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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGTGCTCTTGGGGCAAGGCTTACTGGAGCTGGATGGGGTGGTTGTGCTGTTGCTTTGGTGAAAGAGAGCATAGTTCCACAATTTATCCTTAATTTGAAGgtttgttatcatattattcttgacattcctaattaatcgttggagatttggagctaacaagttgtcaatgctgaattttatatccattgcag

Basic information

species Glycine max
transcript GLYMA07G36610.1
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G36610.1 (Glycine max), 5'ss of exon 12
lower sequence: Vv05s0077g00690.t01 (Vitis vinifera), 5'ss of exon 12
TGGTGCTCTTGGGGCAAGGCTTACTGGAGCTGGATGGGGTGGTTGTGCTGTTGCTTTGGTGAAAGAGAGCATAGTTCCACAATTTATCCTTAATTTGAAGgtttgttatca--tattattcttgacattcctaattaatcgttggagatttggagctaacaagttgtcaatgctgaattttatatccattgcag
||| || ||||| ||||||||||||||||||||||||||||||||||| ||||| ||||||||||||||||| || |||||||| || || ||||||||||| ||||  |   |   |    ||  |||||    |     ||  | |        |   |  ||    ||  ||| ||  ||     |  |||
TGGAGCGCTTGGAGCAAGGCTTACTGGAGCTGGATGGGGTGGTTGTGCAGTTGCCTTGGTGAAAGAGAGCATTGTCCCACAATTCATTCTAAATTTGAAGgtctgtttcctactcccaaagctggaattccactctctctcttacaaaagcaagtttttgacattagacatcatga-ttccatgcttttatcag

upper sequence: GLYMA07G36610.1 (Glycine max), 5'ss of exon 12
lower sequence: PP1S89_154V6.1 (Physcomitrella patens), 5'ss of exon 10
TGGTGCTCTTGGGGCAAGGCTTACTGGAGCTGGATGGGGTGGTTGTGCTGTTGCTTTGGTGAAAGAGAGCATAGTTCCACAATTTATCCTTAATTTGAAGgtttgt-----tatcatattattct-tgacattcctaattaa-----tcgttggag---------atttggagctaacaagtt-gtcaatgctgaatttt----atatccat-tgcag
 |||||  | || |||||| | ||||||||||| ||||||||||||| ||||||| |||| || ||      |||       || |||  |    | ||||| ||       |||     |  || |||       ||| ||     || ||| |          || |  | |||    | |  |||||  |    |||    || ||| | |||||
CGGTGCAATAGGAGCAAGGTTGACTGGAGCTGGTTGGGGTGGTTGTGTTGTTGCTCTGGTCAAGGAAGAGGAAGTGGATTCTTTCATCTCTGCCCTCAAGgtatgcatccccatctccccaccctgtgaacgataaaatcaacgggttcattgaaattggtgtgtatctccaactagtgggctcatcaatattagtgtttctggatgtccttgtgcag
















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|22931426|gb|BU548565.1|BU548565
EST:     TTGCTTTGGTGAAAGAGAGCATAGTTCCACAATTTATCCTTAATTTGAAG                         GAATGTTTCTACCAGTCTAGAATAGACAAGGGCGTTATTAAGAAGAACGAT
genomic: TTGCTTTGGTGAAAGAGAGCATAGTTCCACAATTTATCCTTAATTTGAAGgtttgttatc ... tccattgcagGAATGTTTCTACCAGTCTAGAATAGACAAGGGCGTTATTAAGAAGAACGAT
EST: gi|12774697|gb|BG239624.1|BG239624
EST:     TTGCTTTGGTGAAAGAGAGCATAGTTCCACAATTTATCCTTAATTTGAAG                         GAATGTTTCTACCAGTCTAGAATAGACAAGGGCGTTATTAAGAAGAACGAT
genomic: TTGCTTTGGTGAAAGAGAGCATAGTTCCACAATTTATCCTTAATTTGAAGgtttgttatc ... tccattgcagGAATGTTTCTACCAGTCTAGAATAGACAAGGGCGTTATTAAGAAGAACGAT
EST: gi|151408720|gb|EV278528.1|EV278528
EST:     TTGCTTTGGTGAAAGAGAGCATAGTTCCACAATTTATCCTTAATTTGAAG                         GAACGTTTCTACCAGTCTAGAATAGACAAGGGCGTTATTAAGAAGAACGAT
genomic: TTGCTTTGGTGAAAGAGAGCATAGTTCCACAATTTATCCTTAATTTGAAGgtttgttatc ... tccattgcagGAATGTTTCTACCAGTCTAGAATAGACAAGGGCGTTATTAAGAAGAACGAT
EST: gi|31467576|gb|CD409604.1|CD409604
EST:     TTGCTTTGGTGAAAGAGAGCATAGTTCCACAATTTATCCTTAATTTGAAG                         GAATGTTTCTACCAGTCTAGAATAGACAAGGGCGTTATTAAGAAGAACGAT
genomic: TTGCTTTGGTGAAAGAGAGCATAGTTCCACAATTTATCCTTAATTTGAAGgtttgttatc ... tccattgcagGAATGTTTCTACCAGTCTAGAATAGACAAGGGCGTTATTAAGAAGAACGAT
EST: gi|6746917|gb|AW317373.1|AW317373
EST:     TTGCTTTGGTGAAAGAGAGCATAGTTCCACAATTTATCCTTAATTTGAAG                         GAATGTTTCTACCACTCTAGAATAGACAAGGGCGTTATTAAGAAGAACGAT
genomic: TTGCTTTGGTGAAAGAGAGCATAGTTCCACAATTTATCCTTAATTTGAAGgtttgttatc ... tccattgcagGAATGTTTCTACCAGTCTAGAATAGACAAGGGCGTTATTAAGAAGAACGAT
EST: gi|15661572|gb|BI698943.1|BI698943
EST:     TTGCTTTGGTGAAAGAGAGCATAGTTCCACAATTTATCCTTAATTTGAAG                         GAATGTTTCTACCAGTCTAGAATAGACAAGGGCGTTATTAAGAAGAACGAT
genomic: TTGCTTTGGTGAAAGAGAGCATAGTTCCACAATTTATCCTTAATTTGAAGgtttgttatc ... tccattgcagGAATGTTTCTACCAGTCTAGAATAGACAAGGGCGTTATTAAGAAGAACGAT
EST: gi|213607524|gb|DB978447.1|DB978447
EST:     TTGCTTTGGTGAAAGAGAGCATAGTTCCACAATTTATCCTTAATTTGAAG                         GAATGTTTCTACCAGTCTAGAATAGACAAGGGCGTTATTAAGAAGAACGAT
genomic: TTGCTTTGGTGAAAGAGAGCATAGTTCCACAATTTATCCTTAATTTGAAGgtttgttatc ... tccattgcagGAATGTTTCTACCAGTCTAGAATAGACAAGGGCGTTATTAAGAAGAACGAT
EST: gi|13482134|gb|BG511477.1|BG511477
EST:     TTGCTTTGGTGAAAGAGAGCATAGTTCCACAATTTATCCTTAATTTGAAG                         GAATGTTTCTACCAGTCTAGAATAGACAAGGGCGTTATTAAGAAGAACGAT
genomic: TTGCTTTGGTGAAAGAGAGCATAGTTCCACAATTTATCCTTAATTTGAAGgtttgttatc ... tccattgcagGAATGTTTCTACCAGTCTAGAATAGACAAGGGCGTTATTAAGAAGAACGAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGGTGCTCTTGGGGCAAGGCTTACTGGAGCTGGATGGGGTGGTTGTGCTGTTGCTTTGGTGAAAGAGAGCATAGTTCCACAATTTATCCTTAATTTGAAGgtttgttatcatattattcttgacattcctaattaatcgttggagatttggagctaacaagttgtcaatgctgaattttatatccattgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG