410.1 (Arabidopsis thaliana), 5'ss of exon 11
CTTCCTGTTCGCTGTTATGTTTGGTGATTGGGGGCACGGTATTTGCCTACTTTTGGGGGCGCTTTATTTAGTGTTGAATGAGAAAAAACTTGGAAAACAGgta-catttctgg-----agcatggaagagtcttttga--acagt---tgatt--cttgtggttttgtagaagtt-tgtgtgcgcttacagcatgagcactgtagttcaaaa-ctatcgccggaactgg------agattcgttt------caagtcgtatg-gttaaactaata-ttgtgacattgttgcag---
||||||||| ||||||||||||||||| ||||| || || || ||||| ||  | |   |  | |||||| | ||||  || || ||||||   |  ||||||  |   ||       |||||  |     |   |||  |||||    ||||   || || ||  | | ||||| ||||     ||  |     || |   || ||  | |  | |  |    | |||      |  || || |      |||||  ||   | ||||| |  | |  |  | | ||  ||    
CTTCCTGTTTGCTGTTATGTTTGGTGACTGGGGTCATGGAATCTGCCTGCTGCTTGCAACTATGTATTTAATATTGAGAGAAAAGAAACTTTCCAGCCAGgtaatacccctaattgacagcatctattttccgactgagcacagtataagattggtttctgtttcagaaaaagttgtgtgcaaatttcaaattcaagaaaattattttgagagttgttactttgattggtcatcaatgtttgtctttcttgcaagttctagatgctaaaccatcaatccttgcttcgtgacaacag
















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|162192954|gb|FC371456.1|FC371456
EST:     TTTTGGGGGCGCTTTATTTAGTGTTGAATGAGAAAAAACTTGGAAAACAG                         AAACTCGGTGATATTATGGAGATGGCTTATGGAGGTCGTTATGTAATTCTT
genomic: TTTTGGGGGCGCTTTATTTAGTGTTGAATGAGAAAAAACTTGGAAAACAGgtacatttct ... attgttgcagAAACTCGGTGATATTATGGAGATGGCTTATGGAGGTCGTTATGTAATTCTT
EST: gi|162174814|gb|FC352230.1|FC352230
EST:     TTTTGGGGGCGCTTTATTTAGTGTTGAATGAGAAAAAACTTGGAAAACAG                         AAACTCGGTGATATTATGGAGATGGCTTATGGAGGTCGTTATGTAATTCTT
genomic: TTTTGGGGGCGCTTTATTTAGTGTTGAATGAGAAAAAACTTGGAAAACAGgtacatttct ... attgttgcagAAACTCGGTGATATTATGGAGATGGCTTATGGAGGTCGTTATGTAATTCTT
EST: gi|162156043|gb|FC332210.1|FC332210
EST:     TTTTGGGGGCGCTTTATTTAGTGTTGAATGAGAAAAAACTTGGAAAACAG                         AAACTCGGTGATATTATGGAGATGGCTTATGGAGGTCGTTATGTAATTCTT
genomic: TTTTGGGGGCGCTTTATTTAGTGTTGAATGAGAAAAAACTTGGAAAACAGgtacatttct ... attgttgcagAAACTCGGTGATATTATGGAGATGGCTTATGGAGGTCGTTATGTAATTCTT
EST: gi|162156985|gb|FC333347.1|FC333347
EST:     TTTTGGGGGCGCTTTATTTAGTGTTGAATGAGAAAAAACTTGGAAAACAG                         AAACTCGGTGATATTATGGAGATGGCTTATGGAGGTCGTTATGTAATTCTT
genomic: TTTTGGGGGCGCTTTATTTAGTGTTGAATGAGAAAAAACTTGGAAAACAGgtacatttct ... attgttgcagAAACTCGGTGATATTATGGAGATGGCTTATGGAGGTCGTTATGTAATTCTT
EST: gi|162173250|gb|FC350032.1|FC350032
EST:     TTTTGGGGGCGCTTTATTTAGTGTTGAATGAGAAAAAACTTGNAAAACAG                         AAACTCGGTGATATTATGGAGATGGCTTATGGAGGTCGTTATGTAATTCTT
genomic: TTTTGGGGGCGCTTTATTTAGTGTTGAATGAGAAAAAACTTGGAAAACAGgtacatttct ... attgttgcagAAACTCGGTGATATTATGGAGATGGCTTATGGAGGTCGTTATGTAATTCTT

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: 29 (upstream exon), 35 (downstream exon)
Score: 16

CTTCCTGTTCGCTGTTATGTTTGGTGATTGGGGGCACGGTATTTGCCTACTTTTGGGGGCGCTTTATTTAGTGTTGAATGAGAAAAAACTTGGAAAACAGgtacatttct ... attgttgcagAAACTCGGTGATATTATGGAGATGGCTTATGGAGGTCGTTATGTAATTCTTTTGATGGCTATTTTCTCCATCTACACTGGTTTCATATACAATGAGTTCT




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