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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCCCTTTGAGGAAGATGACAAGGATGCCAGCATATGGTTCTTGGACCACAACTATCATGAGACTATGTTCGACATGTTCAAGAGAATTAACGgtattcttactacttctttcctccaactgattaacttctttgtagttgtttggatgaagaacgcagctgcaagtttagcggtgtgttttaaccaatattttctaattttgactggtatgtctcgtaacattttgagtatggcagatttgttaaatctgtttgtggtaaaactgactgttgtaagacgtgtttgctcag

Basic information

species Physcomitrella patens
transcript PP1S197_115V6.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S197_115V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: GRMZM2G368908_T02 (Zea mays), 5'ss of exon 2
TGCCCTTTGAGGAAGATGACAAGGATGCCAGCATATGGTTCTTGGACCACAACTATCATGAGACTATGTTCGACATGTTCAAGAGAATTAACGgtattct-tactac--ttctttcctccaactgattaacttctttgtagttgtttggatgaagaacgcagctgcaagt--ttagcggtgtgttttaaccaatattttctaattttgactggtatgtctcgtaacattttgagtatggcagatttgttaaatctgtttgtggtaaaactgactgttgtaagacgtgtttgctcag
|||| |||||||| |||||||||||| | || || |||||| | |||||||| || |||||  | ||||||  |||||||||||| ||||||||||| || ||  |   ||||     ||   ||       ||| ||   | | ||   |                ||   || | ||||                                                                                                                   
TGCCGTTTGAGGAGGATGACAAGGATCCTAGGATCTGGTTCCTTGACCACAATTACCATGAATCGATGTTCTCCATGTTCAAGAGGATTAACGgtatgctgtatcaaaattctcggtgcctgttgggcctgctctgtgctatggattctgttgtcctgatgagcatgagctgtttgtggtgcag----------------------------------------------------------------------------------------------------------------

upper sequence: PP1S197_115V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: GRMZM2G061745_T03 (Zea mays), 5'ss of exon 2
TGCCCTTTGAGGAAGATGACAAGGATGCCAGCATATGGTTCTTGGACCACAACTATCATGAGACTATGTTCGACATGTTCAAGAGAATTAACGgtattct-tacta----cttc----tttcctccaactgattaacttctttgtagttgtttggatgaagaacgcag-ctgcaagtttagcggtgtgttttaaccaatattttctaattttgactggtatgtctcgtaacattttgagtatggcagatttgttaaatctgtttgtggtaaaactgactgttgtaagacgtgtttgctcag
|||| |||||||| |||||||||||| | || || |||||| | |||||||| || || ||| | ||||||  |||||||||||| ||||| ||||| || ||  |    | ||    |||  |    |||||        |||    | ||    ||| || | | | |||   ||   || |                                                                                                                     
TGCCGTTTGAGGAGGATGACAAGGATCCTAGGATCTGGTTCCTTGACCACAATTACCACGAGTCAATGTTCTCCATGTTCAAGAGGATTAATGgtatgctctatcaaaatcctcaaattttgttgggcctgatccgtgctattgcttcttttgtcctgatgagcacgggctgtttgtggtgcag---------------------------------------------------------------------------------------------------------------------

upper sequence: PP1S197_115V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: GLYMA11G34980.1 (Glycine max), 5'ss of exon 2
TGCCCTTTGAGGAAGATGACAAGGATGCCAGCATATGGTTCTTGGACCACAACTATCATGAGACTATGTTCGACATGTTCAAGAGAATTAACGgtattcttactacttctttcctccaactgattaacttctttgtagttgtttggatgaagaacgcagctgcaagtttagcggtgtgttttaaccaatattttctaattttgactggtatgtctcgtaacattttgagtatggcagatttgttaaatctgtttgtggtaaaactgactgttgtaagacgtgtttgctcag
|||||||||| ||||||||||||||| | ||||| |||||  | |||||||| || |||||  |||||||   |||||| || ||||| || ||||    ||  |    ||| |              |  | | |   |||||  ||  |  | ||     |   | ||   |    ||||      | |||| |  |||  |                                                                                       
TGCCCTTTGAAGAAGATGACAAGGATCCTAGCATCTGGTTTCTTGACCACAATTACCATGAATCTATGTTTTCCATGTTTAAAAGAATAAATGgtacgagtaggaaaatttttcctt----------ttcttgtatgtctgtttcaattgaatatgc-----ctgatctaattgaacatttt------ttttttttggtttacag--------------------------------------------------------------------------------------

upper sequence: PP1S197_115V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: AT5G05780.1 (Arabidopsis thaliana), 5'ss of exon 2
TGCCCTTTGAGGAAGATGACAAGGATGCCAGCATATGGTTCTTGGACCACAACTATCATGAGACTATGTTCGACATGTTCAAGAGAATTAACGgtat--tcttactacttctttcctccaactgattaacttctttgtagttgtttggatgaagaacgc-agctgcaagtttagcggtgtgttttaaccaatattttctaattttgactggtatgtctcgtaacattttgagtatggcagatttgttaaatctgtttgtggtaaaactgactgttgtaagacgtgtttgctcag
||||||||||||| |||||||| ||  | ||||| |||||  | || |||||||| |||||| | |||||| ||||||||||||||||||| |||||  ||| |  |      | ||   |||| |||    | ||||||   |          ||| | | || |  | ||  | |                                                                                                                     
TGCCCTTTGAGGAGGATGACAAAGACCCAAGCATCTGGTTTCTTGATCACAACTACCATGAGTCAATGTTCCACATGTTCAAGAGAATTAATGgtattttctcaggaaactgatgcttatactgttta-tgacattgtagaaatccatgcttttaacactacctacttgcttttcag---------------------------------------------------------------------------------------------------------------------

upper sequence: PP1S197_115V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: AT3G11270.2 (Arabidopsis thaliana), 5'ss of exon 2
TGCCCTTTGAGGAAGATGACAAGGATGCCAGCATATGGTTCTTGGACCACAACTATCATGAGACTATGTTCGACATGTTCAAGAGAATTAACGgtattcttactacttctttcctccaactgattaacttctttgtagttgtttggatgaagaacgcagctgcaagtttagcggtgtgttttaaccaatattttctaattttgactggtatgtctcgtaacattttgagtatggcagatttgttaaatctgtttgtggtaaaactgactgttgtaagacgtgtttgctcag
|||| |||||||| |||||||| ||  | |||||||||||  | || |||||||| || ||| | |||||  ||||||||||||||||||| ||||||  |               |     ||  | | |||   |||    |  |||  ||| ||  ||     |||  | |    |||| |    |  ||||                                                                                                
TGCCTTTTGAGGAGGATGACAAAGACACAAGCATATGGTTTCTTGATCACAACTACCACGAGTCGATGTTTCACATGTTCAAGAGAATTAATGgtattgct---------------cgggaaatataatgcttaagagta---tatatgtggaaagcctcttt---tttgactg---attttcatatttgctttcag----------------------------------------------------------------------------------------------

upper sequence: PP1S197_115V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: Vv08s0007g01980.t01 (Vitis vinifera), 5'ss of exon 2
TGCCCTTTGAGGAAGATGACAAGGATGCCAGCATATGGTTCTTGGACCACAACTATCATGAGACTATGTTCGACATGTTCAAGAGAATTAACGgtattcttactacttctttcctccaactgattaacttctttgtagttgtttggatgaagaacgcagctgcaagtttagcggtgtgttttaaccaatattttctaattttgactggtatgtctcgtaacattttgagtatggcagatttgttaaatctgtttgtggtaaaactgactgttgtaagacgtgtttgctcag
|||||||||| ||||||||||||||  | |||||||||||  | |||||||||||||||||  | |||||   ||||||||||||||| || |||||| ||        |||| |  || |||| |  |      ||    |||    |  ||   |   ||  | ||||  | | ||||| |                                                                                                            
TGCCCTTTGAAGAAGATGACAAGGACCCAAGCATATGGTTTCTTGACCACAACTATCATGAATCAATGTTTTCCATGTTCAAGAGAATAAATGgtattatt--------tttcgt--aaatgatgaggtctcgcttacaatttttatgggcgatttcttatgggaattta-tgatttgtttcag-----------------------------------------------------------------------------------------------------------

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|162212343|gb|FC388071.1|FC388071
EST:     GGACCACAACTATCATGAGACTATGTTCGACATGTTCAAGAGAATTAACG                         CAAAAGAGCATGTGGTGGGGTGGTACAGCACTGGGCCTAAGCTTCGAGAAA
genomic: GGACCACAACTATCATGAGACTATGTTCGACATGTTCAAGAGAATTAACGgtattcttac ... gtttgctcagCAAAAGAGCATGTGGTGGGGTGGTACAGCACTGGGCCTAAGCTTCGAGAAA
EST: gi|100442139|gb|BY963032.1|BY963032
EST:     GGACCACAACTATCATGAGACTATGTTCGACATGTTCAAGAGAATTAGCG                         CAAAAGAGCATGTGGTGGGGTGGTACAGCACTGGGCCTAAGTTTCGAGAAA
genomic: GGACCACAACTATCATGAGACTATGTTCGACATGTTCAAGAGAATTAACGgtattcttac ... gtttgctcagCAAAAGAGCATGTGGTGGGGTGGTACAGCACTGGGCCTAAGCTTCGAGAAA
EST: gi|18346971|gb|BJ179017.1|BJ179017
EST:     GGACCACAACTATCATGAGACTATGTTCGACATGTTCAAGAGAATTAACG                         CAAAAGAGCATGTGGTGGGGTGGTACAGCACTGG
genomic: GGACCACAACTATCATGAGACTATGTTCGACATGTTCAAGAGAATTAACGgtattcttac ... gtttgctcagCAAAAGAGCATGTGGTGGGGTGGTACAGCACTGG
EST: gi|208368978|gb|DC955063.1|DC955063
EST:     GGACCACAACTATCATGAGACTATGTTCGACATGTTCAAGAGAATTAACG                         CAAAAGAGCATGTGGTGGGGTGGTACAGCACTGGGCCTAAGCTTCGAGAAA
genomic: GGACCACAACTATCATGAGACTATGTTCGACATGTTCAAGAGAATTAACGgtattcttac ... gtttgctcagCAAAAGAGCATGTGGTGGGGTGGTACAGCACTGGGCCTAAGCTTCGAGAAA
EST: gi|208391154|gb|DC942066.1|DC942066
EST:     GGACCACAACTATCATGAGACTATGTTCGACATGTTCAAGAGAATTAACG                         CAAAAGAGCATGTGGTGGGGTGGTACAGCACTGGGCCTAAGCTTCGAGAAA
genomic: GGACCACAACTATCATGAGACTATGTTCGACATGTTCAAGAGAATTAACGgtattcttac ... gtttgctcagCAAAAGAGCATGTGGTGGGGTGGTACAGCACTGGGCCTAAGCTTCGAGAAA
EST: gi|100398742|gb|BY990493.1|BY990493
EST:     GGACCACAACTATCATGAGACTATGTTCGACATGTTCAAGAGAATTAACG                         CAAAAGAGCATGTGGTGGGGTGGTACAGCACTGGGCCTAAGCTTCGAGAAA
genomic: GGACCACAACTATCATGAGACTATGTTCGACATGTTCAAGAGAATTAACGgtattcttac ... gtttgctcagCAAAAGAGCATGTGGTGGGGTGGTACAGCACTGGGCCTAAGCTTCGAGAAA
EST: gi|100426796|gb|BY977367.1|BY977367
EST:     GGACCACAACTATCATGAGACTATGTTCGACATGTTCAAGAGAATTAACG                         CAAAAGAGCATGTGGTGGGGTGGTACAGCACTGGGCCTAAGCTTCGAGAAA
genomic: GGACCACAACTATCATGAGACTATGTTCGACATGTTCAAGAGAATTAACGgtattcttac ... gtttgctcagCAAAAGAGCATGTGGTGGGGTGGTACAGCACTGGGCCTAAGCTTCGAGAAA
EST: gi|100362914|gb|BY947592.1|BY947592
EST:     GGACCACAACTATCATGAGACTATGTTCGACATGTTCAAGAGAATTAACG                         CANAAGAGCATGTGGTGGGGTGGTACAGCACTGGGCCTAAGCTTCGAGAAA
genomic: GGACCACAACTATCATGAGACTATGTTCGACATGTTCAAGAGAATTAACGgtattcttac ... gtttgctcagCAAAAGAGCATGTGGTGGGGTGGTACAGCACTGGGCCTAAGCTTCGAGAAA
EST: gi|100387742|gb|BY951742.1|BY951742
EST:     GGACCACAACTATCATGAGACTATGTTCGACATGTTCAAGAGAATTAACG                         CANAAGAGCATGTGGTGGGGTGGTACAGCACTGGGCCTAAGCTTCGAGAAA
genomic: GGACCACAACTATCATGAGACTATGTTCGACATGTTCAAGAGAATTAACGgtattcttac ... gtttgctcagCAAAAGAGCATGTGGTGGGGTGGTACAGCACTGGGCCTAAGCTTCGAGAAA
EST: gi|100381366|gb|BY950092.1|BY950092
EST:     GGACCACAACTATCATGAGACTATGTTCGACATGTTCAAGAGAATTAACG                         CAAAAGAGCATGTGGTGGGGTGGTACAGCACTGGGCCTAAGCTTCGAGAAA
genomic: GGACCACAACTATCATGAGACTATGTTCGACATGTTCAAGAGAATTAACGgtattcttac ... gtttgctcagCAAAAGAGCATGTGGTGGGGTGGTACAGCACTGGGCCTAAGCTTCGAGAAA
EST: gi|208361519|gb|DC942804.1|DC942804
EST:     GGACCACAACTATCATGAGACTATGTTCGACATGTTCAAGAGAATTAACG                         CAAAAGAGCATGTGGTGGGGTGGTACAGCACTGGGCCTAAGCTTCGAGAAA
genomic: GGACCACAACTATCATGAGACTATGTTCGACATGTTCAAGAGAATTAACGgtattcttac ... gtttgctcagCAAAAGAGCATGTGGTGGGGTGGTACAGCACTGGGCCTAAGCTTCGAGAAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGCCCTTTGAGGAAGATGACAAGGATGCCAGCATATGGTTCTTGGACCACAACTATCATGAGACTATGTTCGACATGTTCAAGAGAATTAACGgtattcttactacttctttcctccaactgattaacttctttgtagttgtttggatgaagaacgcagctgcaagtttagcggtgtgttttaaccaatattttctaattttgactggtatgtctcgtaacattttgagtatggcagatttgttaaatctgtttgtggtaaaactgactgttgtaagacgtgtttgctcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA