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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGCTTGATGACTCCAATAATAAAAAATGCTGATCAGAAGACAATATCTGCTATCTCCTCAGAGgtaattttatctcatttgtgtaggtttctggttaatgactttatgatagaaactggaatataccgtatgctattaactaagaaatcagggagcaaagctc...

Basic information

species Glycine max
transcript GLYMA20G33080.1
intron # 18
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G33080.1 (Glycine max), 5'ss of exon 18
lower sequence: LOC_Os06g30460.4 (Oryza sativa), 5'ss of exon 13
GGCTTGATGACTCCAATAATAAAAAATGCTGATCAGAAGACAATATCTGCTATCTCCTCAGAGgtaattttatctcatttgtgtaggtttctggttaatgactttatgatagaaactggaatataccgtatgctattaac---taagaaatcagggagcaaagctc
||| |||||||||| || |||| |||||| ||||| ||||| ||||| || || |||||||||||| |   |     |||    |||||     ||| || | |  |   ||||  |       |    |||  |    |   |   |     |  | |||   | 
GGCCTGATGACTCCTATTATAAGAAATGCAGATCAAAAGACTATATCAGCAATATCCTCAGAGgta-tgagagaatgtttaaa-aggttcaaccttactgtcatagtttcagaagttctttagcatgaaatgtcacaggcacatgtaacgcttgtaatcaactat-

upper sequence: GLYMA20G33080.1 (Glycine max), 5'ss of exon 18
lower sequence: AT3G52200.1 (Arabidopsis thaliana), 5'ss of exon 18
GGCTTGATGACTCCAATAATAAAAAATGCTGATCAGAAGACAATATCTGCTATCTCCTCAGAGgtaattttatctcatttgt---------------gtaggtttctggttaatgactttatgat-agaaactggaatataccgtatgctattaactaaga-aatcagggagcaaagctc---------------------
||||| ||||||||||| || || ||||| || |||||  | || |||||||| |||| ||||||||||||||    | ||                | ||| |   |    |    | | |||| ||    |   |||| || | || | || |     | | | | | |    |                         
GGCTTAATGACTCCAATTATCAAGAATGCAGACCAGAAATCTATTTCTGCTATTTCCTTAGAGgtaattttattctctctgaagttaaacgaatatggaaggctatagaggcacatatgtttgatcagttcttaccatattccatgtgttgttgatcgctatagttatgaattttaatatgtcaaatgatttttggatcag
















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|27426899|gb|CA938419.1|CA938419
EST:     ATGCTGATCAGAAGACAATATCTGCTATCTCCTCAGAG                         GTCAAGGAACTAGCTGCAAAGGCACGTGCTGGCAAATTGAAGCCACATGAA
genomic: ATGCTGATCAGAAGACAATATCTGCTATCTCCTCAGAGgtaattttat ... ggcattttagGTCAAGGAACTAGCTGCAAAGGCACGTGCTGGCAAATTGAAGCCACATGAA
EST: gi|26058095|gb|CA801009.1|CA801009
EST:     CAATAATAAAAAATGCTGATCAGAAGACAATATCTGCTATCTCCTCAGAG                         GTCAAGGAACTAGCTGCAAAGGCACGTGCTGGCAAATTGAAGCCACATGAA
genomic: CAATAATAAAAAATGCTGATCAGAAGACAATATCTGCTATCTCCTCAGAGgtaattttat ... ggcattttagGTCAAGGAACTAGCTGCAAAGGCACGTGCTGGCAAATTGAAGCCACATGAA
EST: gi|6227678|gb|AW156277.1|AW156277
EST:     CAATAATAAAAAATGCTGATCAGAAGACAATATCTGCTATCTCCTCAGAG                         GTCAAGGAACTAGCTGCAAAGGCACGTGCTGGCAAATTGAAGCCACATGAA
genomic: CAATAATAAAAAATGCTGATCAGAAGACAATATCTGCTATCTCCTCAGAGgtaattttat ... ggcattttagGTCAAGGAACTAGCTGCAAAGGCACGTGCTGGCAAATTGAAGCCACATGAA
EST: gi|192310210|gb|FK000690.1|FK000690
EST:     TGCTGATCAGAAGACAATATCTGCTATCTCCTCAGAG                         GTCAAGGAACTAGCTGCAAAGGCACGTGCTGGCAAATTGAAGCCACATGAA
genomic: TGCTGATCAGAAGACAATATCTGCTATCTCCTCAGAGgtaattttat ... ggcattttagGTCAAGGAACTAGCTGCAAAGGCACGTGCTGGCAAATTGAAGCCACATGAA
EST: gi|51344360|gb|CO985093.1|CO985093
EST:     CAATAATAAAAAATGCTGATCAGAAGACAATANCTGCTATNNNNNCAGAG                         GTCAAGGAACTAGCTGCAAAGGCACGTGCTGGCAAATTGAAGCCACATGAA
genomic: CAATAATAAAAAATGCTGATCAGAAGACAATATCTGCTATCTCCTCAGAGgtaattttat ... ggcattttagGTCAAGGAACTAGCTGCAAAGGCACGTGCTGGCAAATTGAAGCCACATGAA
EST: gi|57575389|gb|CX548364.1|CX548364
EST:     CAATAATAAAAAATGCTGATCAGAAGACAATATCTGCTATCTCTTCAGAG                         GTCAAGGAACTAGCTGCAAAGGCACGTGCTGGCAAATTGAAGCCACATGAA
genomic: CAATAATAAAAAATGCTGATCAGAAGACAATATCTGCTATCTCCTCAGAGgtaattttat ... ggcattttagGTCAAGGAACTAGCTGCAAAGGCACGTGCTGGCAAATTGAAGCCACATGAA
EST: gi|209716666|gb|BW654299.1|BW654299
EST:     CAATAATAAAAAATGCTGATCAGAAGACAATATCTGCTATCTCCTCAGAG                         GTCAAGGAACTAGCTGCAAAGGCACGTGCTGGCAAATTGAAGCCACATGAA
genomic: CAATAATAAAAAATGCTGATCAGAAGACAATATCTGCTATCTCCTCAGAGgtaattttat ... ggcattttagGTCAAGGAACTAGCTGCAAAGGCACGTGCTGGCAAATTGAAGCCACATGAA
EST: gi|120532018|gb|EH260151.1|EH260151
EST:     CAATAATAAAAAATGCTGATCAGAAGACAATATCTGCTATCTCCTCAGAG                         GTCAAGGAACTAGCTGCAAAGGCACGTGCTGGCAAATTGAAGCCACATGAA
genomic: CAATAATAAAAAATGCTGATCAGAAGACAATATCTGCTATCTCCTCAGAGgtaattttat ... ggcattttagGTCAAGGAACTAGCTGCAAAGGCACGTGCTGGCAAATTGAAGCCACATGAA
EST: gi|58023434|gb|CX710175.1|CX710175
EST:     CAATAATAAAAAATGCTGATCAGAAGACAATATCTGCTATCTCTTCAGAG                         GTCAAGGAACTAGCTGCAAAGGCACGTGCTGGCAAA-TGNAAGCCACATGA
genomic: CAATAATAAAAAATGCTGATCAGAAGACAATATCTGCTATCTCCTCAGAGgtaattttat ... ggcattttagGTCAAGGAACTAGCTGCAAAGGCACGTGCTGGCAAATTG-AAGCCACATGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGCTTGATGACTCCAATAATAAAAAATGCTGATCAGAAGACAATATCTGCTATCTCCTCAGAGgtaattttatctcatttgtgtaggtttctggttaatgactttatgatagaaactggaatataccgtatgctattaactaagaaatcagggagcaaagctc

- - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - -  GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC