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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagatttaactttctttatgtcctctattacttttttaattttgtttttcaaaccaagagttattttgtattttatcgtgatgacaattgtattttttgttatttgttatgtttttattggactgtgaaatttcattttttattggtatcaatctttaactatacatttaaacttgtttgatttgtgttttagGTTTTGAGAAGCCATCAGCTATTCAGCAGAGAGGAATAGTTCCTTTCTGCAAGGGACTTGATGTTATACAACAGGCCCAGTCTGGAACTGGGAAGACAGC

Basic information

species Glycine max
transcript GLYMA15G18760.3
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G18760.1 (Glycine max), 3'ss of exon 3
lower sequence: AT1G54270.2 (Arabidopsis thaliana), 3'ss of exon 3
gtagatttaactttctttatgtcctctattacttttttaattttgtttttcaaaccaagagttattttgtattttatcgtgatgacaattgtattttttgttatttgttatgtttttattgg--actgtgaaatttcattttttattggtatcaatctttaactatacatttaaacttgtttgatttgtgttttagGTTTTGAGAAGCCATCAGCTATTCAGCAGAGAGGAATAGTTCCTTTCTGCAAGGGACTTGATGTTATACAACAGGCCCAGTCTGGAACTGGGAAGACAGC
|||| | || | | | || || | | | | | |||| || | | || ||| | || || | | | | || | ||| ||||||| | || ||||||| || ||||| || ||||||||||| |||||||| || || || |||||||| |||||||| || || ||||| |||||||| ||||| || || ||
--------------------------------------------------------------------gtatct-atgcttacggtaagtgaagaaggtttaaagaaacaaccttttgtttgttatgttgggattcctattaactttatcgtatgtgctctttcctgtgattga--ttggttgattttt-ttctagGTTTCGAAAAGCCTTCTGCTATTCAGCAAAGAGGAATTGTACCCTTTTGCAAGGGTCTTGATGTGATCCAGCAGGCACAGTCTGGTACTGGAAAAACCGC

upper sequence: GLYMA15G18760.1 (Glycine max), 3'ss of exon 3
lower sequence: AT3G13920.4 (Arabidopsis thaliana), 3'ss of exon 3
gtagatttaactttctttatgtcctctattacttttttaattttgtttttcaaaccaagagttattttgtattttatcgtgatgacaattgtattttttgttatttgttatgtttttattggactgtgaaa--tttcattttttattggtatca-atctttaactatacatttaaacttgtttgatttgtgttttagGTTTTGAGAAGCCATCAGCTATTCAGCAGAGAGGAATAGTTCCTTTCTGCAAGGGACTTGATGTTATACAACAGGCCCAGTCTGGAACTGGGAAGACAGC
|||||| | ||| || ||||| | || || ||| | || ||| | ||| | || | || | || | | | || || || | | ||||||||||||||||| || ||||||||||| |||||||| || || ||||| ||||| |||||||| || |||||||| |||||||| |||||||| |||||
------------------------------------------------------------------------------------------gtatttatgctta--tggtatgtgtgtaggaacttgaaaaagctatcttttgtgatttatgtcttagattagaacattatctcatgcgtgcttctgttttttcttagGTTTTGAGAAGCCTTCTGCTATTCAGCAAAGAGGAATCGTCCCCTTCTGTAAGGGTCTTGATGTGATTCAACAGGCTCAGTCTGGTACTGGGAAAACAGC

upper sequence: GLYMA15G18760.1 (Glycine max), 3'ss of exon 3
lower sequence: AT3G13920.2 (Arabidopsis thaliana), 3'ss of exon 3
gtagatttaactttctttatgtcctctattacttttttaattttgtttttcaaaccaagagttattttgtattttatcgtgatgacaattgtattttttgttatttgttatgtttttattggactgtgaaatttcattttttattggtatcaatctttaactata-catt----taaacttgtttgatttgtgttttagGTTTTGAGAAGCCATCAGCTATTCAGCAGAGAGGAATAGTTCCTTTCTGCAAGGGACTTGATGTTATACAACAGGCCCAGTCTGGAACTGGGAAGACAGC
| | | | | ||| ||||| | | ||| || | | |||| | || | |||| | | || || || | | ||||||||||||||||| || ||||||||||| |||||||| || || ||||| ||||| |||||||| || |||||||| |||||||| |||||||| |||||
-------------------------------------------------------------------------------------------------------------gtatgtgtgtaggaacttgaaaaagctatcttttgtgatttatgtcttagattagaacattatctcatgcgtgcttctgttttttcttagGTTTTGAGAAGCCTTCTGCTATTCAGCAAAGAGGAATCGTCCCCTTCTGTAAGGGTCTTGATGTGATTCAACAGGCTCAGTCTGGTACTGGGAAAACAGC

upper sequence: GLYMA15G18760.1 (Glycine max), 3'ss of exon 3
lower sequence: AT1G72730.1 (Arabidopsis thaliana), 3'ss of exon 3
gtagatttaactttctttatgtcctctattacttttttaattttgtttttcaaaccaagagttattttgtattttatcgtgatgacaattgtattttttgttatttgttatgtttttattggactgtgaaatttcattttttattggtatcaatctttaactatacatttaaacttgtttgatttgtgttttagGTTTTGAGAAGCCATCAGCTATTCAGCAGAGAGGAATAGTTCCTTTCTGCAAGGGACTTGATGTTATACAACAGGCCCAGTCTGGAACTGGGAAGACAGC
| | | || |||| | | ||| | || | || | | ||| ||| | || | |||| || | ||| |||| ||| | | | | |||| ||| | | || | | |||| | |||||||| |||||||| || ||||||||||| |||||||| |||| ||||||||||| |||||||| || || || || || ||||||||||| ||||| ||
-----------------------------------gtaagtgaagtatttcctttgagaacacattctatacat----------accttcattgtttctgtctagttttgtattttcttttgtttgt-----ttcaaagcttagtactgttactcttaaacaacctcatattggttttgttatttat-cattagGTTTCGAGAAGCCTTCTGCTATTCAGCAAAGAGGAATTATTCCATTCTGCAAGGGTCTTGATGTGATCCAGCAAGCTCAATCTGGAACTGGAAAGACCGC

upper sequence: GLYMA15G18760.1 (Glycine max), 3'ss of exon 3
lower sequence: AT1G54270.1 (Arabidopsis thaliana), 3'ss of exon 3
gtagatttaactttctttatgtcctctattacttttttaattttgtttttcaaaccaagagttattttgtattttatcgtgatgacaattgtattttttgttatttgttatgtttttattggactgtgaaatttcattttttattggtatcaatctttaactatacatttaaacttgtttgatttgtgttttagGTTTTGAGAAGCCATCAGCTATTCAGCAGAGAGGAATAGTTCCTTTCTGCAAGGGACTTGATGTTATACAACAGGCCCAGTCTGGAACTGGGAAGACAGC
||| | | | | || | | || ||||||||||| ||| || | || ||||| | ||| || || | ||| | ||| ||||||| | || ||||||| || ||||| || ||||||||||| |||||||| || || || |||||||| |||||||| || || ||||| |||||||| ||||| || || ||
--------------------------------------------------------------------gtaagtgaagaaggtt-taaagaaacaaccttttgtttgttatgttgggattc--ctattaa--------ctttatcg-tatgtgctctttcctgtg-attga---ttggttgattttt-ttctagGTTTCGAAAAGCCTTCTGCTATTCAGCAAAGAGGAATTGTACCCTTTTGCAAGGGTCTTGATGTGATCCAGCAGGCACAGTCTGGTACTGGAAAAACCGC

upper sequence: GLYMA15G18760.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv11s0016g01920.t01 (Vitis vinifera), 3'ss of exon 2
gtagatttaactttctttatgtcctctattacttttttaattttgtttttcaaaccaagagttattttgtattttatcgtgatgacaattgtattttttgttatttgttatgtttttattggactgtgaaatttcattttttattggtatcaatcttta----actatacatttaaacttgtttgatttgtgttttagGTTTTGAGAAGCCATCAGCTATTCAGCAGAGAGGAATAGTTCCTTTCTGCAAGGGACTTGATGTTATACAACAGGCCCAGTCTGGAACTGGGAAGACAGC
||| ||| |||||||| | | | | | ||| || | || || | || || ||| ||| || | ||| | | |||||||||| || || || || |||||||| |||||||| ||||| || ||||||||||||||||| || || || || ||||| ||||| || ||||| ||
--------------------------------------------------------------------------------------------------tgtatattgatatgttttcgtgaaaatttcttttcctccgtttgttttgcattgctcatgtcagtaccatcaattgaaagatggataattcttcgtgtagGTTTTGAAAAACCTTCTGCAATTCAGCAAAGAGGAATTGTTCCCTTTTGCAAGGGACTTGATGTAATTCAGCAAGCTCAGTCAGGAACAGGAAAGACTGC

upper sequence: GLYMA15G18760.1 (Glycine max), 3'ss of exon 3
lower sequence: PP1S31_150V6.5 (Physcomitrella patens), 3'ss of exon 3
gtagatttaactttctttatgtcctctattacttttttaattttgtttttcaaaccaagagttattttgtattttatcgtgatgacaattgtattttttgt---tatttgttatgtttttattggactgtgaaatttcattttttattggtatcaatctttaactatacatttaaacttgtttgatttgtgttttagGTTTTGAGAAGCCATCAGCTATTCAGCAGAGAGGAATAGTTCCTTTCTGCAAGGGACTTGATGTTATACAACAGGCCCAGTCTGGAACTGGGAAGACAGC
||| || |||||| | |||| |||| || | || | || || || ||| || || || | | || |||| ||| |||||||||||||||||| ||||| || ||| | ||||| ||||| ||| |||||| |||||||| || ||||| ||||||||||||||||| ||||||||
----------------------------------------------------------------------------------------ttgcatgttttgtgggtgcttgtggtgttcgtagtttcctaccgagaaccaattg-----aaccgcactctgctgctcta-atctcattctggttgacctgtac---agGTTTTGAGAAGCCATCTGCTATCCAACAGCGTGGAATCGTTCCCTTCACCAAGGGTCTTGATGTCATTCAACAAGCCCAGTCTGGAACTGGCAAGACAGC

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|298169377|gb|HO020737.1|HO020737
EST:     TGATGCTATGGGCTTGCAAGAGAATCTCCTGAGAGGCATTTATGCATATG                         GTTTTGAGAAGCCATCAGCTATTCAGCAGAGAGGAATAGTTCCTTTCTGCA
genomic: TGATGCTATGGGCTTGCAAGAGAATCTCCTGAGAGGCATTTATGCATATGgtagatttaa ... tgtgttttagGTTTTGAGAAGCCATCAGCTATTCAGCAGAGAGGAATAGTTCCTTTCTGCA
EST: gi|208237128|gb|GE035136.1|GE035136
EST:     AGAATCTCCTGAGAGGCATTTATGCATATG                         GTTTTGAGAAGCCATCAGCTATTCAGCAGAGAGGAATAGTTCCTTTCTGCA
genomic: AGAATCTCCTGAGAGGCATTTATGCATATGgtagatttaa ... tgtgttttagGTTTTGAGAAGCCATCAGCTATTCAGCAGAGAGGAATAGTTCCTTTCTGCA
EST: gi|15814355|gb|BI786630.1|BI786630
EST:     TGATGCTATGGGCTTGCAAGAGAATCTCCTGAGAGGCATTTATGCATATG                         GTTTTGAGAAGCCATCAGCTATTCAGCAGAGAGGAATAGTTCCTTTCTGCA
genomic: TGATGCTATGGGCTTGCAAGAGAATCTCCTGAGAGGCATTTATGCATATGgtagatttaa ... tgtgttttagGTTTTGAGAAGCCATCAGCTATTCAGCAGAGAGGAATAGTTCCTTTCTGCA
EST: gi|6666365|gb|AW277824.1|AW277824
EST:     TGATGCTATGGGCTTGCAAGAGAATCTCCTGAGAGGCATTTATGCATATG                         GTTTTGAGAAGCCATCAGCTATTCAGCAGAGAGGAATAGTTCCTTTCTGCA
genomic: TGATGCTATGGGCTTGCAAGAGAATCTCCTGAGAGGCATTTATGCATATGgtagatttaa ... tgtgttttagGTTTTGAGAAGCCATCAGCTATTCAGCAGAGAGGAATAGTTCCTTTCTGCA
EST: gi|192295033|gb|FG986752.1|FG986752
EST:     TGATGCTATGGGCTTGCAAGACAATCTCCTGAGAGGCATTTATGCATATG                         GTTTTGAGAAGCCA
genomic: TGATGCTATGGGCTTGCAAGAGAATCTCCTGAGAGGCATTTATGCATATGgtagatttaa ... tgtgttttagGTTTTGAGAAGCCA
EST: gi|209712728|gb|BW681582.1|BW681582
EST:     TGATGCTATGGGCTTGCAGGAGAATCTCCTGAGAGGCATTTATGCATATG                         GTTTTGAGAAGCCATCAGCTATTCAGCAGAGAGGAATAGTTCCTTTCTGCA
genomic: TGATGCTATGGGCTTGCAAGAGAATCTCCTGAGAGGCATTTATGCATATGgtagatttaa ... tgtgttttagGTTTTGAGAAGCCATCAGCTATTCAGCAGAGAGGAATAGTTCCTTTCTGCA
EST: gi|213591344|gb|DB959886.1|DB959886
EST:     TGATGCTATGGGCTTGCAGGAGAATCTCCTGAGAGGCATTTATGCATATG                         GTTTTGAGAAGCCATCAGCTATTCAGCAGAGAGGAATAGTTCCTTTCTGCA
genomic: TGATGCTATGGGCTTGCAAGAGAATCTCCTGAGAGGCATTTATGCATATGgtagatttaa ... tgtgttttagGTTTTGAGAAGCCATCAGCTATTCAGCAGAGAGGAATAGTTCCTTTCTGCA
EST: gi|207825765|gb|GD798582.1|GD798582
EST:     AGAATCTCCTGAGAGGCATTTATGCATANG                         GTTTTGAGAAGCCATCAGCTATTCAGCAGAGAGGAATAGTTCCTTTCTGCA
genomic: AGAATCTCCTGAGAGGCATTTATGCATATGgtagatttaa ... tgtgttttagGTTTTGAGAAGCCATCAGCTATTCAGCAGAGAGGAATAGTTCCTTTCTGCA
EST: gi|208275593|gb|GE077793.1|GE077793
EST:     AGAATCTCCTGAGAGGCATTTATGCATATG                         GTTTTGAGAAGCCATCAGCTATTCAGCAGAGAGGAATAGTTCCTTTCTGCA
genomic: AGAATCTCCTGAGAGGCATTTATGCATATGgtagatttaa ... tgtgttttagGTTTTGAGAAGCCATCAGCTATTCAGCAGAGAGGAATAGTTCCTTTCTGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttattggtatcaatctttaactatacatttaaacttgtttgatttgtgttttagGTTTTGAGAAGCCATCAGCTATTCAGCAGAGAGGAATAGTTCCTTTCTGCAAGGGACTTGATGTTATACAACAGGCCCAGTCTGGAACTGGGAAGACAGC
            aatctttaactataca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagatttaactttctttatgtcctctattacttttttaattttgtttttcaaaccaagagttattttgtattttatcgtgatgacaattgtattttttgttatttgttatgtttttattggactgtgaaatttcattttttattggtatcaatctttaactatacatttaaacttgtttgatttgtgttttagGTTTTGAGAAGCCATCAGCTATTCAGCAGAGAGGAATAGTTCCTTTCTGCAAGGGACTTGATGTTATACAACAGGCCCAGTCTGGAACTGGGAAGACAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA