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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttgttataagcattttgagatactttctatcttgtacttaatatcctctcaatcacttgtgaccccaatattaagttgtattttgacttctgtacatatttttctacgctcttagGTTGATGAAGATGATTTTCAGGAGGAGCAGAATTCTGTTGCGCTTCTCATTCATATGTTATATAATGATGACCCAGAAGAGATGTTTAAG

Basic information

species Arabidopsis thaliana
transcript AT2G17790.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G17790.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: LOC_Os03g58700.1 (Oryza sativa), 3'ss of exon 13
gttgttataagcattttgagatact-ttctatcttgtacttaatatcctctcaatcacttgtgaccccaatat---taagttgtattttgacttctgtacatatttttctacgct----cttagGTTGATGAAGATGATTTTCAGGAGGAGCAGAATTCTGTTGCGCTTCTCATTCATATGTTATATAATGATGACCCAGAAGAGATGTTTAAG
  |  ||||  |  ||     |||  || | | | |    | ||||  | ||     ||  | | |  |||      |     |||| |   ||||   ||  |||  ||    |    ||||| ||||||| || |||||| ||||||| ||||||||||| |||| ||| ||||| |||||  | ||||||||||  ||||||||||| |||
-gtaatatacacgcttcattctacaattttctttggcttgttatattgtttctgctgctgttcaactgaatcagcgcacacaatattctattttcttatcaagtttacctgttatattgcttagCTTGATGATGAGGATTTTAAGGAGGAACAGAATTCTGTGGCGCGTCTTATTCACATGTTGCACAATGATGACCATGAAGAGATGTTGAAG

upper sequence: AT2G17790.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GRMZM5G825524_T02 (Zea mays), 3'ss of exon 13
-----------------------------------------gttgttataagcattttg-----agatactttctatcttgtact-taatatcctctcaatcacttgtgaccccaatattaagttgtattt---tgacttctgtacatatttttctacgctcttagGTTGATGAAGATGATTTTCAGGAGGAGCAGAATTCTGTTGCGCTTCTCATTCATATGTTATATAATGATGACCCAGAAGAGATGTTTAAG
                                          ||||| |   |||| ||        | ||  | || |||| |    | |||  | |||    ||   |   || | |    |    |||     || | |    || ||||| ||   | |||| |||||||||| |||||| ||||||| ||||| ||||| || | ||||||||| |||||  | |||||||| || ||||||||||| |||
gtgagttcatacacttcgttagaaaagcgaatttttacttgtttgttgtcttcattctgccgcttagtgctcccaatattgttcagctagatcagcacaacacatttcaatttcattttctcatgaagtttgctcaacctgtaacaatgtttttttattattttagCTTGATGAAGAAGATTTTAAGGAGGAACAGAACTCTGTAGCACGTCTCATTCACATGTTGCACAATGATGAGCCTGAAGAGATGTTGAAG

upper sequence: AT2G17790.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA01G36870.1 (Glycine max), 3'ss of exon 12
----------------------------------------------------------------------gttgttataagcattt----tgagatactttctatcttgtacttaatatcctctcaatcacttgtgaccccaatattaagttgtattttgact-tctgtacatatttttctacgctcttagGTTGATGAAGATGATTTTCAGGAGGAGCAGAATTCTGTTGCGCTTCTCATTCATATGTTATATAATGATGACCCAGAAGAGATGTTTAAG
                                                                       ||  | | | | |||    |   ||  |   ||| || |  | ||| ||   | ||  | |  | |      |  |   || |  ||| | | |   ||  | ||   ||   | ||||| | ||||||||||||||  | ||||||||||||||| |||| |  || ||||  ||| | ||||||||||| |||||||| |||||||||
gtcatttcagtaaccatgactagtctcatttgtcttgtctattttttacaatgcctatttgacttctcccattaatgtcaccttttataatataatgttacatatgttcttataaatgtcagttaaaataatccttatttttgtgatccattctcctttcattatacttattttttcccctttccccttagCTGGATGAAGATGATTTCAAAGAGGAGCAGAATTCTCTTGCCCGCCTAATTCTGATGCTTTATAATGATGATCCAGAAGAAATGTTTAAG

upper sequence: AT2G17790.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA11G08390.1 (Glycine max), 3'ss of exon 12
----------------------------------gttgttataa-gcattttgagatactttctatcttgtacttaatatcctctcaatcacttgtgaccccaatattaagttgtat------tttgactt---ctgtacatatttttctacg-----ctcttagGTTGATGAAGATGATTTTCAGGAGGAGCAGAATTCTGTTGCGCTTCTCATTCATATGTTATATAATGATGACCCAGAAGAGATGTTTAAG
                                   || ||| || || | ||    | ||  |  |  |||   | || | ||   ||      |  |    |||| | | || | |      ||   |||    | ||| ||||||| | |      |  |||| | ||||||||||||||  | ||||||||||| |||||| | | ||| || || ||| | ||||||||||| |||||||| |||||||||
gtcattttagtaccatgactagtctcatttgtctatttttacaatgcctatttgacttctcccattaatgtcacttatgttcttataaatgtaagacaaaataatacttatttttgtgatccattctccttgcattatacttatttttttccctctcccctttagCTGGATGAAGATGATTTCAAAGAGGAGCAGAACTCTGTTTCCCGTCTAATCCAGATGCTTTATAATGATGATCCAGAAGAAATGTTTAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaccccaatattaagttgtattttgacttctgtacatatttttctacgctcttagGTTGATGAAGATGATTTTCAGGAGGAGCAGAATTCTGTTGCGCTTCTCATTCATATGTTATATAATGATGACCCAGAAGAGATGTTTAAG
                    ttttgac  putative branch site (score: 3)
                                      tttttctacgctctt  putative PPT
      aatattaagttgtatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttgttataagcattttgagatactttctatcttgtacttaatatcctctcaatcacttgtgaccccaatattaagttgtattttgacttctgtacatatttttctacgctcttagGTTGATGAAGATGATTTTCAGGAGGAGCAGAATTCTGTTGCGCTTCTCATTCATATGTTATATAATGATGACCCAGAAGAGATGTTTAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG