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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttttattttcgatcctatttctccatcaaattcaatcaggtttaggtttgtgtttaatttccgatcgatgatttcttactggaccttctattttcttgcatcgttatactttcagGCTTGTTCCGGCGCCGTTCATTGTCAGCTTCTCGATGCCGCTCATCCAGGGATCGTGCCTATGCACAAGGTCAATTTCGACGCCAAGAGCGAGTACGAGA

Basic information

species Glycine max
transcript GLYMA11G05560.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G05560.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os10g35580.1 (Oryza sativa), 3'ss of exon 1
gttttattttcgatcctatttctccatcaaattcaatcaggtttaggtttgtgtttaatttcc------------gatcgatgatttcttactggaccttctattt-----tcttgcatcgttata-----ctttcagGCTTGTTCCGGCGCCGTTCATTGTCAGCTTCTCGATGCCGCTCATCCAGGGATCGTGCCTATGCACAAGGTCAATTTCGACGCCAAGAGCGAGTACGAGA
   | | |  || || |  | | || |    ||  ||  ||||  | | | ||||  |||||               | |||  ||| || || |    |  || |     | |    | | | |      | |  |||||   || || || ||    || |||||  | || || || || || |||   ||||| |||||||||||||| |||||||||||||  ||||||||||
--gtaaatcgcgctcttcctcccccttgggttttgattcggtt-ggttgtttgttggatttcttgatgcgcggggcgtggattttttttttctcggttcttgatgtggcgatttgatttgggtgtgggtttcgtgtagGCTGCGTCGGGGGCGGTGGCGTGCCAGCTGATGGACGCGGCGCACCCGGGGGCGGTGCCGATGCACAAGGTCAACTTCGACGCCAAGACGGAGTACGAGA

upper sequence: GLYMA11G05560.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G163409_T02 (Zea mays), 3'ss of exon 1
---------------------------------------------gttttattt-tcgatcctatttctccatcaa--attcaatcaggtttaggtttgtgtttaatttccgatcgat--gatttcttactggaccttctattttcttg-catcgttatactttcagGCTTGTTCCGGCGCCGTTCATTGTCAGCTTCTCGATGCCGCTCATCCAGGGATCGTGCCTATGCACAAGGTCAATTTCGACGCCAAGAGCGAGTACGAGA
                                             |  ||| |  | || || |  | |||   |   ||||     | |    ||| |||        |  | || |  | ||   | |  | || |  |     | | |  | |  |  | ||||||    || ||||| |||   || || ||  | || || || ||||| ||   |||||| |||||||||||||| |||||||||||||  |||||||| |
gtaagcagcgcccgcccgggtccctcttcccgatctgtgccgttcgcgttagtggtggagccaaggtttccgggatctattcggagggttccctgttcgtgcgggcgggctaagcggttgggttctgtgcgagtccctgaaaccagtggtcgacttcgtggtctcagGCGGCGTCAGGCGCGGTTGCGTGCCAACTGATGGACGCGGCGCATCCCGGCGCCGTGCCGATGCACAAGGTCAACTTCGACGCCAAGACGGAGTACGACA

upper sequence: GLYMA11G05560.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv07s0129g01080.t01 (Vitis vinifera), 3'ss of exon 1
gttttattttcgatcctatttctccatcaaattcaatcaggtttaggtttgtgtttaatttccgatcgatgatttcttactggacct-tctattttcttgcatcg-----ttatactttcagGCTTGTTCCGGCGCCGTTCATTGTCAGCTTCTCGATGCCGCTCATCCAGGGATCGTGCCTATGCACAAGGTCAATTTCGACGCCAAGAGCGAGTACGAGA
                                              ||| ||   | ||  |   ||  |   ||||| ||   | | |||| |   | | ||||     ||  | || |||||||||||||| || ||||||||||||||  | ||| | | ||||||||| ||||| || |||||||| |||||||| || ||||||| |||||||||||
----------------------------------------------gttcgtccctgatcacgagtctttttattcttgctcaccgtctctaataaatcgaatcggatttttccaattgcagGCTTGTTCCGGTGCGGTTCATTGTCAGCTCATGGATTCGGTTCATCCAGGTATCGTTCCCATGCACAAAGTCAATTTTGATGCCAAGAACGAGTACGAGA

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|207718682|gb|GD700576.1|GD700576
EST:     TTTCTTGGATCAACTCAACTCTGCAACTCAATCTCTCCAAAGTCGAAGAG                         GCTTGTTCCGGCGCCGTTCATTGTCAGCTTCTCGATGCCGCTCATCCAGGG
genomic: TTTCTTGGATCAACTCAACTCTGCAACTCAATCTCTCCAAAGTCGAAGAGgttttatttt ... atactttcagGCTTGTTCCGGCGCCGTTCATTGTCAGCTTCTCGATGCCGCTCATCCAGGG
EST: gi|208111382|gb|GD909100.1|GD909100
EST:     TTTCTTGGATCAACTCAACTCTGCAACTCAATCTCTCCAAAGTCGAAGAG                         GCTTGTTCCGGCGCCGTTCATTGTCAGCTTCTCGATGCCGCTCATCCAGGG
genomic: TTTCTTGGATCAACTCAACTCTGCAACTCAATCTCTCCAAAGTCGAAGAGgttttatttt ... atactttcagGCTTGTTCCGGCGCCGTTCATTGTCAGCTTCTCGATGCCGCTCATCCAGGG
EST: gi|193581813|gb|FK533140.1|FK533140
EST:     TTTCTTGGATCAACTCAACTCTGCAACTCAATCTCTCCAAAGTCGAAGAG                         GCTTGTTCCGGCGCCGTTCATTGTCAGCTTCTCGATGCCGCTCATCCAGGG
genomic: TTTCTTGGATCAACTCAACTCTGCAACTCAATCTCTCCAAAGTCGAAGAGgttttatttt ... atactttcagGCTTGTTCCGGCGCCGTTCATTGTCAGCTTCTCGATGCCGCTCATCCAGGG
EST: gi|207710806|gb|GD691756.1|GD691756
EST:     TTTCTTGGATCAACTCAACTCTGCAACTCAATCTCTCCAAAGTCGAAGAG                         GCTTGTTCCGGCGCCGTTCATTGTCAGCTTCTCGATGCCGCTCATCCAGGG
genomic: TTTCTTGGATCAACTCAACTCTGCAACTCAATCTCTCCAAAGTCGAAGAGgttttatttt ... atactttcagGCTTGTTCCGGCGCCGTTCATTGTCAGCTTCTCGATGCCGCTCATCCAGGG
EST: gi|151397172|gb|EV267045.1|EV267045
EST:     TTTCTTGGATCAACTCAACTCTGCAACTCAATCTCTCCAAAGTCGAAGAG                         GCTTGTTCCGGCGCCGTTCATTGTCAGCTTCTCGATGCCGCTCATCCAGGG
genomic: TTTCTTGGATCAACTCAACTCTGCAACTCAATCTCTCCAAAGTCGAAGAGgttttatttt ... atactttcagGCTTGTTCCGGCGCCGTTCATTGTCAGCTTCTCGATGCCGCTCATCCAGGG
EST: gi|193416805|gb|FK383309.1|FK383309
EST:     TTTCTTGGATCAACTCAACTCTGCAACTCAATCTCTCCAAAGTCGAAGAG                         GCTTGTTCCGGCGCCGTTCATTGTCAGCTTCTCGATGCCGCTCATCCAGGG
genomic: TTTCTTGGATCAACTCAACTCTGCAACTCAATCTCTCCAAAGTCGAAGAGgttttatttt ... atactttcagGCTTGTTCCGGCGCCGTTCATTGTCAGCTTCTCGATGCCGCTCATCCAGGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccgatcgatgatttcttactggaccttctattttcttgcatcgttatactttcagGCTTGTTCCGGCGCCGTTCATTGTCAGCTTCTCGATGCCGCTCATCCAGGGATCGTGCCTATGCACAAGGTCAATTTCGACGCCAAGAGCGAGTACGAGA
            ttcttac  putative branch site (score: 2)
                                              tactttc  putative PPT
                         ttctatttt  TA-rich tract