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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaactttgcctttcaattcgccttgaaaatttgaagtctcaatggttcatggattccacatcttttgaatggaaacttaaaaccgttttattgaactgcagCGATCCGGAGAATATCTTCCTCACTGATGGAGCTAGCAAAGGTGTAGCACAAGTTTTGAATGCCCTCATCCGCGATGAGAAGGATGGG

Basic information

species Physcomitrella patens
transcript PP1S215_28V6.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S215_28V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: AT1G23310.1 (Arabidopsis thaliana), 3'ss of exon 5
gtgaactttgcctttcaattcgccttgaaaatttgaagtctcaatggttcatggattccacatcttttgaatgga---aacttaaaaccgtt--ttattgaactgcagCGATCCGGAGAATATCTTCCTCACTGATGGAGCTAGCAAAGGTGTAGCACAAGTTTTGAATGCCCTCATCCGCGATGAGAAGGATGGG
                         |||   |||  |    ||       || ||||     |  |   ||   |   | ||||      ||  || || |  |  || || || ||    ||||| ||||||||||||||||||||||||||    ||| | ||||||    | || |||| | |    ||||||
------------------------gtgattgttttcatctgcacaatgaaatagatttt-tgttgtagaaacaaacccagcttaggctttttggttctttatttttagTGACCCAGAACTCATCTTTCTCACTGATGGAGCTAGCAAAGGTGTGATGCAAATCTTGAATTGTGTTATACGCGGTAATGGAGATGGG
















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|162184664|gb|FC361902.1|FC361902
EST:     GTGCGGCAGGAGGTTGCAAATTTTATCCTGCAGCGTGACGGATATCCGAG                         CGATCCGGAGAATATCTTCCTCACTGATGGAGCTAGCAAAGGTGTAGCACA
genomic: GTGCGGCAGGAGGTTGCAAATTTTATCCTGCAGCGTGACGGATATCCGAGgtgaactttg ... tgaactgcagCGATCCGGAGAATATCTTCCTCACTGATGGAGCTAGCAAAGGTGTAGCACA
EST: gi|162207832|gb|FC384125.1|FC384125
EST:     GTGCGGCAGGAGGTTGCAAATTTTATCCTGCAGCGTGACGGATATCCGAG                         CGATCCGGAGAATATCTTCCTCACTGATGGAGCTAGCAAAGGTGTAGCACA
genomic: GTGCGGCAGGAGGTTGCAAATTTTATCCTGCAGCGTGACGGATATCCGAGgtgaactttg ... tgaactgcagCGATCCGGAGAATATCTTCCTCACTGATGGAGCTAGCAAAGGTGTAGCACA
EST: gi|208400418|gb|DC908645.1|DC908645
EST:     GTGCGGCAGGAGGTTGCAAATTTTATCCTGCAGCGTGACGGATATCCGAG                         CGATCCGGAGAATATCTTCCTCACTGATGGAGCTAGCAAAGGTGTAGCACA
genomic: GTGCGGCAGGAGGTTGCAAATTTTATCCTGCAGCGTGACGGATATCCGAGgtgaactttg ... tgaactgcagCGATCCGGAGAATATCTTCCTCACTGATGGAGCTAGCAAAGGTGTAGCACA
EST: gi|100371525|gb|BY968022.1|BY968022
EST:     GTGCGGCAGGAGGTTGCAAATTTTATCCTGCAGCGTGACGGATATCCGAG                         CGATCCGGAGAATATCTTCCTCACTGATGGAGCTAGCAAAGGTGTAGCACA
genomic: GTGCGGCAGGAGGTTGCAAATTTTATCCTGCAGCGTGACGGATATCCGAGgtgaactttg ... tgaactgcagCGATCCGGAGAATATCTTCCTCACTGATGGAGCTAGCAAAGGTGTAGCACA
EST: gi|100395972|gb|BY972219.1|BY972219
EST:     GTGCGGCAGGAGGTTGCAAATTTTATCCTGCAGCGTGACGGATATCCGAG                         CGATCCGGAGAATATCTTCCTCACTGATGGAGCTAGCAAAGGTGTAGCACA
genomic: GTGCGGCAGGAGGTTGCAAATTTTATCCTGCAGCGTGACGGATATCCGAGgtgaactttg ... tgaactgcagCGATCCGGAGAATATCTTCCTCACTGATGGAGCTAGCAAAGGTGTAGCACA
EST: gi|162166511|gb|FC343208.1|FC343208
EST:     GTGCGGCAGGAGGTTGCAAATTTTATCCTGCAGCGTGACGGATATCCGAG                         CGATCCGGAGAATATCTTCCTCACTGATGGAGCTAGCANAGGTGTAGCACA
genomic: GTGCGGCAGGAGGTTGCAAATTTTATCCTGCAGCGTGACGGATATCCGAGgtgaactttg ... tgaactgcagCGATCCGGAGAATATCTTCCTCACTGATGGAGCTAGCAAAGGTGTAGCACA
EST: gi|100448661|gb|CJ972960.1|CJ972960
EST:     GTGCGGCAGGAGGTTGCAAATTTTATCCTGCAGCGTGACGGATATCCGAG                         CGATCCGGAGAATATCTTCCTCACTGATGGAGCTAGCAAAGGTGTAGCACA
genomic: GTGCGGCAGGAGGTTGCAAATTTTATCCTGCAGCGTGACGGATATCCGAGgtgaactttg ... tgaactgcagCGATCCGGAGAATATCTTCCTCACTGATGGAGCTAGCAAAGGTGTAGCACA
EST: gi|100393479|gb|BY953418.1|BY953418
EST:     GTGCGGCAGGAGGTTGCAAATTTTATCCTGCAGCGTGACGGATATCCGAG                         CGATCCGGAGAATATCTTCCTCACTGATGGAGCTAGCAAAGGTGTAGCACA
genomic: GTGCGGCAGGAGGTTGCAAATTTTATCCTGCAGCGTGACGGATATCCGAGgtgaactttg ... tgaactgcagCGATCCGGAGAATATCTTCCTCACTGATGGAGCTAGCAAAGGTGTAGCACA
EST: gi|162214587|gb|FC390618.1|FC390618
EST:     GTGCGGCAGGAGGTTGCAAATTTTATCCTGCAGCGTGACGGATATCCGAG                         CGATCCGGAGAATATCTTCCTCACTGATGGAGCTAGCAAAGGTGTAGCACA
genomic: GTGCGGCAGGAGGTTGCAAATTTTATCCTGCAGCGTGACGGATATCCGAGgtgaactttg ... tgaactgcagCGATCCGGAGAATATCTTCCTCACTGATGGAGCTAGCAAAGGTGTAGCACA
EST: gi|100417952|gb|BY993265.1|BY993265
EST:     GTGCGGCAGGAGGTTGCAAATTTTATCCTGCAGCGTGACGGATATCCGAG                         CGATCCGGAGAATATCTTCCTCACTGATGGAGCTAGCANAGGTGTAGCACA
genomic: GTGCGGCAGGAGGTTGCAAATTTTATCCTGCAGCGTGACGGATATCCGAGgtgaactttg ... tgaactgcagCGATCCGGAGAATATCTTCCTCACTGATGGAGCTAGCAAAGGTGTAGCACA
EST: gi|162155910|gb|FC332459.1|FC332459
EST:     GTGCGGCAGGAGGTTGCAAATTTTATCCTGCAGCGTGACGGATATCCGAG                         CGATCCGGAGAATATCTTCCTCACTGATGGAGCTAGCAAAGGTGTAGCACA
genomic: GTGCGGCAGGAGGTTGCAAATTTTATCCTGCAGCGTGACGGATATCCGAGgtgaactttg ... tgaactgcagCGATCCGGAGAATATCTTCCTCACTGATGGAGCTAGCAAAGGTGTAGCACA
EST: gi|162151638|gb|FC327767.1|FC327767
EST:     GTGCGGCAGGAGGTTGCAAATTTTATCCTGCAGCGTGACGGATATCCGAG                         CGATCCGGAGAATATCTTCCTCACTGATGGAGCTAGCAAAGGTGTAGCACA
genomic: GTGCGGCAGGAGGTTGCAAATTTTATCCTGCAGCGTGACGGATATCCGAGgtgaactttg ... tgaactgcagCGATCCGGAGAATATCTTCCTCACTGATGGAGCTAGCAAAGGTGTAGCACA
EST: gi|162153918|gb|FC329425.1|FC329425
EST:     GTGCGGCAGGAGGTTGCAAATTTTATCCTGCAGCGTGACGGATATCCGAG                         CGATCCGGAGAATATCTTCCTCACTGATGGAGCTAGCAAAGGTGTAGCACA
genomic: GTGCGGCAGGAGGTTGCAAATTTTATCCTGCAGCGTGACGGATATCCGAGgtgaactttg ... tgaactgcagCGATCCGGAGAATATCTTCCTCACTGATGGAGCTAGCAAAGGTGTAGCACA
EST: gi|100392222|gb|BY953255.1|BY953255
EST:     GTGCGGCAGGAGGTTGCAAATTTTATCCTGCAGCGTGACGGATATCCGAG                         CGATCCGGAGAATATCTTCCTCACTGATGGAGCTAGCAAAGGTGTAGCACA
genomic: GTGCGGCAGGAGGTTGCAAATTTTATCCTGCAGCGTGACGGATATCCGAGgtgaactttg ... tgaactgcagCGATCCGGAGAATATCTTCCTCACTGATGGAGCTAGCAAAGGTGTAGCACA
EST: gi|100384799|gb|BY969534.1|BY969534
EST:     GTGCGGCAGGAGGTTGCAAATTTTATCCTGCAGCGTGACGGATATCCGAG                         CGATCCGGAGAATATCTTCCTCACTGATGGAGCTAGCAAAGGTGTAGCACA
genomic: GTGCGGCAGGAGGTTGCAAATTTTATCCTGCAGCGTGACGGATATCCGAGgtgaactttg ... tgaactgcagCGATCCGGAGAATATCTTCCTCACTGATGGAGCTAGCAAAGGTGTAGCACA
EST: gi|162186627|gb|FC363599.1|FC363599
EST:     GTGCGGCAGGAGGTTGCAAATTTTATCCTGCAGCGTGACGGATATCCGAG                         CGATCCGGAGAATATCTTCCTCACTGATGGAGCTAGCAAAGGTGTAGCACA
genomic: GTGCGGCAGGAGGTTGCAAATTTTATCCTGCAGCGTGACGGATATCCGAGgtgaactttg ... tgaactgcagCGATCCGGAGAATATCTTCCTCACTGATGGAGCTAGCAAAGGTGTAGCACA
EST: gi|162152068|gb|FC328463.1|FC328463
EST:     GTGCGGCAGGAGGTTGCAAATTTTATCCTGCAGCGTGACGGATATCCGAG                         CGATCCGGAGAATATCTTCCTCACTGATGGAGCTAGCAAAGGTGTAGCACA
genomic: GTGCGGCAGGAGGTTGCAAATTTTATCCTGCAGCGTGACGGATATCCGAGgtgaactttg ... tgaactgcagCGATCCGGAGAATATCTTCCTCACTGATGGAGCTAGCAAAGGTGTAGCACA
EST: gi|100437194|gb|BY961398.1|BY961398
EST:     GTGCGGCAGGAGGTTGCAAATTTTATCCTGCAGCGTGACGGATATCCGAG                         CGATCCGGAGAATATCTTCCTCACTGATGGAGCTAGCAAAGGTGTAGCACA
genomic: GTGCGGCAGGAGGTTGCAAATTTTATCCTGCAGCGTGACGGATATCCGAGgtgaactttg ... tgaactgcagCGATCCGGAGAATATCTTCCTCACTGATGGAGCTAGCAAAGGTGTAGCACA
EST: gi|162155922|gb|FC332471.1|FC332471
EST:     GTGCGGCAGGAGGTTGCAAATTTTATCCTGCAGCGTGACGGATATCCGAG                         CGATCCGGAGAATATCTTCCTCACTGATGGAGCTAGCAAAGGTGTAGCACA
genomic: GTGCGGCAGGAGGTTGCAAATTTTATCCTGCAGCGTGACGGATATCCGAGgtgaactttg ... tgaactgcagCGATCCGGAGAATATCTTCCTCACTGATGGAGCTAGCAAAGGTGTAGCACA
EST: gi|162176654|gb|FC352499.1|FC352499
EST:     GTGCGGCAGGAGGTTGCAAATTTTATCCTGCAGCGTGACGGATATCCGAG                         CGATCCGGAGAATATCTTCCTCACTGATGGAGCTAGCAAAGGTGTAGCACA
genomic: GTGCGGCAGGAGGTTGCAAATTTTATCCTGCAGCGTGACGGATATCCGAGgtgaactttg ... tgaactgcagCGATCCGGAGAATATCTTCCTCACTGATGGAGCTAGCAAAGGTGTAGCACA
EST: gi|100360719|gb|BY965863.1|BY965863
EST:     GTGCGGCAGGAGGTTGCAAATTTTATCCTGCAGCGTGACGGATATCCGAG                         CGATCCGGAGAATATCT
genomic: GTGCGGCAGGAGGTTGCAAATTTTATCCTGCAGCGTGACGGATATCCGAGgtgaactttg ... tgaactgcagCGATCCGGAGAATATCT
EST: gi|100441845|gb|BY981068.1|BY981068
EST:     GTGCGGCAGGAGGTTGCAAATTTTATCCTGCAGCGTGACGGATATCCGAG                         CGATCCGGAGA-TATCTTCCTCACTGATGGAGCTAGCAAAGGTGTAGCACA
genomic: GTGCGGCAGGAGGTTGCAAATTTTATCCTGCAGCGTGACGGATATCCGAGgtgaactttg ... tgaactgcagCGATCCGGAGAATATCTTCCTCACTGATGGAGCTAGCAAAGGTGTAGCACA
EST: gi|100448584|gb|CJ972883.1|CJ972883
EST:     GTGCGGCAGGAGGTTGCAAATTTTATCCTGCAGCGTGACGGATATCCGAG                         CGATCCGGAGAATATCTTCCTCACTGATGGAGCTAGCAAAGGTGTAGCACA
genomic: GTGCGGCAGGAGGTTGCAAATTTTATCCTGCAGCGTGACGGATATCCGAGgtgaactttg ... tgaactgcagCGATCCGGAGAATATCTTCCTCACTGATGGAGCTAGCAAAGGTGTAGCACA
EST: gi|100448006|gb|CJ972305.1|CJ972305
EST:     GTGCGGCAGGAGGTTGCAAATTTTATCCTGCAGCGTGACGGATATCCGAG                         CGATCCGGAGAATATCTTCCTCACTGATGGAGCTAGCAAAGGTGTAGCACA
genomic: GTGCGGCAGGAGGTTGCAAATTTTATCCTGCAGCGTGACGGATATCCGAGgtgaactttg ... tgaactgcagCGATCCGGAGAATATCTTCCTCACTGATGGAGCTAGCAAAGGTGTAGCACA
EST: gi|162177756|gb|FC354590.1|FC354590
EST:     GTGCGGCAGGAGGTTGCAAATTTTATCCTGCAGCGTGACGGATATCCGAG                         CGATCCGGAGAATATCTTCCTCACTGATGGAGCTAGCAAAGGTGTAGCACA
genomic: GTGCGGCAGGAGGTTGCAAATTTTATCCTGCAGCGTGACGGATATCCGAGgtgaactttg ... tgaactgcagCGATCCGGAGAATATCTTCCTCACTGATGGAGCTAGCAAAGGTGTAGCACA
EST: gi|162178101|gb|FC354403.1|FC354403
EST:     GTGCGGCAGGAGGTTGCAAATTTTATCCTGCAGCGTGACGGATATCCGAG                         CGATCCGGAGAATATCTTCCTCACTGATGGAGCTAGCAAAGGTGTAGCACA
genomic: GTGCGGCAGGAGGTTGCAAATTTTATCCTGCAGCGTGACGGATATCCGAGgtgaactttg ... tgaactgcagCGATCCGGAGAATATCTTCCTCACTGATGGAGCTAGCAAAGGTGTAGCACA
EST: gi|162186048|gb|FC361876.1|FC361876
EST:     GTGCGGCAGGAGGTTGCAAATTTTATCCTGCAGCGTGACGGATATCCGAG                         CGATCCGGAGAATATCTTCCTCACTGATGGAGCTAGCAAAGGTGTAGCACA
genomic: GTGCGGCAGGAGGTTGCAAATTTTATCCTGCAGCGTGACGGATATCCGAGgtgaactttg ... tgaactgcagCGATCCGGAGAATATCTTCCTCACTGATGGAGCTAGCAAAGGTGTAGCACA
EST: gi|162161643|gb|FC339058.1|FC339058
EST:     GTGCGGCAGGAGGTTGCAAATTTTATCCTGCAGCGTGACGGATATCCGAG                         CGATCCGGAGAATATCTTCCTCACTGATGGAGCTAGCAAAGGTGTAGCACA
genomic: GTGCGGCAGGAGGTTGCAAATTTTATCCTGCAGCGTGACGGATATCCGAGgtgaactttg ... tgaactgcagCGATCCGGAGAATATCTTCCTCACTGATGGAGCTAGCAAAGGTGTAGCACA
EST: gi|100390035|gb|BY989115.1|BY989115
EST:     GTGCGGCAGGAGGTTGCAAATTTTATCCTGCAGCGTGACGGATATCCGAG                         CGATCCGGAGAATATCTTCCTCACTGATGGAGCTAGCAAAGGTGTAGCACA
genomic: GTGCGGCAGGAGGTTGCAAATTTTATCCTGCAGCGTGACGGATATCCGAGgtgaactttg ... tgaactgcagCGATCCGGAGAATATCTTCCTCACTGATGGAGCTAGCAAAGGTGTAGCACA
EST: gi|100425083|gb|BY976964.1|BY976964
EST:     GTGCGGCAGGAGGTTGCAAATTTTATCCTGCAGCGTGACGGATATCCGAG                         CGATCCGGAGAATATCTTCCTCACTGATGGAGCTAGCAAAGGTGTAGCACA
genomic: GTGCGGCAGGAGGTTGCAAATTTTATCCTGCAGCGTGACGGATATCCGAGgtgaactttg ... tgaactgcagCGATCCGGAGAATATCTTCCTCACTGATGGAGCTAGCAAAGGTGTAGCACA
EST: gi|162151906|gb|FC328152.1|FC328152
EST:     GTGCGGCAGGAGGTTGCAAATTTTATCCTGCAGCGTGACGGATATCCGAG                         CGATCCGGAGAATATCTTCCTCACTGATGGAGCTAGCAAAGGTGTAGCACA
genomic: GTGCGGCAGGAGGTTGCAAATTTTATCCTGCAGCGTGACGGATATCCGAGgtgaactttg ... tgaactgcagCGATCCGGAGAATATCTTCCTCACTGATGGAGCTAGCAAAGGTGTAGCACA
EST: gi|162181637|gb|FC357939.1|FC357939
EST:     GTGCGGCAGGAGGTTGCAAATTTTATCCTGCAGCGTGACGGATATCCGAG                         CGATCCGGAGAATATCTTCCTCACTGATGGAGCTAGCAAAGGTGTAGCACA
genomic: GTGCGGCAGGAGGTTGCAAATTTTATCCTGCAGCGTGACGGATATCCGAGgtgaactttg ... tgaactgcagCGATCCGGAGAATATCTTCCTCACTGATGGAGCTAGCAAAGGTGTAGCACA
EST: gi|100418930|gb|BY975809.1|BY975809
EST:     GTGCGGCAGGAGGTTGCAAATTTTATCCTGCAGCGTGACGGATATCCGAG                         CGATCCGGAGAATATCTTCCTCACTGATGGAGCTAGCAAAGGTGTAGCACA
genomic: GTGCGGCAGGAGGTTGCAAATTTTATCCTGCAGCGTGACGGATATCCGAGgtgaactttg ... tgaactgcagCGATCCGGAGAATATCTTCCTCACTGATGGAGCTAGCAAAGGTGTAGCACA
EST: gi|100398360|gb|BY972565.1|BY972565
EST:     GTGCGGCAGGAGGTTGCAAATTTTATCCTGCAGCGTGACGGATATCCGAG                         CGATCCGGAGAATATCTTCCTCACTGATGGAGCTAGCAAAGGTGTAGCACA
genomic: GTGCGGCAGGAGGTTGCAAATTTTATCCTGCAGCGTGACGGATATCCGAGgtgaactttg ... tgaactgcagCGATCCGGAGAATATCTTCCTCACTGATGGAGCTAGCAAAGGTGTAGCACA
EST: gi|100437396|gb|BY961497.1|BY961497
EST:     GTGCGGCAGGAGGTTGCAAATTTTATCCTGCAGCGTGACGGATATCCGAG                         CGATCCGGAGAATATCTTCCTCACTGATGGAGCTAGCAAAGGTGTAGCACA
genomic: GTGCGGCAGGAGGTTGCAAATTTTATCCTGCAGCGTGACGGATATCCGAGgtgaactttg ... tgaactgcagCGATCCGGAGAATATCTTCCTCACTGATGGAGCTAGCAAAGGTGTAGCACA

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: 58

GAGCTTACAGTGATTCCAGAGGGCTCCCTGGTGTGCGGCAGGAGGTTGCAAATTTTATCCTGCAGCGTGACGGATATCCGAGgtgaactttg ... tgaactgcagCGATCCGGAGAATATCTTCCTCACTGATGGAGCTAGCAAAGGTGTAGCACAAGTTTTGAATGCCCTCATCCGCGATGAGAAGGATGGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcatggattccacatcttttgaatggaaacttaaaaccgttttattgaactgcagCGATCCGGAGAATATCTTCCTCACTGATGGAGCTAGCAAAGGTGTAGCACAAGTTTTGAATGCCCTCATCCGCGATGAGAAGGATGGG
                                       ttttatt  CT-rich tract
                          aaacttaaaa  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgaactttgcctttcaattcgccttgaaaatttgaagtctcaatggttcatggattccacatcttttgaatggaaacttaaaaccgttttattgaactgcagCGATCCGGAGAATATCTTCCTCACTGATGGAGCTAGCAAAGGTGTAGCACAAGTTTTGAATGCCCTCATCCGCGATGAGAAGGATGGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG