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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTGATTGTGCTGTACGTGGATTTCAAGCTTGATGAGAGTTACACGCCGAGCAAAGTTTCCATCCGTGCCGGTGATGGTTTTCACAACTTGAAGgtaaattttttttttattggtttgggtttgattgggttggttatggttaattatttggtgatgactttgggaacatttttag

Basic information

species Glycine max
transcript GLYMA02G06190.3
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G06190.3 (Glycine max), 5'ss of exon 4
lower sequence: GRMZM2G054247_T01 (Zea mays), 5'ss of exon 3
TTGATTGTGCTGTACGTGGATTTCAAGCTTGATGAGAGTTACACGCCGAGCAAAGTTTCCATCCGTGCCGGTGATGGTTTTCACAACTTGAAGgtaaattttttttttattggtttgggtttgattgggttggttatggttaattatttggtgatgactttgggaacatttttag--------------------
| ||||||| ||||||||||||||||| || |||||||||||||||||||| | |||||||| ||||| ||||| || |||||| | |||||| ||||| | || | | ||||| || || | | | | || || ||| | || ||
CTCGTTGTGCTCTACGTGGATTTCAAGCTCGACGAGAGTTACACGCCGAGCAAGATCTCCATCCGGGCCGGGGATGGCTTCCACAACCTAAAGgtacgctttttctccatgagatatcatttga--aggatgttcagaacctagtcggctgtaatagatttaaacaagattatacatgttgattcgtccgagttg

upper sequence: GLYMA02G06190.3 (Glycine max), 5'ss of exon 4
lower sequence: GRMZM2G174971_T01 (Zea mays), 5'ss of exon 3
TTGATTGTGCTGTACGTGGATTTCAAGCTTGATGAGAGTTACACGCCGAGCAAAGTTTCCATCCGTGCCGGTGATGGTTTTCACAACTTGAAGgtaaattttttttttattggtttgggtttgattgggttggttatggttaattatttggtgatgactttgggaacatttttag------------------
| ||| || ||||||||||||||||| || ||||| |||||||| ||||| | |||||||| ||||| ||||| || |||||| | |||||| || || | || | | |||| || | | | | || | || || | || | ||
CTTGTTGCTCTCTACGTGGATTTCAAGCTCGACGAGAGCTACACGCCCAGCAAGATCTCCATCCGGGCCGGGGATGGCTTCCACAACCTCAAGgtatgcttgttctccatgagatattgttttgaaggatgttcaagaacttgtcgggtgtagtagatttaagcaagagttaacatgttgattcgtccgagtt

upper sequence: GLYMA02G06190.3 (Glycine max), 5'ss of exon 4
lower sequence: Vv04s0023g01940.t01 (Vitis vinifera), 5'ss of exon 3
TTGATTGTGCTGTACGTGGATTTCAAGCTTGATGAGAGTTACACGCCGAGCAAAGTTTCCATCCGTGCCGGTGATGGTTTTCACAACTTGAAGgtaaattttttttttattggtttgggtttg--attgggttggttatggttaattat-ttggtgatgactttgggaacatttttag----------------
|| |||| | || |||||||||||||| || ||||| ||||||||||| || | || || || ||||| ||||| || |||||||||||||| | | ||| |||| | | ||| ||| | | || | | ||| ||||| | | | | | ||
CTGGTTGTAATTTATGTGGATTTCAAGCTGGACGAGAGCTACACGCCGAGTAAGATCTCTATTCGAGCCGGAGATGGCTTCCACAACTTGAAGgtgactacagcattt-ttggctcgttcttgtgattttgaagcttcttaggacttacattggtagtagaatcgtgcttaggactaaatgctatgttcggttg

upper sequence: GLYMA02G06190.3 (Glycine max), 5'ss of exon 4
lower sequence: EFJ26697 (Selaginella moellendorffii), 5'ss of exon 2
-------TTGATTGTGCTGTACGTGGATTTCAAGCTTGATGAGAGTTACACGCCGAGCAAAGTTTCCATCCGTGCCGGTGATGGTTTTCACAACTTGAAGgtaaattttttttttattggtttgggtttgattgggttggttatggttaattatttggtgatgactttgggaacatttttag
|| | | | | ||||||||||||||||| |||||||| |||||||| | ||| | || | || | || || ||| | |||||| |||| ||| |||| || || | | || || || | | | || | | |
CTTGCAGCTGCTGGCGATTTACGTGGATTTCAAGCTGGATGAGAGCTACACGCCCAACAAGATCTCGGTGCGCACTGGAAATTCTTTCTATGACTTGAGGgtatgtttacttttcgtt--cttcgtctcgactgtgtcaacaaaatctctcttttctcttcctcttccaag-----------

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|298182568|gb|HO031303.1|HO031303
EST:     CGCTGAGCAAAGTTTCCATCCGTGCCGGTGA-GGTTTTCACAACTTGAAG                         GAGATTAAGACCGTGGAACTCGTGAAGCCAACTGGGTGGGTTTATCTATCC
genomic: CGCCGAGCAAAGTTTCCATCCGTGCCGGTGATGGTTTTCACAACTTGAAGgtaaattttt ... acatttttagGAGATTAAGACCGTGGAACTCGTGAAGCCAACTGGGTGGGTTTATCTATCC
EST: gi|192310829|gb|FK000315.1|FK000315
EST:     CGCCGAGCAAAGTTTCCATCCGTGCCGGTGATGGTTTTCACAACTTGAAG                         GAGATTAAGACCGTGGAACTCGTGAAGCCAACTGGGTGGGTTTATCTATCC
genomic: CGCCGAGCAAAGTTTCCATCCGTGCCGGTGATGGTTTTCACAACTTGAAGgtaaattttt ... acatttttagGAGATTAAGACCGTGGAACTCGTGAAGCCAACTGGGTGGGTTTATCTATCC
EST: gi|58024926|gb|CX711667.1|CX711667
EST:     CGCCGAGCAAAGTTTCCATCCGTGCCGGTGATGGTTTTCAAAACTTGAAG                         GAGATTAAGACCGTGGAACTCGTGAAGCCAACTGGGTGGGTTTATCTATCC
genomic: CGCCGAGCAAAGTTTCCATCCGTGCCGGTGATGGTTTTCACAACTTGAAGgtaaattttt ... acatttttagGAGATTAAGACCGTGGAACTCGTGAAGCCAACTGGGTGGGTTTATCTATCC
EST: gi|151407570|gb|EV277385.1|EV277385
EST:     CGCCGAGCAAAGTT-CCATCCGTGCCGGTGATGGTTTTCACAACTTGAAG                         GAGATTAAGACCGTGGAACTCGTGAAGCCAACTGGGTGGGTTTATCTATCC
genomic: CGCCGAGCAAAGTTTCCATCCGTGCCGGTGATGGTTTTCACAACTTGAAGgtaaattttt ... acatttttagGAGATTAAGACCGTGGAACTCGTGAAGCCAACTGGGTGGGTTTATCTATCC
EST: gi|193723936|gb|FK656314.1|FK656314
EST:     CGCCGAGCAAAGTTTCCATCCGTGCCGGTGATGGTTTTCACAACTTGAAG                         GAGATTAAGACCGTGGAACTCGTGAAGCCAACTGGGTGGGTTTATCTATCC
genomic: CGCCGAGCAAAGTTTCCATCCGTGCCGGTGATGGTTTTCACAACTTGAAGgtaaattttt ... acatttttagGAGATTAAGACCGTGGAACTCGTGAAGCCAACTGGGTGGGTTTATCTATCC
EST: gi|209711476|gb|BW665228.1|BW665228
EST:     CGCCGAGCAAAGTTTCCATCCGTGCCGGTGATGGTTTTCACAACTTGAAG                         GAGATTAAGACCGTGGAACTCGTGAAGCCAACTGGGTGGGTTTATCTATCC
genomic: CGCCGAGCAAAGTTTCCATCCGTGCCGGTGATGGTTTTCACAACTTGAAGgtaaattttt ... acatttttagGAGATTAAGACCGTGGAACTCGTGAAGCCAACTGGGTGGGTTTATCTATCC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTGATTGTGCTGTACGTGGATTTCAAGCTTGATGAGAGTTACACGCCGAGCAAAGTTTCCATCCGTGCCGGTGATGGTTTTCACAACTTGAAGgtaaattttttttttattggtttgggtttgattgggttggttatggttaattatttggtgatgactttgggaacatttttag

- - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG