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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGCGGAACAACTAAAAGATCTTGGATGCAAGTGGGTTGTTCTTGGACATTCTGAGCGAAGACATATTATTGGAGAAAATGATGAGgtaaagcaaatccagacatcatttttctacagtagctttgctagagaatatgattagtatatttgcaagagatgctaaatatttaagatattaactgaacattgtcaattccag

Basic information

species Glycine max
transcript GLYMA19G36990.2
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G36990.2 (Glycine max), 5'ss of exon 5
lower sequence: GRMZM2G002807_T01 (Zea mays), 5'ss of exon 5
CGCGGAACAACTAAAAGATCTTGGATGCAAGTGGGTTGTTCTTGGACATTCTGAGCGAAGACATATTATTGGAGAAAATGATGAGgtaaagcaaatccagacatcatttttctacagtagctttgctagagaat-atgattagtatatttgcaagagatgctaaatatttaagatattaactgaacattgtcaattccag
 || ||||||||    ||  | || ||  | |||||| |||||||||| |||||||| |||||||||||||| |||||||||||||| |    | |  |  |  ||| |       ||        | |||||| |   ||  | |  || ||| |  |   || |  || | ||                         
TGCCGAACAACTGGTGGACATCGGCTGTCAATGGGTTATTCTTGGACACTCTGAGCGTAGACATATTATTGGTGAAAATGATGAGgtga--ttattttatgcg-catgtgctactggtttgaaacttggagaatcacagtt--tctgattacaata--taacaagttgttcaaatgcag---------------------

upper sequence: GLYMA19G36990.2 (Glycine max), 5'ss of exon 5
lower sequence: GRMZM5G852968_T02 (Zea mays), 5'ss of exon 5
CGCGGAACAACTAAAAGATCTTGGATGCAAGTGGGTTGTTCTTGGACATTCTGAGCGAAGACATATTATTGGAGAAAATGATGAGgtaaagcaaatccagacatcatttttctacagtagctttgctagagaatatgattagtatatttgcaagagatgctaaatatttaagatattaactgaacattgtcaattccag
 || ||||||||    ||  | || ||  | |||||| |||||||||| || ||||| |||||||||||||| |||||||| ||||| |      |     ||| ||  | ||    |     |   ||| || ||  ||  | |  |||||| |  |   || |   | | ||                         
TGCAGAACAACTGGTGGACATCGGTTGTCAATGGGTTATTCTTGGACACTCAGAGCGTAGACATATTATTGGTGAAAATGACGAGgtgattattttatgtgcat-atgctactggtttgatgcttgcaga-aacatagtt--tgtgattgcaata--taacaagttgctcaaatgcag---------------------

upper sequence: GLYMA19G36990.2 (Glycine max), 5'ss of exon 5
lower sequence: AT2G21170.2 (Arabidopsis thaliana), 5'ss of exon 4
CGCGGAACAACTAAAAGATCTTGGATGCAAGTGGGTTGTTCTTGGACATTCTGAGCGAAGACATATTATTGGAGAAAATGATGAGgtaaagcaaatccagacatcatttttctacagtagctttgcta-gagaatatgattagtatatttgcaagagatgctaaatatttaagatattaactgaacattgtcaattccag
|| |||||| || ||||| ||||| |||||||||||  ||||||| ||||| || || |||||| | || |||||||| |||||||| | | |||   | |||   | |    || |  |  || ||| || |   |  | |  | || |        | || || |   ||   ||                       
CGTGGAACAGCTCAAAGACCTTGGCTGCAAGTGGGTCATTCTTGGGCATTCCGAACGGAGACATGTCATCGGAGAAAAAGATGAGgtca-gtaaaataaaacactttataagcactggtgagttactaagaaagggttgtgaaaacatatttgctctgttctcaaca---aaaccatag---------------------

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|192294177|gb|FG986266.1|FG986266
EST:     TTGTTCTTGGACATTCTGAACGAAGACATATTATTGGAGAAAATGATGAG                         TTTATAGGAAAGAAAACTGCCTATGCTTTGAGCCAAGGTCTTGGAGTGATT
genomic: TTGTTCTTGGACATTCTGAGCGAAGACATATTATTGGAGAAAATGATGAGgtaaagcaaa ... tcaattccagTTTATAGGAAAGAAAGCTGCCTATGCTTTGAGCCAAGGTCTTGGAGTGATT
EST: gi|19054173|gb|BM732840.1|BM732840
EST:     TTGTTCTTGGACATTCTGAGCGAAGACATATTATTGGAGAAAATGATGAG                         TTTATAGGAAAGAAAGCTGCCTATGCTTTGAGCCAAGGTCTTGGAGTGATT
genomic: TTGTTCTTGGACATTCTGAGCGAAGACATATTATTGGAGAAAATGATGAGgtaaagcaaa ... tcaattccagTTTATAGGAAAGAAAGCTGCCTATGCTTTGAGCCAAGGTCTTGGAGTGATT
EST: gi|192303891|gb|FG998243.1|FG998243
EST:     TTGTTCTTGGACATTCTGAGCGAAGACATATTATTGGAGAAAATGATGAG                         TTTCTAGGAAAGAAAGCTGCCTATGCTTTGAGCCAAGGTCTTGGAGTGATT
genomic: TTGTTCTTGGACATTCTGAGCGAAGACATATTATTGGAGAAAATGATGAGgtaaagcaaa ... tcaattccagTTTATAGGAAAGAAAGCTGCCTATGCTTTGAGCCAAGGTCTTGGAGTGATT
EST: gi|20814775|gb|BQ299253.1|BQ299253
EST:     TTGTTCTTGGACATTCTGAGCGAAGACATATTATTGGAGAAAATGATGAG                         TTTATAGGAAAGAAAGCTGCCTATGCTTTGAGCCAAGGTCTTGGAGTGATT
genomic: TTGTTCTTGGACATTCTGAGCGAAGACATATTATTGGAGAAAATGATGAGgtaaagcaaa ... tcaattccagTTTATAGGAAAGAAAGCTGCCTATGCTTTGAGCCAAGGTCTTGGAGTGATT
EST: gi|7691290|gb|AW759483.1|AW759483
EST:     TTGTTCTTGGACATTCTGAGCGAAGACATATTATTGGAGAAAATGATGAG                         TTTATAGGAAAGAAAGCTGCCTATGCTTAGAGCCAAGGTCTTGCAGTGATT
genomic: TTGTTCTTGGACATTCTGAGCGAAGACATATTATTGGAGAAAATGATGAGgtaaagcaaa ... tcaattccagTTTATAGGAAAGAAAGCTGCCTATGCTTTGAGCCAAGGTCTTGGAGTGATT
EST: gi|10843866|gb|BF067227.1|BF067227
EST:     TTGTTCTTGGACATTCTGAGCGAAGACATATTATTGGAGAAAATGATGAG                         TTTATAGGAAAGAAAGCTGCCTATGCTTTGAGCCAAGGTCTTGGAGTGATT
genomic: TTGTTCTTGGACATTCTGAGCGAAGACATATTATTGGAGAAAATGATGAGgtaaagcaaa ... tcaattccagTTTATAGGAAAGAAAGCTGCCTATGCTTTGAGCCAAGGTCTTGGAGTGATT
EST: gi|8283483|gb|BE021042.1|BE021042
EST:     TTGTTCTTGGACATTCTGAGCGAAGACATATTATTGGAGAAAATGATGAG                         TTTATAGGAAAGAAAGCTGCCTATGCTTTGAGCCAAGGTCTTGGAGTGATT
genomic: TTGTTCTTGGACATTCTGAGCGAAGACATATTATTGGAGAAAATGATGAGgtaaagcaaa ... tcaattccagTTTATAGGAAAGAAAGCTGCCTATGCTTTGAGCCAAGGTCTTGGAGTGATT
EST: gi|12689031|gb|BG155376.1|BG155376
EST:     TTGTTCTTGGACATTCTGAGCGAAGACATATTATTGGAGAAAATGATGAG                         TTTATAGGAAAGAAAGCTGCCTATGCTTTGAGCCAAGGTCTTGGAGTGATT
genomic: TTGTTCTTGGACATTCTGAGCGAAGACATATTATTGGAGAAAATGATGAGgtaaagcaaa ... tcaattccagTTTATAGGAAAGAAAGCTGCCTATGCTTTGAGCCAAGGTCTTGGAGTGATT
EST: gi|15204307|gb|BI427075.1|BI427075
EST:     TTGTTCTTGGACATTCTGAGCGAAGACATATTATTGGAGAAAATGATGAG                         TTTATAGGAAAGAAAGCTGCCTATGCTTTGAGCCAAGGTCTTGGAGTGATT
genomic: TTGTTCTTGGACATTCTGAGCGAAGACATATTATTGGAGAAAATGATGAGgtaaagcaaa ... tcaattccagTTTATAGGAAAGAAAGCTGCCTATGCTTTGAGCCAAGGTCTTGGAGTGATT
EST: gi|298173868|gb|HO017204.1|HO017204
EST:     TTGTTCTTGGACATTCTGAGCGAAGACATATTATTGGAGAAAATGATGAG                         TTTATAGGAAAGAAAGCTGCCTATGCTTTGAGCCAAGGTCTTGGAGTGATT
genomic: TTGTTCTTGGACATTCTGAGCGAAGACATATTATTGGAGAAAATGATGAGgtaaagcaaa ... tcaattccagTTTATAGGAAAGAAAGCTGCCTATGCTTTGAGCCAAGGTCTTGGAGTGATT
EST: gi|17519271|gb|BM188313.1|BM188313
EST:     TTGTTCTTGGACATTCTGAGCGAAGACATATTATTGGAGAAAATGATGAG                         TTTATAGGAAAGAAAGCTGCCTATGCTTTGAGCCAAGGTCTTGGAGTGATT
genomic: TTGTTCTTGGACATTCTGAGCGAAGACATATTATTGGAGAAAATGATGAGgtaaagcaaa ... tcaattccagTTTATAGGAAAGAAAGCTGCCTATGCTTTGAGCCAAGGTCTTGGAGTGATT
EST: gi|8284792|gb|BE022351.1|BE022351
EST:     TTGTTCTTGGACATTCTGAGCGAAGACATATTATTGGAGAAAATGATGAG                         TTTATAGGAAAGAAAGCTGCCTATGCTTTGAGCCAAGGTCTTGGAGTGATT
genomic: TTGTTCTTGGACATTCTGAGCGAAGACATATTATTGGAGAAAATGATGAGgtaaagcaaa ... tcaattccagTTTATAGGAAAGAAAGCTGCCTATGCTTTGAGCCAAGGTCTTGGAGTGATT
EST: gi|120533074|gb|EH261207.1|EH261207
EST:     TTGTTCTTGGACATTCTGAGCGAAGACATATTATTGGAGAAAATGATGAG                         TTTATAGGAAAGAAAGCTGCCTATGCTTTGAGCCAAGGTCTTGCGAGCTGA
genomic: TTGTTCTTGGACATTCTGAGCGAAGACATATTATTGGAGAAAATGATGAGgtaaagcaaa ... tcaattccagTTTATAGGAAAGAAAGCTGCCTATGCTTTGAGCCAAGGTCTTG-GAG-TGA
EST: gi|209724432|gb|BW666667.1|BW666667
EST:     TTGTTCTTGGACATTCTGAGCGAAGACATATTATTGGAGAAAATGATGAG                         TTTATAGGAAAGAAAGCTGCCTATGCTTTGAGCCAAGGTCTTGGAGTGATT
genomic: TTGTTCTTGGACATTCTGAGCGAAGACATATTATTGGAGAAAATGATGAGgtaaagcaaa ... tcaattccagTTTATAGGAAAGAAAGCTGCCTATGCTTTGAGCCAAGGTCTTGGAGTGATT
EST: gi|192326679|gb|FK018521.1|FK018521
EST:     TTGTTCTTGGACATTCTGAGCGAAGACATATTATTGGAGAAAATGATGAG                         TTTATAGGAAAGAAAGCTGCCTATGCTTTGAGCCAAGGTCTTGGAGTGATT
genomic: TTGTTCTTGGACATTCTGAGCGAAGACATATTATTGGAGAAAATGATGAGgtaaagcaaa ... tcaattccagTTTATAGGAAAGAAAGCTGCCTATGCTTTGAGCCAAGGTCTTGGAGTGATT
EST: gi|192331703|gb|FK022805.1|FK022805
EST:     TTGTTCTTGGACATTCTGAGCGAAGACATATTATTGGAGAAAATGATGAG                         TTTATAGGAAAGAAAGCTGCCTATGCTTTGAGCCAAGGTCTTGGAGTGATT
genomic: TTGTTCTTGGACATTCTGAGCGAAGACATATTATTGGAGAAAATGATGAGgtaaagcaaa ... tcaattccagTTTATAGGAAAGAAAGCTGCCTATGCTTTGAGCCAAGGTCTTGGAGTGATT
EST: gi|21993826|gb|BQ785354.1|BQ785354
EST:     TTGTTCTTGGACATTCTGAGCGAAGACATATTATTGGAGAAAATGATGAG                         TTTATAGGAAAGAAAGCTGCCTATGCTTTGAGC
genomic: TTGTTCTTGGACATTCTGAGCGAAGACATATTATTGGAGAAAATGATGAGgtaaagcaaa ... tcaattccagTTTATAGGAAAGAAAGCTGCCTATGCTTTGAGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGCGGAACAACTAAAAGATCTTGGATGCAAGTGGGTTGTTCTTGGACATTCTGAGCGAAGACATATTATTGGAGAAAATGATGAGgtaaagcaaatccagacatcatttttctacagtagctttgctagagaatatgattagtatatttgcaagagatgctaaatatttaagatattaactgaacattgtcaattccag

- - - - - - - - - - - - - - - - - - - - - - - - - - -  CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA