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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCCCTAGTCAAGGAGTTGGTGAGGTTAATGTAAACCTTGATTGGAAAATTGGAATTGCAGCTAAGGATTGGGATTCAGTGCTAGAAAAGAGAAGATTGAGgtaaacttccaagagatatgtataattttgaatctccctatactataggtagatagaacttaagtgttttacctatcaagggctgacatttgctcaaggt...

Basic information

species Glycine max
transcript GLYMA08G13470.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G13470.1 (Glycine max), 5'ss of exon 2
lower sequence: LOC_Os02g52920.1 (Oryza sativa), 5'ss of exon 2
-GCCCTAGTCAAGGAGTTGGTGAGGTTAATGTAAACCTTGATTGGAAAATTGGAATTGCAGCTAAGGATTGGGAT-TCAGTGCTAGAAAAGAGAAGATTGAGgtaaactt---ccaagagatatgtataattttgaatctccctatactataggtagatagaacttaagtgttttacctatcaagggctgacatttgctcaaggt-----
   |  ||  || | ||  |  |  |   | | || ||||||||||| |||||||||||||| |||||||||||| | |  ||||  || || || |||||||||    |   |  ||  | |    | |   |  || |  | ||| |  |   |  |  |  |||| |   |        ||  ||||  || |  |     |     
TAGCGCAGAGAAAGGGTCAGGAATATC--TATTAATCTTGATTGGAAGATTGGAATTGCAGCAAAGGATTGGGATGTTATCGCTAAGAAGGAAAAAATTGAGgtaggagtaggcttagccaaactgctgacggtccatatgaccatatttcactgatgtccagtttaattcactgcttctctaattgctgcaatctaattccttttgtag

upper sequence: GLYMA08G13470.1 (Glycine max), 5'ss of exon 2
lower sequence: AT1G57620.1 (Arabidopsis thaliana), 5'ss of exon 2
GCCCTAGTCAAGGAGTTGGTGAGGTTAATGTAAACCTTGATTGGAAAATTGGAATTGCAGCTAAGGATTGGGATTC-AGTGCTAGAAAAGAGAAGATTGAGgtaaacttccaagagatatgtataattttgaatctccctatactataggtagat-agaactta-agtgttttacctatcaagggctgacatttgctcaaggt-------------
     ||||| ||       ||  |||   | ||| | || ||||||| |||||| |||||||| |||||||| || | |||||||||||| ||||| ||||| | ||  | |   || |  |    | |||  |     |     |    |||| | | |||| |||   |||      ||   |||||| | | | | |               
-TAAAAGTCATGGTAACAAAGATTTTAGCATCAACATCGACTGGAAAACTGGAATCGCAGCTAAAGATTGGGACTCCATTGCTAGAAAAGAAAAGATCGAGgtcagctctccat--atttccaagcctctgagacaattaaattacttacaagatcacatcttagagtaggttagtctctaa--actgacactcgataatgtcttcaattgtgtag
















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|193535013|gb|FK493069.1|FK493069
EST:     GAATTGCAGCTAAGGATTGGGATTCAGTTGCTAGAAAAGAGAAGATTGAG                         GGAGTTGAGCTTGAGCTGAGAAAGCTAGAGGGAGCAG
genomic: GAATTGCAGCTAAGGATTGGGATTCAG-TGCTAGAAAAGAGAAGATTGAGgtaaacttcc ... tgatacctagGGAGTTGAGCTTGAGCTGAGAAAGCTAGAGGGAGCAG
EST: gi|151394340|gb|EV264211.1|EV264211
EST:     GAATTGCAGCTAAGGATTGGGATTCAGTTGCTAGAAAAGAGAAGATTGAG                         GGAGTTGAGCTTGAGCTGAGAAAGCTAGAGGGAGCAGTA-GAGGCCATCCA
genomic: GAATTGCAGCTAAGGATTGGGATTCAGT-GCTAGAAAAGAGAAGATTGAGgtaaacttcc ... tgatacctagGGAGTTGAGCTTGAGCTGAGAAAGCTAGAGGGAGCAGTAAGAGGCCATCCA
EST: gi|151394089|gb|EV263960.1|EV263960
EST:     GAATTGCAGCTAAGGATTGGGATTCAGTTGCTAGAAAAGAGAAGATTGAG                         GGAGTTGAGCTTGAGCTGAGAAAGCTAGAGGGAGCAGTA-GAGGCCATCCA
genomic: GAATTGCAGCTAAGGATTGGGATTCAGT-GCTAGAAAAGAGAAGATTGAGgtaaacttcc ... tgatacctagGGAGTTGAGCTTGAGCTGAGAAAGCTAGAGGGAGCAGTAAGAGGCCATCCA
EST: gi|192306615|gb|FG998055.1|FG998055
EST:     GAATTGCAGCTAAGGATTGGGATTCAGTTGCCAGAAAAGAGAAGATTGAG                         GGAGTTGAGCTTGAGCTGAGAAAGCTAGAGGGAGCAGTA-GAGGCCATCCA
genomic: GAATTGCAGCTAAGGATTGGGATTCAGT-GCTAGAAAAGAGAAGATTGAGgtaaacttcc ... tgatacctagGGAGTTGAGCTTGAGCTGAGAAAGCTAGAGGGAGCAGTAAGAGGCCATCCA
EST: gi|209708754|gb|BW683778.1|BW683778
EST:     GAATTGCAGCTAAGGATTGGGATTCAGTTGCTAGAAAAGAGAAGATTGAG                         GGAGTTGAGCTTGAGCTGAGAAAGCTAGAGGGAGCAGTA-GAGGCCATCCA
genomic: GAATTGCAGCTAAGGATTGGGATTCAGT-GCTAGAAAAGAGAAGATTGAGgtaaacttcc ... tgatacctagGGAGTTGAGCTTGAGCTGAGAAAGCTAGAGGGAGCAGTAAGAGGCCATCCA
EST: gi|193686122|gb|FK625473.1|FK625473
EST:     TTCAGTTGCTAGAAAAGAGAAGATTGAG                         GGAGTTGAGCTTGAGCTGAGAAAGCTAGAGGGAGCAGT-AGAGGCCATCCA
genomic: TTCAG-TGCTAGAAAAGAGAAGATTGAGgtaaacttcc ... tgatacctagGGAGTTGAGCTTGAGCTGAGAAAGCTAGAGGGAGCAGTAAGAGGCCATCCA
EST: gi|298176386|gb|HO023087.1|HO023087
EST:     GAATTGCAGCTAAGGATTGGGATTCAGTTGCTAGAAAAGAGAAGATTGAG                         GGAGTTGAGCTTGAGCTGAGAAAGCTAGAGGGAGCA
genomic: GAATTGCAGCTAAGGATTGGGATTCAGT-GCTAGAAAAGAGAAGATTGAGgtaaacttcc ... tgatacctagGGAGTTGAGCTTGAGCTGAGAAAGCTAGAGGGAGCA
EST: gi|207689114|gb|GD673467.1|GD673467
EST:     TAATTGCAGCTAAGGATTGGGATTCAGTTGCTAGAAAAGAGAAGATTGAG                         GGAGTTGAGCTTGAGCTGAGAAAGCTAGAGGGAGCAGT-AGAGGCCATCCA
genomic: -AATTGCAGCTAAGGATTGGGATTCAG-TGCTAGAAAAGAGAAGATTGAGgtaaacttcc ... tgatacctagGGAGTTGAGCTTGAGCTGAGAAAGCTAGAGGGAGCAGTAAGAGGCCATCCA
EST: gi|298170194|gb|HO018818.1|HO018818
EST:     GAATTGCAGCTAAGGATTGGGATTCAGTTGCTAGAAAAGAGAAGATTGAG                         GGAGTTGAGCTTGAGCTGAGAAAGCTAGAGGGAGCAGTA-GAGGCCATCCA
genomic: GAATTGCAGCTAAGGATTGGGATTCAGT-GCTAGAAAAGAGAAGATTGAGgtaaacttcc ... tgatacctagGGAGTTGAGCTTGAGCTGAGAAAGCTAGAGGGAGCAGTAAGAGGCCATCCA
EST: gi|298164598|gb|HO014243.1|HO014243
EST:     GAATTGCAGCTAAGGATTGGGATTCAGTTGCTAGAAAAGAGAAGATTGAG                         GGAGTTGAGCTTGAGCTGAGAAAGCTAGAGGGAGCAGTA-GAGGCCATCCA
genomic: GAATTGCAGCTAAGGATTGGGATTCAGT-GCTAGAAAAGAGAAGATTGAGgtaaacttcc ... tgatacctagGGAGTTGAGCTTGAGCTGAGAAAGCTAGAGGGAGCAGTAAGAGGCCATCCA
EST: gi|31474639|gb|CD416667.1|CD416667
EST:     GAATTGCAGCTAAGGATTGGGATTCAGTTGCTAGAAAAGAGAAGATTGAG                         GGAGTTGAGCTTGAGCTGAGAAAGCTAGAGGGAGCAGTA-GAGGCCATCCA
genomic: GAATTGCAGCTAAGGATTGGGATTCAGT-GCTAGAAAAGAGAAGATTGAGgtaaacttcc ... tgatacctagGGAGTTGAGCTTGAGCTGAGAAAGCTAGAGGGAGCAGTAAGAGGCCATCCA
EST: gi|298173881|gb|HO017217.1|HO017217
EST:     GAATTGCAGCTAAGGATTGGGATTCAGTTGCTAGAAAAGAGAAGATTGAG                         GGAGTTGAGCTTGAGCTGAGAAAGCTAGAGGGAGCAGTA-GAGGCCATCCA
genomic: GAATTGCAGCTAAGGATTGGGATTCAGT-GCTAGAAAAGAGAAGATTGAGgtaaacttcc ... tgatacctagGGAGTTGAGCTTGAGCTGAGAAAGCTAGAGGGAGCAGTAAGAGGCCATCCA
EST: gi|192306630|gb|FG998056.1|FG998056
EST:     GAATTGCAGCTAAGGATTGGGATTCAGTTGCCAGAAAAGAGAAGATTGAG                         GGAGTTGAGCTTGAGCTGAGAAAGCTAGAGGGAGCAGT-AGAGGCCATCCA
genomic: GAATTGCAGCTAAGGATTGGGATTCAG-TGCTAGAAAAGAGAAGATTGAGgtaaacttcc ... tgatacctagGGAGTTGAGCTTGAGCTGAGAAAGCTAGAGGGAGCAGTAAGAGGCCATCCA
EST: gi|298176262|gb|HO015667.1|HO015667
EST:     GAATTGCAGCTAAGGATTGGGATTCAGTTGCTAGAAAAGAGAAGATTGAG                         GGAGTTGAGCTTGAGCTGAGAAAGCTAGAGGGAGCAGTA-GAGGCCATCCA
genomic: GAATTGCAGCTAAGGATTGGGATTCAGT-GCTAGAAAAGAGAAGATTGAGgtaaacttcc ... tgatacctagGGAGTTGAGCTTGAGCTGAGAAAGCTAGAGGGAGCAGTAAGAGGCCATCCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCCCTAGTCAAGGAGTTGGTGAGGTTAATGTAAACCTTGATTGGAAAATTGGAATTGCAGCTAAGGATTGGGATTCAGTGCTAGAAAAGAGAAGATTGAGgtaaacttccaagagatatgtataattttgaatctccctatactataggtagatagaacttaagtgttttacctatcaagggctgacatttgctcaaggt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tctcccta