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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttttgtagggcgacaacaaaggttttctggtgtggaagaagaaaatggcaacttctcctgaaattctgtgctgtttttgctcggttccgtttttaaacagACATTTTGGAGATGGTCGCAAATATGAAGTTCGATGAAGAGCCAAACCACGGCAAGCTCGTTCTACTCTTTGATTCCATCTTGAGTCCTAATCCTACTGT

Basic information

species Physcomitrella patens
transcript PP1S176_7V6.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S176_7V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: GLYMA08G21570.1 (Glycine max), 3'ss of exon 9
-----------------------------------------------------------ttttgtagggcgacaacaaaggttttctggtgtggaagaagaaaatggcaacttctcctgaaattctgtgctgtttttgctcggttccgtttttaaacagACATTTTGGAGATGGTCGCAAATATGAAGTTCGATGAAGAGCCAAACCACGGCAAGCTCGTTCTACTCTTTGATTCCATCTTGAGTCCTAATCCTACTGT
                                                           |||| ||||| || |||||||| |||||||| || ||||||||||||| ||| |||||||| |  || ||||| ||| |  |  | ||  |||||| |||   | ||| |                                                                                          
gttggacattaaaataactcttttattcttacgttcagaaggttggtctctaacattatttttttagGGAGAAAACAAAGGATTTCTGGTTTGCAAGAAGAAAATGGGAACATCTCCTGAGACCCTATGCTGCTTTAGTCCCCTCCC--TTTTAAGCAGTT-TGTTGAAC-----------------------------------------------------------------------------------------

upper sequence: PP1S176_7V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: Vv11s0016g04060.t01 (Vitis vinifera), 3'ss of exon 9
-----ttttgtagggcgacaacaaaggttttctggtgtggaagaagaaaatggcaacttctcctgaaattctgtgctgtttttgctcggttccgtttttaaacagACATTTTGGAGATGGTCGCAAATATGAAGTTCG----ATGAAGAGCCAAACCACGGCAAGCTCGTTCTACTCTTTGATTCCATCTTGAGTCCTA-ATCCTACTGT--
     ||   |  ||   |||| |    || ||  | || ||    |     | ||| |||       || | |    ||||   | |  |   |       || ||  |  || ||   |     || |   ||| |    | |||||    |||  |  |      | | |  |  ||   |||  |     | | | |   |  ||   
gtaagttcattcaggattcaaccattcattgctatt-tgcaacttcactgctgtaacctcttagtttcttatttataattttcatt-gccttgatgaactctcaaactgtagGGGGAGAATAAAGGATTTCTTGTTTGTAAGAAGAAGATGGCAACTTCTCCTGAGATGCTTTGTTGCTTATGTCCTCCCCCTTTTCAACAGTTTCTTGAGA


















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggcaacttctcctgaaattctgtgctgtttttgctcggttccgtttttaaacagACATTTTGGAGATGGTCGCAAATATGAAGTTCGATGAAGAGCCAAACCACGGCAAGCTCGTTCTACTCTTTGATTCCATCTTGAGTCCTAATCCTACTGT
                                       ttccgttttt  CT-rich tract
                                            tttttaaaca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttttgtagggcgacaacaaaggttttctggtgtggaagaagaaaatggcaacttctcctgaaattctgtgctgtttttgctcggttccgtttttaaacagACATTTTGGAGATGGTCGCAAATATGAAGTTCGATGAAGAGCCAAACCACGGCAAGCTCGTTCTACTCTTTGATTCCATCTTGAGTCCTAATCCTACTGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT