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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTATGGTCCGCACCTAATTACTGTTACCGTTGTGGAAATGTAGCTTCTATTCTTAGTTTCAATGAAAATATGgtgagccacccgaagcttattttacttttaaatatgttttcaggattatcttggttactgcatctgtctcgtgatgtatatatgtggtgcctttgttttt...

Basic information

species Glycine max
transcript GLYMA0048S00290.1
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA0048S00290.2 (Glycine max), 5'ss of exon 9
lower sequence: AT1G50370.1 (Arabidopsis thaliana), 5'ss of exon 9
GTATGGTCCGCACCTAATTACTGTTACCGTTGTGGAAATGTAGCTTCTATTCTTAGTTTCAATGAAAATATGgtgagccacccgaagcttattttacttttaaatatgttttcaggattatcttggttactgcatctgtctcgtg-atgtatatatgtggtgcctttgttttt----
|| ||||| || ||||||||||| ||||||||||| ||||| ||||||||  | ||||||||||| || |||||||| ||   |     | ||||  |  | |     | | |   | ||||||| ||  ||    | |  | |  ||| |    | |   |  | |  ||||    
GTGTGGTCTGCGCCTAATTACTGCTACCGTTGTGGGAATGTGGCTTCTATATTGAGTTTCAATGACAACATGgtgaggcatttgttttctcttttgttactga-----tctgccacaatatcttgtttcatgttcttcttacttttatgcactcgtcttcggattctacttttcctt

upper sequence: GLYMA0048S00290.2 (Glycine max), 5'ss of exon 9
lower sequence: AT3G19980.1 (Arabidopsis thaliana), 5'ss of exon 9
GTATGGTCCGCACCTAATTACTGTTACCGTTGTGGAAATGTAGCTTCTATTCTTAGTTTCAATGAAAATATGgtgagccacccgaagcttattttacttttaaatat--gttttcaggattatcttggttactgcatctgtctcgtgatgtatatatgtggtgcctttgttttt
|||||||| |||||||||||||||||||| ||||| ||||| ||||||||  | ||||||||||| || |||||||||| | |  ||  | |  ||  |  | |      | |||    | | |  |   |  |  ||| |  | | |   || |   |  |  ||||     |
GTATGGTCTGCACCTAATTACTGTTACCGCTGTGGGAATGTCGCTTCTATATTGAGTTTCAATGACAACATGgtgagcctctcttagtctttcctaaatgaatactctaatcttctctgtcagcaaga--agggattctattacttcagtgattttaatcatttcttttaagat

upper sequence: GLYMA0048S00290.2 (Glycine max), 5'ss of exon 9
lower sequence: Vv10s0071g00950.t01 (Vitis vinifera), 5'ss of exon 9
GTATGGTCCGCACCTAATTACTGTTACCGTTGTGGAAATGTAGCTTCTATTCTTAGTTTCAATGAAAATATGgtgagccacccgaa-------gcttattttacttttaaatatgttttcaggattatcttggttactgcatctgtctcgtgatgtatatatgtggtgcctttgttttt
|| ||||| ||||| || ||||||||||||||||| ||||| ||||| ||  | || |||||||| |||||||| |        ||       |||||| | ||||||  ||    | |    || ||     |||||      ||  | | |     || |    ||   |       
GTCTGGTCTGCACCAAACTACTGTTACCGTTGTGGGAATGTGGCTTCCATATTGAGCTTCAATGAGAATATGgtaaaatgttacaaatcatgtgcttatatcacttttggatggtctatggaaatcatgagatttactattatcgtgccctcactaccattttccctgttat-------

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|254340656|gb|GR854384.1|GR854384
EST:     GTTACCGTTGTGGAAATGTAGCTTCTATTCTTAGTTTCAATGAAAATATG                         GAAAGAGAAGTTAAATTTTTCACTGAAACAGAGG
genomic: GTTACCGTTGTGGAAATGTAGCTTCTATTCTTAGTTTCAATGAAAATATGgtgagccacc ... cttctaacagGAAAGAGAAGTTAAATTTTTCACTGAAACAGAGG
EST: gi|213611336|gb|DB983956.1|DB983956
EST:     GTTACCGTTGTGGAAATGTAGCTTCTATTCTTAGTTTCAATGAAAATATG                         GAAAGAGAAGTTAAATTTTTCACTGAAACAGAGGAGAACAACCAGATGAGA
genomic: GTTACCGTTGTGGAAATGTAGCTTCTATTCTTAGTTTCAATGAAAATATGgtgagccacc ... cttctaacagGAAAGAGAAGTTAAATTTTTCACTGAAACAGAGGAGAACAACCAGATGAGA
EST: gi|209728925|gb|BW651715.1|BW651715
EST:     TTAGTTTCAATGAAAATAT-                         ----GAGAAGTTAAATTTTTCACTGAAACAGAGGAGAACAACCAGATGAGA
genomic: TTAGTTTCAATGAAAATATGgtgagccacc ... cttctaacagGAAAGAGAAGTTAAATTTTTCACTGAAACAGAGGAGAACAACCAGATGAGA
EST: gi|193346878|gb|FK310146.1|FK310146
EST:     TTACCGTTGTGGAAATGTAGCTTCTATTCTTAGTTTCAATGAAAAATATG                         GAAAGAGAAGTTAAATTTTTCACTGAAACAGAGGAGAACA
genomic: TTACCGTTGTGGAAATGTAGCTTCTATTCTTAGTTTCAATGAAAA-TATGgtgagccacc ... cttctaacagGAAAGAGAAGTTAAATTTTTCACTGAAACAGAGGAGAACA
EST: gi|207746865|gb|GD721124.1|GD721124
EST:     GTTACCGTTGTGGAAATGTAGCTTCTATTCTTAGTTTCAATGAAAATATG                         GAAAGAGAAGTTAAATTTTTCACTGAAACAGAGGAGAACAACCAGATGAGA
genomic: GTTACCGTTGTGGAAATGTAGCTTCTATTCTTAGTTTCAATGAAAATATGgtgagccacc ... cttctaacagGAAAGAGAAGTTAAATTTTTCACTGAAACAGAGGAGAACAACCAGATGAGA
EST: gi|31464149|gb|CD406177.1|CD406177
EST:     GTTACCGTTGTGGAAATGTAGCTTCTATTCTTAGTTTCAATGAAAATATG                         GAAAGAGAAGTTAAATTTTTCACTGAAACAGAGGAGAACAACCAGTATGAG
genomic: GTTACCGTTGTGGAAATGTAGCTTCTATTCTTAGTTTCAATGAAAATATGgtgagccacc ... cttctaacagGAAAGAGAAGTTAAATTTTTCACTGAAACAGAGGAGAACAACCAG-ATGAG
EST: gi|254340657|gb|GR854385.1|GR854385
EST:     GTTACCGTTGTGGAAATGTAGCTTCTATTCTTAGTTTCAATGAAAATATG                         GAAAGAGAAGTTAAATTTTTCACTGAAACAGAGGAGAACAACCAGATGAGA
genomic: GTTACCGTTGTGGAAATGTAGCTTCTATTCTTAGTTTCAATGAAAATATGgtgagccacc ... cttctaacagGAAAGAGAAGTTAAATTTTTCACTGAAACAGAGGAGAACAACCAGATGAGA
EST: gi|209728248|gb|BW651683.1|BW651683
EST:     GTTACCGTTGTGGAAATGTAGCTTCTATTCTTAGTTTCAATGAAAATAT-                         ----GAGAAGTTAAATTTTTCACTGAAACAGAGGAGAACAACCAGATGAGA
genomic: GTTACCGTTGTGGAAATGTAGCTTCTATTCTTAGTTTCAATGAAAATATGgtgagccacc ... cttctaacagGAAAGAGAAGTTAAATTTTTCACTGAAACAGAGGAGAACAACCAGATGAGA
EST: gi|213593175|gb|DB975366.1|DB975366
EST:     GTTACCGTTGTGGAAATGTAGCTTCTATTCTTAGTTTCAATGAAAATATG                         GAAAGAGAAGTTAAATTTTTCACTGAAACAGAGGAGAACAACCAGATGAGA
genomic: GTTACCGTTGTGGAAATGTAGCTTCTATTCTTAGTTTCAATGAAAATATGgtgagccacc ... cttctaacagGAAAGAGAAGTTAAATTTTTCACTGAAACAGAGGAGAACAACCAGATGAGA
EST: gi|16345163|gb|BI970758.1|BI970758
EST:     GTTACCGTTGTGGAAATGTAGCTTCTATTCTTAGTTTCAATGAAAATATG                         GAAAGAGAAGTTAAATTTTTCACTGAAACAGAGGAGAACAACCAGATGAGA
genomic: GTTACCGTTGTGGAAATGTAGCTTCTATTCTTAGTTTCAATGAAAATATGgtgagccacc ... cttctaacagGAAAGAGAAGTTAAATTTTTCACTGAAACAGAGGAGAACAACCAGATGAGA
EST: gi|207791752|gb|GD763659.1|GD763659
EST:     TTAGTTTCAATGAAAATATG                         GAAAGAGAAGTTAAATTTTTCACTGAAACAGAGGAGAACAACCAGATGAGA
genomic: TTAGTTTCAATGAAAATATGgtgagccacc ... cttctaacagGAAAGAGAAGTTAAATTTTTCACTGAAACAGAGGAGAACAACCAGATGAGA
EST: gi|31473271|gb|CD415284.1|CD415284
EST:     GTTACCGTTGTGGAAATGTAGCTTCTATTCTTAGTTTCAATGAAAATATG                         GAAAGAGAAGTTAAATTTTTCACTGAAACAGAGGAGAACAACCAGATGAGA
genomic: GTTACCGTTGTGGAAATGTAGCTTCTATTCTTAGTTTCAATGAAAATATGgtgagccacc ... cttctaacagGAAAGAGAAGTTAAATTTTTCACTGAAACAGAGGAGAACAACCAGATGAGA
EST: gi|254337376|gb|GR849329.1|GR849329
EST:     GTTACCGTTGTGGAAATGTAGCTTCTATTCTTAGTTTCAATGAAAATATG                         GAAAGAGAAGTTAAATTTTTCACTGAAACAGAGGAGAACAACCAGATGAGA
genomic: GTTACCGTTGTGGAAATGTAGCTTCTATTCTTAGTTTCAATGAAAATATGgtgagccacc ... cttctaacagGAAAGAGAAGTTAAATTTTTCACTGAAACAGAGGAGAACAACCAGATGAGA
EST: gi|5753202|gb|AI960489.1|AI960489
EST:     GTTACCGTTGTGGAAATGTAGCTTCTATTCTTAGTTTCAATGAAAATATG                         AAAAGAGAAGTTAAATTTTTCACTGAAACAGAGGAGAACAACCAGATGAGA
genomic: GTTACCGTTGTGGAAATGTAGCTTCTATTCTTAGTTTCAATGAAAATATGgtgagccacc ... cttctaacagGAAAGAGAAGTTAAATTTTTCACTGAAACAGAGGAGAACAACCAGATGAGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTATGGTCCGCACCTAATTACTGTTACCGTTGTGGAAATGTAGCTTCTATTCTTAGTTTCAATGAAAATATGgtgagccacccgaagcttattttacttttaaatatgttttcaggattatcttggttactgcatctgtctcgtgatgtatatatgtggtgcctttgttttt

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