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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAAGCTGGTACTATCTCATGACCTAGCAACCGAGAAAGAGCTTAAGGATATGGAGAAGGAAATTAGAAAAGAAGTAGATGACGCCATTGCCAAAGCTAAGgtaaaacaacagttacattactactttcaaagcgtaaactcgagacccttatgcgaaaatctctgtaccgtttcag

Basic information

species Arabidopsis thaliana
transcript AT1G59900.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G59900.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: LOC_Os02g50620.1 (Oryza sativa), 5'ss of exon 6
GAAGCTGGTACTATCTCATGACCTAGCAACCGAGAAAGAGCTTAAGGATATGGAGAAGGAAATTAGAAAAGAAGTAGATGACGCCATTGCCAAAGCTAAGgtaaa-acaacagttacattactactttcaaagcgta--------aactcgagacccttatgcgaaaatctctgtaccgtttcag---------
                                              || |||||||| ||||| ||||||||||| ||||| |||||||| ||||| |||||     |  || ||   ||  |  |||    |  ||           | ||      | | |    |  | |   || ||| |          
----------------------------------------------GACATGGAGAAAGAAATCAGAAAAGAAGTCGATGATGCCATTGCGAAAGCAAAGgttcttgctgcattttgcttctttttttttttgtttacttgttttgctttgaattagattttcactcacatatacccctttttaatatttgcag

upper sequence: AT1G59900.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GRMZM2G140150_T01 (Zea mays), 5'ss of exon 6
GAAGCTGGTACTATCTCATGACCTAGCAACCGAGAAAGAGCTTAAGGATATGGAGAAGGAAATTAGAAAAGAAGTAGATGACGCCATTGCCAAAGCTAAGgtaaaacaacagttacattactactttcaaagcgtaaactcgagaccc-ttatgcgaaaatctctgtaccgtttcag-------
                                              ||||||||||| ||||| || ||| ||||||||||||||||||| ||||| |||||   ||| || ||| ||      ||  |   | |   ||  | |    ||||||  |    |   | |  | |          
----------------------------------------------GATATGGAGAAAGAAATCAGGAAACAAGTAGATGACGCCATTGCAAAAGCAAAGgtcccaca-catttagatatgcctttatagttcttgtgcttcaaattagttatgcttaccatttcattcgctcttgttctgcag

upper sequence: AT1G59900.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GRMZM2G361693_T01 (Zea mays), 5'ss of exon 6
GAAGCTGGTACTATCTCATGACCTAGCAACCGAGAAAGAGCTTAAGGATATGGAGAAGGAAATTAGAAAAGAAGTAGATGACGCCATTGCCAAAGCTAAGgtaaaacaacagttacat-tactactttcaaagcgtaaactcgagacccttatgcgaaaatctctgtaccgtttcag----------
                                               |||||||||| ||||| || ||| ||||||||||||| ||||| ||||| |||||   |   || ||| || | ||  | ||      |    || |     ||||||  |   ||   ||   |               
----------------------------------------------AATATGGAGAAAGAAATCAGGAAACAAGTAGATGACGCTATTGCTAAAGCAAAGgtcccattgcatttagatatgcttttgtcgttcttttgcttcaaattagttatgcttaccactgcatatactcctgttgatctgcag

upper sequence: AT1G59900.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GLYMA08G40380.1 (Glycine max), 5'ss of exon 6
GAAGCTGGTACTATCTCATGACCTAGCAACCGAGAAAGAGCTTAAGGATATGGAGAAGGAAATTAGAAAAGAAGTAGATGACGCCATTGCCAAAGCTAAGgtaaaacaacagttacattact-actttcaaagcgtaaact-cgagacccttatgcgaaaatctctgtaccgtttcag-------------------------------------------------------
                                              || || || |||||||| ||||||||||| ||||| |||||||||||||| ||||| |||| | |  |  |||  | | | |   |   | || |  |  | ||  ||      |||||  | | ||| |                                                         
----------------------------------------------GACATTGAAAAGGAAATAAGAAAAGAAGTTGATGAAGCCATTGCCAAAGCAAAGgtgaaactatatcttgattgtttattcttctaatattaattatggtatccacatattttcatctcc-tgcagttgccctatcatcctatgtgatttacaatctcagagttctgtgttcatttctgatttccag

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|164204319|gb|ES012570.1|ES012570
EST:     TGGAGAAGGAAATTAGAAAAGAAGTAGATGACGCCATTGCCAAAGCTAAG                         GATTGCCCAATGCCAGAGCCTTCTGAGCTCTTTACCAA
genomic: TGGAGAAGGAAATTAGAAAAGAAGTAGATGACGCCATTGCCAAAGCTAAGgtaaaacaac ... accgtttcagGATTGCCCAATGCCAGAGCCTTCTGAGCTCTTTACCAA
EST: gi|124739960|gb|EH831122.1|EH831122
EST:     AGAAGGAAATTAGAAAAGAAGTAGATGACGCCATTGCCAAAGCTAAG                         GATTGCCCAATGCCAGAGCCTTCTGAGCTCTTTACCAATGTGTATGTGAAG
genomic: AGAAGGAAATTAGAAAAGAAGTAGATGACGCCATTGCCAAAGCTAAGgtaaaacaac ... accgtttcagGATTGCCCAATGCCAGAGCCTTCTGAGCTCTTTACCAATGTGTATGTGAAG
EST: gi|164056257|gb|ES149172.1|ES149172
EST:     GAAGG-AATTAGAAAAGAAGTAGATGACGCCATTGTCCAAAGCTAAG                         GATTGCCCAATGCCAGAGCCTTCTGAGCTCTTTACCAATGTGTATGTGAAG
genomic: GAAGGAAATTAGAAAAGAAGTAGATGACGCCATTG-CCAAAGCTAAGgtaaaacaac ... accgtttcagGATTGCCCAATGCCAGAGCCTTCTGAGCTCTTTACCAATGTGTATGTGAAG
EST: gi|164061722|gb|ES117889.1|ES117889
EST:     CGCCATTGCCAAAGCTAAG                         GATTGCCCAATGCCAGAGCCTTCTGAGCTCTTTACCAATGTGTATGTGAAG
genomic: CGCCATTGCCAAAGCTAAGgtaaaacaac ... accgtttcagGATTGCCCAATGCCAGAGCCTTCTGAGCTCTTTACCAATGTGTATGTGAAG
EST: gi|124766215|gb|EH856345.1|EH856345
EST:     CCATTGCCAAAGCTAAG                         GATTGCCCAATGCCAGAGCCTTCTGAGCTCTTTACCAATGTGTATGTGAAG
genomic: CCATTGCCAAAGCTAAGgtaaaacaac ... accgtttcagGATTGCCCAATGCCAGAGCCTTCTGAGCTCTTTACCAATGTGTATGTGAAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAAGCTGGTACTATCTCATGACCTAGCAACCGAGAAAGAGCTTAAGGATATGGAGAAGGAAATTAGAAAAGAAGTAGATGACGCCATTGCCAAAGCTAAGgtaaaacaacagttacattactactttcaaagcgtaaactcgagacccttatgcgaaaatctctgtaccgtttcag

- - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT