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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGACATGTTATTTGGAAAGCGTGGCAAAAGTGGTTTGGTTGCCTTGAATTTGGATTTTGCACAAGTTGTTTCATTTGTGAAGGAGCGTCTTGGAAAAGAGgtgctttatcctcgtggttttccctctttatttttttagttgttcggggtgtttccctttccacccttgatgtatttagttatgtctttctctaatatatag

Basic information

species Glycine max
transcript GLYMA02G04120.2
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G04120.2 (Glycine max), 5'ss of exon 3
lower sequence: Vv01s0127g00260.t01 (Vitis vinifera), 5'ss of exon 4
TGACATGTTATTTGGAAAGCGTGGCAAAAGTGGTTTGGTTGCCTTGAATTTGGATTTTGCACAAGTTGTTTCATTTGTGAAGGAGCGTCTTGGAAAAGAGgtgcttta------tcctcgtggttttccctctttattttttta-------gttgttcggggtgt-ttccctttccacccttga--tgtat---ttagttatgtctttctctaatatatag---------------------
||||||||||||||| |||||||| || |||||||| |||||| ||||||| ||||| || ||||||| | | || ||||| || |||||||| ||||||||  || |      ||  | ||    ||  | || ||  ||| |       |||  |  | || | ||   |||  | | ||||  |  ||   ||  | | ||   | ||| ||   |                       
TGACATGTTATTTGGCAAGCGTGGGAAGAGTGGTTTAGTTGCCCTGAATTTAGATTTGGCTCAAGTTGGTACTTTCGTGAAAGAACGTCTTGGCAAAGAGgtatttaaactctttcaccatgtgactcatttttaatcctttgatgagtatgttaatatgagtatgttatatttttatcattgaattccatcccttgatgaagtggatttcttatgcttctattatccatttgggtttctag
















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|209701247|gb|BW652225.1|BW652225
EST:     TGGATTTTGCACAAGTTGTTTCATTTGTGAAGGAGCGTCTTGGAAAAGAG                         GTTGAGATGAGTGGATGCAAAGGACCCATAACAACTTTCATTGTTGAACCT
genomic: TGGATTTTGCACAAGTTGTTTCATTTGTGAAGGAGCGTCTTGGAAAAGAGgtgctttatc ... taatatatagGTTGAGATGAGTGGATGCAAAGGACCCATAACAACTTTCATTGTTGAACCT
EST: gi|192305509|gb|FG994303.1|FG994303
EST:     TGGATTTTGCACAAGTTGTTTCATTTGTGAAGGAGCGTCTTGGAAAGGAG                         GTTGAGATGAGTGGATGCAAAGGACCCATAACAACTTTCATTGTTGAACCT
genomic: TGGATTTTGCACAAGTTGTTTCATTTGTGAAGGAGCGTCTTGGAAAAGAGgtgctttatc ... taatatatagGTTGAGATGAGTGGATGCAAAGGACCCATAACAACTTTCATTGTTGAACCT
EST: gi|213590555|gb|DB973314.1|DB973314
EST:     TGGATTTTGCACAAGTTGTTTCATTTGTGAAGGAGCGTCTTGGAAAAGAG                         GTTGAGATGAGTGGATGCAAAGGACCCATAACAACTTTCATTGTTGAACCT
genomic: TGGATTTTGCACAAGTTGTTTCATTTGTGAAGGAGCGTCTTGGAAAAGAGgtgctttatc ... taatatatagGTTGAGATGAGTGGATGCAAAGGACCCATAACAACTTTCATTGTTGAACCT
EST: gi|5753577|gb|AI960864.1|AI960864
EST:     TGGATTTTGCACAAGTTGTTTCATTTGTGAAGGAGCGTCTTGGAAAAGAG                         GTTGAGATGAGTGGATGCAAAGGACCCATAACAACTTTCATTGTTGAACCT
genomic: TGGATTTTGCACAAGTTGTTTCATTTGTGAAGGAGCGTCTTGGAAAAGAGgtgctttatc ... taatatatagGTTGAGATGAGTGGATGCAAAGGACCCATAACAACTTTCATTGTTGAACCT
EST: gi|213601137|gb|DB956473.1|DB956473
EST:     TGGATTTTGCACAAGTTGTTTCATTTGTGAAGGAGCGTCTTGGAAAAGAG                         GTTGAGATGAGTGGATGCAAAGGACCCATAACAACTTTCATTGTTGAACCT
genomic: TGGATTTTGCACAAGTTGTTTCATTTGTGAAGGAGCGTCTTGGAAAAGAGgtgctttatc ... taatatatagGTTGAGATGAGTGGATGCAAAGGACCCATAACAACTTTCATTGTTGAACCT
EST: gi|213598625|gb|DB964247.1|DB964247
EST:     TGGATCTTGCACAAGTTGTTTCATTTGTGAAGGAGCGTCTTGGAAAAGAG                         GTTGAGATGAGTGGATGCAAAGGACCCATAACAACTTTCATTGTTGAACCT
genomic: TGGATTTTGCACAAGTTGTTTCATTTGTGAAGGAGCGTCTTGGAAAAGAGgtgctttatc ... taatatatagGTTGAGATGAGTGGATGCAAAGGACCCATAACAACTTTCATTGTTGAACCT
EST: gi|6566938|gb|AW234569.1|AW234569
EST:     GGATTTTGCACAAGTTGTTTCATTTGTGAAGGAGCCTCTTGGAAAAGAG                         GTTGAGATGAGTGGATGCAAAGGACCCATAACAACTTTCATTGTTGAACCT
genomic: GGATTTTGCACAAGTTGTTTCATTTGTGAAGGAGCGTCTTGGAAAAGAGgtgctttatc ... taatatatagGTTGAGATGAGTGGATGCAAAGGACCCATAACAACTTTCATTGTTGAACCT
EST: gi|20498839|gb|BQ273769.1|BQ273769
EST:     TGGATTTTGCACAAGTTGTTTCATTTGTGAAGGAGCGTCTTGGAAAAGAG                         GTTGAGATGAGTGGATGCAAAGGACCCATAACAACTTTCATTGTTGAACCT
genomic: TGGATTTTGCACAAGTTGTTTCATTTGTGAAGGAGCGTCTTGGAAAAGAGgtgctttatc ... taatatatagGTTGAGATGAGTGGATGCAAAGGACCCATAACAACTTTCATTGTTGAACCT
EST: gi|17519242|gb|BM188284.1|BM188284
EST:     TGGATTTTGCACAAGTTGTTTCATTTGTGAAGGAGCGTCTTGGAAAAGAG                         GTTGAGATGAGTGGATGCAAAGGACCCATAACAACTTTCATTGTTGAACCT
genomic: TGGATTTTGCACAAGTTGTTTCATTTGTGAAGGAGCGTCTTGGAAAAGAGgtgctttatc ... taatatatagGTTGAGATGAGTGGATGCAAAGGACCCATAACAACTTTCATTGTTGAACCT
EST: gi|192306307|gb|FG995101.1|FG995101
EST:     TGGATTTTGCACAAGTTGTTTCATTTGTGAAGGAGCGTCTTGGAAAAGAG                         GTTGTGATGAGTGGATGCAAAGGACCCATAACAACTTTCATTGTTGAACCT
genomic: TGGATTTTGCACAAGTTGTTTCATTTGTGAAGGAGCGTCTTGGAAAAGAGgtgctttatc ... taatatatagGTTGAGATGAGTGGATGCAAAGGACCCATAACAACTTTCATTGTTGAACCT
EST: gi|7589883|gb|AW705648.1|AW705648
EST:     TGGATTTTGCACAAGTTGTTTCATTTGTGAAGGAGCGTCTTGGAAAAGAG                         GTTGAGATGAGTGGATGCAAAGGACCCATAACAACTTTCATTGTTGAACCT
genomic: TGGATTTTGCACAAGTTGTTTCATTTGTGAAGGAGCGTCTTGGAAAAGAGgtgctttatc ... taatatatagGTTGAGATGAGTGGATGCAAAGGACCCATAACAACTTTCATTGTTGAACCT
EST: gi|298178311|gb|HO024046.1|HO024046
EST:     TGGATTTTGCACAAGTTGTTTCATTTGTGAAGGAGCGTCTTGGAAAAGAG                         GTTGAGATGAGTGGTTGCAAAGGACCCATAACAACTTTCATTGTTGAACCT
genomic: TGGATTTTGCACAAGTTGTTTCATTTGTGAAGGAGCGTCTTGGAAAAGAGgtgctttatc ... taatatatagGTTGAGATGAGTGGATGCAAAGGACCCATAACAACTTTCATTGTTGAACCT
EST: gi|151410816|gb|EV280631.1|EV280631
EST:     TGGATTTTGCACAAGTTGTTTCATTTGTGAAGGAGCGTCTTGGAAAAGAG                         GTTGAGATGAGTGGATGCAAAGGACCCATAACAACTTTCATTGTTGAACCT
genomic: TGGATTTTGCACAAGTTGTTTCATTTGTGAAGGAGCGTCTTGGAAAAGAGgtgctttatc ... taatatatagGTTGAGATGAGTGGATGCAAAGGACCCATAACAACTTTCATTGTTGAACCT
EST: gi|298174335|gb|HO017671.1|HO017671
EST:     TGGATTTTGCACAAGTTGTTTCATTTGTGAAGGAGCGTCTTGGAAAAGAG                         GTTGAGATGAGTGGATGCAAAGGACCCATAACAACTTTCATTGTTGAACCT
genomic: TGGATTTTGCACAAGTTGTTTCATTTGTGAAGGAGCGTCTTGGAAAAGAGgtgctttatc ... taatatatagGTTGAGATGAGTGGATGCAAAGGACCCATAACAACTTTCATTGTTGAACCT
EST: gi|6566595|gb|AW234236.1|AW234236
EST:     TGGATTTTGCACAAGTTGTTTCATTTGTGAAGGAGCGTCTTGGAAAAGAG                         GTTGAGATGAGTGGATGCAAAGGACCCATAACAACTTTCATTGTTGAACCT
genomic: TGGATTTTGCACAAGTTGTTTCATTTGTGAAGGAGCGTCTTGGAAAAGAGgtgctttatc ... taatatatagGTTGAGATGAGTGGATGCAAAGGACCCATAACAACTTTCATTGTTGAACCT
EST: gi|213600410|gb|DB970304.1|DB970304
EST:     TGGATTTTGCACAAGTTGTTTCATTTGTGAAGGAGCGTCTTGGAAAAGAG                         GTTGAGATGAGTGGATGCAAAGGACCCATAACAACTTTCATTGTTGAACCT
genomic: TGGATTTTGCACAAGTTGTTTCATTTGTGAAGGAGCGTCTTGGAAAAGAGgtgctttatc ... taatatatagGTTGAGATGAGTGGATGCAAAGGACCCATAACAACTTTCATTGTTGAACCT
EST: gi|209697931|gb|BW670133.1|BW670133
EST:     TGGATTTTGCACAAGTTGTTTCATTTGTGAAGGAGCGTCTTGGAAAAGAG                         GTTGAGATGAGTGGATGCAAAGGACCCATAACAACTTTCATTGTTGAACCT
genomic: TGGATTTTGCACAAGTTGTTTCATTTGTGAAGGAGCGTCTTGGAAAAGAGgtgctttatc ... taatatatagGTTGAGATGAGTGGATGCAAAGGACCCATAACAACTTTCATTGTTGAACCT
EST: gi|213600535|gb|DB960083.1|DB960083
EST:     TGGATTTTGCACAAGTTGTTTCATTTGTGAAGGAGCGTCTTGGAAAAGAG                         GTTGAGATGAGTGGATGCAAAGGACCCATAACAACTTTCATTGTTGAACCT
genomic: TGGATTTTGCACAAGTTGTTTCATTTGTGAAGGAGCGTCTTGGAAAAGAGgtgctttatc ... taatatatagGTTGAGATGAGTGGATGCAAAGGACCCATAACAACTTTCATTGTTGAACCT
EST: gi|213593143|gb|DB969885.1|DB969885
EST:     TGGATTTTGCACAAGTTGTTTCATTTGTGAAGGAGCGTCTTGGAAAAGAG                         GTTGAGATGAGTGGATGCAAAGGACCCATAACAACTTTCATTGTTGAACCT
genomic: TGGATTTTGCACAAGTTGTTTCATTTGTGAAGGAGCGTCTTGGAAAAGAGgtgctttatc ... taatatatagGTTGAGATGAGTGGATGCAAAGGACCCATAACAACTTTCATTGTTGAACCT
EST: gi|213601183|gb|DB956491.1|DB956491
EST:     TGGATTTTGCACAAGTTGTTTCATTTGTGAAGGAGCGTCTTGGAAAAGAG                         GTTGAGATGAGTGGATGCAAAGGACCCATAACAACTTTCATTGTTGAACCT
genomic: TGGATTTTGCACAAGTTGTTTCATTTGTGAAGGAGCGTCTTGGAAAAGAGgtgctttatc ... taatatatagGTTGAGATGAGTGGATGCAAAGGACCCATAACAACTTTCATTGTTGAACCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGACATGTTATTTGGAAAGCGTGGCAAAAGTGGTTTGGTTGCCTTGAATTTGGATTTTGCACAAGTTGTTTCATTTGTGAAGGAGCGTCTTGGAAAAGAGgtgctttatcctcgtggttttccctctttatttttttagttgttcggggtgtttccctttccacccttgatgtatttagttatgtctttctctaatatatag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG