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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAAGATTTTGATAACATAGTGGAGCTTCAACTAGGTGCTCCGTGGCCCCTACCACCCCTTGAAGCGACTGCCACATTAGCTCACAAATTTGAACTCATAGgttggttttatcattttatgttttgtgtttttgtttcttatctgtatgtgcgtgctaaattttgcatgattactactaattgccagttatgagaattgtagtattgtatagtctttgagagtgcctttttatcttttgtgggttttgtaaatgtcccag

Basic information

species Glycine max
transcript GLYMA20G34960.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G34960.1 (Glycine max), 5'ss of exon 3
lower sequence: Vv05s0049g01360.t01 (Vitis vinifera), 5'ss of exon 3
AAAGATTTTGATAACATAGTGGAGCTTCAACTAGGTGCTCCGTGGCCCCTACCACCCCTTGAAGCGACTGCCACATTAGCTCACAAATTTGAACTCATAGgttggttttatcattttatgttttgtgtttttgtttcttat-ctgtatgtgcgtgctaaattttgcatgattactactaattgccagttatgagaattgtagtattgtatagtctttgagagtgcctttttatcttttgtgggttttgtaaatgtcccag
||||||||||| || ||||| || || ||  ||||||| || |||||||| |||||  |||||   |||||||||||||| ||||| ||||||||||||||||  |||      |   |   |   | || |    ||| | ||| || |       |  |||  ||    ||     ||    |   ||    |||| || | |  | |||                                                
AAAGATTTTGACAATATAGTAGATCTCCAGATAGGTGCCCCATGGCCCCTTCCACCAATTGAACTCACTGCCACATTAGCCCACAAGTTTGAACTCATAGgttcatttccaagctcatttcatgaggcttgtacagcttcttctgcatttttacttcatttttcacagaggtatcctgaaaatgctacta----aattttaatgt-atgtag------------------------------------------------
















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|120495475|gb|EH223642.1|EH223642
EST:     ACCACCCCTTGAAGCGACTGCCACATTAGCTCACAAATTTGAACTCATAG                         GATCTTCAAAGATAAAGATAGTATTTGAGAAAACCACTGTGAAGACAGCTG
genomic: ACCACCCCTTGAAGCGACTGCCACATTAGCTCACAAATTTGAACTCATAGgttggtttta ... aatgtcccagGATCTTCAAAGATAAAGATAGTATTTGAGAAAACCACTGTGAAGACAGCTG
EST: gi|120530629|gb|EH258762.1|EH258762
EST:     ACCACCCCTTGAAGCGACTGCCACATTAGCTCACAAATTTGAACTCATAG                         GATCTTCAAAGATAAAGATAGTATTTGAGAAAACCACTGTGAAGACAGCTG
genomic: ACCACCCCTTGAAGCGACTGCCACATTAGCTCACAAATTTGAACTCATAGgttggtttta ... aatgtcccagGATCTTCAAAGATAAAGATAGTATTTGAGAAAACCACTGTGAAGACAGCTG
EST: gi|23728495|gb|BU762303.1|BU762303
EST:     ACCACCCCTTGAAGCGACTGCCACATTAGCTCACAAATTTGAACTCATAG                         GATCTTCAAAGATAAAGATAGTATTTGAGAAAACCACTGTGAAGACAGCTG
genomic: ACCACCCCTTGAAGCGACTGCCACATTAGCTCACAAATTTGAACTCATAGgttggtttta ... aatgtcccagGATCTTCAAAGATAAAGATAGTATTTGAGAAAACCACTGTGAAGACAGCTG
EST: gi|15813996|gb|BI786271.1|BI786271
EST:     ACCACCCCTTGAAGCGACTGCCACATTAGCTCACAAATTTGAACTCATAG                         GATCTTCAAAGATAAAGATAGTATTTGAGAAAACCACTGTGAA
genomic: ACCACCCCTTGAAGCGACTGCCACATTAGCTCACAAATTTGAACTCATAGgttggtttta ... aatgtcccagGATCTTCAAAGATAAAGATAGTATTTGAGAAAACCACTGTGAA
EST: gi|20498481|gb|BQ273411.1|BQ273411
EST:     ACCACCCCTTGAAGCGACTGCCACATTAGCTCACAAATTTGAACTCATAG                         GATCTTCAAAGATAAAGATAGTATTTGAGAAAACCACTGTGAAGACAGCTG
genomic: ACCACCCCTTGAAGCGACTGCCACATTAGCTCACAAATTTGAACTCATAGgttggtttta ... aatgtcccagGATCTTCAAAGATAAAGATAGTATTTGAGAAAACCACTGTGAAGACAGCTG
EST: gi|23057257|gb|BU577932.1|BU577932
EST:     ACCACCCCTTGAAGCGACTGCCACATTAGCTCACAAATTTGAACTCATAG                         GATCTTCAAAGATAAAGATAGTATTTGAGAAAACCACTGTGAAGACAGCTG
genomic: ACCACCCCTTGAAGCGACTGCCACATTAGCTCACAAATTTGAACTCATAGgttggtttta ... aatgtcccagGATCTTCAAAGATAAAGATAGTATTTGAGAAAACCACTGTGAAGACAGCTG
EST: gi|13562464|gb|BG550684.1|BG550684
EST:     ACCACCCCTTGAAGCGACTGCCACATTAGCTCACAAATTTGAACTCATAG                         GATCTTCAAAGATAAAGATAGTATTTGAGAAAACCACTGTGAAGACAGCTG
genomic: ACCACCCCTTGAAGCGACTGCCACATTAGCTCACAAATTTGAACTCATAGgttggtttta ... aatgtcccagGATCTTCAAAGATAAAGATAGTATTTGAGAAAACCACTGTGAAGACAGCTG
EST: gi|31474640|gb|CD416668.1|CD416668
EST:     ACCACCCCTTGAAGCGACTGCCACATTAGCTCACAAATTTGAACTCATAG                         GATCTTCAAAGATAAAGATAGTATTTGAGAAAACCACTGTGAAGACAGCTG
genomic: ACCACCCCTTGAAGCGACTGCCACATTAGCTCACAAATTTGAACTCATAGgttggtttta ... aatgtcccagGATCTTCAAAGATAAAGATAGTATTTGAGAAAACCACTGTGAAGACAGCTG
EST: gi|151403502|gb|EV273312.1|EV273312
EST:     ACCACCCCTTGAAGCGACTGCCACATTAGCTCACAAATTTGAACTCATAG                         GATCTTCAAAGATAAAGATAGTATTTGAGAAAACCACTGTGAAGACAGCTG
genomic: ACCACCCCTTGAAGCGACTGCCACATTAGCTCACAAATTTGAACTCATAGgttggtttta ... aatgtcccagGATCTTCAAAGATAAAGATAGTATTTGAGAAAACCACTGTGAAGACAGCTG
EST: gi|120495329|gb|EH223496.1|EH223496
EST:     ACCACCCCTTGAAGCGACTGCCACATTAGCTCACAAATTTGAACTCATAG                         GATCTTCAAAGATAAAGATAGTATTTGAGAAAACCACTGTGAAGACAGCTG
genomic: ACCACCCCTTGAAGCGACTGCCACATTAGCTCACAAATTTGAACTCATAGgttggtttta ... aatgtcccagGATCTTCAAAGATAAAGATAGTATTTGAGAAAACCACTGTGAAGACAGCTG
EST: gi|58016590|gb|CX703332.1|CX703332
EST:     TCCACCCCTTGAAGCGACTGCCACATTAGCTCACAAATTTGAACTCATAG                         GATCTTCAAAGATAAAGATAGTATTTGAGAAAACCACTGTGAAGACAGCTG
genomic: ACCACCCCTTGAAGCGACTGCCACATTAGCTCACAAATTTGAACTCATAGgttggtttta ... aatgtcccagGATCTTCAAAGATAAAGATAGTATTTGAGAAAACCACTGTGAAGACAGCTG
EST: gi|120530496|gb|EH258629.1|EH258629
EST:     ACCACCCCTTGAAGCGACTGCCACATTAGCTCACAAATTTGAACTCATAG                         GATCTTCAAAGATAAAGATAGTATTTGAGAAAACCACTGTGAAGACAGCTG
genomic: ACCACCCCTTGAAGCGACTGCCACATTAGCTCACAAATTTGAACTCATAGgttggtttta ... aatgtcccagGATCTTCAAAGATAAAGATAGTATTTGAGAAAACCACTGTGAAGACAGCTG
EST: gi|27425259|gb|CA936779.1|CA936779
EST:     ACCACCCCTTGAAGCGACTGCCACATTAGCTCACAAATTTGAACTCATAG                         GATCTTCAAAGATAAAGATAGTATTTGAGAAAACCACTGTGAAGACAGCTG
genomic: ACCACCCCTTGAAGCGACTGCCACATTAGCTCACAAATTTGAACTCATAGgttggtttta ... aatgtcccagGATCTTCAAAGATAAAGATAGTATTTGAGAAAACCACTGTGAAGACAGCTG
EST: gi|33389199|gb|CA852406.1|CA852406
EST:     ACCACCCCTTGAAGCGACTGCCACATTAGCTCACAAATTTGAACTCATAG                         GATCTTCAAAGATAAAGATAGTATTTGAGAAAACCACTGTGAAGACAGCTG
genomic: ACCACCCCTTGAAGCGACTGCCACATTAGCTCACAAATTTGAACTCATAGgttggtttta ... aatgtcccagGATCTTCAAAGATAAAGATAGTATTTGAGAAAACCACTGTGAAGACAGCTG
EST: gi|26060099|gb|CA803013.1|CA803013
EST:     ACCACCCCTTGAAGCGACTGCCACATTAGCTCACAAATTTGAACTCATAG                         GATCTTCAAAGATAAAGATAGTATTTGAGAAAACCACTGTGAAGACAGCTG
genomic: ACCACCCCTTGAAGCGACTGCCACATTAGCTCACAAATTTGAACTCATAGgttggtttta ... aatgtcccagGATCTTCAAAGATAAAGATAGTATTTGAGAAAACCACTGTGAAGACAGCTG
EST: gi|7283325|gb|AW595933.1|AW595933
EST:     ACCACCCCTTGAAGCGACTGCCACATTAGCTCACAAATATGAACTCATAG                         GATCTTCAAAGATAAAGATAGTATTTGAGATAACCACTGTGAAGACAGCTG
genomic: ACCACCCCTTGAAGCGACTGCCACATTAGCTCACAAATTTGAACTCATAGgttggtttta ... aatgtcccagGATCTTCAAAGATAAAGATAGTATTTGAGAAAACCACTGTGAAGACAGCTG
EST: gi|20498880|gb|BQ273810.1|BQ273810
EST:     ACCACCCCTTGAAGCGACTGCCACATTAGCTCACAAATTTGAACTCATAG                         GATCTTCAAAGATAAAGATAGTATTTGAGAAAACCACTGTGAAGACAGCTG
genomic: ACCACCCCTTGAAGCGACTGCCACATTAGCTCACAAATTTGAACTCATAGgttggtttta ... aatgtcccagGATCTTCAAAGATAAAGATAGTATTTGAGAAAACCACTGTGAAGACAGCTG
EST: gi|120491766|gb|EH219933.1|EH219933
EST:     ACCACCCCTTGAAGCGACTGCCACATTAGCTCACAAATTTGAACTCATAG                         GATCTTCAAAGATAAAGATAGTATTTGAGAAAACCACTGTGAAGACAGCTG
genomic: ACCACCCCTTGAAGCGACTGCCACATTAGCTCACAAATTTGAACTCATAGgttggtttta ... aatgtcccagGATCTTCAAAGATAAAGATAGTATTTGAGAAAACCACTGTGAAGACAGCTG
EST: gi|120491718|gb|EH219885.1|EH219885
EST:     ACCACCCCTTGAAGCGACTGCCACATTAGCTCACAAATTTGAACTCATAG                         GATCTTCAAAGATAAAGATAGTATTTGAGAAAACCACTGTGAAGACAGCTG
genomic: ACCACCCCTTGAAGCGACTGCCACATTAGCTCACAAATTTGAACTCATAGgttggtttta ... aatgtcccagGATCTTCAAAGATAAAGATAGTATTTGAGAAAACCACTGTGAAGACAGCTG
EST: gi|12489972|gb|BG043493.1|BG043493
EST:     ACCACCCCTTGAAGCGACTGCCACATTAGCTCACAAATTTGAACTCATAG                         GATCTTCACAGATAAAGATAGTATTTGAGAAAACCACTGTG
genomic: ACCACCCCTTGAAGCGACTGCCACATTAGCTCACAAATTTGAACTCATAGgttggtttta ... aatgtcccagGATCTTCAAAGATAAAGATAGTATTTGAGAAAACCACTGTG
EST: gi|120530540|gb|EH258673.1|EH258673
EST:     ACCACCCCTTGAAGCGACTGCCACATTAGCTCACAAATTTGAACTCATAG                         GATCTTCAAAGATAAAGATAGTATTTGAGAAAACCACTGTGAAGACAGCTG
genomic: ACCACCCCTTGAAGCGACTGCCACATTAGCTCACAAATTTGAACTCATAGgttggtttta ... aatgtcccagGATCTTCAAAGATAAAGATAGTATTTGAGAAAACCACTGTGAAGACAGCTG
EST: gi|151397186|gb|EV267059.1|EV267059
EST:     ACCACCCCTTGAAGCGACTGCCACATTAGCTCACAAATTTGAACTCATAG                         GATCTTCAAAGATAAAGATAGTATTTGAGAAAACCACTGTGAAGACAGCTG
genomic: ACCACCCCTTGAAGCGACTGCCACATTAGCTCACAAATTTGAACTCATAGgttggtttta ... aatgtcccagGATCTTCAAAGATAAAGATAGTATTTGAGAAAACCACTGTGAAGACAGCTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAAGATTTTGATAACATAGTGGAGCTTCAACTAGGTGCTCCGTGGCCCCTACCACCCCTTGAAGCGACTGCCACATTAGCTCACAAATTTGAACTCATAGgttggttttatcattttatgttttgtgtttttgtttcttatctgtatgtgcgtgctaaattttgcatgattactactaattgccagttatgagaattgtagtattgtatagtctttgagagtgcctttttatcttttgtgggttttgtaaatgtcccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA