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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tccgactttgtgtcttagtatagtaaaccatctaattctgtgtaggtcgactgagatcattctttattaaatggaaagtgtttaatatcttgtgctttagGATTCAGATGCTTCAATTCAGAAAAGGGCACTTGAGCTTATTTACCTTCTAGTGAATGAGAATAACGTGAAGCCACTAGCAAAGGAGCTTATAGAATATT

Basic information

species Arabidopsis thaliana
transcript AT1G60070.2
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G60070.2 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA02G03800.1 (Glycine max), 3'ss of exon 6
tccgactttgtgtcttagtatagtaaaccatctaattctgtgtaggtcgactgagatca-ttctttatta-aatggaaagtgtttaatatcttgt-----gctttagGATTCAGATGCTTCAATTCAGAAAAGGGCACTTGAGCTTATTTACCTTCTAGTGAATGAGAATAACGTGAAGCCACTAGCAAAGGAGCTTATAGAATATT
                 ||||  | |    |||       |  ||   |||  |||| |  ||| | ||| |||  || | ||| |  || |         ||| |||||||||||||||| |||| |||||| || ||||| ||| ||||  || | |||||||||| ||| ||||||||  | ||||| ||||||||||| ||| 
-----------------gtatt-tgatttgtcttccctcattcag--tgacaaagatgagctctgttttacaatccaaggggttgatcatttgactcttaacttcagGATTCAGATGCTTCGATTCGGAAAAGAGCCCTTGAACTTGTTTATGTTTTGGTGAATGAGACTAATGTGAAGCCCTTGGCAAAAGAGCTTATAGATTATC

upper sequence: AT1G60070.2 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA01G03890.1 (Glycine max), 3'ss of exon 7
tccgactttgtgtcttagtatagtaaaccatctaattctgtgtaggtcgactgagatcattctttattaaatggaaagtgtttaatatcttgtg-ctttagGATTCAGATGCTTCAATTCAGAAAAGGGCACTTGAGCTTATTTACCTTCTAGTGAATGAGAATAACGTGAAGCCACTAGCAAAGGAGCTTATAGAATATT
           || || |  | ||   || ||  |||| ||| |    ||      |  || |  | |  | |||     |    |  ||  |  ||| |||||||||||||||| ||||||||||| || ||||| ||| ||||  || | |||||||| | ||| ||||||||  | ||||| ||||||||||| ||| 
-----------gtatttgatttgtcttccctc--attcagtg-acaaagatgagctttgttttacaatccaaggagttgatcatttgactcttaacttcagGATTCAGATGCTTCGATTCAGAAAAGAGCCCTTGAACTTGTTTATGTTTTGGTGAATGAAACTAATGTGAAGCCCTTGGCAAAAGAGCTTATAGATTATC

upper sequence: AT1G60070.2 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA08G39930.1 (Glycine max), 3'ss of exon 7
tccgactttgtgtcttagtatagtaaac---catctaattctgtgta---ggtcgactgagatcattctttattaaatggaaagtgtttaat---atcttgtgctttagGATTCAGATGCTTCAATTCAGAAAAGGGCACTTGAGCTTATTTACCTTCTAGTGAATGAGAATAACGTGAAGCCACTAGCAAAGGAGCTTATAGAATATT
           || ||| |  || |  |   | ||  |||   | ||   |   |||| || |  |  ||||  |  || |||||   | |    |  || || |||||||||| ||||||||||||| |||||| || ||||| ||| |||   |||| |||||||| | ||| |||||| |  || |||| |||||  |||||||| 
-----------gtattaattgagcagtctttcttcctatttcttataatggagagactcagctt-tgttttacaatgtgaaaagttagtgacttaactttttggtttagGATTCTGATGCTTCAATTCGGAAAAGAGCTCTTGAACTTGTTTGTATTCTGGTGAATGAAACTAATGTGAAGGCCTTAACAAAAGAGCTAGTAGAATATC

upper sequence: AT1G60070.2 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv01s0026g00310.t01 (Vitis vinifera), 3'ss of exon 7
tccgactttgtgtcttagtatagtaa-accatctaattctgtgtaggtcgactgagatcattctt-tat-taaatggaaagtgtttaat----atcttgtgctttagGATTCAGATGCTTCAATTCAGAAAAGGGCACTTGAGCTTATTTACCTTCTAGTGAATGAGAATAACGTGAAGCCACTAGCAAAGGAGCTTATAGAATATT
       | ||||  |  | ||||      |||  ||| |||  |  | | |  ||    ||||  |||  | || |||||  | |||     || || |  || ||||||||||||||||||||| ||||||||| ||||| ||||||||  ||||||||||||| |  || ||||||||  | ||||| ||||| || || ||| 
-------tcgtgtagttttttagttgtgttatcggattgtgtcaaaattgccacagccacttctaatatacatatagaaagcttgtaactttaatattctctttcagGATTCAGATGCTTCAATTCGGAAAAGGGCCCTTGAACTTATTTATGTTCTAGTGAATGACAGCAATGTGAAGCCTTTGGCAAAAGAGCTAATTGATTATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtcgactgagatcattctttattaaatggaaagtgtttaatatcttgtgctttagGATTCAGATGCTTCAATTCAGAAAAGGGCACTTGAGCTTATTTACCTTCTAGTGAATGAGAATAACGTGAAGCCACTAGCAAAGGAGCTTATAGAATATT
                                  gtttaat  putative branch site (score: 4)
          atcattctttattaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tccgactttgtgtcttagtatagtaaaccatctaattctgtgtaggtcgactgagatcattctttattaaatggaaagtgtttaatatcttgtgctttagGATTCAGATGCTTCAATTCAGAAAAGGGCACTTGAGCTTATTTACCTTCTAGTGAATGAGAATAACGTGAAGCCACTAGCAAAGGAGCTTATAGAATATT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT