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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgcagagccgtgatgttttctatttcatttacttaagcttctttgatttctattaatctaaactttctttcatttgtaattagGCAATAAATAAAAGTCTGTCATCATTAAGTGATGTAATATTTGCCTTGGCCAAGAAGGAGGATCATATCCCATTCAGGAACTCAAAGCTCACATACCTAC

Basic information

species Glycine max
transcript GLYMA13G36230.1
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G36230.2 (Glycine max), 3'ss of exon 15
lower sequence: AT5G54670.1 (Arabidopsis thaliana), 3'ss of exon 15
gtatgcagagccgtgatgttttctatttcatttacttaagcttctttgatttctattaatctaaactttctttcatttgtaattagGCAATAAATAAAAGTCTGTCATCATTAAGTGATGTAATATTTGCCTTGGCCAAGAAGGAGGATCATATCCCATTCAGGAACTCAAAGCTCACATACCTAC
||| |       |  |       ||   |||     |    |  |   |||| || |    ||||||||| ||| ||     | ||||||| || |||||| |||| ||  || | ||||| ||||| ||||| || ||||| || |||||| | |||||| | ||||||||||||||||| || |
gtacgtttgatagaaaca-----taaaacatgattatggtttcttgcaatttttagtctcttaaactttcattctttc---ttcagGCAATCAACAAAAGTTTGTCGTCGCTAGGCGATGTCATATTCGCCTTAGCAAAGAAAGAAGATCATGTACCATTCCGAAACTCAAAGCTCACATATCTTC

upper sequence: GLYMA13G36230.2 (Glycine max), 3'ss of exon 15
lower sequence: Vv19s0014g05070.t01 (Vitis vinifera), 3'ss of exon 14
---------gtatgcagagccgtgatgttttctatttcatttacttaagcttctttgatttc-tattaatctaaactttctttcatttgtaattagGCAATAAATAAAAGTCTGTCATCATTAAGTGATGTAATATTTGCCTTGGCCAAGAAGGAGGATCATATCCCATTCAGGAACTCAAAGCTCACATACCTAC
           |  | ||  |  | |   |||| ||   ||||||||   || |     ||  |||| || || | | | ||||| || | |  |||| || ||||| ||||||||||||||||||||||| ||||||||| |||| ||||||||||| ||| | ||||| |||||||||||||| || || || |
gtatttgagaaacactgatacaagcttaattctgttaattttacttatcattatgcatctttatatttatatatattct-tttcaattatgac-agGCCATCAATAAGAGTCTGTCATCATTAAGTGATGTTATATTTGCCCTGGCAAAGAAGGAGGACCATGTACCATTTAGGAACTCAAAGCTTACGTATCTTC
















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|6667670|gb|AW279121.1|AW279121
EST:     AACGTCTTTCAAGGAGTGGATCAACCGGGGACCGATTGAAAGAGACTCAA                         GCAATAAATAAAAGTCTGTCATCATTAAGTGATGTAATATTTGCCTTGGCC
genomic: AACGTCTTTCAAGGAGTGGATCAACCGGGGACCGATTGAAAGAGACTCAAgtatgcagag ... ttgtaattagGCAATAAATAAAAGTCTGTCATCATTAAGTGATGTAATATTTGCCTTGGCC
EST: gi|193419543|gb|FK383193.1|FK383193
EST:     ACCGGGGACCGATTGAAAGAGACTCAA                         GCAATAAATAAAAGTCTGTCATCATTAAGTGATGTAATATTTGCCTTGGCC
genomic: ACCGGGGACCGATTGAAAGAGACTCAAgtatgcagag ... ttgtaattagGCAATAAATAAAAGTCTGTCATCATTAAGTGATGTAATATTTGCCTTGGCC
EST: gi|208072762|gb|GD872363.1|GD872363
EST:     AACGTCTTTCAAGGAGTGGATCAACCGGGGACCGATTGAAAGAGACTCAA                         GCAATAAATAAAAGTCTGTCATCATTAAGTGATGTAATATTTGCCTTGGCC
genomic: AACGTCTTTCAAGGAGTGGATCAACCGGGGACCGATTGAAAGAGACTCAAgtatgcagag ... ttgtaattagGCAATAAATAAAAGTCTGTCATCATTAAGTGATGTAATATTTGCCTTGGCC
EST: gi|10255088|gb|BE822854.1|BE822854
EST:     AACGTCTTTCAAGGAGTGGATCAACCGGGGACCGATTGAAAGAGACTCAA                         GCAATAAATAAAAGTCTGTCATCATTAAGTGATGTAATATTTGCCTTGGCC
genomic: AACGTCTTTCAAGGAGTGGATCAACCGGGGACCGATTGAAAGAGACTCAAgtatgcagag ... ttgtaattagGCAATAAATAAAAGTCTGTCATCATTAAGTGATGTAATATTTGCCTTGGCC
EST: gi|16996302|gb|BM085674.1|BM085674
EST:     AACGTCTTTCAAGGAGTGGATCAACCGGGGACCGATTGAAAGAGACTCAA                         GCAATAAATAAAAGTCTGTCATCATTAAGTGATGTAATATTTGCCTTGGCC
genomic: AACGTCTTTCAAGGAGTGGATCAACCGGGGACCGATTGAAAGAGACTCAAgtatgcagag ... ttgtaattagGCAATAAATAAAAGTCTGTCATCATTAAGTGATGTAATATTTGCCTTGGCC
EST: gi|193542299|gb|FK497517.1|FK497517
EST:     AACGTCTTTCAAGGAGTGGATCAACCGGGGACCGATTGAAAGGGACTCAA                         GCAATAAATAAAAGTCTGTCATCATTAAGTGATGTAATATTTGCCTTGGCC
genomic: AACGTCTTTCAAGGAGTGGATCAACCGGGGACCGATTGAAAGAGACTCAAgtatgcagag ... ttgtaattagGCAATAAATAAAAGTCTGTCATCATTAAGTGATGTAATATTTGCCTTGGCC
EST: gi|5820092|gb|AI988298.1|AI988298
EST:     AACGTCTTTCAAGGAGTGGATCAACCGGGGACCGATTGAAAGAGACTCAA                         GCAATAAATAAAAGTCTGTCATCATTAAGTGATGTAATATTTGCCTTGGCC
genomic: AACGTCTTTCAAGGAGTGGATCAACCGGGGACCGATTGAAAGAGACTCAAgtatgcagag ... ttgtaattagGCAATAAATAAAAGTCTGTCATCATTAAGTGATGTAATATTTGCCTTGGCC
EST: gi|207785336|gb|GD759087.1|GD759087
EST:     AACGTC-TTCAAGGAGTGGATCAACCGGGGACCGATTGAAAGAGACTCAA                         GCAATAAATAAAAGTCTGTCATCATTAAGTGATGTAATATTTGCCTTGGCC
genomic: AACGTCTTTCAAGGAGTGGATCAACCGGGGACCGATTGAAAGAGACTCAAgtatgcagag ... ttgtaattagGCAATAAATAAAAGTCTGTCATCATTAAGTGATGTAATATTTGCCTTGGCC
EST: gi|208305868|gb|GE109547.1|GE109547
EST:     GGGACCGA-TGAAAGAGACTCAA                         GCAATAAATAAAAGTCTGTCATCATTAAGTGATGTAATATTTGCCTTGGCC
genomic: GGGACCGATTGAAAGAGACTCAAgtatgcagag ... ttgtaattagGCAATAAATAAAAGTCTGTCATCATTAAGTGATGTAATATTTGCCTTGGCC
EST: gi|208218829|gb|GE016147.1|GE016147
EST:     AACGTCTTTCAAGGAGTGGATCAACCGGGGACCGATTGAAAGAGACTCAA                         GCAATAAATAAAAGTCTGTCATCATTAAGTGATGTAATATTTGCCTTGGCC
genomic: AACGTCTTTCAAGGAGTGGATCAACCGGGGACCGATTGAAAGAGACTCAAgtatgcagag ... ttgtaattagGCAATAAATAAAAGTCTGTCATCATTAAGTGATGTAATATTTGCCTTGGCC
EST: gi|51344240|gb|CO984973.1|CO984973
EST:     AACGTCTTTCAAGGAGTGGATCAACCGGGGACCGATTGAAAGAGACTCAA                         GCAATAAATAAAAGTCTGTCATCATTAAGTGATGTAATATTTGCCTTGGCC
genomic: AACGTCTTTCAAGGAGTGGATCAACCGGGGACCGATTGAAAGAGACTCAAgtatgcagag ... ttgtaattagGCAATAAATAAAAGTCTGTCATCATTAAGTGATGTAATATTTGCCTTGGCC
EST: gi|208186092|gb|GD985433.1|GD985433
EST:     ATCAACCGGGGACCGATTGAAAGAGACTCAA                         GCAATAAAATAAAAGTCTGTCATCATTAAGTGATGTAATATTTGCCTTGGC
genomic: ATCAACCGGGGACCGATTGAAAGAGACTCAAgtatgcagag ... ttgtaattagGCAAT-AAATAAAAGTCTGTCATCATTAAGTGATGTAATATTTGCCTTGGC
EST: gi|14205310|gb|BG838988.1|BG838988
EST:     ACGTTTTTTCAAGGAGTGGATCAACCGGGGACCGATTGAAAGAGACTCAA                         GCAATAAATAAAAGTCTGTCATCATTAAGTGATGTAATATTTGCCTTGGCC
genomic: ACG-TCTTTCAAGGAGTGGATCAACCGGGGACCGATTGAAAGAGACTCAAgtatgcagag ... ttgtaattagGCAATAAATAAAAGTCTGTCATCATTAAGTGATGTAATATTTGCCTTGGCC
EST: gi|11687964|gb|BF595640.1|BF595640
EST:     AACGTCTTTCAAGGAGTGGATCAACCGGGGACCGATTGAAAGAGACTCAA                         GCAATAAATAAAAGTCTGTCATCATTAAGTGATGTAATATTTGCCTTGGCC
genomic: AACGTCTTTCAAGGAGTGGATCAACCGGGGACCGATTGAAAGAGACTCAAgtatgcagag ... ttgtaattagGCAATAAATAAAAGTCTGTCATCATTAAGTGATGTAATATTTGCCTTGGCC
EST: gi|207687107|gb|GD669795.1|GD669795
EST:     AACGTCTTTCAAGGAGTGGATCAACCGGGGACCGATTGAAAGAGACTCAA                         GCAATAAATAAAAGTCTGTCATCATTAAGTGATGTAATATTTGCCTTGGCC
genomic: AACGTCTTTCAAGGAGTGGATCAACCGGGGACCGATTGAAAGAGACTCAAgtatgcagag ... ttgtaattagGCAATAAATAAAAGTCTGTCATCATTAAGTGATGTAATATTTGCCTTGGCC
EST: gi|208323722|gb|GE122293.1|GE122293
EST:     AACGTCTTTCAAGGAGTGGATCAACCGGGGACCGATTGAAAGAGACTCAA                         GCAATAAATAAAAGTCTGTCATCATTAAGTGATGTAATATTTGCCTTGGCC
genomic: AACGTCTTTCAAGGAGTGGATCAACCGGGGACCGATTGAAAGAGACTCAAgtatgcagag ... ttgtaattagGCAATAAATAAAAGTCTGTCATCATTAAGTGATGTAATATTTGCCTTGGCC
EST: gi|193306454|gb|FK273379.1|FK273379
EST:     AACGTCTTTCAAGGAGTGGATCAACCGGGGACCGATTGAAAGAGACTCAA                         GCAATAAATAAAAGTCTGTCATCATTAAG
genomic: AACGTCTTTCAAGGAGTGGATCAACCGGGGACCGATTGAAAGAGACTCAAgtatgcagag ... ttgtaattagGCAATAAATAAAAGTCTGTCATCATTAAG
EST: gi|208326181|gb|GE121095.1|GE121095
EST:     CCGGGGACCGATTGTAAAGAGTACTTCAA                         GCAATAAATAAAAGTCTGTCATCATTAAGTGATGTGATATTTGCCTTGGC
genomic: CCGGGGACCGATTG-AAAGAG-AC-TCAAgtatgcagag ... ttgtaattagGCAATAAATAAAAGTCTGTCATCATTAAGTGATGTAATATTTGCCTTGGC
EST: gi|193696453|gb|FK636629.1|FK636629
EST:     CCGGGGACCGATTGAAAGAGACTCAA                         GCAATAAATAAAAGTCTGTCATCATTAAGTGATGTAATATTTGCCTTGGCC
genomic: CCGGGGACCGATTGAAAGAGACTCAAgtatgcagag ... ttgtaattagGCAATAAATAAAAGTCTGTCATCATTAAGTGATGTAATATTTGCCTTGGCC
EST: gi|193571531|gb|FK532762.1|FK532762
EST:     GACCGATTGAAAGAGACTCAA                         GCAATAAAATAAAAGTCTGTCATCATTAAGTGATGTAATATTTGCCTTGGC
genomic: GACCGATTGAAAGAGACTCAAgtatgcagag ... ttgtaattagGCAAT-AAATAAAAGTCTGTCATCATTAAGTGATGTAATATTTGCCTTGGC
EST: gi|51334869|gb|CO978735.1|CO978735
EST:     AACGTCTTTCAAGGAGTGGATCAACCGGGGACCGATTGAAAGAGACTCAA                         GCAATAAATAAAAGTCTGTCATCATTAAGTGATGTAATATTTGCCTTGGCC
genomic: AACGTCTTTCAAGGAGTGGATCAACCGGGGACCGATTGAAAGAGACTCAAgtatgcagag ... ttgtaattagGCAATAAATAAAAGTCTGTCATCATTAAGTGATGTAATATTTGCCTTGGCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttacttaagcttctttgatttctattaatctaaactttctttcatttgtaattagGCAATAAATAAAAGTCTGTCATCATTAAGTGATGTAATATTTGCCTTGGCCAAGAAGGAGGATCATATCCCATTCAGGAACTCAAAGCTCACATACCTAC
                                  ctttctttcatttgt  CT-rich tract
             tttgatttctattaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgcagagccgtgatgttttctatttcatttacttaagcttctttgatttctattaatctaaactttctttcatttgtaattagGCAATAAATAAAAGTCTGTCATCATTAAGTGATGTAATATTTGCCTTGGCCAAGAAGGAGGATCATATCCCATTCAGGAACTCAAAGCTCACATACCTAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA