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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaatattcaagatacttgtattttttttaattagtccatctgattaatttctctaattatttcaaaatgtgataaattgtccactcaacgctgcagGCTGTGATGCTGATATACACGTCATTGTAAAAATTGAAAGTGCAGACTCTATACCAAACTTGCATTCAATTATTACAGCGTCTGATGGG

Basic information

species Glycine max
transcript GLYMA20G30430.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G30430.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os01g47080.1 (Oryza sativa), 3'ss of exon 5
gtaaatattcaagatacttgtattttttttaattagtccatctgattaatttctctaattatttcaa-aatgtgataaattgtccactcaacgctgcagGCTGTGATGCTGATATACACGTCATTGTAAAAATTGAAAGTGCAGACTCTATACCAAACTTGCATTCAATTATTACAGCGTCTGATGGG
     || | |  || |   ||  || |  || |  |||| |      | || |  || | | | || | |||| |   ||||    |  |  || ||||||   |||| |||||||| || |||||||| |||||||||||||| || || |||||| | || ||||| || ||||| || ||||||
----gtaataattatcccc-tacattatgaaaattatccagc------acttattcaactgtcttaatagtgtgtt---ttgtt---ttgattct-cagGCTCCAATGCCGATATACATGTAATTGTAAAGATTGAAAGTGCAGATTCCATTCCAAACCTACACTCAATCATCACAGCATCGGATGGG

upper sequence: GLYMA20G30430.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G152686_T01 (Zea mays), 3'ss of exon 5
gtaaatattcaagatacttgtattttttttaattagtccatctgattaatttctctaattatttcaaaatgtgataaattgtccactcaacgctgcagGCTGTGATGCTGATATACACGTCATTGTAAAAATTGAAAGTGCAGACTCTATACCAAACTTGCATTCAATTATTACAGCGTCTGATGGG
|||| | |||||   |  |       || |||  | ||         |  || | | |  ||||    |  | ||      || | || |  || |||| ||  ||||||| ||||| || || |||||||| |||||||||||||| || || ||||| |||||||| || ||||| |||||||||
gtaa-tcttcaacccaact-------ttgtaaaaaatcatatcatgcacctttttttacaatttactgagctcat------tctattctattct-cagGTTGCAATGCTGACATACATGTTATCGTAAAAATAGAAAGTGCAGACTCCATCCCCAACTTACATTCAATCATCACAGCATCTGATGGG

upper sequence: GLYMA20G30430.1 (Glycine max), 3'ss of exon 5
lower sequence: AT5G52920.1 (Arabidopsis thaliana), 3'ss of exon 5
gtaaatattcaagatac-ttgtattttttttaattagtccatctgattaatttctctaattatttcaaaatgtgataaattgtccactcaacgctgcagGCTGTGATGCTGATATACACGTCATTGTAAAAATTGAAAGTGCAGACTCTATACCAAACTTGCATTCAATTATTACAGCGTCTGATGGG
||||||| |    |    ||  ||  |   | | |  |    ||     |||||  |  |  | | |   || |||   ||||  ||  |    |||||   ||| ||||||||||||||| || || |||||||| ||||||||||| ||||| |||||||| || ||||| ||||| || ||||||
gtaaatacttggaacctattccatcctaagtgaatgatttgcctatgatatttcctttttggtctaaccttgagattgtttgtt-acaaatatttgcagATAGTGGTGCTGATATACACGTGATAGTGAAAATTGAGAGTGCAGACTCCATACCTAACTTGCACTCCATTATCACAGCATCAGATGGG

upper sequence: GLYMA20G30430.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv16s0050g02180.t01 (Vitis vinifera), 3'ss of exon 5
gtaaatattcaagatacttgtattttttttaattagtccatctgattaatttctctaattatttcaaaatgtgata-----aattgtccactcaacgctgcagGCTGTGATGCTGATATACACGTCATTGTAAAAATTGAAAGTGCAGACTCTATACCAAACTTGCATTCAATTATTACAGCGTCTGATGGG
||||||| | | |||| |  | ||     ||| ||    |  || || || | |  | ||  |||||| | |   |     |||  |   ||     | ||||||||| |||| ||||| || |||||||| |||||||||||||| ||||| || || ||  | |||||||||||||| || |||||||||
gtaaatacttaggatattcat-ttggaaataactaaataacttgcttgatctgta-atttgcttcaaattttaccacttataatctttaccttgtttcggcagGCTGTAATGCAGATATCCATGTCATTGTTAAAATTGAAAGTGCCGACTCCATTCCCAATCTACATTCAATTATTACCGCATCTGATGGG

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|17022372|gb|BM093406.1|BM093406
EST:     TTTTGTTAAGGATGCACAAGTAGTTCATGAACTGAAGAATTATTTGAAAA                         GCTGTGATGCTGATATACACGTCATTGTAAAAATTGAAAGTGCAGACTCTA
genomic: TTTTGTTAAGGATGCACAAGTAGTTCATGAACTGAAGAATTATTTGAAAAgtaaatattc ... aacgctgcagGCTGTGATGCTGATATACACGTCATTGTAAAAATTGAAAGTGCAGACTCTA
EST: gi|26048943|gb|CA785396.1|CA785396
EST:     TTTTGTTAAGGATGCACAAGTAGTTCATGAACTGAAGAATTATTTGAAAA                         GCTGTGATGCTGATATACACGTCATTGTAAAAATTGAAAGTGCAGACTCTA
genomic: TTTTGTTAAGGATGCACAAGTAGTTCATGAACTGAAGAATTATTTGAAAAgtaaatattc ... aacgctgcagGCTGTGATGCTGATATACACGTCATTGTAAAAATTGAAAGTGCAGACTCTA
EST: gi|26048715|gb|CA785168.1|CA785168
EST:     GTTCATGAACTGAAGAATTATTTGAAAA                         GCTGTGATGCTGATATACACGTCATTGTAAAAATTGAAAGTGCAGACTCTA
genomic: GTTCATGAACTGAAGAATTATTTGAAAAgtaaatattc ... aacgctgcagGCTGTGATGCTGATATACACGTCATTGTAAAAATTGAAAGTGCAGACTCTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gattaatttctctaattatttcaaaatgtgataaattgtccactcaacgctgcagGCTGTGATGCTGATATACACGTCATTGTAAAAATTGAAAGTGCAGACTCTATACCAAACTTGCATTCAATTATTACAGCGTCTGATGGG
         ctctaat  putative branch site (score: 3)
          tctaattatttcaaaa  TA-rich tract