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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGAGTCGTCGCTACAGTATTTGGAGCTACTGGATTTCTAGGGCGTTATGTGGTTCAGCAACTTGgtacgtcctcattccgttgattttgaggtatagcatttgccgagcttcgaggtagttcgtcgaacgggtttctattctgttgcaaaattttgaacgttgtgcggatactgtaatccgagacattggttgataatgtgaaatggcaaatattggatcattagttaaagcaaacataggtcattttggcag

Basic information

species Physcomitrella patens
transcript PP1S79_105V6.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S79_105V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: GLYMA13G18950.1 (Glycine max), 5'ss of exon 3
TGGAGTCGTCGCTACAGTATTTGGAGCTACTGGATTTCTAGGGCGTTATGTGGTTCAGCAACTTGgtacgtcctcattccgttgattttgaggtatagcatttgccgagcttcgaggtagttcgtcgaacgggtttctattctgttgcaaaattttgaacgttgtgcggatactgtaatccgagacattggttgataatgtgaaatggcaaatattggatcattagttaaagcaaacataggtcattttggcag-
|||  |  | |||||||||||||| || ||||||||  |||| |||||||| || || |||||||||| ||           || || || | | ||  |||        || ||   |  |  ||  |  | |   | || | || |   |  |  ||  || ||     | |    |   ||   ||  ||         || ||     |||||  |   | |||   |   |  | | |    ||| |   
TGGCATTATTGCTACAGTATTTGGGGCAACTGGATTCTTAGGTCGTTATGTTGTCCAACAACTTGgtatgta----------tgtttctgggatttataatt-----gttttagaaaaatgttatcagaatgttaattttttttttcctgtaaataaaatattttggaatgaattctgttacagcttttacttttcccccctaactg-----tattgtgttgattgtttttggtgatgttgtttcccttgtctag
















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|67578524|gb|BJ950691.1|BJ950691
EST:     AGTATTTGGAGCTACTGGATTTCTAGGGCGTTATGTGGTTCAGCAACTTG                         CAAGAATGGGGTCCCAAGTTATGGTACCTTACNGAGGTTTGGACGANNAAT
genomic: AGTATTTGGAGCTACTGGATTTCTAGGGCGTTATGTGGTTCAGCAACTTGgtacgtcctc ... attttggcagCAAGAATGGGGTCCCAAGTTATGGTACCTTACAGAGGTTTGGACGAAGAAT
EST: gi|100439315|gb|BY980202.1|BY980202
EST:     AGTATTTGGAGCTACTGGATTTCTAGGGCGTTATGTGGTTCAGCAACTTG                         CAAGAATGGGGTCCCAAGTTATGGTACCTTACAGAGGTTTGGACGAAGAAT
genomic: AGTATTTGGAGCTACTGGATTTCTAGGGCGTTATGTGGTTCAGCAACTTGgtacgtcctc ... attttggcagCAAGAATGGGGTCCCAAGTTATGGTACCTTACAGAGGTTTGGACGAAGAAT
EST: gi|208383362|gb|DC907537.1|DC907537
EST:     AGTATTTGGAGCTACTGGATTTCTAGGGCGTTATGTGGTTCAGCAACTTG                         CAAGAATGGGGTCCCAAGTTATGGTACCTTACAGAGGTTTGGACGAAGAAT
genomic: AGTATTTGGAGCTACTGGATTTCTAGGGCGTTATGTGGTTCAGCAACTTGgtacgtcctc ... attttggcagCAAGAATGGGGTCCCAAGTTATGGTACCTTACAGAGGTTTGGACGAAGAAT
EST: gi|100381811|gb|BY950184.1|BY950184
EST:     AGTATTTGGAGCTACTGGATTTCTAGGGCGTTATGTGGTTCAGCAACTTG                         CAAGAATGGGGTCCCAAGTTATGGTACCTTACAGAGGTTTGGACGAAGAAT
genomic: AGTATTTGGAGCTACTGGATTTCTAGGGCGTTATGTGGTTCAGCAACTTGgtacgtcctc ... attttggcagCAAGAATGGGGTCCCAAGTTATGGTACCTTACAGAGGTTTGGACGAAGAAT
EST: gi|162256292|gb|FC432198.1|FC432198
EST:     AGTATTTGGAGCTACTGGATTTCTAGGGCGTTATGTGGTTCAGCAACTTG                         CAAGAATGGGGTCCCAAGTTATGGTACCTTACAGAGGTTTGGACGAAGAAT
genomic: AGTATTTGGAGCTACTGGATTTCTAGGGCGTTATGTGGTTCAGCAACTTGgtacgtcctc ... attttggcagCAAGAATGGGGTCCCAAGTTATGGTACCTTACAGAGGTTTGGACGAAGAAT
EST: gi|67507649|gb|BJ940529.1|BJ940529
EST:     AGTATTTGGAGCTACTGGATTTCTAGGGCGTTATGTGGTTCAGCAACTTG                         CAAGAATGGGGTCCCAAGTTATGGTACCTTACAGAGGTTTGGACGAAGAAT
genomic: AGTATTTGGAGCTACTGGATTTCTAGGGCGTTATGTGGTTCAGCAACTTGgtacgtcctc ... attttggcagCAAGAATGGGGTCCCAAGTTATGGTACCTTACAGAGGTTTGGACGAAGAAT
EST: gi|162259819|gb|FC435954.1|FC435954
EST:     AGTATTTGGAGCTACTGGATTTCTAGGGCGTTATGTGGTTCAGCAACTTG                         CAAGAATGGGGTCCCAAGTTATGGTACCTTACAGAGGTTTGGACGAAGAAT
genomic: AGTATTTGGAGCTACTGGATTTCTAGGGCGTTATGTGGTTCAGCAACTTGgtacgtcctc ... attttggcagCAAGAATGGGGTCCCAAGTTATGGTACCTTACAGAGGTTTGGACGAAGAAT
EST: gi|100440199|gb|BY980445.1|BY980445
EST:     AGTATTTGGAGCTACTGGATTTCTAGGGCGTTATGTGGTTCAGCAACTTG                         CAAGAATGGGGTCCCAAGTTATGGTACCTTACAGAGGTTTGGACGAAGAAT
genomic: AGTATTTGGAGCTACTGGATTTCTAGGGCGTTATGTGGTTCAGCAACTTGgtacgtcctc ... attttggcagCAAGAATGGGGTCCCAAGTTATGGTACCTTACAGAGGTTTGGACGAAGAAT
EST: gi|100364138|gb|BY966734.1|BY966734
EST:     AGTATTTGGAGCTACTGGATTTCTAGGGCGTTATGTGGTTCAGCAACTTG                         CAAGAATGGGGTCCCAAGTTATGGTACCTTACAGAGGTTTGGACGAAGAAT
genomic: AGTATTTGGAGCTACTGGATTTCTAGGGCGTTATGTGGTTCAGCAACTTGgtacgtcctc ... attttggcagCAAGAATGGGGTCCCAAGTTATGGTACCTTACAGAGGTTTGGACGAAGAAT
EST: gi|162276087|gb|FC452363.1|FC452363
EST:     AGTATTTGGAGCTACTGGATTTCTAGGGCGTTATGTGGTTCAGCAACTTG                         CAAGAATGGGGTCCCAAGTTATGGTACCTTACAGAGGTTTGGACGAAGAAT
genomic: AGTATTTGGAGCTACTGGATTTCTAGGGCGTTATGTGGTTCAGCAACTTGgtacgtcctc ... attttggcagCAAGAATGGGGTCCCAAGTTATGGTACCTTACAGAGGTTTGGACGAAGAAT
EST: gi|67577930|gb|BJ950097.1|BJ950097
EST:     AGTATTTGGAGCTACTGGATTTCTAGGGCGTTATGTGGTTCAGCAACTTG                         CAAGAATGGGGTCCCAAGTTATGGTACCTTACAGAGGTTTGGACGAAGAAT
genomic: AGTATTTGGAGCTACTGGATTTCTAGGGCGTTATGTGGTTCAGCAACTTGgtacgtcctc ... attttggcagCAAGAATGGGGTCCCAAGTTATGGTACCTTACAGAGGTTTGGACGAAGAAT
EST: gi|18362228|gb|BJ194298.1|BJ194298
EST:     AGTATTTGGAGCTACTGGATTTCTAGGGCGTTATGTGGTTCAGCAACTTG                         CAAGAATGGGGTCCCAAGTTATGGTACCTTACAGAGGTTTGGACGAAGAAT
genomic: AGTATTTGGAGCTACTGGATTTCTAGGGCGTTATGTGGTTCAGCAACTTGgtacgtcctc ... attttggcagCAAGAATGGGGTCCCAAGTTATGGTACCTTACAGAGGTTTGGACGAAGAAT
EST: gi|18365271|gb|BJ197345.1|BJ197345
EST:     AGTATTTGGAGCTACTGGATTTCTAGGGCGTTATGTGGTTCAGCAACTTG                         CAAGAATGGGGTCCCAAGTTATGGTACCTTACAGAGGTTTGGACGAAGAAT
genomic: AGTATTTGGAGCTACTGGATTTCTAGGGCGTTATGTGGTTCAGCAACTTGgtacgtcctc ... attttggcagCAAGAATGGGGTCCCAAGTTATGGTACCTTACAGAGGTTTGGACGAAGAAT
EST: gi|18366348|gb|BJ198427.1|BJ198427
EST:     AGTATTTGGAGCTACTGGATTTCTAGGGCGTTATGTGGTTCAGCAACTTG                         CAAGAATGGGGTCCCAAGTTATGGTACCTTACAGAGGTTTGGACGAAGAAT
genomic: AGTATTTGGAGCTACTGGATTTCTAGGGCGTTATGTGGTTCAGCAACTTGgtacgtcctc ... attttggcagCAAGAATGGGGTCCCAAGTTATGGTACCTTACAGAGGTTTGGACGAAGAAT
EST: gi|100427489|gb|BY977523.1|BY977523
EST:     AGTATTTGGAGCTACTGGATTTCTAGGGCGTTATGTGGTTCAGCAACTTG                         CAAGAATGGGGTCCCAAGTTATGGTACCTTACAGAGGTTTGGACGAAGAAT
genomic: AGTATTTGGAGCTACTGGATTTCTAGGGCGTTATGTGGTTCAGCAACTTGgtacgtcctc ... attttggcagCAAGAATGGGGTCCCAAGTTATGGTACCTTACAGAGGTTTGGACGAAGAAT
EST: gi|100374683|gb|BY949018.1|BY949018
EST:     AGTATTTGGAGCTACTGGATTTCTAGGGCGTTATGTGGTTCAGCAACTTG                         CAAGAATGGGGTCCCAAGTTATGGTACCTTACAGAGGTTTGGACGAAGAAT
genomic: AGTATTTGGAGCTACTGGATTTCTAGGGCGTTATGTGGTTCAGCAACTTGgtacgtcctc ... attttggcagCAAGAATGGGGTCCCAAGTTATGGTACCTTACAGAGGTTTGGACGAAGAAT
EST: gi|100387000|gb|BY951399.1|BY951399
EST:     AGTATTTGGAGCTACTGGATTTCTAGGGCGTTATGTGGTTCAGCAACTTG                         CAAGAATGGGGTCCCAAGTTATGGTACCTTACAGAGGTTTGGACGAAGAAT
genomic: AGTATTTGGAGCTACTGGATTTCTAGGGCGTTATGTGGTTCAGCAACTTGgtacgtcctc ... attttggcagCAAGAATGGGGTCCCAAGTTATGGTACCTTACAGAGGTTTGGACGAAGAAT
EST: gi|100448979|gb|CJ973278.1|CJ973278
EST:     AGTATTTGGAGCTACTGGATTTCTAGGGCGTTATGTGGTTCAGCAACTTG                         CAAGAATGGGGTCCCAAGTTATGGTACCTTACAGAGGTTTGGACGAAGAAT
genomic: AGTATTTGGAGCTACTGGATTTCTAGGGCGTTATGTGGTTCAGCAACTTGgtacgtcctc ... attttggcagCAAGAATGGGGTCCCAAGTTATGGTACCTTACAGAGGTTTGGACGAAGAAT
EST: gi|100400631|gb|BY972916.1|BY972916
EST:     AGTATTTGGAGCTACTGGATTTCTAGGGCGTTATGTGGTTCAGCAACTTG                         CAAGAATGGGGTCCCAAGTTATGGTACCTTACAGAGGTTTGGACGAAGAAT
genomic: AGTATTTGGAGCTACTGGATTTCTAGGGCGTTATGTGGTTCAGCAACTTGgtacgtcctc ... attttggcagCAAGAATGGGGTCCCAAGTTATGGTACCTTACAGAGGTTTGGACGAAGAAT
EST: gi|208393451|gb|DC942521.1|DC942521
EST:     AGTATTTGGAGCTACTGGATTTCTAGGGCGTTATGTGGTTCAGCAACTTG                         CAAGAATGGGGTCCCAAGTTATGGTACCTTACAGAGGTTTGGACGAAGAAT
genomic: AGTATTTGGAGCTACTGGATTTCTAGGGCGTTATGTGGTTCAGCAACTTGgtacgtcctc ... attttggcagCAAGAATGGGGTCCCAAGTTATGGTACCTTACAGAGGTTTGGACGAAGAAT

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), 28 (downstream exon)
Score: 10

TGGAGTCGTCGCTACAGTATTTGGAGCTACTGGATTTCTAGGGCGTTATGTGGTTCAGCAACTTGgtacgtcctc ... attttggcagCAAGAATGGGGTCCCAAGTTATGGTACCTTACAGAGGTTTGGACGAAGAATGGAGGCATCTTAAGCTCATGGGAGACCTCGGACAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGGAGTCGTCGCTACAGTATTTGGAGCTACTGGATTTCTAGGGCGTTATGTGGTTCAGCAACTTGgtacgtcctcattccgttgattttgaggtatagcatttgccgagcttcgaggtagttcgtcgaacgggtttctattctgttgcaaaattttgaacgttgtgcggatactgtaatccgagacattggttgataatgtgaaatggcaaatattggatcattagttaaagcaaacataggtcattttggcag

- - - - - - - - - - TTGGAG
- - - - - - - - - - - GGAGCT