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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTAGCAAGGTGCACAAAGATCATAAACCCGAACTCAGAAGATGCCAAATATGTAATCAACGTGAAGCAGATTGCAAAGgtaatctatattttcaacaatgtgaagatgccaaactgtcccattgtttttcaccacatctatcccgtgttcttgttttgaagatgttagacttcacttactgttatgaaattatcaatgggttggcaaagctgttgattctttgattatgctgtcaggactagtaatccttctgcttttttttaatgacag

Basic information

species Glycine max
transcript GLYMA03G42370.4
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G42370.2 (Glycine max), 5'ss of exon 4
lower sequence: LOC_Os06g09290.2 (Oryza sativa), 5'ss of exon 4
GTAGCAAGGTGCACAAAGATCATAAACCCGAACTCAGAAGATGCCAAATATGTAATCAACGTGAAGCAGATTGCAAAGgtaatctatattttcaacaatgtgaagatgccaaactgtcccattgtttttcaccacatctatcccgtgttcttgttttgaagatgttagacttcacttactgttatgaaattatcaatgggttggcaaagctgttgattctttgattatgctgtcaggactagtaatccttctgcttttttttaatgacag
|| ||||| |||||||||||||| | ||| ||| | || ||||| |||||||| ||||| || ||||| ||||| ||||| |   ||  ||| |  | |       |||||  || || |  ||    |    | |   |    | || |||    || || | |||    | | || || | || |  ||||| |||||       ||                                                             
GTTGCAAGATGCACAAAGATCATCAGCCCTAACACGGACGATGCTAAATATGTCATCAATGTCAAGCAAATTGCGAAGgtgagtcatgcttttattact-------tgccagcctttctctgtggaggttcatataaaaaa---gagtactt---ctggaggt-ttatcgctgattttctctgat-attttatctatgggacattgcag-------------------------------------------------------------

upper sequence: GLYMA03G42370.2 (Glycine max), 5'ss of exon 4
lower sequence: PP1S152_13V6.2 (Physcomitrella patens), 5'ss of exon 4
GTAGCAAGGTGCACAAAGATCATAAACCCGAACTCAGAAGATGCCAAATATGTAATCAACGTGAAGCAGATTGCAAAGgtaatctatattttcaacaatgtgaagatgccaaactgtcccattgtttttcaccacatctatcccgtgttcttgttttgaagatgttagacttcacttactgttatgaaattatcaatgggttggcaaagctgttgattctttgattatgctgtcaggactagtaatccttctgcttttttttaatgacag
|| || ||||| |||||||| || ||| | ||  | || ||  ||||||| || |||||||||||||||||||| ||||||   ||   |||    ||    || |      |  |     | |||||    |      ||   | | || |||| |  | ||  |  ||||     | |                                                                                          
GTTGCCAGGTGTACAAAGATAATCAACGCCAATACGGATGACTCCAAATACGTCATCAACGTGAAGCAGATTGCCAAGgtatcataccgtttttgtaagaccaa-acagttcatcgcttggtcgttttgtttc-tgctgatgttgggatcgtgttcttcaaat--tcaactttgagcattca----------------------------------------------------------------------------------------
















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|192301329|gb|FG990219.1|FG990219
EST:     CGAACTCAGAAGATGCCAAATATGTAATCAACGTGAAGCAGATTGCAAAG                         TTTGTCGTTGGGCTGGGCGACAAAGTTTCACCCACCGACATTGAGGAAGGG
genomic: CGAACTCAGAAGATGCCAAATATGTAATCAACGTGAAGCAGATTGCAAAGgtaatctata ... ttaatgacagTTTGTCGTTGGGCTGGGCGACAAAGTTTCACCCACCGACATTGAGGAAGGG
EST: gi|213602675|gb|DB956611.1|DB956611
EST:     CGAACTCAGAAGATGCCAAATATGTAATCAACGTGAAGCAGATTGCAAAG                         TTTGTCGTTGGGCTGGGCGACAAAGTTTCACCCACCGACATTGAGGAAGGG
genomic: CGAACTCAGAAGATGCCAAATATGTAATCAACGTGAAGCAGATTGCAAAGgtaatctata ... ttaatgacagTTTGTCGTTGGGCTGGGCGACAAAGTTTCACCCACCGACATTGAGGAAGGG
EST: gi|213589227|gb|DB957759.1|DB957759
EST:     CGAACTCAGAAGATGCCAAATATGTAATCAACGTGAAGCAGATTGCAAAG                         TTTGTCGTTGGGCTGGGCGACAAAGTTTCACCCACCGACATTGAGGAAGGG
genomic: CGAACTCAGAAGATGCCAAATATGTAATCAACGTGAAGCAGATTGCAAAGgtaatctata ... ttaatgacagTTTGTCGTTGGGCTGGGCGACAAAGTTTCACCCACCGACATTGAGGAAGGG
EST: gi|151405667|gb|EV275481.1|EV275481
EST:     CGAACTCAGAAGATGCCAAATATGTAATCAACGTGAAGCAGATTGCAAAG                         TTTGTCGTTGGGCTGGGCGACAAAGTTTCACCCACCGACATTGAGGAAGGG
genomic: CGAACTCAGAAGATGCCAAATATGTAATCAACGTGAAGCAGATTGCAAAGgtaatctata ... ttaatgacagTTTGTCGTTGGGCTGGGCGACAAAGTTTCACCCACCGACATTGAGGAAGGG
EST: gi|209702899|gb|BW667434.1|BW667434
EST:     CGAACTCAGAAGATGCCAAATATGTAATCAACGTGAAGCAGATTGCAAAG                         TTTGTCGTTGGGCTGGGCGACAAAGTTTCACCCACCGACATTGAGGAAGGG
genomic: CGAACTCAGAAGATGCCAAATATGTAATCAACGTGAAGCAGATTGCAAAGgtaatctata ... ttaatgacagTTTGTCGTTGGGCTGGGCGACAAAGTTTCACCCACCGACATTGAGGAAGGG
EST: gi|193314171|gb|FK280098.1|FK280098
EST:     GAAGATGCCAAATATGTAATCAACGTGAAGCAGATTGCAAAG                         TTTGTCGTTGGGCTGGGCGACAAAGTTTCACCCACCGACATTGAGGAAGGG
genomic: GAAGATGCCAAATATGTAATCAACGTGAAGCAGATTGCAAAGgtaatctata ... ttaatgacagTTTGTCGTTGGGCTGGGCGACAAAGTTTCACCCACCGACATTGAGGAAGGG
EST: gi|208155594|gb|GD951999.1|GD951999
EST:     CGAACTCAGAAGATGCCAAATATGTAATCAACGTGAAGCAGATTGCAAAG                         TTTGTCGTTGGGCTG
genomic: CGAACTCAGAAGATGCCAAATATGTAATCAACGTGAAGCAGATTGCAAAGgtaatctata ... ttaatgacagTTTGTCGTTGGGCTG
EST: gi|208228908|gb|GE024272.1|GE024272
EST:     CGAACTCAGAAGATGCCAAATATGTAATCAACGTGAAGCAGATTGCAAAG                         TTTGTCGTTGGGCTG
genomic: CGAACTCAGAAGATGCCAAATATGTAATCAACGTGAAGCAGATTGCAAAGgtaatctata ... ttaatgacagTTTGTCGTTGGGCTG
EST: gi|208215664|gb|GE008516.1|GE008516
EST:     CGAACTCAGAAGATGCCAAATATGTAATCAACGTGAAGCAGATTGCAAAG                         TTTGTCGTTGGGCTGGGCGACAAAGTTTCACCCACCGACATTGAGGAAGGG
genomic: CGAACTCAGAAGATGCCAAATATGTAATCAACGTGAAGCAGATTGCAAAGgtaatctata ... ttaatgacagTTTGTCGTTGGGCTGGGCGACAAAGTTTCACCCACCGACATTGAGGAAGGG
EST: gi|213600299|gb|DB970277.1|DB970277
EST:     CGAACTCAGAAGATGCCAAATATGTAATCAACGTGAAGCAGATTGCAAAG                         TTTGTCGTTGGGCTGGGCGACAAAGTTTCACCCACCGACATTGAGGAAGGG
genomic: CGAACTCAGAAGATGCCAAATATGTAATCAACGTGAAGCAGATTGCAAAGgtaatctata ... ttaatgacagTTTGTCGTTGGGCTGGGCGACAAAGTTTCACCCACCGACATTGAGGAAGGG
EST: gi|213611619|gb|DB969007.1|DB969007
EST:     CGAACTCAGAAGATGCCAAATATGTAATCAACGTGAAGCAGATTGCAAAG                         TTTGTCGTTGGGCTGGGCGACAAAGTTTCACCCACCGACATTGAGGAAGGG
genomic: CGAACTCAGAAGATGCCAAATATGTAATCAACGTGAAGCAGATTGCAAAGgtaatctata ... ttaatgacagTTTGTCGTTGGGCTGGGCGACAAAGTTTCACCCACCGACATTGAGGAAGGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTAGCAAGGTGCACAAAGATCATAAACCCGAACTCAGAAGATGCCAAATATGTAATCAACGTGAAGCAGATTGCAAAGgtaatctatattttcaacaatgtgaagatgccaaactgtcccattgtttttcaccacatctatcccgtgttcttgttttgaagatgttagacttcacttactgttatgaaattatcaatgggttggcaaagctgttgattctttgattatgctgtcaggactagtaatccttctgcttttttttaatgacag

- - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG