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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGATAGACAGCAACGAGACCATAAAGGTTTATAGAAGTGGTGGAGCAGATCCTGATGGAGATCAACCTGGTGATCTTTATGTTACTATCAAGgtacttcaatagcttggaagtcgctatttttttgttgatacttttaaacttgacatttttatttgtttgtcctttttgcag

Basic information

species Glycine max
transcript GLYMA09G00580.1
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G00580.1 (Glycine max), 5'ss of exon 13
lower sequence: LOC_Os12g07060.1 (Oryza sativa), 5'ss of exon 13
GGATAGACAGCAACGAGACCATAAAGGTTTATAGAAGTGGTGGAGCAGATCCTGATGGAGATCAACCTGGTGATCTTTATGTTACTATCAAGgtac-------ttcaatagcttggaagtcgcta--tttttttgttgatacttttaaa-cttgacatttttatttgtttgtcctttttgcag-----
| || ||   ||| || || || ||||||| | | |  ||||| ||||||  |||  |  || ||||||||||||| |||||||||||||||||         ||   |   ||  ||    | |  | ||| |||   |    | |   |||  ||  |  | ||  |  || ||||   ||     
GCATCGATGACAATGACACTATGAAGGTTTTTGGCAAGGGTGGTGCAGATGTTGAGCGCAATAAACCTGGTGATCTCTATGTTACTATCAAGgtttggttccttttttttttttccaaaatacaaactctttatgtcagtttgatcagttctttgcaaatgaactttgtattcattttcctagtacag

upper sequence: GLYMA09G00580.1 (Glycine max), 5'ss of exon 13
lower sequence: GRMZM2G118316_T01 (Zea mays), 5'ss of exon 13
GGATAGACAGCAACGAGACCATAAAGGTTTATAGAAGTGGTGGAGCAGATCCTGATGGAGATCAACCTGGTGATCTTTATGTTACTATCAAGgtacttcaatagcttggaagtcgctatt-tttttgttgatacttttaaacttgacatttttatttgtttgtcctttttgcag-----------------------------------
| |  |||   || || | ||| ||||||| | | |  ||||| ||||||  |||  || || | |||||||| ||||||||||||||||||||   | |||  ||   | |  |  | |  |  |  |  | |  | |   | | || |  |||  |   |  ||  | | ||                                   
GAAGTGACGATAATGACATCATGAAGGTTTTTGGTAAGGGTGGTGCAGATGTTGACCGAAATAAGCCTGGTGACCTTTATGTTACTATCAAGgt---ttaatttctgaaatgctgtgaatgctcctactcgtgccctaagtttagtcagtactat--gcaaggtctcatggaagtataaaacgaaattcactttcatttcctattacag

upper sequence: GLYMA09G00580.1 (Glycine max), 5'ss of exon 13
lower sequence: GRMZM2G118316_T02 (Zea mays), 5'ss of exon 13
GGATAGACAGCAACGAGACCATAAAGGTTTATAGAAGTGGTGGAGCAGATCCTGATGGAGATCAACCTGGTGATCTTTATGTTACTATCAAGgtacttcaatagcttggaagtcgcta-tttttttgttgatacttttaaacttgacatttttatttgtttgtcctttttgcag-----------------------------------
     |||   || || | ||| ||||||| | | |  ||||| ||||||  |||  || || | |||||||| ||||||||||||||||||||   | |||  ||   | |  |  | |  |  |  |  | |  | |   | | || |  |||  |   |  ||  | | ||                                   
----TGACGATAATGACATCATGAAGGTTTTTGGTAAGGGTGGTGCAGATGTTGACCGAAATAAGCCTGGTGACCTTTATGTTACTATCAAGgt---ttaatttctgaaatgctgtgaatgctcctactcgtgccctaagtttagtcagtactat--gcaaggtctcatggaagtataaaacgaaattcactttcatttcctattacag

upper sequence: GLYMA09G00580.1 (Glycine max), 5'ss of exon 13
lower sequence: Vv13s0064g01360.t01 (Vitis vinifera), 5'ss of exon 13
GGATAGACAGCAACGAGACCATAAAGGTTTATAGAAGTGGTGGAGCAGATCCTGATGGAGATCAACCTGGTGATCTTTATGTTACTATCAAGgta-cttcaatagcttggaa-gtcgctatttttttgttgatacttttaaact-----tgacatttttatttgtttgtcctttttgcag------------
|  | |||  ||| || ||  ||||||| ||||||||||||||||| |||||||| ||| |||||||||||||||||||||||||||||| |||| |||  |||||||      ||  | ||||||| || ||    |  || |     ||| |     | |   | | |     || |             
GAGTGGACGACAATGAAACTCTAAAGGTGTATAGAAGTGGTGGAGCTGATCCTGAAGGAAATCAACCTGGTGATCTTTATGTTACTATCAGGgtaacttgcatagcttctttcatcaattttttttttttaatgaaatggaaatattactgaaaaaggaaatccatcggcaaaggtggattagatattccac

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|208059639|gb|GD858369.1|GD858369
EST:     GAGCAGATCCTGATGGAGATCGACCTGGTGATCTTTATGTTACTATCAAG                         GTTAGAGAAGACCCTGTTTTTCGCAGAGAAGGATCTGATATTCATGTAGAT
genomic: GAGCAGATCCTGATGGAGATCAACCTGGTGATCTTTATGTTACTATCAAGgtacttcaat ... ctttttgcagGTTAGAGAAGACCCTGTTTTTCGCAGAGAAGGATCTGATATTCATGTAGAT
EST: gi|7796591|gb|AW781988.1|AW781988
EST:     GAGCAGATCCTGATGGAGATCAACCTGGTGATCTTTATGTTACTATCAAG                         GTTAGAGAAGACCCTGTTTTTCGCAGAGAAGGATCTGATATTCATGTAGAT
genomic: GAGCAGATCCTGATGGAGATCAACCTGGTGATCTTTATGTTACTATCAAGgtacttcaat ... ctttttgcagGTTAGAGAAGACCCTGTTTTTCGCAGAGAAGGATCTGATATTCATGTAGAT
EST: gi|193368090|gb|FK331656.1|FK331656
EST:     GAGCAGATCCTGATGGAGATCAACCTGGTGATCTTTATGTTACTATCAAG                         GTTAGAGAAGACCCTGTTTTTCGCAGAGAAGGATCTGATTATTCATGTAGA
genomic: GAGCAGATCCTGATGGAGATCAACCTGGTGATCTTTATGTTACTATCAAGgtacttcaat ... ctttttgcagGTTAGAGAAGACCCTGTTTTTCGCAGAGAAGGATCTGAT-ATTCATGTAGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGATAGACAGCAACGAGACCATAAAGGTTTATAGAAGTGGTGGAGCAGATCCTGATGGAGATCAACCTGGTGATCTTTATGTTACTATCAAGgtacttcaatagcttggaagtcgctatttttttgttgatacttttaaacttgacatttttatttgtttgtcctttttgcag

- - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA