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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGGTTGTGGTGTGAATCCTGGTGTGGAAACGCCACAAAAGCCAAGGCCAGAACAATCGATCTTTGCAATAATCCCATGACAAAGGAACCAAAGCTTCAGgtaaaatgatggctttcctcatatctacaacactcacaaagcgttgtttgttataatgcggtgttcttctgcag

Basic information

species Arabidopsis thaliana
transcript AT1G71220.2
intron # 36
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G71220.2 (Arabidopsis thaliana), 5'ss of exon 36
lower sequence: LOC_Os02g44510.1 (Oryza sativa), 5'ss of exon 16
GTGGTTGTGGTGTGAATCCTGGTGTGGAAACGCCACAAAAGCCAAGGCCAGAACAATCGATCTTTGCAATAATCCCATGACAAAGGAACCAAAGCTTCAGgtaaaatgatg--gctttcctcatatctacaacactcacaaagcgttgtttgtta-taatgcggtgttcttctgcag---------
 ||| | ||||||||||| ||||||||||| |||||||| || |  || | ||| || ||||||||||| || || ||||||||||| ||||||||||||||||||| ||   ||  |  |  |   ||      |  |      |||| |   | ||||     | |  |     |         
ATGGCTATGGTGTGAATCTTGGTGTGGAAATGCCACAAAGGCAAGAGCAAAAACCATTGATCTTTGCAACAACCCAATGACAAAGGAGCCAAAGCTTCAGgtaaaattattttgcagtaatagtccatattttgtttcctgtttcttgtctagaactaattttaaggttataaatcgactttctag

upper sequence: AT1G71220.2 (Arabidopsis thaliana), 5'ss of exon 36
lower sequence: GRMZM5G846198_T02 (Zea mays), 5'ss of exon 9
GTGGTTGTGGTGTGAATCCTGGTGTGGAAACGCCACAAAAGCCAAGGCCAGAACAATCGATCTTTGCAATAATCCCATGACAAAGGAACCAAAGCTTCAGgtaaaatgatggctttcctcatatctacaacactcacaaagcgttgtttgttataat-gcggtgttcttctgcag
 ||| ||||||||||||| ||||||||||| ||||||||||| |  || |  || || ||||| ||||| ||||| ||||||||||| ||||||||||||||||||| |||  |  |     || |       |       | |  | || || | | |   ||    | | |||
ATGGCTGTGGTGTGAATCTTGGTGTGGAAATGCCACAAAAGCAAGAGCAAAGACCATTGATCTATGCAACAATCCAATGACAAAGGAGCCAAAGCTTCAGgtaaaattatg--taccagtggattt------tttttttgtcttgatctgctaaacttgtactgcctctttccag

upper sequence: AT1G71220.2 (Arabidopsis thaliana), 5'ss of exon 36
lower sequence: GLYMA08G20020.1 (Glycine max), 5'ss of exon 36
GTGGTTGTGGTGTGAATCCTGGTGTGGAAACGCCACAAAAGCCAAGGCCAGAACAATCGATCTTTGCAATAATCCCATGACAAAGGAACCAAAGCTTCAGgtaaaatgatggctttcctcatatctacaacactca-caaagcgttgtttgttataatgcgg-tgttcttctgcag-----------------------------------
 ||| | |||||||| || |||||||| || || |||||| | ||||| | |||||| ||||| ||||| |||||||||||||| ||||| || |||||||| ||| |     | || |  |   |  || ||||| || |   | | |        ||| | |  |   || ||                                    
ATGGCTTTGGTGTGAGTCATGGTGTGGTAATGCTACAAAATCAAAGGCGAAAACAATTGATCTGTGCAACAATCCCATGACAAAAGAACCCAAACTTCAGgtgaaaag-----tctctttgttcttgtaa-actcatcatattatcgctgacatgtttgcagctccttcacttcacacatatttttaacttgcctccactttgatctttag

upper sequence: AT1G71220.2 (Arabidopsis thaliana), 5'ss of exon 36
lower sequence: GLYMA08G13400.1 (Glycine max), 5'ss of exon 39
GTGGTTGTGGTGTGAATCCTGGTGTGGAAACGCCACAAAAGCCAAGGCCAGAACAATCGATCTTTGCAATAATCCCATGACAAAGGAACCAAAGCTTCAGgtaaaa----tgatggctttcctcatatctaca-acactcacaaagcgttgtttgttataatgcggtgttcttctgcag-------------------------------------------
|||| | ||||||||||| |||||||| || || ||||||  |||||| | ||| || ||||| ||||| |||||||||||||| ||||| || || ||||||||     || ||  ||      | || |   | |||       | | |    ||||  |   |   || |||                                               
GTGGCTATGGTGTGAATCATGGTGTGGTAATGCTACAAAATACAAGGCAAAAACCATTGATCTGTGCAACAATCCCATGACAAAAGAACCCAAACTGCAGgtaaatgttttgctgttttatggtgtgtccatggaaacttgtttcacatcgcagcttatgtttttgcactcctctttgtcttctatgtccatttttttactacttttatctcggaacattag

upper sequence: AT1G71220.2 (Arabidopsis thaliana), 5'ss of exon 36
lower sequence: GLYMA05G30230.1 (Glycine max), 5'ss of exon 37
GTGGTTGTGGTGTGAATCCTGGTGTGGAAACGCCACAAAAGCCAAGGCCAGAACAATCGATCTTTGCAATAATCCCATGACAAAGGAACCAAAGCTTCAGgtaaaatgatggctttcctcatatctacaacactcacaaagcgttgtttgttataatgcggtgttcttctgcag-----------------------------------------------------
|||| | ||||||||||| |||||||| || || ||||||  |||||| | ||| || ||||| ||||| |||||||||||||| ||||| || || |||||||| || |    |   | |  | |       |||   |   ||||||  |||       | |  || ||||                                                      
GTGGCTATGGTGTGAATCATGGTGTGGTAATGCTACAAAATACAAGGCAAAAACCATTGATCTGTGCAACAATCCCATGACAAAAGAACCCAAACTGCAGgtaaa-tgtttttctgttttaagtttt--gtgttcatggaaacttgtttcctatcgcaacttatgtttttgcactcctctttgtcttctatggccattttttttactactttatctcggaacattag

upper sequence: AT1G71220.2 (Arabidopsis thaliana), 5'ss of exon 36
lower sequence: Vv12s0034g02230.t01 (Vitis vinifera), 5'ss of exon 37
GTGGTTGTGGTGTGAATCCTGGTGTGGAAACGCCACAAAAGCCAAGGCCAGAACAATCGATCTTTGCAATAATCCCATGACAAAGGAACCAAAGCTTCAGgtaaaa--tgatggctttcctcatatctacaacactcacaaagcgttgt-ttgttataatgcggtgttcttctgcag---------------------------------
|||||| ||||||||||| ||||| ||||| || |||||| ||||||| | ||| || ||||||||||| |||||||||||||||||||| ||||||||||||||   | ||  | ||   | ||||| |        ||||    | |      |   |      |||||   |                                   
GTGGTTATGGTGTGAATCATGGTGCGGAAATGCTACAAAATCCAAGGCAAAAACCATTGATCTTTGCAACAATCCCATGACAAAGGAACCCAAGCTTCAGgtaaacattcatatccttgagcttatcttccctctcttcaaataactttaccaccaccgtcatcacttctttccctttccatttctgtttgctctttgtcattctcccag

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|164100523|gb|ES017718.1|ES017718
EST:     GAACAATCGATCTTTGCAATAATCCCATGACAAAGGAACCAAAGCTTCAG                         GGTGCCCGAAGAATCGTAACCGAATGGCCCGATC
genomic: GAACAATCGATCTTTGCAATAATCCCATGACAAAGGAACCAAAGCTTCAGgtaaaatgat ... tcttctgcagGGTGCCCGAAGAATCGTAACCGAATGGCCCGATC
EST: gi|47832064|gb|CK121748.1|CK121748
EST:     GAACAATCGATCTTTGCAATAATCCCATGACAAAGGAACCAAAGCTTCAG                         GGTGCCCGAAGAATCGTAACCGAATGGCCCGATCTTGATCTCGAAGCACGA
genomic: GAACAATCGATCTTTGCAATAATCCCATGACAAAGGAACCAAAGCTTCAGgtaaaatgat ... tcttctgcagGGTGCCCGAAGAATCGTAACCGAATGGCCCGATCTTGATCTCGAAGCACGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGGTTGTGGTGTGAATCCTGGTGTGGAAACGCCACAAAAGCCAAGGCCAGAACAATCGATCTTTGCAATAATCCCATGACAAAGGAACCAAAGCTTCAGgtaaaatgatggctttcctcatatctacaacactcacaaagcgttgtttgttataatgcggtgttcttctgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA