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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtatttgccacatgatcttgatgcatgataatgttttgaacttatagacatttctgatggttctgtttttggctaatgatgtttcttcacttagGTTGGGAGTGCACTTTCAGATCCATATCTTTCATTTGCTGCTGCATTGAATGGTTTAGCTGGGCCACTCCATGGTTTGGCTAATCAG

Basic information

species Arabidopsis thaliana
transcript AT3G60100.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G60100.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: LOC_Os11g33240.2 (Oryza sativa), 3'ss of exon 13
gtatgtatttgccacatgatcttgatg--cat-gataatgttttg-aacttatagacattt-ctgatggttctgtttttggctaatgatgtttcttcacttagGTTGGGAGTGCACTTTCAGATCCATATCTTTCATTTGCTGCTGCATTGAATGGTTTAGCTGGGCCACTCCATGGTTTGGCTAATCAG
  || || ||      |  | ||| ||  ||| |   || | |    ||| ||         || |    |   |      ||  |||| ||   | ||  ||||||| ||||| || |||||||| |||||||| ||||| |||||| |||||||||||||||| ||| | || ||  |||||||||||
-gatatactttttttttacttttgttggccattgcctatctctcatgactcatctctgggcactaacctcttcatcccatacttgtgatattcaattac--agGTTGGAAGTGCTCTGTCAGATCCTTATCTTTCTTTTGCAGCTGCACTGAATGGTTTAGCTGGACCATTGCACGGCCTGGCTAATCAG

upper sequence: AT3G60100.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: LOC_Os02g10070.1 (Oryza sativa), 3'ss of exon 13
--gtatgtatttgccac--atgatcttgatgcatgataatgttttga---acttatagacatttctgatggttctgtttttggctaatgatgtttcttcacttagGTTGGGAGTGCACTTTCAGATCCATATCTTTCATTTGCTGCTGCATTGAATGGTTTAGCTGGGCCACTCCATGGTTTGGCTAATCAG
   | |   |||||     ||   ||   |   |     | |  |||   |  ||| | ||   ||||    |   ||    ||| ||||| ||   | ||  ||||||| ||||| || ||||| || |||||||| ||||| |||||| |||||||||||||||| ||  | || ||  |||||||||||
ttattttcttttgctggcaattgcctctctctctctctctctcatgactcatctatgggca---ctgacctcttcattccgtgctcatgatattcaattac--agGTTGGAAGTGCTCTGTCAGACCCTTATCTTTCTTTTGCAGCTGCACTGAATGGTTTAGCTGGACCGTTGCACGGCCTGGCTAATCAG

upper sequence: AT3G60100.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA15G42300.2 (Glycine max), 3'ss of exon 13
-----------------------------------------------------------------------------gtatgtattt-------gccacatgatcttgatgcatgataatgttt-tgaacttatagacatttctgatggttctgtttttggctaatgatgtttcttcac-ttagGTTGGGAGTGCACTTTCAGATCCATATCTTTCATTTGCTGCTGCATTGAATGGTTTAGCTGGGCCACTCCATGGTTTGGCTAATCAG
                                                                              ||| ||||        | |   || | ||  |  ||    || | | |  |  |||| | || | | ||   | | ||  ||  |  |  ||| | ||| | | ||||||  ||| | || |||||||| |||||| ||||||| ||||| |||||||| ||||||||||| || ||||||||||| ||||||
gtaagttacttcctttaatcaagccctttccattctgtcataatttagaattgtaaaacattaaaaaggattttttaatatatattgtggtaaaggcctgtgtttttattatatatatatatatatatatatatatatatatat-atatatatattaatgtattgtactgtgtgttcccgtcagGTTGCTAGTCCGCTATCAGATCCTTATCTTGCATTTGCAGCTGCTTTGAATGGGTTAGCTGGGCCCCTGCATGGTTTGGCCAATCAG

upper sequence: AT3G60100.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA08G16770.1 (Glycine max), 3'ss of exon 13
--------------gtatgtatttgccacatgatcttgatgcatgataatgttttgaacttatagacatttct-gatggttctgtttttggctaatgatgtttcttcacttagGTTGGGAGTGCACTTTCAGATCCATATCTTTCATTTGCTGCTGCATTGAATGGTTTAGCTGGGCCACTCCATGGTTTGGCTAATCAG
               ||   |    |       |  || |  |||     ||||| |   |||| | || | | |||  || |   | |      |  ||| |   |  | ||||||  ||  | || |||||||| |||||| ||||||| ||||| |||||||| ||||||||||| || |||||| |||| ||||||
gtaagttacttcctttaatcaagctctctccacttgtggtaaatggctgcgtttttattatatatatatatatagattttttttaatgtattgtgtactgtgttcccg-tcagGTTGCTAGCCCGCTATCAGATCCTTATCTTGCATTTGCGGCTGCTTTGAATGGGTTAGCTGGGCCCCTGCATGGTCTGGCCAATCAG

upper sequence: AT3G60100.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: Vv13s0156g00180.t01 (Vitis vinifera), 3'ss of exon 13
--------------------------------------------------------------------------------------------------gtatgtatttgccacatgatcttgatgcatgataatgttttgaacttatagacatttctgatggttctgttt-ttggctaatgatgtttcttcacttagGTTGGGAGTGCACTTTCAGATCCATATCTTTCATTTGCTGCTGCATTGAATGGTTTAGCTGGGCCACTCCATGGTTTGGCTAATCAG
                                                                                                   |     | || | |||  | |   |   ||    |||| | |  |  |   |||         |  | | | ||| || ||  | |  ||  | | ||||||  |||||| |  ||||||| || ||||||||||| |||||||| |||||| ||||||| |||||||||||||||||||| |||
gtaagtgagcctagattcgttctaattagttaaatggaaatgtgtaattttgttgtatttccgagggtaaagtcattattttatcctgaagttatttaatggaattatggctcatattttcagtcagtgtgtttgttattatttagtgatcatgaagaggaatgttctctattgactgatattatg-ctcaattcagGTTGCTAGTGCATTGGCAGATCCTTACCTTTCATTTGCAGCTGCATTAAATGGTCTAGCTGGCCCACTCCATGGTTTGGCTAACCAG

upper sequence: AT3G60100.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: PP1S37_33V6.2 (Physcomitrella patens), 3'ss of exon 12
--------gtatgtatttgccacatgatcttgatgcatgataatgttttgaacttatagacatttctgatggttctgtttttggctaatgatgtttcttcacttagGTTGGGAGTGCACTTTCAGATCCATATCTTTCATTTGCTGCTGCATTGAATGGTTTAGCTGGGCCACTCCATGGTTTGGCTAATCAG
        || |     || |   | || | |||| ||  |  | || |||| ||  |     ||||     ||       |  || |  ||||| | ||    ||||||||||||| || || ||||||||||| || |||||||||| | |||| |||||||| || || || || ||  | || ||||||
atttgagagtgttctgctgtcgtttcatttcgatgaatatt--tattatgaattttaacctggttct----ttttaacacctatctgaaaatgttacctctgccagGTTGGGAGTGCTCTATCGGATCCATATCTGTCTTTTGCTGCTGGAATGAACGGTTTAGCAGGCCCTCTGCACGGGCTTGCAAATCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acttatagacatttctgatggttctgtttttggctaatgatgtttcttcacttagGTTGGGAGTGCACTTTCAGATCCATATCTTTCATTTGCTGCTGCATTGAATGGTTTAGCTGGGCCACTCCATGGTTTGGCTAATCAG
                               ggctaat  putative branch site (score: 3)
                                          tttcttcactt  putative PPT
                        tgttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtatttgccacatgatcttgatgcatgataatgttttgaacttatagacatttctgatggttctgtttttggctaatgatgtttcttcacttagGTTGGGAGTGCACTTTCAGATCCATATCTTTCATTTGCTGCTGCATTGAATGGTTTAGCTGGGCCACTCCATGGTTTGGCTAATCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC