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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGGATGATCCTCGTTTGATGACACTAGCTGGTTTGCGGCGTAGAGGCATGACCCCAACTGCAATCAATGCTTTTGTCCGAGGAATTGGAATAACTAGAAGgtatgatatcaatttccaactacagctgtttgtataaatatactatttctaagttattgacgtggaaaagtacttgaaacatctcactcttttgtttata...

Basic information

species Glycine max
transcript GLYMA20G25120.2
intron # 16
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G25120.2 (Glycine max), 5'ss of exon 16
lower sequence: Vv15s0021g01230.t01 (Vitis vinifera), 5'ss of exon 16
GGGATGATCCTCGTTTGATGACACTAGCTGGTTTGCGGCGTAGAGGCATGACCCCAACTGCAATCAATGCTTTTGTCCGAGGAATTGGAATAACTAGAAGgtatgatatcaatt-tccaactacagct---gtttgtataaatatact--atttctaagttattgacgtggaaaagtacttgaaacatctcactcttttgtttata-
|||||||||||||| | |||||| ||||||||||||| ||||| ||  ||||  ||||  |||| ||| ||||| | |||||||||||||| ||||||||||  |  ||   || |      | | ||   | ||    ||||||  |   ||||| |  | || |  ||| |   |  |||| |    | |  ||||    || | 
GGGATGATCCTCGTCTTATGACATTAGCTGGTTTGCGACGTAGGGGGGTGACTTCAACATCAATAAATACTTTTATTCGAGGAATTGGAATCACTAGAAGgttgggcatattttgtttgggcatatctaaagatttaccaaatatctttagtttcttatctttttatttggtattatcattgatattcattatactttgtggtacag

upper sequence: GLYMA20G25120.2 (Glycine max), 5'ss of exon 16
lower sequence: Vv01s0011g03740.t01 (Vitis vinifera), 5'ss of exon 16
GGGATGATCCTCGTTTGATGACACTAGCTGGTTTGCGGCGTAGAGGCATGACCCCAACTGCAATCAATGCTTTTGTCCGAGGAATTGGAATAACTAGAAGgtatgatatcaatttccaactacagctgtttgtataaatatactatttctaagttattgacgtggaaaagtacttgaaacat-----ctcactcttttgtttata----
||||||| |||||| | |||||| |||||||||| || ||||||||  ||||  | ||  | || ||||||||||| |||||||||||||| |||||||||| ||| ||  ||| |          | ||   |     | |  || || || ||  | | |   | | || |||    |||      | |  ||    |||       
GGGATGACCCTCGTCTTATGACATTAGCTGGTTTACGACGTAGAGGGGTGACTTCGACCTCCATAAATGCTTTTGTTCGAGGAATTGGAATCACTAGAAGgt-tgacat--attccttgtggtgtttattcagaagttcaaaaaatatcaaattttatcatgcc-acatgtgcttttgtcatagatattaatgctaccttttgccacag
















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|33389687|gb|CA852894.1|CA852894
EST:     ACCCCAACTGCAATCAATGCTTTTGTCCGAGGAATTGGAATAACTAGAAG                         TGATGGCACTTTGATTTCTGTGGAACGCCTTGAATATCATGTTAGGCAAGA
genomic: ACCCCAACTGCAATCAATGCTTTTGTCCGAGGAATTGGAATAACTAGAAGgtatgatatc ... cttgctgtagTGATGGCACTTTGATTTCTGTGGAACGCCTTGAATATCATGTTAGGGAAGA
EST: gi|151409608|gb|EV279416.1|EV279416
EST:     ACCCCAACTGCAATCAATGCTTTTGTCCGAGGAATTGGAATAACTAGAAG                         TGATGGCACTTTGATTTCTGTGGAACGCCTTGAATATCATGTTAGGGAAGA
genomic: ACCCCAACTGCAATCAATGCTTTTGTCCGAGGAATTGGAATAACTAGAAGgtatgatatc ... cttgctgtagTGATGGCACTTTGATTTCTGTGGAACGCCTTGAATATCATGTTAGGGAAGA
EST: gi|5753691|gb|AI960978.1|AI960978
EST:     ACCCCAACTGCAATCAATGCTTTTGTCCGAGGAATTGGAATAACTAGAAG                         TGATGGCACTTTGATTTCTGTGGAACGCCTTGAATATCATGTTAGGGAAGA
genomic: ACCCCAACTGCAATCAATGCTTTTGTCCGAGGAATTGGAATAACTAGAAGgtatgatatc ... cttgctgtagTGATGGCACTTTGATTTCTGTGGAACGCCTTGAATATCATGTTAGGGAAGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGGATGATCCTCGTTTGATGACACTAGCTGGTTTGCGGCGTAGAGGCATGACCCCAACTGCAATCAATGCTTTTGTCCGAGGAATTGGAATAACTAGAAGgtatgatatcaatttccaactacagctgtttgtataaatatactatttctaagttattgacgtggaaaagtacttgaaacatctcactcttttgtttata

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tctcactc