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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtactactttgagatatttttatttgttctgttttttgccattagtagtggaaatgcactttttgaacactgattgtacaatgagaggtttatatagaagtgaggtgcatttaatattgaagcacaactgatgatgacaattgtgtttctccatggttgtagGTTGTCAGATGGGGGCGGTCTGTATATGCAAATATTCAGAAATTTATCCAGTTTCAGCTTACAGTAAATGTGGCCGCTCTAGTGATTAATGTTGTTGCTG

Basic information

species Glycine max
transcript GLYMA09G06890.1
intron # 25
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G06890.1 (Glycine max), 3'ss of exon 25
lower sequence: LOC_Os04g51610.3 (Oryza sativa), 3'ss of exon 26
gtttgtactactttgagatatttttatttgttctgttttttgccattagtagtggaaatgcactttttgaacactgattgtacaatgagaggtttatatagaagtgaggtgcatttaatattgaagcacaactgatgatgacaattgtgtttctccatggttgtagGTTGTCAGATGGGGGCGGTCTGTATATGCAAATATTCAGAAATTTATCCAGTTTCAGCTTACAGTAAATGTGGCCGCTCTAGTGATTAATGTTGTTGCTG
                                                                                                |||  |      || |  ||| |       ||  ||||    | | | |  | |||   |  | || ||||||||||||||||| || || || |||||||| |||||||||||||| ||||||||| | || || || || || ||  |  | ||||| ||||||||||
-----------------------------------------------------------------------------------------------gtatgtacactgtgttctgttattggccttccatgactgcaacttatagtattcttttctctcgcttttagGTTGTCAGATGGGGTCGCTCGGTTTATGCAAACATTCAGAAATTTATACAGTTTCAGTTAACCGTCAACGTTGCAGCCTTGATTATTAACGTTGTTGCTG

upper sequence: GLYMA09G06890.1 (Glycine max), 3'ss of exon 25
lower sequence: GRMZM5G893864_T01 (Zea mays), 3'ss of exon 5
gtttgtactactttgagatatttttatttgttctgttttttgccattagtagtggaaatgcactttttgaacactgattgtacaatgagaggtttatatagaagtgaggtgcatttaatattgaagcacaac-tgatgatgacaattgtgtttctccatggttgtagGTTGTCAGATGGGGGCGGTCTGTATATGCAAATATTCAGAAATTTATCCAGTTTCAGCTTACAGTAAATGTGGCCGCTCTAGTGATTAATGTTGTTGCTG
                                                                 ||||  |  |  || || |||   |||   || | ||    | | |||    ||    ||  ||||| |  |  |     || | | |||      || ||||| ||  | ||||| || ||||| ||||||||||| || || ||||| ||||| |||||||| |||||||| || ||||| || || |||||||||||||
----------------------------------------------------------------gtttggcc--tatttttagaatctaagg---atcttgataatacgcgcac---atgcctaa-tacaacgttgtcttacatgttctttatcttttatattctagGTGGTTCGCTGGGGTCGCTCTGTTTATGCAAATATCCAAAAGTTTATTCAGTTCCAGCTTACCGTAAATGTTGCAGCTCTTGTCATCAATGTTGTTGCTG

upper sequence: GLYMA09G06890.1 (Glycine max), 3'ss of exon 25
lower sequence: AT5G57110.1 (Arabidopsis thaliana), 3'ss of exon 27
---------------gtttgtactactttgagatatttttatttgttctgttttttgccattagtagtggaaatgcactttttga---acactgattgtaca---atgagaggtttatatagaagtgagg-tgcatttaatat---tgaagc----acaactgatgatgacaattgtgtttctccatggt--------tgtagGTTGTCAGATGGGGGCGGTCTGTATATGCAAATATTCAGAAATTTATCCAGTTTCAGCTTACAGTAAATGTGGCCGCTCTAGTGATTAATGTTGTTGCTG
                ||| | |||||||   |||  || |||||||   |      |    ||      |||| |    ||  |   |   |  ||||  |   |||     | | | ||||    ||  |||||||    |   ||||       | ||| |  ||  |||   |  ||     || |        | ||||||||  |||||||||| || || ||||| || |||||||| || ||||| |||||||| ||||| ||||| |||||||| || ||||||||||| ||||
gtttattcaaattcacttttttctacttt---atagattcatttgttggataaaggtctgcaagacacataaatccctacttcaatagattttttttgtgaatccatgtatactatgtgtagatccaagaatgcatttttcgtaactgaatttgttgctactaagtattccaaccttaatttgtggtgatatatattatatagGTTGTTCGATGGGGGCGATCAGTGTATGCCAACATTCAGAAGTTCATCCAATTTCAGCTCACAGTCAATGTCGCCGCTCTCGTAATTAATGTTGTAGCTG

upper sequence: GLYMA09G06890.1 (Glycine max), 3'ss of exon 25
lower sequence: AT4G29900.1 (Arabidopsis thaliana), 3'ss of exon 27
gtttgtactactttgagat-----atttttatttgtt----------ctgttttttgccattagta-gtggaaatgcactttttgaacactgattgtacaatgagaggtttatatagaagtgaggtgcatttaatat----tgaagcacaactgat--gatgacaattgtgtttctc----catggttgtagGTTGTCAGATGGGGGCGGTCTGTATATGCAAATATTCAGAAATTTATCCAGTTTCAGCTTACAGTAAATGTGGCCGCTCTAGTGATTAATGTTGTTGCTG
||||||| | ||| || |      |||   |||| ||          ||  ||||||  | |  |  || |      |||||| |||      ||   |    |     |  | | |   |  ||   ||||   ||    | ||  |      ||  |||  | ||| |  |  ||    |||   | ||||||||| | ||||| || ||||| ||||| |||||||| || || |||||||||||||| || || ||||| || ||||| || || ||||| || ||||
gtttgta-tccttagaaaccaaggattcaaatttcttataaaagaagctcctttttgatactcttctgttgcgtgatacttttggaatttcttttcctcgtaaatgtcctcctttgggctttggggctatttgtgatctttttaattatcctgaattagatatccattttaataatcgtctcattcctatagGTTGTCCGTTGGGGTCGATCTGTGTATGCGAATATTCAAAAGTTCATCCAGTTTCAGCTCACGGTTAATGTCGCAGCTCTTGTCATCAATGTGGTGGCTG

upper sequence: GLYMA09G06890.1 (Glycine max), 3'ss of exon 25
lower sequence: Vv11s0052g00320.t01 (Vitis vinifera), 3'ss of exon 28
gtttgtactactttgagatatttttatttgttctgttttttgccattagtagtggaaatgcactttttgaacactgattgtacaatgagaggtttatatagaagtgaggtgcatttaatattgaagcacaactgatgatgacaattg-tgtttctccatggttgtagGTTGTCAGATGGGGGCGGTCTGTATATGCAAATATTCAGAAATTTATCCAGTTTCAGCTTACAGTAAATGTGGCCGCTCTAGTGATTAATGTTGTTGCTG
                                                           |   || |||| ||  | ||   |  |  || |  ||   || | |  | |   || ||    |||||     |  |  | ||  ||| | | |||   ||  | ||||||||||||||||| || ||||||||||||||||| |||||||| |||||||||||||| ||||| ||||| || |||||| | |||||||| || || |
----------------------------------------------------------cgagtttgttgatcaaagttt---cccttcgatgcctac--agcatttggataagttgaa----gaagctgggatctttgtaactgttgatttctcttgttgcatttagGTTGTCAGATGGGGACGATCTGTATATGCAAATATACAGAAATTCATCCAGTTTCAGCTCACAGTTAATGTTGCAGCTCTAATAATTAATGTCGTGGCAG

upper sequence: GLYMA09G06890.1 (Glycine max), 3'ss of exon 25
lower sequence: EFJ22392 (Selaginella moellendorffii), 3'ss of exon 22
gtttgtactactttgagatatttttatttgttctgttttttgccattagtagtggaaatgcactttttgaacactgattgtacaatgagaggtttatatagaagtgaggtgcatttaatattgaagcacaactgatgatgacaatt--gtgtttctccatggttgtagGTTGTCAGATGGGGGCGGTCTGTATATGCAAATATTCAGAAATTTATCCAGTTTCAGCTTACAGTAAATGTGGCCGCTCTAGTGATTAATGTTGTTGCTG
                                                                                                                        |   |  ||| ||  || ||  | |     |  ||   ||  ||| |||||||  | ||||| ||||| || ||||| ||||||||||| ||||||||||| ||||| || |||||||| |  || || ||  | || || || || |
-----------------------------------------------------------------------------------------------------------------------gtaagataacagcttttggtgcgagtctgaaggatcgaaattcttgcagGTTGTACGCTGGGGTCGGTCCGTGTATGCCAATATTCAGAAGTTTATCCAGTTCCAGCTGACTGTAAATGTTGTTGCGCTGGTTCTCAACGTCGTGGCCG

upper sequence: GLYMA09G06890.1 (Glycine max), 3'ss of exon 25
lower sequence: EFJ25508 (Selaginella moellendorffii), 3'ss of exon 23
gtttgtactactttgagatatttttatttgttctgttttttgccattagtagtggaaatgcactttttgaacactgattgtacaatgagaggtttatatagaagtgaggtgcatttaatattgaagcacaactgatgatgacaatt--gtgtttctccatggttgtagGTTGTCAGATGGGGGCGGTCTGTATATGCAAATATTCAGAAATTTATCCAGTTTCAGCTTACAGTAAATGTGGCCGCTCTAGTGATTAATGTTGTTGCTG
                                                                                                                        |   |  ||| ||  || ||  | |     |  ||   ||  ||| |||||||  | ||||| ||||| || ||||| ||||||||||| ||||||||||| ||||| || |||||||| |  || || ||  | || || || || |
-----------------------------------------------------------------------------------------------------------------------gtaagataacagcttttggtgcgagtctgaaggatcgaaattcttgcagGTTGTACGCTGGGGTCGGTCCGTGTATGCCAATATTCAGAAGTTTATCCAGTTCCAGCTGACTGTAAATGTAGTTGCGCTGGTTCTCAACGTCGTGGCCG

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|208053841|gb|GD853110.1|GD853110
EST:     AGAGCTCCGATATCATTATTTTGGATGACAATTTTGCTTCAGTTGTGAAG                         GTTGTCAGATGGGGGCGGTCTGTATATGCAAATATTCAGAAATTTATCCAG
genomic: AGAGCTCTGATATCATTATTTTGGATGACAATTTTGCTTCAGTTGTGAAGgtttgtacta ... atggttgtagGTTGTCAGATGGGGGCGGTCTGTATATGCAAATATTCAGAAATTTATCCAG
EST: gi|193626264|gb|FK573107.1|FK573107
EST:     AGAGCTCTGATATCATTATTTTGGATGACAATTTTGCTTCAGTTGTGAAG                         GTTGTCAGATGGGGGCGGTCTGTATATGCAAATATTCAGAAATTTATCCAG
genomic: AGAGCTCTGATATCATTATTTTGGATGACAATTTTGCTTCAGTTGTGAAGgtttgtacta ... atggttgtagGTTGTCAGATGGGGGCGGTCTGTATATGCAAATATTCAGAAATTTATCCAG
EST: gi|193683076|gb|FK621010.1|FK621010
EST:     AGAGCTCTGATATCATTATTTTGGATGACAATTTTGCTTCAGTTGTGAAG                         GTTGTCAGATGGGGGCGGTCTGTATATGCAAATATTCAGAAATTTATCCAG
genomic: AGAGCTCTGATATCATTATTTTGGATGACAATTTTGCTTCAGTTGTGAAGgtttgtacta ... atggttgtagGTTGTCAGATGGGGGCGGTCTGTATATGCAAATATTCAGAAATTTATCCAG
EST: gi|26049080|gb|CA785533.1|CA785533
EST:     AGAGCTCTGATATCATTATTTTGGATGACAATTTTGCTTCAGTTGTGAAG                         GTTGTCAGATGGGGGCGGTCTGTATATGCAAATATTC
genomic: AGAGCTCTGATATCATTATTTTGGATGACAATTTTGCTTCAGTTGTGAAGgtttgtacta ... atggttgtagGTTGTCAGATGGGGGCGGTCTGTATATGCAAATATTC
EST: gi|207788931|gb|GD760279.1|GD760279
EST:     AGAGCTCTGATATCATTATTTTGGATGACAATTTTGCTTCAGTTGTGAAG                         GTTGTCAGATGGGGGCGGTCTGTATATGCAGATATTCAGAAATTTATCCAG
genomic: AGAGCTCTGATATCATTATTTTGGATGACAATTTTGCTTCAGTTGTGAAGgtttgtacta ... atggttgtagGTTGTCAGATGGGGGCGGTCTGTATATGCAAATATTCAGAAATTTATCCAG
EST: gi|193615719|gb|FK561932.1|FK561932
EST:     AGAGCTCTGATATCATTATTTTGGATGACAATTTTGCTTCAGTTGTGAAG                         GTTGTCAGATGGGGGCGGTCTGTATATGCAAATATTCAGAAATTTATCCAG
genomic: AGAGCTCTGATATCATTATTTTGGATGACAATTTTGCTTCAGTTGTGAAGgtttgtacta ... atggttgtagGTTGTCAGATGGGGGCGGTCTGTATATGCAAATATTCAGAAATTTATCCAG
EST: gi|9820234|gb|BE555744.1|BE555744
EST:     AGAGCTCTGATATCATTATTTTGGATGACAATTTTGCTTCAGTTGTGAAG                         GTTGTCAGATGGGGGCGGTCTGTATATGCAAATATTCAGAAATTTATCCAG
genomic: AGAGCTCTGATATCATTATTTTGGATGACAATTTTGCTTCAGTTGTGAAGgtttgtacta ... atggttgtagGTTGTCAGATGGGGGCGGTCTGTATATGCAAATATTCAGAAATTTATCCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catttaatattgaagcacaactgatgatgacaattgtgtttctccatggttgtagGTTGTCAGATGGGGGCGGTCTGTATATGCAAATATTCAGAAATTTATCCAGTTTCAGCTTACAGTAAATGTGGCCGCTCTAGTGATTAATGTTGTTGCTG
                  aactgat  putative branch site (score: 3)
                                      tttctccat  putative PPT
     aatattgaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgtactactttgagatatttttatttgttctgttttttgccattagtagtggaaatgcactttttgaacactgattgtacaatgagaggtttatatagaagtgaggtgcatttaatattgaagcacaactgatgatgacaattgtgtttctccatggttgtagGTTGTCAGATGGGGGCGGTCTGTATATGCAAATATTCAGAAATTTATCCAGTTTCAGCTTACAGTAAATGTGGCCGCTCTAGTGATTAATGTTGTTGCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT