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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTTCTTTGGATGATGGCAGTTCTTACCATATTGTGTGCATCATATTGGTCAGCTTGGACGACCCGAGAAGCAGCTATTGAACAGGATAAGTTGCTAAAGgtctgtttttcctattcatttagtatttactcaagttggattttcatttcttttcttaatatgttgtcgattctactacttactctcatttttttcttttcttatag

Basic information

species Glycine max
transcript GLYMA01G42940.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA01G42940.1 (Glycine max), 5'ss of exon 5
lower sequence: GRMZM2G096343_T01 (Zea mays), 5'ss of exon 5
ATTTCTTTGGATGATGGCAGTTCTTACCATATTGTGTGCATCATATTGGTCAGCTTGGACGACCCGAGAAGCAGCTATTGAACAGGATAAGTTGCTAAAGgtctgtttttcctattcatttagtatttactcaagttggattttcatttcttttcttaatatgttgtcgattctactacttactctcatttttttcttttcttatag
 ||||| ||| | |||||||||  ||||||  | ||||||||||| |||||||| ||||   |||||||||||| ||||||||| || ||| | || |||||        || | || | |   |||| ||   | | | ||| | |   |      ||     || |   |  | |||||  |                       
GTTTCTGTGGCTTATGGCAGTTGGTACCATTCTTTGTGCATCATACTGGTCAGCATGGAGTGCCCGAGAAGCAGATATTGAACAAGAGAAGCTTCTGAAGgttctaaaccccaaatcttgtttgattt-ctattgctagttttgcgtacttgaaaaaaagggactgacaggttcaatacttgttag---------------------

upper sequence: GLYMA01G42940.1 (Glycine max), 5'ss of exon 5
lower sequence: AT1G63690.1 (Arabidopsis thaliana), 5'ss of exon 5
ATTTCTTTGGATGATGGCAGTTCTTACCATATTGTGTGCATCATATTGGTCAGCTTGGACGACCCGAGAAGCAGCTATTGAACAGGATAAGTTGCTAAAGgtctgtt-tttcctattcatttagtatttactcaagttggattttcatttcttttcttaatatgttgtcgattctactacttactctcatttttttcttttcttatag
 ||| | ||| | |||||| ||  |||||| || |||||||| |||||||| || ||||   |||||||||||||||||||||| |||||| | || |||||| |   ||| ||| | |||| | | | | | |  || |  |   |    ||   |  ||  ||    |||   |  |  | |    |  |   || |||       
CTTTTTGTGGTTAATGGCAATTGGTACCATTTTATGTGCATCTTATTGGTCTGCATGGAGTGCCCGAGAAGCAGCTATTGAACATGATAAGCTACTGAAGgtcagacattttctacttatttgggaataa-taatattaggctaggaagatttagttcgatgggtaag-gataacataaactgccaataagtaagtcctttg------
















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|209699604|gb|BW655710.1|BW655710
EST:     CAGCTTGGACGACCCGAGAAGCAGCTATTGAACAGGATAAGTTGCTAAAG                         GATGCTTCAGATGAACTCCCAAACACTAAATATGCTAGTGTTAGTGGAGTT
genomic: CAGCTTGGACGACCCGAGAAGCAGCTATTGAACAGGATAAGTTGCTAAAGgtctgttttt ... tttcttatagGATGCTTCAGATGAACTCCCAAACACTAAATATGCTAGTGTTAGTGGAGTT
EST: gi|21601179|gb|BQ611510.1|BQ611510
EST:     CAGCTTGGACGACCCGAGAAGCAGCTATTGAACAGGATAAGTTGCTAAAG                         GATGCTTCAGATGAACTCCCAAACACTAAATATGCTAGTGTTAGTGGAGTT
genomic: CAGCTTGGACGACCCGAGAAGCAGCTATTGAACAGGATAAGTTGCTAAAGgtctgttttt ... tttcttatagGATGCTTCAGATGAACTCCCAAACACTAAATATGCTAGTGTTAGTGGAGTT
EST: gi|151407819|gb|EV277634.1|EV277634
EST:     CAGCTTGGACGACCCGAGAAGCAGCTATTGAACAGGATAAGTTGCTAAAG                         GATGCTTCAGATGAACTCCCAAACACTAAATATGCTAGTGTTAGTGGAGTT
genomic: CAGCTTGGACGACCCGAGAAGCAGCTATTGAACAGGATAAGTTGCTAAAGgtctgttttt ... tttcttatagGATGCTTCAGATGAACTCCCAAACACTAAATATGCTAGTGTTAGTGGAGTT
EST: gi|298165710|gb|HO008681.1|HO008681
EST:     CAGCTTGGACGACCCGAGAAGCAGCTATTGAACAGGATAAGTTGCTAAAG                         GATGCTTCAGATGAACTCCCAAACACTAAATATGCTAGTGTTAGTGGAGTT
genomic: CAGCTTGGACGACCCGAGAAGCAGCTATTGAACAGGATAAGTTGCTAAAGgtctgttttt ... tttcttatagGATGCTTCAGATGAACTCCCAAACACTAAATATGCTAGTGTTAGTGGAGTT
EST: gi|192315508|gb|FK009688.1|FK009688
EST:     CAGCTTGGACGACCCGAGAAGCAGCTATTGAACAGGATAAGTTGCTAAAG                         GATGCTTCAGATGAACTCCCAAACACTAAATATGCTAGTGTTAGTGGAGTT
genomic: CAGCTTGGACGACCCGAGAAGCAGCTATTGAACAGGATAAGTTGCTAAAGgtctgttttt ... tttcttatagGATGCTTCAGATGAACTCCCAAACACTAAATATGCTAGTGTTAGTGGAGTT
EST: gi|193566132|gb|FK524607.1|FK524607
EST:     CGACCCGAGAAGCAGCTATTGAACAGGATAAGTTGCTAAAG                         GATGCTTCAGATGAACTCCCAAACACTAAATATGCTAGTGTTAGTGGAGTT
genomic: CGACCCGAGAAGCAGCTATTGAACAGGATAAGTTGCTAAAGgtctgttttt ... tttcttatagGATGCTTCAGATGAACTCCCAAACACTAAATATGCTAGTGTTAGTGGAGTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATTTCTTTGGATGATGGCAGTTCTTACCATATTGTGTGCATCATATTGGTCAGCTTGGACGACCCGAGAAGCAGCTATTGAACAGGATAAGTTGCTAAAGgtctgtttttcctattcatttagtatttactcaagttggattttcatttcttttcttaatatgttgtcgattctactacttactctcatttttttcttttcttatag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT