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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTTGATGAGAAGTGGGTTCCTGATTCAGATGTTATTACTCAAACATTGGAAGAGAAGTATCCCAGCCCACCATTGGTGACCCCACCTGAAAGGGCCACAGcgtatgcatttggcttgtagatctagttgttcttagtggtacactgctttgaacttttagaaaaatggatgatgaactcatacacgcttaaacaaagtgg...

Basic information

species Glycine max
transcript GLYMA18G04510.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G04510.1 (Glycine max), 5'ss of exon 3
lower sequence: AT5G16710.1 (Arabidopsis thaliana), 5'ss of exon 3
TTTGATGAGAAGTGGGTTCCTGATTCAGATGTTATTACTCAAACATTGGAAGAGAAGTATCCCAGCCCACCATTGGTGACCCCACCTGAAAGGGCCACAGcgtatgcattt---------------ggcttgtagatctagttgttctta-gtggtacactgctttgaacttttag---aaaaatggatgatg----aactcatacacgcttaaacaaagtgg--------------------------------------------
 |||||||||| |||||||| |||||||||||||| || ||  | || ||||||||||||||    || ||  | |  ||||||||||||| |||  ||| ||| |||||                ||  |   |||  | ||||| ||  |   |  ||    | |   | || |   ||||| || | ||     ||||   | ||    |   ||                                                 
-TTGATGAGAAATGGGTTCCGGATTCAGATGTTATAACACAGGCTTTAGAAGAGAAGTATCCTGAGCCTCCTCTTGCTACCCCACCTGAAAAGGCTTCAGTgtaagcattccttcttctttttttcggtcttatgatgcacttgtttttgtgcaattgaccttctagtgttctttgttgaaaaagggttcatttgacaacttgcatacttccagctaagaatttgcgtgtggacgtttaattctttaatttatgtctgtttctgcag
















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|213588679|gb|DB957687.1|DB957687
EST:     AGAGAAGTATCCCAGCCCACCATTGGTGACCCCACCTGANAGGGCCACAG                         CGGGGTCAAAGATCTTTTCTACATTTATTGGATTTCTCAAGAGCAAGGATC
genomic: AGAGAAGTATCCCAGCCCACCATTGGTGACCCCACCTGAAAGGGCCACAGcgtatgcatt ... ttattttgtaGGGGGTCAAAGATCTTTTCTACATTTATTGGATTTCTCAAGAGCAAGGATC
EST: gi|14011388|gb|BG726302.1|BG726302
EST:     ATTGGTGACCCCACCTGAAAGGGCCACAG                         CGGGGTCAAAGATCTTTTCTACATTTATTGGATTTCTCAAGAGCAAGGATC
genomic: ATTGGTGACCCCACCTGAAAGGGCCACAGcgtatgcatt ... ttattttgtaGGGGGTCAAAGATCTTTTCTACATTTATTGGATTTCTCAAGAGCAAGGATC
EST: gi|23064418|gb|BU579191.1|BU579191
EST:     AGAGAAGTATCCCAGCCCACCATTGGTGACCCCACCTGAAAGGGCCACAG                         CGGGGTCAAAGATCTTTTCTACATTTATTGGATTTCTCAAGAGCAAGGATC
genomic: AGAGAAGTATCCCAGCCCACCATTGGTGACCCCACCTGAAAGGGCCACAGcgtatgcatt ... ttattttgtaGGGGGTCAAAGATCTTTTCTACATTTATTGGATTTCTCAAGAGCAAGGATC
EST: gi|192322908|gb|FK014839.1|FK014839
EST:     AGAGAAGTATCCCAGCCCACCATTGGTGACCCCACCTGAAAGGGCCACAG                         CGGGGTCAAAGATCTTTTCTACATTTATTGGATTTCTCGAGAGCAAGGATC
genomic: AGAGAAGTATCCCAGCCCACCATTGGTGACCCCACCTGAAAGGGCCACAGcgtatgcatt ... ttattttgtaGGGGGTCAAAGATCTTTTCTACATTTATTGGATTTCTCAAGAGCAAGGATC
EST: gi|298177053|gb|HO023414.1|HO023414
EST:     AGAGAAGTATCCCAGCCCACCATTGGTGACCCCACCTGAAAGGGCCACAG                         CGGGGTCAAAGATCTTTTCTACATTTATTGGATTTCTCAAGA
genomic: AGAGAAGTATCCCAGCCCACCATTGGTGACCCCACCTGAAAGGGCCACAGcgtatgcatt ... ttattttgtaGGGGGTCAAAGATCTTTTCTACATTTATTGGATTTCTCAAGA
EST: gi|207764166|gb|GD737981.1|GD737981
EST:     AGAGAAGTATCCCAGCCCACCATTGGTGACCCCACCTGAAAGGGCCACAG                         CGGGGTCAAAGATCTTTTCTACATTTATTGGATTTCTCAAGAGCAAGGATC
genomic: AGAGAAGTATCCCAGCCCACCATTGGTGACCCCACCTGAAAGGGCCACAGcgtatgcatt ... ttattttgtaGGGGGTCAAAGATCTTTTCTACATTTATTGGATTTCTCAAGAGCAAGGATC
EST: gi|13480266|gb|BG509609.1|BG509609
EST:     AGAGAAGTATCCCAGCCCACCATTGGTGACCCCACCTGAAAGGGCCACAG                         CGGGGTCAAAGATCTTTTCTACATTTATTGGATTTCTCAAGAGCAAGGATC
genomic: AGAGAAGTATCCCAGCCCACCATTGGTGACCCCACCTGAAAGGGCCACAGcgtatgcatt ... ttattttgtaGGGGGTCAAAGATCTTTTCTACATTTATTGGATTTCTCAAGAGCAAGGATC
EST: gi|151410703|gb|EV280518.1|EV280518
EST:     AGAGAAGTATCCCAGCCCACCATTGGTGACCCCACCTGAAAGGGCCACAG                         CGGGGTCAAAGATCTTTTCTACATTTATTGGATTTCTCAAGAGCAAGGATC
genomic: AGAGAAGTATCCCAGCCCACCATTGGTGACCCCACCTGAAAGGGCCACAGcgtatgcatt ... ttattttgtaGGGGGTCAAAGATCTTTTCTACATTTATTGGATTTCTCAAGAGCAAGGATC
EST: gi|23726127|gb|BU761045.1|BU761045
EST:     AGAGAAGTATCCCAGCCCACCATTGGTGACCCCACCTGAAAGGGCCACAG                         CGGGGTCAAAGATCTTTTCTACATTTATTGGATTTCTCAAGAGCAAGGATC
genomic: AGAGAAGTATCCCAGCCCACCATTGGTGACCCCACCTGAAAGGGCCACAGcgtatgcatt ... ttattttgtaGGGGGTCAAAGATCTTTTCTACATTTATTGGATTTCTCAAGAGCAAGGATC
EST: gi|209721279|gb|BW665773.1|BW665773
EST:     AGAGAAGTATCCCAGCCCACCATTGGTGACCCCACCTGAAAGGGCCACAG                         CGGGGTCAAAGATCTTTTCTACATTTATTGGATTTCTCAAGAGCAAGGATC
genomic: AGAGAAGTATCCCAGCCCACCATTGGTGACCCCACCTGAAAGGGCCACAGcgtatgcatt ... ttattttgtaGGGGGTCAAAGATCTTTTCTACATTTATTGGATTTCTCAAGAGCAAGGATC
EST: gi|298194148|gb|HO040796.1|HO040796
EST:     AGAGAAGTATCCCAGCCCACCATTGGTGACCCCACCTGAAAGGGCCACAG                         CGGGGTCAAAGATCTTTTCTACATTTATTGGATTTCTCAAGAGCAAGGATC
genomic: AGAGAAGTATCCCAGCCCACCATTGGTGACCCCACCTGAAAGGGCCACAGcgtatgcatt ... ttattttgtaGGGGGTCAAAGATCTTTTCTACATTTATTGGATTTCTCAAGAGCAAGGATC
EST: gi|9259381|gb|BE347528.1|BE347528
EST:     AGAGAAGTATCCCAGCCCACCATTGGTGACCCCACCTGAAAGGGCCACAG                         CGGGGTCAAAGATCTTTTCTACATTTATTGGATTTCTCAAGAGCAAGGATC
genomic: AGAGAAGTATCCCAGCCCACCATTGGTGACCCCACCTGAAAGGGCCACAGcgtatgcatt ... ttattttgtaGGGGGTCAAAGATCTTTTCTACATTTATTGGATTTCTCAAGAGCAAGGATC
EST: gi|298199108|gb|HO042471.1|HO042471
EST:     AGAGAAGTATCCCAGCCCACCATTGGTGACCCCACCTGAAAGGGCCACAG                         CGGGGTCAAAGATCTTTTCTACATTTATTGGATTTCTCAAGAGCAAGGATC
genomic: AGAGAAGTATCCCAGCCCACCATTGGTGACCCCACCTGAAAGGGCCACAGcgtatgcatt ... ttattttgtaGGGGGTCAAAGATCTTTTCTACATTTATTGGATTTCTCAAGAGCAAGGATC
EST: gi|117557695|gb|EG702080.1|EG702080
EST:     AGAGAAGTATCCCAGCCCACCATTGGTGACCCCACCTGAAAGGGCCACAG                         CGGGGTCAAAGATCTTTTCTACACTTATTGGATTTCTCAAGAGCAAGGATC
genomic: AGAGAAGTATCCCAGCCCACCATTGGTGACCCCACCTGAAAGGGCCACAGcgtatgcatt ... ttattttgtaGGGGGTCAAAGATCTTTTCTACATTTATTGGATTTCTCAAGAGCAAGGATC
EST: gi|15285066|gb|BI468957.1|BI468957
EST:     AGAGAAGTATCCCAGCCCACCATTGGTGACCCCACCTGAAAGGGCCACAG                         CGGGGTCAAAGATCTTTTCTACATTTATTGGATTTCTCAAGAGCAAGGATC
genomic: AGAGAAGTATCCCAGCCCACCATTGGTGACCCCACCTGAAAGGGCCACAGcgtatgcatt ... ttattttgtaGGGGGTCAAAGATCTTTTCTACATTTATTGGATTTCTCAAGAGCAAGGATC
EST: gi|6070095|gb|AW099652.1|AW099652
EST:     AGAGAAGTATCCCAGCCCACCATTGGTGACCCCACCTGAAAGGGCCACAG                         CGGGGTCAAAGATCTTTTCTACATTTATTGGATTTCTCAAGAGCAAGGATC
genomic: AGAGAAGTATCCCAGCCCACCATTGGTGACCCCACCTGAAAGGGCCACAGcgtatgcatt ... ttattttgtaGGGGGTCAAAGATCTTTTCTACATTTATTGGATTTCTCAAGAGCAAGGATC
EST: gi|5820109|gb|AI988315.1|AI988315
EST:     AGAGAAGTATCCCAGCCCACCATTGGTGACCCCACCTGAAAGGGCCACAG                         CGGGGTCAAAGATCTTTTCTACATTTATTGGATTTCTCAAGAGCAAGGATC
genomic: AGAGAAGTATCCCAGCCCACCATTGGTGACCCCACCTGAAAGGGCCACAGcgtatgcatt ... ttattttgtaGGGGGTCAAAGATCTTTTCTACATTTATTGGATTTCTCAAGAGCAAGGATC
EST: gi|17963072|gb|BM269825.1|BM269825
EST:     AGAGAAGTATCCCAGCCCACCATTGGTGACCCCACCTGAAAGGGCCACAG                         CGGGGTCAAAGATCTTTTCTACATTTATTGGATTTCTCAAGAGCAAGGATC
genomic: AGAGAAGTATCCCAGCCCACCATTGGTGACCCCACCTGAAAGGGCCACAGcgtatgcatt ... ttattttgtaGGGGGTCAAAGATCTTTTCTACATTTATTGGATTTCTCAAGAGCAAGGATC
EST: gi|151395906|gb|EV265783.1|EV265783
EST:     AGAGAAGTATCCCAGCCCACCATTGGTGACCCCACCTGAAAGGGCCACAG                         CGGGGTCAAAGATCTTTTCTACATTTATTGGATTTCTCAAGAGCAAGGATC
genomic: AGAGAAGTATCCCAGCCCACCATTGGTGACCCCACCTGAAAGGGCCACAGcgtatgcatt ... ttattttgtaGGGGGTCAAAGATCTTTTCTACATTTATTGGATTTCTCAAGAGCAAGGATC
EST: gi|298168940|gb|HO009870.1|HO009870
EST:     AGAGAAGTATCCCAGCCCACCATTGGTGACCCCACCTGAAAGGGCCACAG                         CGGGGTCAAAGATCTTTTCTACATTTATTGGATTTCTCAAGAGCAAGGATC
genomic: AGAGAAGTATCCCAGCCCACCATTGGTGACCCCACCTGAAAGGGCCACAGcgtatgcatt ... ttattttgtaGGGGGTCAAAGATCTTTTCTACATTTATTGGATTTCTCAAGAGCAAGGATC
EST: gi|7796708|gb|AW782102.1|AW782102
EST:     AGAGAAGTATCCCAGCCCACCATTGGTGACCCCACCTGAAAGGGCCACAG                         CGGGGTCAAAGATCTTTTCTACATTTATTGGATTTCTCAAGAGCAAGGATC
genomic: AGAGAAGTATCCCAGCCCACCATTGGTGACCCCACCTGAAAGGGCCACAGcgtatgcatt ... ttattttgtaGGGGGTCAAAGATCTTTTCTACATTTATTGGATTTCTCAAGAGCAAGGATC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTTGATGAGAAGTGGGTTCCTGATTCAGATGTTATTACTCAAACATTGGAAGAGAAGTATCCCAGCCCACCATTGGTGACCCCACCTGAAAGGGCCACAGcgtatgcatttggcttgtagatctagttgttcttagtggtacactgctttgaacttttagaaaaatggatgatgaactcatacacgcttaaacaaagtgg

- - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT