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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aacacttagtaaatatcataaactccttagacctctaaacccattgctcgaattacatttcttaatgcaaagttcctcatattcaattttgatgttacagGTTGTCCAGCGGTTCCAAGAGTTATTTGCTCAAACAAAGTACAAGGAGGCTGCTGAGCTTGCTGCTGAATCTCCTCAGGGCATTCTACGGACACCTGATA

Basic information

species Arabidopsis thaliana
transcript AT3G11130.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: LOC_Os12g01390.1 (Oryza sativa), 3'ss of exon 10
-------------------------------aacact-tagtaaatatcataaactccttagacctctaaacccattgctcgaattacatttcttaatgcaaagttc---ctcatattcaat-tttgatgttacagGTTGTCCAGCGGTTCCAAGAGTTATTTGCTCAAACAAAGTACAAGGAGGCTGCTGAGCTTGCTGCTGAATCTCCTCAGGGCATTCTACGGACACCTGATA
                                |  || |   || |   ||  || | |   |||| |       ||    |    | || | ||  |||||  |       |   || ||| ||| || || |||||||| ||  |||| ||||| || ||||| |||||||| |||||||| || |||||| | ||||| ||||||||||| ||  |||| || || |||||||
gtaagttccattacttctatgcttttgttgtgatgctgttacaattgcaatttacgcttgttacctatgctggttttatcagtggcatatattttcctgcaagatatgatagcgagtttaatgttttatattgcagGTTGTGCAAAGGTTTCAAGAATTGTTTGCACAAACAAAATACAAGGAAGCAGCTGAGTTGGCTGCAGAATCTCCTCAAGGTCTTCTCCGAACTCCTGATA

upper sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 10
-------------------------------aacact-tagtaaatatcataaactccttagacctctaaacccattgctcgaattacatttcttaatgcaaagttc---ctcatattcaat-tttgatgttacagGTTGTCCAGCGGTTCCAAGAGTTATTTGCTCAAACAAAGTACAAGGAGGCTGCTGAGCTTGCTGCTGAATCTCCTCAGGGCATTCTACGGACACCTGATA
                                |  || |   ||     ||  || | |   |||| |       ||    |    | || | ||  |||||  |       |   || |||  || || || |||||||| ||  |||| ||||| || ||||| |||||||| |||||||| || |||||| | ||||| ||||||||||| ||  |||| || || ||||| |
gtaagttccattacttctatgcttttgttgtgatgctgttacaatcgcaatttacgcttgttacctatgctggttttatcagtggcatatattttcctgcaagatatgatagcgagtttaatgctttatattgcagGTTGTGCAAAGGTTTCAAGAATTGTTTGCACAAACAAAATACAAGGAAGCAGCTGAGTTGGCTGCAGAATCTCCTCAAGGTCTTCTCCGAACTCCTGAGA

upper sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA02G42560.1 (Glycine max), 3'ss of exon 10
aacacttagtaaatatcataaactcctt---agacctctaaacccattgctcgaattacatttcttaatgcaaagttcctcatattca-attt--tgatgttacagGTTGTCCAGCGGTTCCAAGAGTTATTTGCTCAAACAAAGTACAAGGAGGCTGCTGAGCTTGCTGCTGAATCTCCTCAGGGCATTCTACGGACACCTGATA
      |  |   |||  | | || |||   | |        |   ||  |  | ||    |||||      | |    | || | || ||||  |||  |||||||| ||  | || || || ||  | ||||| |||||||| || ||||| ||||| |||||||| ||||||||||| || || || || || || ||||| |
------tgattgctatgtttagcttcttaagaaatgctctctcttgttattgtatttttggttcttttattcatgaatatgatgtccatatttgttgacattacagGTAGTGGAACGTTTTCATGAACTGTTTGCCCAAACAAAATATAAGGAAGCTGCAGAGCTTGCAGCTGAATCTCCACAAGGAATCCTTCGAACTCCTGACA

upper sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: Vv13s0067g01290.t01 (Vitis vinifera), 3'ss of exon 10
aacacttagtaaatatcataaactcct--tagacctctaaacccattgctcgaattacatttctta-atgcaaagttcctcatattcaatt-ttgatgttacagGTTGTCCAGCGGTTCCAAGAGTTATTTGCTCAAACAAAGTACAAGGAGGCTGCTGAGCTTGCTGCTGAATCTCCTCAGGGCATTCTACGGACACCTGATA
       |  |  | ||||| | || |  | ||  | || ||   |   ||    |  | |  ||  ||     |   || |||  |     ||  | |  |||||||||||||| |||||||| || |||||||| |||||||| |||||||||||||||||||||||||||||||| || || ||||| || ||||| || |
----agaatcatgtttcatatagtcatggtggaaatttatactgttaaatcattatgtagtctttgcatatttggaatctgatagcctgccatttctatatcagGTTGTCCAGCGTTTCCAAGAATTGTTTGCTCAGACAAAGTATAAGGAGGCTGCTGAGCTTGCTGCTGAATCTCCACAAGGAATTCTCCGTACACCGGACA

upper sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: PP1S7_102V6.1 (Physcomitrella patens), 3'ss of exon 10
aacacttagtaaatatcataaactccttagacctctaaacccattgctcgaattacatttcttaatgcaaagttcctcatattc----aattttgatgtta----cagGTTGTCCAGCGGTTCCAAGAGTTATTTGCTCAAACAAAGTACAAGGAGGCTGCTGAGCTTGCTGCTGAATCTCCTCAGGGCATTCTACGGACACCTGATA
     | |     | |  |||  | | |||   | |||     |      ||      ||  | |  ||      ||||| ||     ||   | |  ||     |||||||| || || || ||||| || ||  | || |  |||||||||||||| || || |||||||| || || |||||||||||||| || || |||||||
----gtcatatcgtgttgtaatttacctag---tataagtg-gtgagcgaaaaagtccttactgacacacgagatctcatttttcggtaacggttacattggaatcagGTTGTACAACGTTTTCAAGAATTGTTCTCCCAGATGAAGTACAAGGAGGCAGCAGATCTTGCTGCAGAGTCGCCTCAGGGCATTCTTCGAACTCCTGATA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctcgaattacatttcttaatgcaaagttcctcatattcaattttgatgttacagGTTGTCCAGCGGTTCCAAGAGTTATTTGCTCAAACAAAGTACAAGGAGGCTGCTGAGCTTGCTGCTGAATCTCCTCAGGGCATTCTACGGACACCTGATA
     aattacatttcttaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aacacttagtaaatatcataaactccttagacctctaaacccattgctcgaattacatttcttaatgcaaagttcctcatattcaattttgatgttacagGTTGTCCAGCGGTTCCAAGAGTTATTTGCTCAAACAAAGTACAAGGAGGCTGCTGAGCTTGCTGCTGAATCTCCTCAGGGCATTCTACGGACACCTGATA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - - - cataaac
- - - - - - - - - - - - - - - - - ctaaacc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - atgcaaa