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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TAGTTACTATGCAGTAATACTAAAGGTTGATGAGGAAGAGTTTGGCGGTCATGGAGCCCTCCTTCAAGAGGGGCTATTTGCTTCCATAACTCTTTTCCTGgtaatttactatgttggtcattgctttgtccactctagaaaatgaggcttttactgttctacaatctgacttcacttttgatatctgtgcag

Basic information

species Glycine max
transcript GLYMA11G14780.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G14780.1 (Glycine max), 5'ss of exon 3
lower sequence: LOC_Os05g01994.1 (Oryza sativa), 5'ss of exon 3
TAGTTACTATGCAGTAATACTAAAGGTTGATGAGGAAGAGTTTGGCGGTCATGGAGCCCTCCTTCAAGAGGGGCTATTTGCTTCCATAACTCTTTTCCTGgtaattt--actatgttggtcattgctttgtccactctagaaaatgaggcttttactgttctacaatctgacttcacttttgatatctgtgcag
  | |||||||||    |  | ||| ||||||||||||| ||||| || |||||||| || ||||| |||||  | ||||| ||  | ||||||||||||||||     |  |  |     ||| || |  | || ||      |   | || |  || |    || |||| ||  ||| |  | |   |||||
CTGGTACTATGCATACCTGTTGAAGATTGATGAGGAAGACTTTGGAGGCCATGGAGCACTACTTCAGGAGGGAATGTTTGCCTCTTTCACTCTTTTCCTGgtaaaaagaaaaacataaccaatttctgtaactaccctgt----ttccgtttgttttggttcgaaa-ctgaatttgcttct--ttttgctgcag

upper sequence: GLYMA11G14780.1 (Glycine max), 5'ss of exon 3
lower sequence: Vv06s0004g04920.t01 (Vitis vinifera), 5'ss of exon 3
TAGTTACTATGCAGTAATACTAAAGGTTGATGAGGAAGAGTTTGGCGGTCATGGAGCCCTCCTTCAAGAGGGGCTATTTGCTTCCATAACTCTTTTCCTGgtaatttactatgttggtcattgctttgtccactctagaaaatgaggcttt-tactgttctacaatctgacttcacttttgatatctgtgcag----
| |||| |||||| ||||||||||| ||||||| ||||| ||||| |||||||| |||||||| ||||||||||| |||||||| ||||| || ||||||||| ||  |    |   ||  |  ||||||      |     |   | | | ||  |    |  |    | ||    |||| |||||    |     
TGGTTATTATGCAATAATACTAAAGATTGATGAAGAAGATTTTGGTGGTCATGGGGCCCTCCTCCAAGAGGGGCTTTTTGCTTCTATAACGCTCTTCCTGgtacttatcgccatatctcggttatttgtcgttgggaatctttcttgttatgtatggagtgagtaatgaattttttctttggtatcttcttattcag
















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|10255455|gb|BE823221.1|BE823221
EST:     ATGGAGCNNNNNTTCAAGAGGGGCTATTTGCTTCCATAACTCTTTTCCTG                         CTTTCCTGGATTTTAGTTTACAGTTTAGCACACTTCTGATTGGCTGGGCAT
genomic: ATGGAGCCCTCCTTCAAGAGGGGCTATTTGCTTCCATAACTCTTTTCCTGgtaatttact ... atctgtgcagCTTTCCTGGATTTTAGTTTACAGTTTAGCACACTTCTGATTGGCTGGGCAT
EST: gi|6341410|gb|AW164234.1|AW164234
EST:     ATGGAGCCCTCCTTCAAGAGGGGCTATTTGCTTCCATAACTCTTTTCCTG                         CTGTCCTGGATTTTAGTTTACAGTTTAGCACACTTCTGATTGGCTGGGCAT
genomic: ATGGAGCCCTCCTTCAAGAGGGGCTATTTGCTTCCATAACTCTTTTCCTGgtaatttact ... atctgtgcagCTTTCCTGGATTTTAGTTTACAGTTTAGCACACTTCTGATTGGCTGGGCAT
EST: gi|209706551|gb|BW667816.1|BW667816
EST:     ATGGAGCCCTCCTTCAAGAGGGGCTATTTGCTTCCATAACTCTTTTCCTG                         CTTTCCTGGATTTTAGTTTACAGTTTAGCACACTTCTGATTGGCTGGGCAT
genomic: ATGGAGCCCTCCTTCAAGAGGGGCTATTTGCTTCCATAACTCTTTTCCTGgtaatttact ... atctgtgcagCTTTCCTGGATTTTAGTTTACAGTTTAGCACACTTCTGATTGGCTGGGCAT
EST: gi|213589493|gb|DB973201.1|DB973201
EST:     ATGGAGCCCTCCTTCAAGAGGGGCTATTTGCTTCCATAACTCTTTTCCTG                         CTTTCCTGGATTTTAGTTTACAGTTTAGCACACTTCTGATTGGCTGGGCAT
genomic: ATGGAGCCCTCCTTCAAGAGGGGCTATTTGCTTCCATAACTCTTTTCCTGgtaatttact ... atctgtgcagCTTTCCTGGATTTTAGTTTACAGTTTAGCACACTTCTGATTGGCTGGGCAT
EST: gi|209708896|gb|BW673905.1|BW673905
EST:     TTGCTTCCATAACTCTTTTCCTG                         CTTTCCTGGATTTTAGTTTACAGTTTAGCACACTTCTGATTGGCTGGGCAT
genomic: TTGCTTCCATAACTCTTTTCCTGgtaatttact ... atctgtgcagCTTTCCTGGATTTTAGTTTACAGTTTAGCACACTTCTGATTGGCTGGGCAT
EST: gi|192320694|gb|FK012776.1|FK012776
EST:     ATGGAGCCCTCCTTCGAGAGGGGCTATTTGCTTCCATAACTCTTTTCCTG                         CTTTCCTGGATTTTAGTTTACAGTTTAGCACACTTCTGATTGGCTGGGCAT
genomic: ATGGAGCCCTCCTTCAAGAGGGGCTATTTGCTTCCATAACTCTTTTCCTGgtaatttact ... atctgtgcagCTTTCCTGGATTTTAGTTTACAGTTTAGCACACTTCTGATTGGCTGGGCAT
EST: gi|26058544|gb|CA801458.1|CA801458
EST:     ATGGAGCCCTCCTTCAAGAGGGGCTATTTGCTTCCATAACTCTTTTCCTG                         CTTTCCCTGGATTT-AGTTTACAGTTTAGCACACTTC
genomic: ATGGAGCCCTCCTTCAAGAGGGGCTATTTGCTTCCATAACTCTTTTCCTGgtaatttact ... atctgtgcagCTTTCC-TGGATTTTAGTTTACAGTTTAGCACACTTC
EST: gi|209712747|gb|BW681601.1|BW681601
EST:     ATGGAGCCCTCCTTCAAGAGGGGCTATTTGCTTCCATAACTCTTTTCCTG                         CTTTCCTGGATTTTAGTTTACAGTTTAGCACACTTCTGATTGGCTGGGCAT
genomic: ATGGAGCCCTCCTTCAAGAGGGGCTATTTGCTTCCATAACTCTTTTCCTGgtaatttact ... atctgtgcagCTTTCCTGGATTTTAGTTTACAGTTTAGCACACTTCTGATTGGCTGGGCAT
EST: gi|192320693|gb|FK012775.1|FK012775
EST:     ATGGAGCCCTCCTTCGAGAGGGGCTATTTGCTTCCATAACTCTTTTCCTG                         CTTTCCTGGATTTTAGTTTACAGTTTAGCACACTTCTGATTGGCTGGGCAT
genomic: ATGGAGCCCTCCTTCAAGAGGGGCTATTTGCTTCCATAACTCTTTTCCTGgtaatttact ... atctgtgcagCTTTCCTGGATTTTAGTTTACAGTTTAGCACACTTCTGATTGGCTGGGCAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TAGTTACTATGCAGTAATACTAAAGGTTGATGAGGAAGAGTTTGGCGGTCATGGAGCCCTCCTTCAAGAGGGGCTATTTGCTTCCATAACTCTTTTCCTGgtaatttactatgttggtcattgctttgtccactctagaaaatgaggcttttactgttctacaatctgacttcacttttgatatctgtgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG