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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgaaaaacatttttggaattatatgttcaaatggacattagaattcactgtgttggctaggcttgcattgttgatacttttttccatatcatgtttgcagATAAGATACATAGCAAAATGGGTGAAGGAACTTTTGGGCAGGTCTTAGAATGCTGGGATAGAGAAAGGAAGGAAATGGTTGCCGTAAAAATTGTCCGTGG

Basic information

species Glycine max
transcript GLYMA17G13440.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G13440.1 (Glycine max), 3'ss of exon 2
lower sequence: AT4G24740.1 (Arabidopsis thaliana), 3'ss of exon 3
tgaaaaacatttttggaattatatgttcaaatggacattagaattcactgt-gttggctaggcttgcattgttgatacttttttccatatcatgtttgcagATAAGATACATAGCAAAATGGGTGAAGGAACTTTTGGGCAGGTCTTAGAATGCTGGGATAGAGAAAGGAAGGAAATGGTTGCCGTAAAAATTGTCCGTGG---------------------------
                                     |  ||||| |  || ||||   | | |    |  | | | |   | |   |||| | | ||        ||       |   |   || ||| |||||||| || ||  ||||||| |||||||| || |||||||||||||| || |||||||||||||||||                           
------------------------------------gtatgaatttatggttgttgtacaagttattttcataggt-ccggtgtagttatcgtatctg--------atttcctaaattttccttgtagGTACTTTTGGTCAAGTGCTAGAATGTTGGGATAGGGAGAGGAAGGAAATGGTGGCAGTAAAAATTGTCCGTGGTGTGAAGAAATACCGTGAGGCTGCTAT

upper sequence: GLYMA17G13440.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv17s0000g09500.t01 (Vitis vinifera), 3'ss of exon 3
tgaaaaacatttttggaattatatgttcaaatggacattagaattcactgtgt-tggctaggcttgcattgttgatacttttttccatatcatgtttgcagATAAGATACATAGCAAAATGGGTGAAGGAACTTTTGGGCAGGTCTTAGAATGCTGGGATAGAGAAAGGAAGGAAATGGTTGCCGTAAAAATTGTCCGTGG---------------------------
                               |   | || | ||  | | | | | | |     |  ||| |  | |   |  | |||      |   | |||   ||  ||  |    |   || |||||| ||||| ||||| || ||||||||||| ||||| |||||||||||||||||||| ||||||||||||||                           
------------------------------gtacccctttggatctattatttcttgatcattctcaattttctacatcataattcatcatgcatcccc-gatccaatttatttcc---tttttgtagGAACCTTTGGTCAGGTTTTGGAATGCTGGGACAGAGAGAGGAAGGAAATGGTTGCCGTCAAAATTGTCCGTGGTATTAAGAAGTATCGTGAGGCTGCCAT
















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|209715198|gb|BW668526.1|BW668526
EST:     CAAAGATGGGCATTACATGTTTGCGCTTGGAGAAAATTTAACTTCTCGCT                         ATAAGATACATAGCAAAATGGGTGAAGGAACTTTTGGGCAGGTCTTAGAAT
genomic: CAAAGATGGGCATTACATGTTTGCGCTTGGAGAAAATTTAACTTCTCGCTgtaattacac ... atgtttgcagATAAGATACATAGCAAAATGGGTGAAGGAACTTTTGGGCAGGTCTTAGAAT
EST: gi|207832960|gb|GD805246.1|GD805246
EST:     CAAAGATGGGCATTACATGTTTGCGCTTGGAGAAAATTTAACTTCTCGCT                         ATAAGATACATAGCAAAATGGGTGAGGGAACTTTTGGGCAGGTCTTAGAAT
genomic: CAAAGATGGGCATTACATGTTTGCGCTTGGAGAAAATTTAACTTCTCGCTgtaattacac ... atgtttgcagATAAGATACATAGCAAAATGGGTGAAGGAACTTTTGGGCAGGTCTTAGAAT
EST: gi|192295348|gb|FG986002.1|FG986002
EST:     CAAAGATGGGCATTACATGTTTGCGCTTGGAGAAAATTTAACTTCTCGCT                         ATAAGATACATAGCAAAATGGGTGAAGGAACTTTTGGGCAGGTCTTAGAAT
genomic: CAAAGATGGGCATTACATGTTTGCGCTTGGAGAAAATTTAACTTCTCGCTgtaattacac ... atgtttgcagATAAGATACATAGCAAAATGGGTGAAGGAACTTTTGGGCAGGTCTTAGAAT
EST: gi|193485971|gb|FK452158.1|FK452158
EST:     CAAAGATGGGCATTACATGTTTGCGCTTGGAGAAAATTTAACTTCTCGCT                         ATAAGATACATAGCAAAATGGGTGAAGGAACTTTTGGGCAGGTCTTAGAAT
genomic: CAAAGATGGGCATTACATGTTTGCGCTTGGAGAAAATTTAACTTCTCGCTgtaattacac ... atgtttgcagATAAGATACATAGCAAAATGGGTGAAGGAACTTTTGGGCAGGTCTTAGAAT
EST: gi|207701006|gb|GD682321.1|GD682321
EST:     CAAAGATGGGCATTACATGTTTGCGCTTGGAGAAAATTTAACTTCTCGCT                         ATAAGATACATAGCAAAATGGGTGAAGGAACTTTTGGGCAGGTCTTAGAAT
genomic: CAAAGATGGGCATTACATGTTTGCGCTTGGAGAAAATTTAACTTCTCGCTgtaattacac ... atgtttgcagATAAGATACATAGCAAAATGGGTGAAGGAACTTTTGGGCAGGTCTTAGAAT
EST: gi|6454636|gb|AW185319.1|AW185319
EST:     CAAAGATGGGCATTACATGTTTGCGCTTGGAGAAAATTTAACTTCTCGCT                         ATAAGATACATAGCAAAATGGGTGAAGGAACTTTTGGGCAGGTCTTAGAAT
genomic: CAAAGATGGGCATTACATGTTTGCGCTTGGAGAAAATTTAACTTCTCGCTgtaattacac ... atgtttgcagATAAGATACATAGCAAAATGGGTGAAGGAACTTTTGGGCAGGTCTTAGAAT
EST: gi|15286579|gb|BI470470.1|BI470470
EST:     CAAAGATGGGCATTACATGTTTGCGCTTGGAGAAAATTTAACTTCTCGCT                         ATAAGATACATAGCAAAATGGGTGAAGGAACTTTTGGGCAGGTCTTAGAAT
genomic: CAAAGATGGGCATTACATGTTTGCGCTTGGAGAAAATTTAACTTCTCGCTgtaattacac ... atgtttgcagATAAGATACATAGCAAAATGGGTGAAGGAACTTTTGGGCAGGTCTTAGAAT
EST: gi|17022467|gb|BM093501.1|BM093501
EST:     CAAAGATGGGCATTACATGTTTGCGCTTGGAGAAAATTTAACTTCTCGCT                         ATAAGATACATAGCAAAATGGGTGAAGGAACTTTTGGGCAGGTCTTAGAAT
genomic: CAAAGATGGGCATTACATGTTTGCGCTTGGAGAAAATTTAACTTCTCGCTgtaattacac ... atgtttgcagATAAGATACATAGCAAAATGGGTGAAGGAACTTTTGGGCAGGTCTTAGAAT
EST: gi|9986568|gb|BE660676.1|BE660676
EST:     CAAAGATGGGCATTACATGTTTGCGCTTGGAGAAAATTTAACTTCTCGCT                         ATAAGATACATAGCAAAATGGGTGAAGGAACTTTTGGGCAGGTCTTAGAAT
genomic: CAAAGATGGGCATTACATGTTTGCGCTTGGAGAAAATTTAACTTCTCGCTgtaattacac ... atgtttgcagATAAGATACATAGCAAAATGGGTGAAGGAACTTTTGGGCAGGTCTTAGAAT
EST: gi|23064326|gb|BU579099.1|BU579099
EST:     CAAAGATGGGCATTACATGTTTGCGCTTGGAGAAAATTTAACTTCTCGCT                         ATAAGATACATAGCAAAATGGGTGAAGGAACTTTTGGGCAGGTCTTAGAAT
genomic: CAAAGATGGGCATTACATGTTTGCGCTTGGAGAAAATTTAACTTCTCGCTgtaattacac ... atgtttgcagATAAGATACATAGCAAAATGGGTGAAGGAACTTTTGGGCAGGTCTTAGAAT
EST: gi|9901661|gb|BE610629.1|BE610629
EST:     CAAAGATGGGCATTACATGTTTGCGCTTGGAGAAAATTTAACTTCTCGCT                         ATAAGATACATAGCAAAATGGGTGAAGGAACTTTTGGGCAGGTCTTAGAAT
genomic: CAAAGATGGGCATTACATGTTTGCGCTTGGAGAAAATTTAACTTCTCGCTgtaattacac ... atgtttgcagATAAGATACATAGCAAAATGGGTGAAGGAACTTTTGGGCAGGTCTTAGAAT
EST: gi|23064408|gb|BU579181.1|BU579181
EST:     CAAAGATGGGCATTACATGTTTGCGCTTGGAGAAAATTTAACTTCTCGCT                         ATAAGATACATAGCAAAATGGGTGAAGGAACTTTTGGGCAGGTCTTAGAAT
genomic: CAAAGATGGGCATTACATGTTTGCGCTTGGAGAAAATTTAACTTCTCGCTgtaattacac ... atgtttgcagATAAGATACATAGCAAAATGGGTGAAGGAACTTTTGGGCAGGTCTTAGAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cactgtgttggctaggcttgcattgttgatacttttttccatatcatgtttgcagATAAGATACATAGCAAAATGGGTGAAGGAACTTTTGGGCAGGTCTTAGAATGCTGGGATAGAGAAAGGAAGGAAATGGTTGCCGTAAAAATTGTCCGTGG
                       tgttgat  putative branch site (score: 4)
                            atactttttt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgaaaaacatttttggaattatatgttcaaatggacattagaattcactgtgttggctaggcttgcattgttgatacttttttccatatcatgtttgcagATAAGATACATAGCAAAATGGGTGAAGGAACTTTTGGGCAGGTCTTAGAATGCTGGGATAGAGAAAGGAAGGAAATGGTTGCCGTAAAAATTGTCCGTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- aaaaaca
- - - - - - - - - - - - - - - - - - - - - - - - -gtgttgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcttgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgttgat