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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcttcttgaattctttcaagacatttcatgctttcaaacgcttgcatgatcccatgatggctacgtttcactgagtcagtctcatggtgggcgcgtgcagCTTCTCCTGGTGGATAAGAAGATCGTAACTGCCCGTGACATGATTGGAATTCTGGAGGAATCCATCCGTGGTGGATTCCCACTTTTGATTATTGCTGAGG

Basic information

species Physcomitrella patens
transcript PP1S14_298V6.1
intron # 5
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|162171350|gb|FC346443.1|FC346443
EST:     ATTTTGTGACTGACCCAGAGAAGATGTCTGTGGAGTATGATAACTGCAGG                         CTTCTCCTGGTGGATAAGAAGATCGTAACTGCCCGTGACATGATTGGAATT
genomic: ATTTTGTGACTGACCCAGAGAAGATGTCTGTGGAGTATGATAACTGCAGGgtatgctcct ... gcgcgtgcagCTTCTCCTGGTGGATAAGAAGATCGTAACTGCCCGTGACATGATTGGAATT
EST: gi|162246717|gb|FC422710.1|FC422710
EST:     ATTTTGTGACTGACCCAGAGAAGATGTCTGTGGAGTATGATAACTGCAGG                         CTTCTCCTGGTGGATAAGAAGATCGTAACTGCCCGTGACATGATTGGAATT
genomic: ATTTTGTGACTGACCCAGAGAAGATGTCTGTGGAGTATGATAACTGCAGGgtatgctcct ... gcgcgtgcagCTTCTCCTGGTGGATAAGAAGATCGTAACTGCCCGTGACATGATTGGAATT
EST: gi|162203804|gb|FC379901.1|FC379901
EST:     ATTTTGTGACTGACCCAGAGAAGATGTCTGTGGAGTATGATAACTGCAGG                         CTTCTCCTGGTGGATAAGAAGATCGTAACTGCCCGTGACATGATTGGAATT
genomic: ATTTTGTGACTGACCCAGAGAAGATGTCTGTGGAGTATGATAACTGCAGGgtatgctcct ... gcgcgtgcagCTTCTCCTGGTGGATAAGAAGATCGTAACTGCCCGTGACATGATTGGAATT
EST: gi|162195954|gb|FC372151.1|FC372151
EST:     ATTTTGTGACTGACCCAGAGAAGATGTCTGTGGAGTATGATAACTGCAGG                         CTTCTCCTGGTGGATAAGAAGATCGTAACTGCCCGTGACATGATTGGAATT
genomic: ATTTTGTGACTGACCCAGAGAAGATGTCTGTGGAGTATGATAACTGCAGGgtatgctcct ... gcgcgtgcagCTTCTCCTGGTGGATAAGAAGATCGTAACTGCCCGTGACATGATTGGAATT
EST: gi|162170824|gb|FC347438.1|FC347438
EST:     ATTTTGTGACTGACCCAGAGAAGATGTCTGTGGAGTATGATAACTGCAGG                         CTTCTCCTGGTGGATAAGAAGATCGTAACTGCCCGTGACATGATTGGAATT
genomic: ATTTTGTGACTGACCCAGAGAAGATGTCTGTGGAGTATGATAACTGCAGGgtatgctcct ... gcgcgtgcagCTTCTCCTGGTGGATAAGAAGATCGTAACTGCCCGTGACATGATTGGAATT
EST: gi|162157418|gb|FC333195.1|FC333195
EST:     ATTTTGTGACTGACCCAGAGAAGATGTCTGTGGAGTATGATAACTGCAGG                         CTTCTCCTGGTGGATAAGAAGATCGTAACTGCCCGTGACATGATTGGAATT
genomic: ATTTTGTGACTGACCCAGAGAAGATGTCTGTGGAGTATGATAACTGCAGGgtatgctcct ... gcgcgtgcagCTTCTCCTGGTGGATAAGAAGATCGTAACTGCCCGTGACATGATTGGAATT
EST: gi|162187436|gb|FC362658.1|FC362658
EST:     ATTTTGTGACTGACCCAGAGAAGATGTCTGTGGAGTATGATAACTGCAGG                         CTTCTCCTGGTGGATAAGAAGATCGTAACTGCCCGTGACATGATTGGAATT
genomic: ATTTTGTGACTGACCCAGAGAAGATGTCTGTGGAGTATGATAACTGCAGGgtatgctcct ... gcgcgtgcagCTTCTCCTGGTGGATAAGAAGATCGTAACTGCCCGTGACATGATTGGAATT
EST: gi|162193667|gb|FC371246.1|FC371246
EST:     ATTTTGTGACTGACCCAGAGAAGATGTCTGTGGAGTATGATAACTGCAGG                         CTTCTCCTGGTGGATAAGAAGATCGTAACTGCCCGTGACATGATTGGAATT
genomic: ATTTTGTGACTGACCCAGAGAAGATGTCTGTGGAGTATGATAACTGCAGGgtatgctcct ... gcgcgtgcagCTTCTCCTGGTGGATAAGAAGATCGTAACTGCCCGTGACATGATTGGAATT
EST: gi|162173847|gb|FC349439.1|FC349439
EST:     ATTTTGTGACTGACCCAGAGAAGATGTCTGTGGAGTATGATAACTGCAGG                         CTTCTCCTGGTGGATAAGAAGATCGTAACTGCCCGTGACATGATTGGAATT
genomic: ATTTTGTGACTGACCCAGAGAAGATGTCTGTGGAGTATGATAACTGCAGGgtatgctcct ... gcgcgtgcagCTTCTCCTGGTGGATAAGAAGATCGTAACTGCCCGTGACATGATTGGAATT
EST: gi|162158432|gb|FC334227.1|FC334227
EST:     ATTTTGTGACTGACCCAGAGAAGATGTCTGTGGAGTATGATAACTGCAGG                         CTTCTCCTGGTGGATAAGAAGATCGTAACTGCCCGTGACATGATTGGAATT
genomic: ATTTTGTGACTGACCCAGAGAAGATGTCTGTGGAGTATGATAACTGCAGGgtatgctcct ... gcgcgtgcagCTTCTCCTGGTGGATAAGAAGATCGTAACTGCCCGTGACATGATTGGAATT
EST: gi|162195933|gb|FC372143.1|FC372143
EST:     ATTTTGTGACTGACCCAGAGAAGATGTCTGTGGAGTATGATAACTGCAGG                         CTTCTCCTGGTGGATAAGAAGATCGTAACTGCCCGTGACATGATTGGAATT
genomic: ATTTTGTGACTGACCCAGAGAAGATGTCTGTGGAGTATGATAACTGCAGGgtatgctcct ... gcgcgtgcagCTTCTCCTGGTGGATAAGAAGATCGTAACTGCCCGTGACATGATTGGAATT
EST: gi|162255992|gb|FC431756.1|FC431756
EST:     ATTTTGTGACTGACCCAGAGAAGATGTCTGTGGAGTATGATAACTGCAGG                         CTTCTCCTGGTGGATAAGAAGATCGTAACTGCCCGTGACATGATTGGAATT
genomic: ATTTTGTGACTGACCCAGAGAAGATGTCTGTGGAGTATGATAACTGCAGGgtatgctcct ... gcgcgtgcagCTTCTCCTGGTGGATAAGAAGATCGTAACTGCCCGTGACATGATTGGAATT
EST: gi|162175554|gb|FC350972.1|FC350972
EST:     ATTTTGTGACTGACCCAGAGAAGATGTCTGTGGAGTATGATAACTGCAGG                         CTTCTCCTGGTGGATAAGAAGATCGTAACTGCCCGTGACATGATTGGAATT
genomic: ATTTTGTGACTGACCCAGAGAAGATGTCTGTGGAGTATGATAACTGCAGGgtatgctcct ... gcgcgtgcagCTTCTCCTGGTGGATAAGAAGATCGTAACTGCCCGTGACATGATTGGAATT
EST: gi|162227587|gb|FC403529.1|FC403529
EST:     ATTTTGTGACTGACCCAGAGAAGATGTCTGTGGAGTATGATAACTGCAGG                         CTTCTCCTGGTGGATAAGAAGATCGTAACTGCCCGTGACATGATTGGAATT
genomic: ATTTTGTGACTGACCCAGAGAAGATGTCTGTGGAGTATGATAACTGCAGGgtatgctcct ... gcgcgtgcagCTTCTCCTGGTGGATAAGAAGATCGTAACTGCCCGTGACATGATTGGAATT
EST: gi|208362500|gb|DC939480.1|DC939480
EST:     ATTTTGTGACTGACCCAGAGAAGATGTCTGTGGAGTATGATAACTGCAGG                         CTTCTCCTGGTGGATAAGAAGATCGTAACTGCCCGTGACATGATTGGAATT
genomic: ATTTTGTGACTGACCCAGAGAAGATGTCTGTGGAGTATGATAACTGCAGGgtatgctcct ... gcgcgtgcagCTTCTCCTGGTGGATAAGAAGATCGTAACTGCCCGTGACATGATTGGAATT
EST: gi|162158158|gb|FC333953.1|FC333953
EST:     ATTTTGTGACTGACCCAGAGAAGATGTCTGTGGAGTATGATAACTGCAGG                         CTTCTCCTGGTGGATAAGAAGATCGTAACTGCCCGTGACATGATTGGAATT
genomic: ATTTTGTGACTGACCCAGAGAAGATGTCTGTGGAGTATGATAACTGCAGGgtatgctcct ... gcgcgtgcagCTTCTCCTGGTGGATAAGAAGATCGTAACTGCCCGTGACATGATTGGAATT
EST: gi|162149659|gb|FC326710.1|FC326710
EST:     ATTTTGTGACTGACCCAGAGAAGATGTCTGTGGAGTATGATAACTGCAGG                         CTTCTCCTGGTGGATAAGAAGATCGTAACTGCCCGTGACATGATTGGAATT
genomic: ATTTTGTGACTGACCCAGAGAAGATGTCTGTGGAGTATGATAACTGCAGGgtatgctcct ... gcgcgtgcagCTTCTCCTGGTGGATAAGAAGATCGTAACTGCCCGTGACATGATTGGAATT

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: 18

CCTGTACGTGGTCGAGGGCATGCAGTTTGACAGAGGCTACATTTCCCCCTATTTTGTGACTGACCCAGAGAAGATGTCTGTGGAGTATGATAACTGCAGGgtatgctcct ... gcgcgtgcagCTTCTCCTGGTGGATAAGAAGATCGTAACTGCCCGTGACATGATTGGAATTCTGGAGGAATCCATCCGTGGTGGATTCCCACTTTTGATTATTGCTGAGG




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Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcttcttgaattctttcaagacatttcatgctttcaaacgcttgcatgatcccatgatggctacgtttcactgagtcagtctcatggtgggcgcgtgcagCTTCTCCTGGTGGATAAGAAGATCGTAACTGCCCGTGACATGATTGGAATTCTGGAGGAATCCATCCGTGGTGGATTCCCACTTTTGATTATTGCTGAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA