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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TATATTGCGTGTGTGAGAGATGCAGCAGCACCTGATGCAGATGCAGCCCATGATGGCAGCCTACTACCCCAACAACGTCACCACTGATCACATTCAGCAGgtccgtttctctcttcttcttctgcactgctactactgctaccactaccattccccttcatctgcttatcttatctcttctgctagctttggatatactc...

Basic information

species Glycine max
transcript GLYMA19G43580.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G43580.1 (Glycine max), 5'ss of exon 1
lower sequence: AT5G28640.1 (Arabidopsis thaliana), 5'ss of exon 1
TATATTGCGT-GTGTGAGAGATGCAGCAGCACCTGATGCAGATGCAGCCCATGATGGCAGCCTACTACCCCAACAACGTCACCACTGATCACATTCAGCAGgtccgtttctctcttcttcttctgcactgctactactgctaccactaccattccccttcatctgcttatcttatctcttctgctagctttggatatactc---
 ||||    | |    ||| ||||| |||||||||||||||||||||||||||||||| |  |||||||||| ||| || ||| ||||||| || || ||||| |  |||||  |        |   || || || ||  ||  | || |  |  | ||  |||  ||||  ||| | |  |   |    |  |   |      
-ATATAAAATAGCAAAAGAAATGCAACAGCACCTGATGCAGATGCAGCCCATGATGGCTGGTTACTACCCCAGCAATGTTACCTCTGATCATATCCAACAGgttctcttctccttctcctccttctccttcttcttctattat-attatctctttcttttttct--ttattatatgtttctttgaattcataaaggaaagtgaa

upper sequence: GLYMA19G43580.1 (Glycine max), 5'ss of exon 1
lower sequence: Vv14s0081g00200.t01 (Vitis vinifera), 5'ss of exon 1
TATATTGCGTGTGTGAGAGATGCAGCAGCACCTGATGCAGATGCAGCCCATGATGGCAGCCTACTACCCCAACAACGTCACCACTGATCACATTCAGCAGgtccgtttctctcttcttcttctgcactgctactactgctaccactaccattccccttcatctgcttatcttatctcttctgctagctttggatatactc--
   ||   | | | |||| |||||||||||||||||||||||||||||||||||||||||||| ||||||| |||||||||||||||||||||||||||||| |  |  ||||||||   |||   || || || ||    |   |    || || ||  | ||         ||| |  | ||   |||   | |  ||  
GGGATATAGAGAGAGAGAAATGCAGCAGCACCTGATGCAGATGCAGCCCATGATGGCAGCCTATTACCCCAGCAACGTCACCACTGATCACATTCAGCAGgttc-ctcttctcttctctctcttt-cttctccttctctctcttttttttttgccttttttttgggggagggttctttgttcctgtttttccctttcttcct
















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|208180264|gb|GD975807.1|GD975807
EST:     TGATGGCAGCCTACTACCCCAACAACGTCACCACTGATCACATTCAACAG                         TATCTGGATGAGAACAAGTCCTTAATTCTGAAGATTGTTGAAAGCCAGAAT
genomic: TGATGGCAGCCTACTACCCCAACAACGTCACCACTGATCACATTCAGCAGgtccgtttct ... ttacatgcagTATCTGGATGAGAACAAGTCCTTAATTCTGAAGATTGTTGAAAGCCAGAAT
EST: gi|298199270|gb|HO042633.1|HO042633
EST:     TGATGGCAGCCTACTACCCCAACAACGTCACCACTGATCACATTCAGCAG                         TATCTGGATGAGAACAAGTCCTTAATTCTGAAGATTGTTGAAAGCCAGAAT
genomic: TGATGGCAGCCTACTACCCCAACAACGTCACCACTGATCACATTCAGCAGgtccgtttct ... ttacatgcagTATCTGGATGAGAACAAGTCCTTAATTCTGAAGATTGTTGAAAGCCAGAAT
EST: gi|207719536|gb|GD703491.1|GD703491
EST:     TGATGGCAGCCTACTACCCCAACAACGTCACCACTGATCACATTCAGCAG                         TATCTGGATGAGAACAAGTCCTTAATTCTGAAGATCGTTGAAAGCCAGAAT
genomic: TGATGGCAGCCTACTACCCCAACAACGTCACCACTGATCACATTCAGCAGgtccgtttct ... ttacatgcagTATCTGGATGAGAACAAGTCCTTAATTCTGAAGATTGTTGAAAGCCAGAAT
EST: gi|208290307|gb|GE082735.1|GE082735
EST:     TGATGGCAGCCTACTACCCCAACAACGTCACCACTGATCACATTCAGCAG                         TATCTGGATGAGAACAAGTCCTTAATTCTGAAGATTGTTGAAAGCCAGAAT
genomic: TGATGGCAGCCTACTACCCCAACAACGTCACCACTGATCACATTCAGCAGgtccgtttct ... ttacatgcagTATCTGGATGAGAACAAGTCCTTAATTCTGAAGATTGTTGAAAGCCAGAAT
EST: gi|207804600|gb|GD777759.1|GD777759
EST:     TGATGGCAGCCTACTACCCCAACAACGTCACCACTGATCACATTCAGCAG                         TATCTGGATGAGAACAAGTCCTTAATTCTGAAGATTGTTGAAAGCCAGAAT
genomic: TGATGGCAGCCTACTACCCCAACAACGTCACCACTGATCACATTCAGCAGgtccgtttct ... ttacatgcagTATCTGGATGAGAACAAGTCCTTAATTCTGAAGATTGTTGAAAGCCAGAAT
EST: gi|208116462|gb|GD914521.1|GD914521
EST:     TGATGGCAGCCTACTACCCCAACAACGTCACCACTGATCACATTCAGCAG                         TATCTGGATGAGAACAAGTCCTTAATTCTGAAGATTGTTGAAAGCCAGAAT
genomic: TGATGGCAGCCTACTACCCCAACAACGTCACCACTGATCACATTCAGCAGgtccgtttct ... ttacatgcagTATCTGGATGAGAACAAGTCCTTAATTCTGAAGATTGTTGAAAGCCAGAAT
EST: gi|208070376|gb|GD870913.1|GD870913
EST:     TGATGGCAGCCTACTACCCCAACAACGTCACCACTGATCACATTCAGCAG                         TATCTGGATGNGAACAAGTCCTTAATTCTGAAGATTGTTGAAAGCCAGAAT
genomic: TGATGGCAGCCTACTACCCCAACAACGTCACCACTGATCACATTCAGCAGgtccgtttct ... ttacatgcagTATCTGGATGAGAACAAGTCCTTAATTCTGAAGATTGTTGAAAGCCAGAAT
EST: gi|207776266|gb|GD749587.1|GD749587
EST:     TGATGGCAGCCTACTACCCCAACAACGTCACCACTGATCACATTCAGCAG                         TATCTGGATGAGAACAAAGTCCTTAAATTCTGAAGATTGTTGAAAGCCAGA
genomic: TGATGGCAGCCTACTACCCCAACAACGTCACCACTGATCACATTCAGCAGgtccgtttct ... ttacatgcagTATCTGGATGAGAACAA-GTCCTTAA-TTCTGAAGATTGTTGAAAGCCAGA
EST: gi|20075691|gb|BQ094474.1|BQ094474
EST:     TGATGGCAGCCTACTACCCCAACAACGTCACCACTGATCACATTCAGCAG                         TATCTGGATGAGAACAAGTCCTTAATTCTGAAGATTGTTGAAAGCCAGAAT
genomic: TGATGGCAGCCTACTACCCCAACAACGTCACCACTGATCACATTCAGCAGgtccgtttct ... ttacatgcagTATCTGGATGAGAACAAGTCCTTAATTCTGAAGATTGTTGAAAGCCAGAAT
EST: gi|298164608|gb|HO014253.1|HO014253
EST:     TGATGGCAGCCTACTACCCCAACAACGTCACCACTGATCACATTCAGCAG                         TATCTGGATGAGAACAAGTCCTTAATTCTGAAGATTGTTGAAAGCCAGAAT
genomic: TGATGGCAGCCTACTACCCCAACAACGTCACCACTGATCACATTCAGCAGgtccgtttct ... ttacatgcagTATCTGGATGAGAACAAGTCCTTAATTCTGAAGATTGTTGAAAGCCAGAAT
EST: gi|208301413|gb|GE100268.1|GE100268
EST:     TGATGGCAGCCTACTACCCCAACAACGTCACCACTGATCACATTCAGCAG                         TATCTGGATGAGAACAAGTCCTTAATTCTGAAGATTGTTGAAAGCCAGAAT
genomic: TGATGGCAGCCTACTACCCCAACAACGTCACCACTGATCACATTCAGCAGgtccgtttct ... ttacatgcagTATCTGGATGAGAACAAGTCCTTAATTCTGAAGATTGTTGAAAGCCAGAAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TATATTGCGTGTGTGAGAGATGCAGCAGCACCTGATGCAGATGCAGCCCATGATGGCAGCCTACTACCCCAACAACGTCACCACTGATCACATTCAGCAGgtccgtttctctcttcttcttctgcactgctactactgctaccactaccattccccttcatctgcttatcttatctcttctgctagctttggatatactc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctctcttc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttcccct