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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttgaaaagagttgccaccttttacttctctgtgctttccctactcaccttcctttcttagaccttttagtgcactctcaacacagGTTTTGGAGATCAATTTGGTAACCTTTCCTAATGTGGCTGATGCAATCTTAGCAAATGGGATGTTCAGCCATTATGACCGGCCTCGTGTTGCTCAGCTTT

Basic information

species Arabidopsis thaliana
transcript AT3G11130.1
intron # 16
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 16
lower sequence: LOC_Os12g01390.1 (Oryza sativa), 3'ss of exon 16
--------------------------------gttgaaaagagttgccacctt--ttacttctctgtgctttccctactcaccttcctttcttagaccttttagtgcactctcaacacagGTTTTGGAGATCAATTTGGTAACCTTTCCTAATGTGGCTGATGCAATCTTAGCAAATGGGATGTTCAGCCATTATGACCGGCCTCGTGTTGCTCAGCTTT
                                 |      |  ||||||  ||  | | |    | |  |  |  ||  |   |   || || ||   |||  ||      | |    |||||||||||||||| ||||| || |  || ||||| |||||||| ||| | || ||||| |||||||| |||||||| || |||||||||||||||||||
gttagcagttttttcccaataagttcggccttttacctttgcattgccatgttgctcagtggcttcttttacctttatactgttgtgttgctcagtagtttctgtttgaattgattgtagGTTTTGGAGATCAACTTGGTCACTTACCCAAATGTTGCTGATGCCATCCTTGCTAATGGTATGTTCAGTCATTATGATCGCCCTCGTGTTGCTCAGCTTT

upper sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 16
-------------------------------------gttgaaaagagttgccaccttttacttctctgtgctttcc--ctact-caccttcctttcttagaccttttagtgcactctcaacacagGTTTTGGAGATCAATTTGGTAACCTTTCCTAATGTGGCTGATGCAATCTTAGCAAATGGGATGTTCAGCCATTATGACCGGCCTCGTGTTGCTCAGCTTT
                                      ||| |  |   ||   |    |   |   | | | ||    ||  |     |   || || ||   |||  ||      |      |||||||||||||||| ||||| || |  || ||||| |||||||| ||| | || ||||| |||||||| |||||||| || |||||||||||||||||||
gttagcagttttttcccaataagttaggccttttgcctttgcattgccatgttgctcagtggcttcttttacctttatactgttgtgtttgtgttgctcagtagtttctgtttgaattggttgtagGTTTTGGAGATCAACTTGGTCACTTACCCAAATGTTGCTGATGCCATCCTTGCTAATGGTATGTTCAGTCATTATGATCGCCCTCGTGTTGCTCAGCTTT

upper sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 14
gttgaaaagagttgccaccttttacttc-----tctgtgctttccctactcac--cttcctttcttag-accttttagtgcactctcaacacagGTTTTGGAGATCAATTTGGTAACCTTTCCTAATGTGGCTGATGCAATCTTAGCAAATGGGATGTTCAGCCATTATGACCGGCCTCGTGTTGCTCAGCTTT
|||   |   | |    | ||| | |       | ||   |   ||| |   |  |||   | || |    ||| |  |    |        |||||||||||||||| || || || |  || ||||| || ||||| ||  | || ||||| |||||||| ||||||||||| |||||| |||||||||| |
gttagtatttgattgttcatttcaatatgaacatttgccttagacctgcatgctgcttaactactcaatgtcttctgcttggattgtcttgtagGTTTTGGAGATCAACTTAGTGACTTACCCAAATGTTGCAGATGCCATTCTTGCGAATGGTATGTTCAGTCATTATGACCGTCCTCGTATTGCTCAGCTCT

upper sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: GLYMA02G42560.1 (Glycine max), 3'ss of exon 16
gttgaaaagagttgccacctttta-cttctctgtgctttccctactcaccttcctttcttagaccttttagtgcactctcaaca------cagGTTTTGGAGATCAATTTGGTAACCTTTCCTAATGTGGCTGATGCAATCTTAGCAAATGGGATGTTCAGCCATTATGACCGGCCTCGTGTTGCTCAGCTTT
   |      |        | | | |   | || || |||    || |   | ||||||| || || |||      | | ||        ||||| |||||||| ||| |||| || || || ||||| ||||||||||| || || ||||| |||||||||||||||||||| |||||| |||| |||||||
---gtgtgtggcctttgtttctcatccgttatgggcattctactctgaaaattctttctttgaactgttacgatcttgtgaattgctgttcagGTGTTGGAGATAAATCTGGTGACTTTCCCCAATGTTGCTGATGCAATATTGGCTAATGGCATGTTCAGCCATTATGACCGTCCTCGTATTGCCCAGCTTT

upper sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: GLYMA14G06340.2 (Glycine max), 3'ss of exon 16
gttgaaaagagttgccacctttta-cttctctgtgctttccctactcaccttcctttcttagaccttttagtgcactctcaaca------cagGTTTTGGAGATCAATTTGGTAACCTTTCCTAATGTGGCTGATGCAATCTTAGCAAATGGGATGTTCAGCCATTATGACCGGCCTCGTGTTGCTCAGCTTT
          |        | | | ||  | || || ||     || |   | ||||||| ||  | |||      | | ||        ||||| |||||||| ||| |||| || || || ||||| ||||||||||| || || ||||| |||||||||||||||||||| |||||| |||| || ||||
-----gtgtggcctttgtttctcatctgttatgggcattttactctgaaaattctttctttgaagtgttacgatgttgtgaatcactgttcagGTGTTGGAGATAAATCTGGTGACTTTCCCCAATGTTGCTGATGCAATATTGGCTAATGGCATGTTCAGCCATTATGACCGTCCTCGTATTGCCCAACTTT

upper sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: Vv13s0067g01290.t01 (Vitis vinifera), 3'ss of exon 16
gttgaaaagagttgccaccttttacttctctgtgctttccctactcaccttcctttcttagaccttttagtgcactct-caacacagGTTTTGGAGATCAATTTGGTAACCTTTCCTAATGTGGCTGATGCAATCTTAGCAAATGGGATGTTCAGCCATTATGACCGGCCTCGTGTTGCTCAGCTTT
         | ||    ||| | |      | |  |||| ||| ||| | |  ||| ||        ||        |     ||||||  |||| |||||| ||||||| |  || ||||| || ||||| || ||||||||||||||||| ||||||||||| || || ||  |||| |||||||
------gttacttttttcctctgatgcaattttattttcactattcatcatttttttttcagttccataacatttcttgttttacagGTCCTGGAAATCAATCTGGTAACTTACCCAAATGTTGCAGATGCTATATTAGCAAATGGGATGTTTAGCCATTATGATCGTCCACGGATTGCCCAGCTTT

upper sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: PP1S452_30V6.1 (Physcomitrella patens), 3'ss of exon 17
--------------------------------------------------------------------------------------------------------gttgaaaagagttgccaccttttacttctctgtgctttccctactcaccttcctttcttagaccttttagtgcactctcaa-cacagGTTTTGGAGATCAATTTGGTAACCTTTCCTAATGTGGCTGATGCAATCTTAGCAAATGGGATGTTCAGCCATTATGACCGGCCTCGTGTTGCTCAGCTTT
                                                                                                         |  |   |||||   |  |   | |    | |    | |  | | ||||   ||||| | |  ||  | ||   || ||  | |||||  |||||||||||||||| || ||||| |||||||||||||||||  | || ||||| ||||||  ||||||||| || |||||  ||||||| || |
gtgtgtgttggcttgctgcaagctacgactttgtagtactatcaggacattggaatcagttcagtatttgtcatgctagttatctccattactcctactaatgaatctaggggagtttttatgtac-attatcttttaaaattcgaaatgacctaagtttctgatat-ttagattgatgtcacattctcagGTACTGGAGATCAATTTGGTCACATTTCCCAATGTGGCTGATGCAATTCTGGCGAATGGCATGTTCTCCCATTATGATCGTCCTCGCATTGCTCAACTCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgctttccctactcaccttcctttcttagaccttttagtgcactctcaacacagGTTTTGGAGATCAATTTGGTAACCTTTCCTAATGTGGCTGATGCAATCTTAGCAAATGGGATGTTCAGCCATTATGACCGGCCTCGTGTTGCTCAGCTTT
          tactcac  putative branch site (score: 1)
                                         cactctc  putative PPT
                      tttctta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttgaaaagagttgccaccttttacttctctgtgctttccctactcaccttcctttcttagaccttttagtgcactctcaacacagGTTTTGGAGATCAATTTGGTAACCTTTCCTAATGTGGCTGATGCAATCTTAGCAAATGGGATGTTCAGCCATTATGACCGGCCTCGTGTTGCTCAGCTTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT