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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTATTGTTGGGACGTGGATTATATCAATTGTGGGGAGCTGGTGCAATTTCTTGACCTTGTTCTACATTGgtaagaacaatctattccgtttcatatataatgttttcaaagttatgaatatgaactatgaagttttacttatttcttcatttgcag

Basic information

species Glycine max
transcript GLYMA07G06830.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G06830.1 (Glycine max), 5'ss of exon 4
lower sequence: LOC_Os05g45050.2 (Oryza sativa), 5'ss of exon 3
------------------------------GTTATTGTTGGGACGTGGATTATATCAATTGTGGGGAGCTGGTGCAATTTCTTGACCTTGTTCTACATTGgtaagaacaatctattccgtttcatatataatgttttcaaagttatgaatatgaacta-tgaagttttacttatttcttcatttgcag
                              ||| | || ||    ||| || | ||  || | |||||||| ||||||||| |||||||||||||||| |||||  |   | |  | |      | || || |||  || | |||  | | | | | | |  ||||||  || || |           
AATTTGCTTATGCTGGTCCTCTTTATTAAGGTTGTCGTGGGTCTCTGGGTTCTCTCTGTTCTTGGGAGCTGCTGCAATTTCCTGACCTTGTTCTACATAGgtaattat--tttggtacaacaactgtacaa-gttaccacatttagcactgttaccaactacagttttctttcttgcag---------

upper sequence: GLYMA07G06830.1 (Glycine max), 5'ss of exon 4
lower sequence: LOC_Os05g45050.1 (Oryza sativa), 5'ss of exon 4
GTTATTGTTGGGACGTGGATTATATCAATTGTGGGGAGCTGGTGCAATTTCTTGACCTTGTTCTACATTGgtaagaacaatctattccgtttcatatataatgttttcaaagttatgaatatgaacta-tgaagttttacttatttcttcatttgcag
||| | || ||    ||| || | ||  || | |||||||| ||||||||| |||||||||||||||| |||||  |   | |  | |      | || || |||  || | |||  | | | | | | |  ||||||  || || |           
GTTGTCGTGGGTCTCTGGGTTCTCTCTGTTCTTGGGAGCTGCTGCAATTTCCTGACCTTGTTCTACATAGgtaattat--tttggtacaacaactgtacaa-gttaccacatttagcactgttaccaactacagttttctttcttgcag---------

upper sequence: GLYMA07G06830.1 (Glycine max), 5'ss of exon 4
lower sequence: Vv15s0046g01760.t01 (Vitis vinifera), 5'ss of exon 4
GTTATTGTTGGGACGTGGATTATATCAATTGTGGGGAGCTGGTGCAATTTCTTGACCTTGTTCTACATTGgtaagaacaatctattccgtttcatatata-atgttttcaaagttatgaatatgaactatga-agttttacttatttcttcatttgcag----
 |||||| |||   |||| |  | || ||  ||||||| || |||||||||||||||||||| |||||  ||| ||    |   ||   ||| | | ||  ||  | | ||   ||||   ||   | |||  | ||||  |||||      || | |     
ATTATTGCTGGCCTGTGGGTACTGTCGATCCTGGGGAGTTGCTGCAATTTCTTGACCTTGTTTTACATAAgtatgactgctggttttatttttaaacatttataatatgaactatatgttgatctgccatgttaatttttgttattatgattttggaaaacag

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|16344603|gb|BI970198.1|BI970198
EST:     TATATCAATTGTGGGGAGCTGGTGCAATTTCTTGACCTTGTTCTACATTG                         CTTTTGTTTTGTTGCATACGGTTCCTGTCTTGTATGACAAGTATGAGGATA
genomic: TATATCAATTGTGGGGAGCTGGTGCAATTTCTTGACCTTGTTCTACATTGgtaagaacaa ... tcatttgcagCTTTTGTTTTGTTGCATACGGTTCCTGTCTTGTATGACAAGTATGAGGATA
EST: gi|16346040|gb|BI971635.1|BI971635
EST:     TATATCAATTGTGGGGAGCTGGTGCAATTTCTTGACCTTGTTCTACATTG                         CTTTTGTTTTGTTGCATACGGTTCCTGTCTTGTATGACAAGTATGAGGATA
genomic: TATATCAATTGTGGGGAGCTGGTGCAATTTCTTGACCTTGTTCTACATTGgtaagaacaa ... tcatttgcagCTTTTGTTTTGTTGCATACGGTTCCTGTCTTGTATGACAAGTATGAGGATA
EST: gi|13790242|gb|BG652833.1|BG652833
EST:     TATATCAATTGTGGGGAGCTGGTGCAATTTCTTGACCTTGTTCTACATTG                         CTTTTGTTTTGTTGCATACGGTTCCTGTCTTGTATGACAAGTATGAGGATA
genomic: TATATCAATTGTGGGGAGCTGGTGCAATTTCTTGACCTTGTTCTACATTGgtaagaacaa ... tcatttgcagCTTTTGTTTTGTTGCATACGGTTCCTGTCTTGTATGACAAGTATGAGGATA
EST: gi|151403313|gb|EV273123.1|EV273123
EST:     TATATCAATTGTGGGGAGCTGGTGCAATTTCTTGACCTTGTTCTACATTG                         CTTTTGTTTTGTTGCATACGGTTCCTGTCTTGTATGACAAGTATGAGGATA
genomic: TATATCAATTGTGGGGAGCTGGTGCAATTTCTTGACCTTGTTCTACATTGgtaagaacaa ... tcatttgcagCTTTTGTTTTGTTGCATACGGTTCCTGTCTTGTATGACAAGTATGAGGATA
EST: gi|192320226|gb|FK014240.1|FK014240
EST:     TATATCAATTGTGGGGAGCTGGTGCAATTTCTTGACCTTGTTTTACATTG                         CTTTTGTTTTGTTGCATACGGTTCCTGTCTTGTATGACTAGTATGAGGATA
genomic: TATATCAATTGTGGGGAGCTGGTGCAATTTCTTGACCTTGTTCTACATTGgtaagaacaa ... tcatttgcagCTTTTGTTTTGTTGCATACGGTTCCTGTCTTGTATGACAAGTATGAGGATA
EST: gi|192325037|gb|FK016163.1|FK016163
EST:     TATATCAATTGTGGGGAGCTGGTGCAATTTCTTGACCTTGTTCTACATTG                         CTTTTGTTTTGTTGCATACGGTTCCTGTCTTGTATGACAAGTATGAGGATA
genomic: TATATCAATTGTGGGGAGCTGGTGCAATTTCTTGACCTTGTTCTACATTGgtaagaacaa ... tcatttgcagCTTTTGTTTTGTTGCATACGGTTCCTGTCTTGTATGACAAGTATGAGGATA
EST: gi|192320241|gb|FK014241.1|FK014241
EST:     TATATCAATTGTGGGGAGCTGGTGCAATTTCTTGACCTTGTTCTACATTG                         CTTTTGTTTTGTTGCATACGGTTCCTGTCTTGTATGACTAGTATGAGGATA
genomic: TATATCAATTGTGGGGAGCTGGTGCAATTTCTTGACCTTGTTCTACATTGgtaagaacaa ... tcatttgcagCTTTTGTTTTGTTGCATACGGTTCCTGTCTTGTATGACAAGTATGAGGATA
EST: gi|26057729|gb|CA800643.1|CA800643
EST:     TATATCAATTGTGGGGAGCTGGTGCAATTTCTTGACCTTGTTCTACATTG                         CTTTTGTTTTGTTGCATACGGTTCCTGTCTTGTATGACAAGTATGAGGATA
genomic: TATATCAATTGTGGGGAGCTGGTGCAATTTCTTGACCTTGTTCTACATTGgtaagaacaa ... tcatttgcagCTTTTGTTTTGTTGCATACGGTTCCTGTCTTGTATGACAAGTATGAGGATA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTATTGTTGGGACGTGGATTATATCAATTGTGGGGAGCTGGTGCAATTTCTTGACCTTGTTCTACATTGgtaagaacaatctattccgtttcatatataatgttttcaaagttatgaatatgaactatgaagttttacttatttcttcatttgcag

- - - - - - - - - - - - - - - - - GGAGCT