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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTGTAAGTGAGTATGCTGTGACTGGAAAAGATGCTGGGACAGGAAGCCTCTTGGCAGCCCTAGCTGAAGCTGGGTTCCTTATTGGACTGGAAAAGAACAGgtttacatttattatgaagttttcattaagtattttatctagggcaaggtttgaaactttgaacttttgcccaaaccacacatgcaagagattttttata...

Basic information

species Glycine max
transcript GLYMA03G27460.2
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G27460.2 (Glycine max), 5'ss of exon 13
lower sequence: LOC_Os07g48750.1 (Oryza sativa), 5'ss of exon 15
TTGTAAGTGAGTATGCTGTGACTGGAAAAGATGCTGGGACAGGAAGCCTCTTGGCAGCCCTAGCTGAAGCTGGGTTCCTTATTGGACTGGAAAAGAACAGgtttacatttattatgaagttttcattaagtattttatctagggcaaggtttgaaactttgaacttt--tgcccaaaccacacatgcaagagattttttata
||||||||||||| |||||||||||||| |||||||| | |||||  ||  | | ||| ||||| || || |  || ||  ||||| | ||||  |||||||| | | | ||  |    ||||     | |||||   ||         | |  | | | ||  | |  ||   || |    |    ||  | |   | |||
TTGTAAGTGAGTACGCTGTGACTGGAAAGGATGCTGGCAAAGGAACACTGGTAGAAGCACTAGCAGAGGCAGCATTTCTCGTTGGATTAGAAAGAAACAGgttaataatcatacttt--ttttagaggaatatttatacttttattttctctccatcatggatttctgctgtgtaagctctgccataaattggtccatgata

upper sequence: GLYMA03G27460.2 (Glycine max), 5'ss of exon 13
lower sequence: AT3G10740.1 (Arabidopsis thaliana), 5'ss of exon 14
TTGTAAGTGAGTATGCTGTGACTGGAAAAGATGCTGGGACAGGAAGCCTCTTGGCAGCCCTAGCTGAAGCTGGGTTCCTTATTGGACTGGAAAAGAACAGgtttacatttattatgaagttttcattaagtattttatctagggcaaggtttgaaactttgaacttttgcccaaaccacacatgcaagagattttttata-
|||| ||||| |||||||| ||||||||||||||||| |||||||||||  | ||  | || || ||||||| ||| || ||||| || |||||||| |||||  | || | | |     | |    | |  ||| ||||     ||      |||| |  ||         ||   | ||||   |  || |||||  | 
TTGTCAGTGAATATGCTGTTACTGGAAAAGATGCTGGTACAGGAAGCCTTCTTGCCTCTCTTGCAGAAGCTGCGTTTCTCATTGGTCTTGAAAAGAATAGgttccctttgaattt----ctcttcccaggc-tttgatctcaactaa------aaacatcaaat--------aagttaaacatcttat-gactttttgcag

upper sequence: GLYMA03G27460.2 (Glycine max), 5'ss of exon 13
lower sequence: Vv08s0040g00320.t01 (Vitis vinifera), 5'ss of exon 15
TTGTAAGTGAGTATGCTGTGACTGGAAAAGATGCTGGGACAGGAAGCCTCTTGGCAGCCCTAGCTGAAGCTGGGTTCCTTATTGGACTGGAAAAGAACAGgtttacatttatt--------atgaagttttcatt-aagtattttatctagggcaaggtttgaaactttgaacttttgccca-aaccacacatgcaagagattttttata
|||| ||||||||||||||||| || |||||||||||  ||||||  || ||||||||  | ||||||||||  ||||| |||||  ||||||||||||||| | |  |  |         |  | ||||||||| || |  || |  |   ||    ||    | ||  ||||| ||  |  ||   |   ||  |   |         
TTGTCAGTGAGTATGCTGTGACAGGTAAAGATGCTGGTTCAGGAACTCTTTTGGCAGCATTGGCTGAAGCTGCATTCCTCATTGGGGTGGAAAAGAACAGgtctgctctgctctcctgaggaaaaggttttcattcaaatgcttgagtttttgcgtaatt----atttcaaacttctgttctcaatttcttttgagaagaaaaa------

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|7796787|gb|AW782181.1|AW782181
EST:     TTGGCAGCCCTAGCTGAAGCTAGGTTCCTTATTGGACTGGAAAAGAACAG                         TGATGTTATCCAAATGGCCAGCTATGCTCCACTTTTTGTTAATGCCAATGA
genomic: TTGGCAGCCCTAGCTGAAGCTGGGTTCCTTATTGGACTGGAAAAGAACAGgtttacattt ... tctggtgcagTGATGTTATCCAAATGGCCAGCTATGCTCCACTTTTTGTTAATGCCAATGA
EST: gi|6134767|gb|AW133160.1|AW133160
EST:     TTGGCAGCCCTAGCTGAAGCTGGGTTCCTTATTGGACTGGAAAAGAACAG                         TGATGTTATCCAAATGGCCAGCTATGCTCCACTTTTTGTTAATGCCAATGA
genomic: TTGGCAGCCCTAGCTGAAGCTGGGTTCCTTATTGGACTGGAAAAGAACAGgtttacattt ... tctggtgcagTGATGTTATCCAAATGGCCAGCTATGCTCCACTTTTTGTTAATGCCAATGA
EST: gi|9819826|gb|BE555402.1|BE555402
EST:     TTGGCAGCCCTAGCTGAAGCTGGGTTCCTTATTGGACTGGAAAAGAACAG                         TGATGTTATCCAAATGGCCAGCTATGCTCCACTTTTTGTTAATGCCAATGA
genomic: TTGGCAGCCCTAGCTGAAGCTGGGTTCCTTATTGGACTGGAAAAGAACAGgtttacattt ... tctggtgcagTGATGTTATCCAAATGGCCAGCTATGCTCCACTTTTTGTTAATGCCAATGA
EST: gi|19348102|gb|BM892634.1|BM892634
EST:     TTGGCAGCCCTAGCTGAAGCTGGGTTCCTTATTGGACTGGAAAAGAACAG                         TGATGTTATCCAAATGGCCAGCTATGCTCCACTTTTTGTTAATGCCAATGA
genomic: TTGGCAGCCCTAGCTGAAGCTGGGTTCCTTATTGGACTGGAAAAGAACAGgtttacattt ... tctggtgcagTGATGTTATCCAAATGGCCAGCTATGCTCCACTTTTTGTTAATGCCAATGA
EST: gi|9899023|gb|BE607991.1|BE607991
EST:     TTGGCAGCCCTAGCTGAAGCTGGGTTCCTTATTGGACTGGAAAAGAACAG                         TGATGTTATCCAAATGGCCAGCTATGCTCCACTTTTTGTTAATGCCAATGA
genomic: TTGGCAGCCCTAGCTGAAGCTGGGTTCCTTATTGGACTGGAAAAGAACAGgtttacattt ... tctggtgcagTGATGTTATCCAAATGGCCAGCTATGCTCCACTTTTTGTTAATGCCAATGA
EST: gi|9819476|gb|BE554989.1|BE554989
EST:     T-GGCAGCCCTAGCTGAAGCTGGTTTC-TTATTGGACTGGAAAAGAACAG                         TGATGT-ATCCAAATG-CCAGCTATTCTTCACTT
genomic: TTGGCAGCCCTAGCTGAAGCTGGGTTCCTTATTGGACTGGAAAAGAACAGgtttacattt ... tctggtgcagTGATGTTATCCAAATGGCCAGCTATGCTCCACTT
EST: gi|298166525|gb|HO009964.1|HO009964
EST:     GGAAAAGAACAG                         TGATGTTATCCAAATGGCCAGCTATGCTCCACTTTTTGTTAATGCCAATGA
genomic: GGAAAAGAACAGgtttacattt ... tctggtgcagTGATGTTATCCAAATGGCCAGCTATGCTCCACTTTTTGTTAATGCCAATGA
EST: gi|9899207|gb|BE608105.1|BE608105
EST:     TTGGCAGCCCTAGCTGAAGCTGGGTTCCTTATTGGACTGGAAAAGAACAG                         TGATGTTATCCAAATGGCCAGCTATGCTCCACTTTTTGTTAATGCCAATGA
genomic: TTGGCAGCCCTAGCTGAAGCTGGGTTCCTTATTGGACTGGAAAAGAACAGgtttacattt ... tctggtgcagTGATGTTATCCAAATGGCCAGCTATGCTCCACTTTTTGTTAATGCCAATGA
EST: gi|22523744|gb|BU082555.1|BU082555
EST:     TTGGCAGCCCTAGCTGAAGCTGGGTTCCTTATTGGACTGGAAAAGAACAG                         TGATGTTATCCAAATGGCCAGCTATGCTCCACTTTTTGTTAATGCCAATGA
genomic: TTGGCAGCCCTAGCTGAAGCTGGGTTCCTTATTGGACTGGAAAAGAACAGgtttacattt ... tctggtgcagTGATGTTATCCAAATGGCCAGCTATGCTCCACTTTTTGTTAATGCCAATGA
EST: gi|51335508|gb|CO979374.1|CO979374
EST:     NTGGCAGCCCTAGCTGAAGCTGGGTTCCTTATTGGACTGGAAAAGAACAG                         TGATGTTATCCAAATGGCCAGCTATGCTCCACTTTTTGTTAATGCCAATGA
genomic: TTGGCAGCCCTAGCTGAAGCTGGGTTCCTTATTGGACTGGAAAAGAACAGgtttacattt ... tctggtgcagTGATGTTATCCAAATGGCCAGCTATGCTCCACTTTTTGTTAATGCCAATGA
EST: gi|27424547|gb|CA936067.1|CA936067
EST:     TTGGCAGCCCTAGCTGAAGCTGGGTTCCTTATTGGACTGGAAAAGAACAG                         TGATGTTATCCAAATGGCCAGCTATGCTCCACTTTTTGTTAATGCCAATGA
genomic: TTGGCAGCCCTAGCTGAAGCTGGGTTCCTTATTGGACTGGAAAAGAACAGgtttacattt ... tctggtgcagTGATGTTATCCAAATGGCCAGCTATGCTCCACTTTTTGTTAATGCCAATGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTGTAAGTGAGTATGCTGTGACTGGAAAAGATGCTGGGACAGGAAGCCTCTTGGCAGCCCTAGCTGAAGCTGGGTTCCTTATTGGACTGGAAAAGAACAGgtttacatttattatgaagttttcattaagtattttatctagggcaaggtttgaaactttgaacttttgcccaaaccacacatgcaagagattttttata

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC