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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGATGATAACACTATAGACTTCATTGGTCATGCTTTGGCGCTTCATAGTGATGATCGCTACTTGGCTGAGCCAGCACTGGACACTGTGAAGAGAATGAAGgtaagtttactgggttattatgcacttgtaatttattctcagtcgtggattcttcttaattgaaaatttcttctgttccatttggttcccattagctatattttgtttcctacttgtag

Basic information

species Glycine max
transcript GLYMA08G13300.3
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G13300.3 (Glycine max), 5'ss of exon 6
lower sequence: Vv05s0094g01550.t01 (Vitis vinifera), 5'ss of exon 6
TGATGATAACACTATAGACTTCATTGGTCATGCTTTGGCGCTTCATAGTGATGATCGCTACTTGGCTGAGCCAGCACTGGACACTGTGAAGAGAATGAAGgt---aagtttactgggttattat-gcacttgtaatttattctcagtcgtggattcttcttaattgaaaatttcttctgttccatttggttcccattagctatattttgtttcctacttg-tag
 ||||| |||||||| || || |||||||||||  | ||||||||||| |||||  ||||| |   |||||| ||| | || ||||||||||||||||||||   || |  |  |||||  |||   ||||     ||   ||  ||  || ||||      | |  || || | ||  ||    |  | | |||| |  |   |  | ||  |||  || |||
CGATGACAACACTATTGATTTTATTGGTCATGCAATAGCGCTTCATAGAGATGACTGCTACCTAAATGAGCCTGCAATTGATACTGTGAAGAGAATGAAGgtgaaaaatgcatagggttcatattatactt----ctttcccttggttttgaattccctcacaatagaagttccatc-atttttgtgagcttccatgaagttcttccttttgactatgtgatag

upper sequence: GLYMA08G13300.3 (Glycine max), 5'ss of exon 6
lower sequence: PP1S20_16V6.1 (Physcomitrella patens), 5'ss of exon 6
TGATGATAACACTATAGACTTCATTGGTCATGCTTTGGCGCTTCATAGTGATGATCGCTACTTGGCTGAGCCAGCACTGGACACTGTGAAGAGAATGAAGgtaag--tttactgggttattatgcact------tgtaatttattctcagtcgtggattcttcttaattg-aaaatttct-tctgttcca----tttggttcccattagctatatt-ttgtttcctacttgtag---
 ||||  ||||| || ||||||||||| ||| |||||||| | ||| |||| ||||| | |||| ||||||||||  |||| || ||||||||| |||||||| |  |||| |   |  | |  ||||      | ||  | |||||   |  |  |  | |  |  |   || |||| | || | || |    |||| |  | |  | ||   || |  |||  | ||||  |   
CGATGCCAACACAATTGACTTCATTGGGCATTCTTTGGCGTTGCATCGTGACGATCGTTTCTTGTCTGAGCCAGCGTTGGATACAGTGAAGAGAGTGAAGgtatgcctttatttcctgctaacacactccctgttatagctcattctgtttaatccacacgttatcttcacaagatttttatcagctctacagttttgttcgctacaacctgagttgtcttttttttcttggtgcag
















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|8404346|gb|BE059980.1|BE059980
EST:     CAGCACTGGACACTGTGAAGAGAATGAAG                         TTATATGCAGAGTCTCTTGCACGCTTTCAAGGAGGGTCACCTTACATATAT
genomic: CAGCACTGGACACTGTGAAGAGAATGAAGgtaagtttac ... ctacttgtagTTATATGCAGAGTCTCTTGCACGCTTTCAAGGAGGGTCACCTTACATATAT
EST: gi|207734492|gb|GD712443.1|GD712443
EST:     ATGATCGCTACTTGGCTGAGCCAGCACTGGACACTGTGAAGAGAATGAAG                         TTATATGCAGAGTCTCTTGCACGCTTTCAA
genomic: ATGATCGCTACTTGGCTGAGCCAGCACTGGACACTGTGAAGAGAATGAAGgtaagtttac ... ctacttgtagTTATATGCAGAGTCTCTTGCACGCTTTCAA
EST: gi|163927330|gb|EH040145.1|EH040145
EST:     ATGATCGCTACTTGGCTGAGCCAGCACTGGACACTGTGAAGAGAATGAAG                         TTATATGCAGAGTCTCTTGCACGCTTTCAAGGAGGGTCACCTTACATATAT
genomic: ATGATCGCTACTTGGCTGAGCCAGCACTGGACACTGTGAAGAGAATGAAGgtaagtttac ... ctacttgtagTTATATGCAGAGTCTCTTGCACGCTTTCAAGGAGGGTCACCTTACATATAT
EST: gi|151394091|gb|EV263962.1|EV263962
EST:     ATGATCGCTACTTGGCTGAGCCAGCACTGGACACTGTGAAGAGAATGAAG                         TTATATGCAGAGTCTCTTGCACGCTTT
genomic: ATGATCGCTACTTGGCTGAGCCAGCACTGGACACTGTGAAGAGAATGAAGgtaagtttac ... ctacttgtagTTATATGCAGAGTCTCTTGCACGCTTT
EST: gi|192326977|gb|FK019239.1|FK019239
EST:     ATGATCGCTACTTGGCTGAGCCAGCACTGGACACTGTGAAGAGAATGAAG                         TTATATGCAGAGTCTCTTGCACGCTTTCAAGGAGGGTCACCTTACATATAT
genomic: ATGATCGCTACTTGGCTGAGCCAGCACTGGACACTGTGAAGAGAATGAAGgtaagtttac ... ctacttgtagTTATATGCAGAGTCTCTTGCACGCTTTCAAGGAGGGTCACCTTACATATAT
EST: gi|4283991|gb|AI440725.1|AI440725
EST:     ATGATCGCTACTTGGCTGAGCCAGCACTGGACACTGTGAAGAGAATGAAG                         TTATATGCAGAGTCTCTTGCACGCTTTCAAGGAGGGTCACCTTACATATAT
genomic: ATGATCGCTACTTGGCTGAGCCAGCACTGGACACTGTGAAGAGAATGAAGgtaagtttac ... ctacttgtagTTATATGCAGAGTCTCTTGCACGCTTTCAAGGAGGGTCACCTTACATATAT
EST: gi|192328654|gb|FK023154.1|FK023154
EST:     ATGATCGCTACTTGGCTGAGC-AGCACTGGACACTGTGA-GAGA-TGA-G                         T-ATATGCAGAGTCTCTTGCACG
genomic: ATGATCGCTACTTGGCTGAGCCAGCACTGGACACTGTGAAGAGAATGAAGgtaagtttac ... ctacttgtagTTATATGCAGAGTCTCTTGCACG
EST: gi|24136625|gb|BU927135.1|BU927135
EST:     ATGATCGCTACTTGGCTGAGCCAGCACTGGACACTGTGAAGAGAATGAAG                         TTATATGCAGAGTCTCTTGCACGCTTTCAAGGAGGGTCACCTTACATATAT
genomic: ATGATCGCTACTTGGCTGAGCCAGCACTGGACACTGTGAAGAGAATGAAGgtaagtttac ... ctacttgtagTTATATGCAGAGTCTCTTGCACGCTTTCAAGGAGGGTCACCTTACATATAT
EST: gi|151407978|gb|EV277793.1|EV277793
EST:     ATGATCGCTACTTGGCTGAGCCAGCACTGGACACTGTGAAGAGAATGAAG                         TTATATGCAGAGTCTCTTGCACGCTTTCAAGGAGGGTCACCTTACATATAT
genomic: ATGATCGCTACTTGGCTGAGCCAGCACTGGACACTGTGAAGAGAATGAAGgtaagtttac ... ctacttgtagTTATATGCAGAGTCTCTTGCACGCTTTCAAGGAGGGTCACCTTACATATAT
EST: gi|151411945|gb|EV281756.1|EV281756
EST:     ATGATCGCTACTTGGCTGAGCCAGCACTGGACACTGTGAAGAGAATGAAG                         TTATATGCAGAGTCTCTTGCACGCTTT
genomic: ATGATCGCTACTTGGCTGAGCCAGCACTGGACACTGTGAAGAGAATGAAGgtaagtttac ... ctacttgtagTTATATGCAGAGTCTCTTGCACGCTTT
EST: gi|254321748|gb|GR825065.1|GR825065
EST:     ATGATCGCTACTTGGCTGAGCCAGCACTGGACACTGTGAAGAGAATGAAG                         TTATATGGAGAGTCTCTTGCACGCTTT
genomic: ATGATCGCTACTTGGCTGAGCCAGCACTGGACACTGTGAAGAGAATGAAGgtaagtttac ... ctacttgtagTTATATGCAGAGTCTCTTGCACGCTTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGATGATAACACTATAGACTTCATTGGTCATGCTTTGGCGCTTCATAGTGATGATCGCTACTTGGCTGAGCCAGCACTGGACACTGTGAAGAGAATGAAGgtaagtttactgggttattatgcacttgtaatttattctcagtcgtggattcttcttaattgaaaatttcttctgttccatttggttcccattagctatattttgtttcctacttgtag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA