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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtccgtgctatcccattccatttcgtagtttctactatttcccattgtttcatttcattcgatgattatgctccgattgaagcagCTCGCGGGAGTTTTACTATTCTCCGCGATTCCTTTCACTGCCGTGAAAGCTATAGCTAATAGTCCGCTAGGGGAGTCGCTTCAGAGGAAAATGGAGGAGA

Basic information

species Glycine max
transcript GLYMA17G38220.2
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G38220.2 (Glycine max), 3'ss of exon 1
lower sequence: Vv18s0122g00430.t01 (Vitis vinifera), 3'ss of exon 1
gtccgtgctatcccattccatttcgtagtttctactatttccc--attgtttcatttcattcgatgattatgctccgattgaagcagCTCGCGGGAGTTTTACTATTCTCCGCGATTCCTTTCACTGCCGTGAAAGCTATAGCTAATAGTCCGCTAGGGGAGTCGCTTCAGAGGAAAATGGAGGAGA
||| | |   | | |     |||| | || ||  ||  || |   | |||   | ||   || |     ||  |    ||   | ||||||| || |||||| ||||||| |||||||||||||| ||||| ||||| ||||| ||||| || || || ||||||||||||||   |||||||||||
gtctgcgaatttctagg--gtttctttgtctcctctcgtttcagaactgtgaaacttatctctacttacatttttttttttgggaagCTCGCCGGCGTTTTAATATTCTCAGCGATTCCTTTCACCGCCGTTAAAGCCATAGCGAATAGCCCTCTCGGAGAGTCGCTTCAGAGCCGAATGGAGGAGA
















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|151404614|gb|EV274428.1|EV274428
EST:     CTGCCCCGAAGCGAAGAAGAAGCAGCTTCATTACTGCTTCGTGGCAAGAG                         CTCGCGGGAGTTTTACTATTCTCCGCGATTCCTTTCACTGCCGTGAAAGCT
genomic: CTGCCCCGAAGCGAAGAAGAAGCAGCTTCATTACTGCTTCGTGGCAAGAGgtccgtgcta ... attgaagcagCTCGCGGGAGTTTTACTATTCTCCGCGATTCCTTTCACTGCCGTGAAAGCT
EST: gi|209718155|gb|BW677426.1|BW677426
EST:     CTGCCCCGAAGCGAAGAAGAAGCAGCTTCATTACTGCTTCGTGGCAAGAG                         CTCGCGGGAGTTTTACTATTCTCCGCGATTCCTTTCACTGCCGTGAAAGCT
genomic: CTGCCCCGAAGCGAAGAAGAAGCAGCTTCATTACTGCTTCGTGGCAAGAGgtccgtgcta ... attgaagcagCTCGCGGGAGTTTTACTATTCTCCGCGATTCCTTTCACTGCCGTGAAAGCT
EST: gi|15285088|gb|BI468979.1|BI468979
EST:     CTGCCCCGAAGCGAAGAAGAAGCAGCTTCATTACTGCTTCGTGGCAAGAG                         CTCGCGGGAGTTTTACTATTCTCCGCGATTCCTTTCACTGCCGTGAAAGCT
genomic: CTGCCCCGAAGCGAAGAAGAAGCAGCTTCATTACTGCTTCGTGGCAAGAGgtccgtgcta ... attgaagcagCTCGCGGGAGTTTTACTATTCTCCGCGATTCCTTTCACTGCCGTGAAAGCT
EST: gi|208074776|gb|GD869547.1|GD869547
EST:     CTGCCCCGAAGCGAAGAAGAAGCAGCTTCATTACTGCTTCGTGGCAAGAG                         CTCGCGGGAGTTTTACTATTCTCCGCGATTCCTTTCACTGCCGTGAAAGCT
genomic: CTGCCCCGAAGCGAAGAAGAAGCAGCTTCATTACTGCTTCGTGGCAAGAGgtccgtgcta ... attgaagcagCTCGCGGGAGTTTTACTATTCTCCGCGATTCCTTTCACTGCCGTGAAAGCT
EST: gi|209716259|gb|BW657562.1|BW657562
EST:     CTGCCCCGAAGCGAAGAAGAAGCAGCTTCATTACTGCTTCGTGGCAAGAG                         CTCGCGGGAGTTTTACTATTCTCCGCGATTCCTTTCACTGCCGTGAAAGCT
genomic: CTGCCCCGAAGCGAAGAAGAAGCAGCTTCATTACTGCTTCGTGGCAAGAGgtccgtgcta ... attgaagcagCTCGCGGGAGTTTTACTATTCTCCGCGATTCCTTTCACTGCCGTGAAAGCT
EST: gi|151395535|gb|EV265412.1|EV265412
EST:     CTGCCCCGAAGCGAAGAAGAAGCAGCTTCATTACTGCTTCGTGGCAAGAG                         CTCGCGGGAGTTTTACTATTCTCCGCGATTCCTTTCACTGCCGTGAAAGCT
genomic: CTGCCCCGAAGCGAAGAAGAAGCAGCTTCATTACTGCTTCGTGGCAAGAGgtccgtgcta ... attgaagcagCTCGCGGGAGTTTTACTATTCTCCGCGATTCCTTTCACTGCCGTGAAAGCT
EST: gi|120491971|gb|EH220138.1|EH220138
EST:     CTGCCCCGAAGCGAAGAAGAAGCAGCTTCATTACTGCTTCGTGGCAAGAG                         CTCGCGGGAGTTTTACTATTCTCCGCGATTCCTTTCACTGCCGTGAAAGCT
genomic: CTGCCCCGAAGCGAAGAAGAAGCAGCTTCATTACTGCTTCGTGGCAAGAGgtccgtgcta ... attgaagcagCTCGCGGGAGTTTTACTATTCTCCGCGATTCCTTTCACTGCCGTGAAAGCT
EST: gi|10846954|gb|BF069679.1|BF069679
EST:     CTGCCCCGAAGCGAAGAAGAAGCAGCTTCATTACTGCTTCGTGGCAAGAG                         CTCGCGGGAGTTTTACTATTCTCCGCGATTCCTTTCACTGCCGTGAAAGCT
genomic: CTGCCCCGAAGCGAAGAAGAAGCAGCTTCATTACTGCTTCGTGGCAAGAGgtccgtgcta ... attgaagcagCTCGCGGGAGTTTTACTATTCTCCGCGATTCCTTTCACTGCCGTGAAAGCT
EST: gi|207796870|gb|GD770248.1|GD770248
EST:     CTGCCCCGAAGCGAAGAAGAAGCAGCTTCATTACTGCTTCGTGGCAAGAG                         CTCGCGGGAGTTTTACTATTCTCCGCGATTCCATTCACTGCCGTGAAAGCT
genomic: CTGCCCCGAAGCGAAGAAGAAGCAGCTTCATTACTGCTTCGTGGCAAGAGgtccgtgcta ... attgaagcagCTCGCGGGAGTTTTACTATTCTCCGCGATTCCTTTCACTGCCGTGAAAGCT
EST: gi|209714192|gb|BW679521.1|BW679521
EST:     CTGCCCCGAAGCGAAGAAGAAGCAGCTTCATTACTGCTTCGTGGCAAGAG                         CTCGCGGGAGTTTTACTATTCTCCGCGATTCCTTTCACTGCCGTGAAAGCT
genomic: CTGCCCCGAAGCGAAGAAGAAGCAGCTTCATTACTGCTTCGTGGCAAGAGgtccgtgcta ... attgaagcagCTCGCGGGAGTTTTACTATTCTCCGCGATTCCTTTCACTGCCGTGAAAGCT
EST: gi|22539788|gb|BU089631.1|BU089631
EST:     CTGCCCCGAAGCGAAGAAGAAGCAGCTTCATTACTGCTTCGTGGCAAGAG                         CTCGCGGGAGTTTTACTATTCTCCGCGATTCCTTTCACTGCCGTGAAAGCT
genomic: CTGCCCCGAAGCGAAGAAGAAGCAGCTTCATTACTGCTTCGTGGCAAGAGgtccgtgcta ... attgaagcagCTCGCGGGAGTTTTACTATTCTCCGCGATTCCTTTCACTGCCGTGAAAGCT
EST: gi|22540334|gb|BU090177.1|BU090177
EST:     CTGCCCCGAAGCGAAGAAGAAGCAGCTTCATTACTGCTTCGTGGCAAGAG                         CTCGCGGGAGTTTTACTATTCTCCGCGATTCCTTTCACTGCCGTGAAAGCT
genomic: CTGCCCCGAAGCGAAGAAGAAGCAGCTTCATTACTGCTTCGTGGCAAGAGgtccgtgcta ... attgaagcagCTCGCGGGAGTTTTACTATTCTCCGCGATTCCTTTCACTGCCGTGAAAGCT
EST: gi|192297292|gb|FG990626.1|FG990626
EST:     CTGCCCCGAAGCGAAGAAGAAGCAGCTTCATTACTGCTTCGTGGCAAGAG                         CTCGCGGGAGTTTTACTATTCTCCGCGATTCCTTTCACTGCCGTGAAAGCT
genomic: CTGCCCCGAAGCGAAGAAGAAGCAGCTTCATTACTGCTTCGTGGCAAGAGgtccgtgcta ... attgaagcagCTCGCGGGAGTTTTACTATTCTCCGCGATTCCTTTCACTGCCGTGAAAGCT
EST: gi|20075945|gb|BQ094728.1|BQ094728
EST:     CTGCCCCGAAGCGAAGAAGAAGCAGCTTCATTACTGCTTCGTGGCAAGAG                         CTCGCGGGAGTTTTACTATTCTCCGCGATTCCTTTCACTGCCGTGAAAGCT
genomic: CTGCCCCGAAGCGAAGAAGAAGCAGCTTCATTACTGCTTCGTGGCAAGAGgtccgtgcta ... attgaagcagCTCGCGGGAGTTTTACTATTCTCCGCGATTCCTTTCACTGCCGTGAAAGCT
EST: gi|209703879|gb|BW667920.1|BW667920
EST:     CTGCCCCGAAGCGAAGAAGAAGCAGCTTCATTACTGCTTCGTGGCAAGAG                         CTCGCGGGAGTTTTACTATTCTCCGCGATTCCTTTCACTGCCGTGAAAGCT
genomic: CTGCCCCGAAGCGAAGAAGAAGCAGCTTCATTACTGCTTCGTGGCAAGAGgtccgtgcta ... attgaagcagCTCGCGGGAGTTTTACTATTCTCCGCGATTCCTTTCACTGCCGTGAAAGCT
EST: gi|151404020|gb|EV273830.1|EV273830
EST:     CTGCCCCGAAGCGAAGAAGAAGCAGCTTCATTACTGCTTCGTGGCAAGAG                         CTCGCGGGAGTTTTACTATTCTCCGCGATTCCTTTCACTGCCGTGAAAGCT
genomic: CTGCCCCGAAGCGAAGAAGAAGCAGCTTCATTACTGCTTCGTGGCAAGAGgtccgtgcta ... attgaagcagCTCGCGGGAGTTTTACTATTCTCCGCGATTCCTTTCACTGCCGTGAAAGCT
EST: gi|120533754|gb|EH261887.1|EH261887
EST:     CTGCCCCGAAGCGAAGAAGAAGCAGCTTCATTACTGCTTCGTGGCAAGAGCAG                       
genomic: CTGCCCCGAAGCGAAGAAGAAGCAGCTTCATTACTGCTTCGTGGC-A-AG-AGgtccgtgcta ... attgaagc
EST: gi|6727137|gb|AW311491.1|AW311491
EST:     CTGCCCCGAAGCGAAGAAGAAGCAGCTTCATTACTGCTTCGTGGCAAGAG                         CTCGCGGGAGTTTTACTATTCTCCGCGATTCCTTTCACTGCCGTGAAAGCT
genomic: CTGCCCCGAAGCGAAGAAGAAGCAGCTTCATTACTGCTTCGTGGCAAGAGgtccgtgcta ... attgaagcagCTCGCGGGAGTTTTACTATTCTCCGCGATTCCTTTCACTGCCGTGAAAGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctactatttcccattgtttcatttcattcgatgattatgctccgattgaagcagCTCGCGGGAGTTTTACTATTCTCCGCGATTCCTTTCACTGCCGTGAAAGCTATAGCTAATAGTCCGCTAGGGGAGTCGCTTCAGAGGAAAATGGAGGAGA
                 tttcattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtccgtgctatcccattccatttcgtagtttctactatttcccattgtttcatttcattcgatgattatgctccgattgaagcagCTCGCGGGAGTTTTACTATTCTCCGCGATTCCTTTCACTGCCGTGAAAGCTATAGCTAATAGTCCGCTAGGGGAGTCGCTTCAGAGGAAAATGGAGGAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA