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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgatttctaatggtttaatgaacccctcagctagtagcttgatatcgttacgaatcaatgacattttccgacacggttcaacatgctggcggcggtgcagCACTTGCAATGTGGGGATTTTATAGTGAAGGAACCCATGGTTATTGGCCATGAATGTGCTGGTACCATTGAGGAAGTTGGGAAGGCTGTGAAGAATGTTG

Basic information

species Physcomitrella patens
transcript PP1S36_261V6.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S36_261V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA16G32360.2 (Glycine max), 3'ss of exon 1
tgatttctaatggtttaatgaacccctcagctagtagcttgatatcgttacgaatcaatgacattttccgacacggttcaacatgctggcggcggtgcagCACTTGCAATGTGGGGATTTTATAGTGAAGGAACCCATGGTTATTGGCCATGAATGTGCTGGTACCATTGAGGAAGTTGGGAAGGCTGTGAAGAATGTTG-------------------------
         | |||||| |    ||  |   ||     |  || |  |  | | | ||     |           |||  |  | ||        | |||    ||   ||||   | |||||||| || ||||| ||||||||||| ||||| |||||||| | ||| || |||||||| |     || |||| | | |                         
---------agggtttatt---tcctgcgttta-----tctatgttttctctagtgaaaagtttcaaattttgttgtttcatttact--------ttcagacactgaggtgtgctcactttatagTTAAAGAACCAATGGTTATTGGTCATGAGTGTGCTGGGATCATAGAAGAAGTTGGTAGTCAGGTAAAGAGTTTGGTGCCTGGTGACCGTGTGGCAATTGA

upper sequence: PP1S36_261V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA09G27310.1 (Glycine max), 3'ss of exon 2
-----tgatttctaatggtttaatgaacccctcagctagtagcttgatatcgttacgaatcaatgacattttccgacacggttcaacatgctggcggcggtgcagCACTTGCAATGTGGGGATTTTATAGTGAAGGAACCCATGGTTATTGGCCATGAATGTGCTGGTACCATTGAGGAAGTTGGGAAGGCTGTGAAGAATGTTG
     || ||   |||  | || || |    | |  |  |   || || |   |       | ||  | ||||       |||     |        |  |    |||| |   ||||   | |||||||| || ||||| ||||||||||| ||||| |||||||| | ||| || |||||||| |     ||||||| | | |
tgttttggttggaaattttatattggaggggttatttcctgcgtttatctatgttttctctagtggaagtttcaatttttgtt----gtttcatttactttcagACACT-GAGGTGTGCTCACTTTATAGTTAAAGAACCAATGGTTATTGGTCATGAGTGTGCTGGGATCATAGAAGAAGTTGGCAGTCAAGTGAAGAGTTTGG

upper sequence: PP1S36_261V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA16G32360.3 (Glycine max), 3'ss of exon 1
-----tgatttctaatggtttaatgaacccctcagctagtagcttgatatcgttacgaatcaatgacattttccgacacggttcaacatgctggcggcggtgcagCACTTGCAATGTGGGGATTTTATAGTGAAGGAACCCATGGTTATTGGCCATGAATGTGCTGGTACCATTGAGGAAGTTGGGAAGGCTGTGAAGAATGTTG
     || ||   |||  || |||| |    | |  |  |   || || |   |       | ||| |  || | |     ||     |        |  |    |||| |   ||||   | |||||||| || ||||| ||||||||||| ||||| |||||||| | ||| || |||||||| |     || |||| | | |
tgttttggttggaaatt-ttaaatggagggtttatttcctgcgtttatctatgttttctctagtgaaaagtttcaa---attttgttgtttcatttactttcagACACT-GAGGTGTGCTCACTTTATAGTTAAAGAACCAATGGTTATTGGTCATGAGTGTGCTGGGATCATAGAAGAAGTTGGTAGTCAGGTAAAGAGTTTGG

upper sequence: PP1S36_261V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: AT5G51970.1 (Arabidopsis thaliana), 3'ss of exon 2
tgatttctaatg-gtttaatgaacccctcagctagtagcttgatatcgttacgaatcaatgacattt-tccgacacggttcaacatgctggcggcggtgcagCACTTGCAATGTGGGGATTTTATAGTGAAGGAACCCATGGTTATTGGCCATGAATGTGCTGGTACCATTGAGGAAGTTGGGAAGGCTGTGAAGAATGTTG
  | || | ||    | |  ||     |  | |  |   ||||| | | || |  ||  |||||||  |     | || |    ||| ||          ||  | ||  ||||| ||||||| | ||||| || || ||||| ||||| |||||||||||||| | |||||| ||||| ||  | |  |||||  || | |
gtacttatgatataatcagagagatatttggttttttctttgat-ttggtatggctct-tgacattggtttttgatgggtgtgaatgttgcaaa--acaaagACCATGAGATGTGCGGATTTTGTGGTGAAAGAGCCGATGGTGATTGGACATGAATGTGCTGGGATCATTGAAGAAGTAGGTGAAGAAGTGAAACATTTAG

upper sequence: PP1S36_261V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: Vv16s0100g00300.t01 (Vitis vinifera), 3'ss of exon 2
tgatttctaa-tggtttaatgaacccctcagctagtagcttgatatcgttacga-atcaatgacattttccgacacggttcaacatgctggcggcggtg-cagCACTTGCAATGTGGGGATTTTATAGTGAAGGAACCCATGGTTATTGGCCATGAATGTGCTGGTACCATTGAGGAAGTTGGGAAGGCTGTGAAGAATGTTG
   ||||| |       ||  ||      |  ||  |    |   ||    |    |      ||| |   |||     |   | ||     ||   |  ||| | |||  |||||  |||||||| || || || || ||||| || ||||||||||||||||| | |||||| ||||||||       ||||||  | | |
-attttctgagcaaccaaacaaagggagtatttaaaataaaggggtcccccctttgttccctccatctattgacct--ctagtcttgtgattggtattttcagAAATTGAGATGTGCAGATTTTATTGTTAAAGAGCCTATGGTGATCGGCCATGAATGTGCTGGGATCATTGATGAAGTTGGTCCCCAGGTGAAGTCTCTGG

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|208376602|gb|DC932066.1|DC932066
EST:     TGGGAATCAAAGCTGTAGGTATTTGCGGCAGCGATGTCCATTATTACAGG                         CACTTGCAATGTGGGGATTTTATAGTGAAGGAACCCATGGTTATTGGCCAT
genomic: TGGGAATCAAAGCTGTAGGTATTTGCGGCAGCGATGTCCATTATTACAGGgtaggattat ... ggcggtgcagCACTTGCAATGTGGGGATTTTATAGTGAAGGAACCCATGGTTATTGGCCAT
EST: gi|100410799|gb|BY956193.1|BY956193
EST:     TGGGAATCAAAGCTGTAGGTATTTGCGGCAGCGATGTCCATTATTACAGG                         CACTTGCAATGTGGGGATTTTATAGTGAAGGAACCCATGGTTATTGGCCAT
genomic: TGGGAATCAAAGCTGTAGGTATTTGCGGCAGCGATGTCCATTATTACAGGgtaggattat ... ggcggtgcagCACTTGCAATGTGGGGATTTTATAGTGAAGGAACCCATGGTTATTGGCCAT
EST: gi|100384783|gb|BY950773.1|BY950773
EST:     TGGGAATCAAAGCTGTAGGTATTTGCGGCAGCGATGTCCATTATTACAGG                         CACTTGCAATGTGGGGATTTTATAGTGAAGGAACCCATGGTTATTGGCCAT
genomic: TGGGAATCAAAGCTGTAGGTATTTGCGGCAGCGATGTCCATTATTACAGGgtaggattat ... ggcggtgcagCACTTGCAATGTGGGGATTTTATAGTGAAGGAACCCATGGTTATTGGCCAT
EST: gi|208393643|gb|DC907794.1|DC907794
EST:     TGGGAATCAAAGCTGTAGGTATTTGCGGCAGCGATGTCCATTATTACAGG                         CACTTGCAATGTGGGGATTTTATAGTGAAGGAACCCATGGTTATTGGCCAT
genomic: TGGGAATCAAAGCTGTAGGTATTTGCGGCAGCGATGTCCATTATTACAGGgtaggattat ... ggcggtgcagCACTTGCAATGTGGGGATTTTATAGTGAAGGAACCCATGGTTATTGGCCAT
EST: gi|100447536|gb|CJ971835.1|CJ971835
EST:     TGGGAATCAAAGCTGTAGGTATTTGCGGCAGCGATGTCCATTATTACAGG                         CACTTGCAATGTGGGGATTTTATAGTGAAGGAACCCATGGTTATTGGCCAT
genomic: TGGGAATCAAAGCTGTAGGTATTTGCGGCAGCGATGTCCATTATTACAGGgtaggattat ... ggcggtgcagCACTTGCAATGTGGGGATTTTATAGTGAAGGAACCCATGGTTATTGGCCAT
EST: gi|100373071|gb|BY949206.1|BY949206
EST:     TGGGAATCAAAGCTGTAGGTATTTGCGGCAGCGATGTCCATTATTACAGG                         CACTTGCAATGTGGGGATTTTATAGTGAAGGAACCCATGGTTATTGGCCAT
genomic: TGGGAATCAAAGCTGTAGGTATTTGCGGCAGCGATGTCCATTATTACAGGgtaggattat ... ggcggtgcagCACTTGCAATGTGGGGATTTTATAGTGAAGGAACCCATGGTTATTGGCCAT
EST: gi|100406268|gb|BY991623.1|BY991623
EST:     TGGGAATCAAAGCTGTAGGTATTTGCGGCAGCGATGTCCATTATTACAGG                         CACTTGCAATGTGGGGATTTTATAGTGAAGGAACCCATGGTTATTGGCCAT
genomic: TGGGAATCAAAGCTGTAGGTATTTGCGGCAGCGATGTCCATTATTACAGGgtaggattat ... ggcggtgcagCACTTGCAATGTGGGGATTTTATAGTGAAGGAACCCATGGTTATTGGCCAT
EST: gi|100403388|gb|BY991178.1|BY991178
EST:     TGGGAATCAAAGCTGTAGGTATTTGCGGCAGCGATGTCCATTATTACAGG                         CACTTGCAATGTGGGGATTTTATAGTGAAGGAACCCATGGTTATTGGCCAT
genomic: TGGGAATCAAAGCTGTAGGTATTTGCGGCAGCGATGTCCATTATTACAGGgtaggattat ... ggcggtgcagCACTTGCAATGTGGGGATTTTATAGTGAAGGAACCCATGGTTATTGGCCAT
EST: gi|100440063|gb|BY980377.1|BY980377
EST:     TGGGAATCAAAGCTGTAGGTATTTGCGGCAGCGATGTCCATTATTACAGG                         CGCTTGCAATGTGGGGATTTTATAGTGAAGGAACCCATGGTTATTGGCCAT
genomic: TGGGAATCAAAGCTGTAGGTATTTGCGGCAGCGATGTCCATTATTACAGGgtaggattat ... ggcggtgcagCACTTGCAATGTGGGGATTTTATAGTGAAGGAACCCATGGTTATTGGCCAT
EST: gi|67569739|gb|BJ942563.1|BJ942563
EST:     TGGGAATCAAAGCTGTAGGTATTTGCGGCAGCGATGTCCATTATTACAGG                         CACTTGCAATGTGGGGATTTTATAGTGAAGGAACCCATGGTTATTGGCCAT
genomic: TGGGAATCAAAGCTGTAGGTATTTGCGGCAGCGATGTCCATTATTACAGGgtaggattat ... ggcggtgcagCACTTGCAATGTGGGGATTTTATAGTGAAGGAACCCATGGTTATTGGCCAT
EST: gi|100410247|gb|BY974482.1|BY974482
EST:     TGGGAATCAAAGCTGTAGGTATTTGCGGCAGCGATGTCCATTATTACAGG                         CACTTGCAATGTGGGGATTTTATAGTGAAGGAACCCATGGTTATTGGCCAT
genomic: TGGGAATCAAAGCTGTAGGTATTTGCGGCAGCGATGTCCATTATTACAGGgtaggattat ... ggcggtgcagCACTTGCAATGTGGGGATTTTATAGTGAAGGAACCCATGGTTATTGGCCAT
EST: gi|100356878|gb|BY965324.1|BY965324
EST:     TGGGAATCAAAGCTGTAGGTATTTGCGGCAGCGATGTCCATTATTACAGG                         CACTTGCAATGTGGGGATTTTATAGTGAAGGAACCCATGGTTATTGGCCAT
genomic: TGGGAATCAAAGCTGTAGGTATTTGCGGCAGCGATGTCCATTATTACAGGgtaggattat ... ggcggtgcagCACTTGCAATGTGGGGATTTTATAGTGAAGGAACCCATGGTTATTGGCCAT
EST: gi|208346881|gb|DC913106.1|DC913106
EST:     TGGGAATCAAAGCTGTAGGTATTTGCGGCAGCGATGTCCATTATTACAGG                         CACTTGCAATGTGGGGATTTTATAGTGAAGGAACCCATGGTTATTGGCCAT
genomic: TGGGAATCAAAGCTGTAGGTATTTGCGGCAGCGATGTCCATTATTACAGGgtaggattat ... ggcggtgcagCACTTGCAATGTGGGGATTTTATAGTGAAGGAACCCATGGTTATTGGCCAT
EST: gi|208351787|gb|DC910355.1|DC910355
EST:     TGGGAATCAAAGCTGTAGGTATTTGCGGCAGCGATGTCCATTATTACAGG                         CACTTGCAATGTGGGGATTTTATAGTGAAGGAACCCATGGTTATTGGCCAT
genomic: TGGGAATCAAAGCTGTAGGTATTTGCGGCAGCGATGTCCATTATTACAGGgtaggattat ... ggcggtgcagCACTTGCAATGTGGGGATTTTATAGTGAAGGAACCCATGGTTATTGGCCAT
EST: gi|100388202|gb|BY951804.1|BY951804
EST:     TGGGAATCAAAGCTGTAGGTATTTGCGGCAGCGATGTCCATTATTACAGG                         CACTTGCAATGTGGGGATTTTATAGTGAAGGAACCCATGGTTATTGGCCAT
genomic: TGGGAATCAAAGCTGTAGGTATTTGCGGCAGCGATGTCCATTATTACAGGgtaggattat ... ggcggtgcagCACTTGCAATGTGGGGATTTTATAGTGAAGGAACCCATGGTTATTGGCCAT
EST: gi|100390881|gb|BY989364.1|BY989364
EST:     TGGGAATCAAAGCTGTAGGTATTTGCGGCAGCGATGTCCATTATTACAGG                         CACTTGCAATGTGGGGATTTTATAGTGAAGGAACCCATGGTTATTGGCCAT
genomic: TGGGAATCAAAGCTGTAGGTATTTGCGGCAGCGATGTCCATTATTACAGGgtaggattat ... ggcggtgcagCACTTGCAATGTGGGGATTTTATAGTGAAGGAACCCATGGTTATTGGCCAT
EST: gi|100425325|gb|BY977086.1|BY977086
EST:     TGGGAATCAAAGCTGTAGGTATTTGCGGCAGCGATGTCCATTATTACAGG                         CACTTGCAATGTGGGGATTTTATAGTGAAGGAACCCATGGTTATTGGCCAT
genomic: TGGGAATCAAAGCTGTAGGTATTTGCGGCAGCGATGTCCATTATTACAGGgtaggattat ... ggcggtgcagCACTTGCAATGTGGGGATTTTATAGTGAAGGAACCCATGGTTATTGGCCAT
EST: gi|18326861|gb|BJ158861.1|BJ158861
EST:     TGGGAATCAAAGCTGTAGGTATTTGCGGCAGCGATGTCCATTATTACAGG                         CACTTGCAATGTGGGGATTTTATAGTGAAGGAACCCATGGTTATTGGCCAT
genomic: TGGGAATCAAAGCTGTAGGTATTTGCGGCAGCGATGTCCATTATTACAGGgtaggattat ... ggcggtgcagCACTTGCAATGTGGGGATTTTATAGTGAAGGAACCCATGGTTATTGGCCAT
EST: gi|162219194|gb|FC396633.1|FC396633
EST:     CAGCGATGTCCATTATTACAGG                         CACTTGCAATGTGGGGATTTTATAGTGAAGGAACCCATGGTTATTGGCCAT
genomic: CAGCGATGTCCATTATTACAGGgtaggattat ... ggcggtgcagCACTTGCAATGTGGGGATTTTATAGTGAAGGAACCCATGGTTATTGGCCAT
EST: gi|100432486|gb|BY960480.1|BY960480
EST:     TGGGAATCAAAGCTGTAGGTATTTGCGGCAGCGATGTCCATTATTACAGG                         CACTTGCAATGTGGGGATTTTATAGTGAAGGAACCCATGGTTATTGGCCAT
genomic: TGGGAATCAAAGCTGTAGGTATTTGCGGCAGCGATGTCCATTATTACAGGgtaggattat ... ggcggtgcagCACTTGCAATGTGGGGATTTTATAGTGAAGGAACCCATGGTTATTGGCCAT
EST: gi|208384337|gb|DC903404.1|DC903404
EST:     TGGGAATCAAAGCTGTAGGTATTTGCGGCAGCGATGTCCATTATTACAGG                         CACTTGCAATGTGGGGATTTTATAGTGAAGGAACCCATGGTTATTGGCCAT
genomic: TGGGAATCAAAGCTGTAGGTATTTGCGGCAGCGATGTCCATTATTACAGGgtaggattat ... ggcggtgcagCACTTGCAATGTGGGGATTTTATAGTGAAGGAACCCATGGTTATTGGCCAT
EST: gi|100395443|gb|BY953711.1|BY953711
EST:     TGGGAATCAAAGCTGTAGGTATTTGCGGCAGCGATGTCCATTATTACAGG                         CACTTGCAATGTGGGGATTTTATAGTGAAGGAACCCATGGTTATTGGCCAT
genomic: TGGGAATCAAAGCTGTAGGTATTTGCGGCAGCGATGTCCATTATTACAGGgtaggattat ... ggcggtgcagCACTTGCAATGTGGGGATTTTATAGTGAAGGAACCCATGGTTATTGGCCAT
EST: gi|100412210|gb|BY956468.1|BY956468
EST:     TGGGAATCAAAGCTGTAGGTATTTGCGGCAGCGATGTCCATTATTACAGG                         CACTTGCAATGTGGGGATTTTATAGTGAAGGAACCCATGGTTATTGGCCAT
genomic: TGGGAATCAAAGCTGTAGGTATTTGCGGCAGCGATGTCCATTATTACAGGgtaggattat ... ggcggtgcagCACTTGCAATGTGGGGATTTTATAGTGAAGGAACCCATGGTTATTGGCCAT
EST: gi|100356741|gb|BY965257.1|BY965257
EST:     TGGGAATCAAAGCTGTAGGTATTTGCGGCAGCGATGTCCATTATTACAGG                         CACTTGCAATGTGGGGATTTTATAGTGAAGGAACCCATGGTTATTGGCCAT
genomic: TGGGAATCAAAGCTGTAGGTATTTGCGGCAGCGATGTCCATTATTACAGGgtaggattat ... ggcggtgcagCACTTGCAATGTGGGGATTTTATAGTGAAGGAACCCATGGTTATTGGCCAT
EST: gi|18331202|gb|BJ163211.1|BJ163211
EST:     TGGGAATCAAAGCTGTAGGTATTTGCGGCAGCGATGTCCATTATTACAGG                         CACTTGCAATGTGGGGATTTTATAGTGAAGGAA
genomic: TGGGAATCAAAGCTGTAGGTATTTGCGGCAGCGATGTCCATTATTACAGGgtaggattat ... ggcggtgcagCACTTGCAATGTGGGGATTTTATAGTGAAGGAA
EST: gi|208387112|gb|DC941284.1|DC941284
EST:     TGGGAATCAAAGCTGTAGGTATTTGCGGCAGCGATGTCCATTATTACAGG                         CACTTGCAATGTGGGGATTTTATAGTGAAGGAACCCATGGTTATTGGCCAT
genomic: TGGGAATCAAAGCTGTAGGTATTTGCGGCAGCGATGTCCATTATTACAGGgtaggattat ... ggcggtgcagCACTTGCAATGTGGGGATTTTATAGTGAAGGAACCCATGGTTATTGGCCAT
EST: gi|100355845|gb|BY946067.1|BY946067
EST:     TGGGAATCAAAGCTGTAGGTATTTGCGGCAGCGATGTCCATTATTACAGG                         CACTTGCAATGTGGGGATTTTATAGTGAAGGAACCCATGGTTATTGGCCAT
genomic: TGGGAATCAAAGCTGTAGGTATTTGCGGCAGCGATGTCCATTATTACAGGgtaggattat ... ggcggtgcagCACTTGCAATGTGGGGATTTTATAGTGAAGGAACCCATGGTTATTGGCCAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgttacgaatcaatgacattttccgacacggttcaacatgctggcggcggtgcagCACTTGCAATGTGGGGATTTTATAGTGAAGGAACCCATGGTTATTGGCCATGAATGTGCTGGTACCATTGAGGAAGTTGGGAAGGCTGTGAAGAATGTTG
       aatcaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgatttctaatggtttaatgaacccctcagctagtagcttgatatcgttacgaatcaatgacattttccgacacggttcaacatgctggcggcggtgcagCACTTGCAATGTGGGGATTTTATAGTGAAGGAACCCATGGTTATTGGCCATGAATGTGCTGGTACCATTGAGGAAGTTGGGAAGGCTGTGAAGAATGTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA