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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttggtttttgtaattttgaatttcgaatttcaatttgagtgcataatcgttggttccgtgatttcgttttatacagtttgaaattttcgtttgtggtttctgatttacgagatctggtttcagatctgcaatacctgtgcttgtgcgtttgatttttgaattggtatggtttttttgttgtttttttttcagATGTGTTTCGATTGCAATGCGAAGAACCCTACCTGGGCGTCCGTCACGTATGGGATCTTTCTCTGCATCGATTGCTCCGCCGTACACCGCAGTCTCGGCG

Basic information

species Glycine max
transcript GLYMA08G36700.2
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G36700.2 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os03g63710.2 (Oryza sativa), 3'ss of exon 1
gtttggtttttgtaattttgaatttcgaatttcaatttgagtgcataatcgttggttccgtgatttcgttttatacagtttgaaattttcgtttgtggtttctgatttacgagatctggtttcagatctgcaatacctgtgcttgtgcgtttgatttt-tgaattggtatggtttttttgttgtttttttttcagATGTGTTTCGATTGCAATGCGAAGAACCCTACCTGGGCGTCCGTCACGTATGGGATCTTTCTCTGCATCGATTGCTCCGCCGTACACCGCAGTCTCGGCG
                                                                                              ||   |||    |  | ||||||  ||     ||| |    |||        | ||  ||| |  || | | |||| ||  | |  |||||  |||  |||||||| ||||| ||||  || |||||||| |||||||| |||||||| || || ||||| |||||| |||| ||||||||||| |||||||| |||||||
----------------------------------------------------------------------------------------------gtaacttcctcctctc-agatcttcttcttcttcttcttcgcct-----caagagtcagatctcatgtactagtattgtcgtgtgcttgttaatttcccagATGTGCTTCGACTGCAGCGCCAAGAACCCCACCTGGGCCTCCGTCACCTACGGCATCTTCCTCTGCCTCGACTGCTCCGCCGTCCACCGCAGCCTCGGCG

upper sequence: GLYMA08G36700.2 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os10g42420.1 (Oryza sativa), 3'ss of exon 1
gtttggtttttgtaattttgaatttcgaatttcaatttgagtgcataatcgttggttccgtgatttcgttttatacagtttgaaattttcgtttgtggtttctgatttacgagatctggtttcagatctgcaatacctgtgcttgtgcgtttgatttttgaattggtatggtttttttgt-----tgtttttttttcagATGTGTTTCGATTGCAATGCGAAGAACCCTACCTGGGCGTCCGTCACGTATGGGATCTTTCTCTGCATCGATTGCTCCGCCGTACACCGCAGTCTCGGCG
                                                                                                ||||     | |  ||||    || |    |||| ||| | |||| || |   | |   ||  || | |      ||| | |||     ||  |  ||| |||||||| ||||| ||||| || |||||||| |||||||| |||||||| || ||  |||| ||||||||||| ||||| ||||| ||||| || |||||||
------------------------------------------------------------------------------------------------ggttgtgtgtgtgagagagactgtgttct-tctgtaattcgtgtgattttttttct--cttacgagtcgactatatttatatgtgcgtatgcctaatttgcagATGTGCTTCGACTGCAACGCCAAGAACCCGACCTGGGCCTCCGTCACCTACGGCGTCTTCCTCTGCATCGACTGCTCTGCCGTCCACCGTAGCCTCGGCG

upper sequence: GLYMA08G36700.2 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G134045_T02 (Zea mays), 3'ss of exon 1
gtttggtttttgtaattttgaatttcgaatttcaatttgagtgcataatcgttggttccgtgatttcgttttatacagtttgaaattttcgt-ttgtggtttctgatttacgagatctggtttcagatctgcaatacctgtgcttgtgcgtttgatttttgaattggtatggtttttttgttgtttttt--tttcagATGTGTTTCGATTGCAATGCGAAGAACCCTACCTGGGCGTCCGTCACGTATGGGATCTTTCTCTGCATCGATTGCTCCGCCGTACACCGCAGTCTCGGCG
                                                                                          ||  ||| | |||   |   || | | |   |     | ||  |   | || |  |||  |||  ||| ||     | || ||| |  || || |       | |||||||| |||||||| || || |||||||| || |||||||||||||| || ||  |||| ||||||||||| ||||| || || |||||||| |||||||
------------------------------------------------------------------------------------------gtactgttgattcaattgatcgcgctttctatcgctctgtgtgagtgccgtccacgtgacttttttttctgtgcgcgaatcgttctgatggtggtgcacgcgtgcagATGTGCTTCGATTGTAACGCCAAGAACCCGACGTGGGCGTCCGTCACCTACGGTGTCTTCCTCTGCATCGACTGCTCGGCGGTGCACCGCAGCCTCGGCG

upper sequence: GLYMA08G36700.2 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G094390_T01 (Zea mays), 3'ss of exon 1
gtttggtttttgtaattttgaatttcgaatttcaatttgagtgcataatcgttggttccgtgatttcgttttatacagtttgaaattttcgtttgtggtttctgatttacgagatctggtttcagatctgcaatacctgtgcttgtgcgtttgatttttgaattggtatggtttttttgttgtttttttttcagATGTGTTTCGATTGCAATGCGAAGAACCCTACCTGGGCGTCCGTCACGTATGGGATCTTTCTCTGCATCGATTGCTCCGCCGTACACCGCAGTCTCGGCG
                           | | |  ||| || || ||  |   ||| |    |||||  ||   |  |||  | | |  |||    |  ||| || | |  | ||    ||  |   | |||||||  | |   |||| ||  || ||  |  |  | ||||   |      ||        |||||||| ||||||||||| || |||||||| || |||||||||||||| || ||  |||| ||||||||||| ||||| || |  |||||||| |||||||
-------------------------gtactgtggattagattggat--tttatgggtgatcgatttgatt--gtggagtcgggattgatcgcactttcttt-tgctctgtgtga----gtgccgcctgtgcaatattttt-tgtgtgtgtgcgaattccgtttctg-atggcggtgcaagcgtg-------cagATGTGCTTCGATTGCAACGCCAAGAACCCGACGTGGGCGTCCGTCACCTACGGCGTCTTCCTCTGCATCGACTGCTCGGCGGCGCACCGCAGCCTCGGCG

upper sequence: GLYMA08G36700.2 (Glycine max), 3'ss of exon 1
lower sequence: AT2G35210.2 (Arabidopsis thaliana), 3'ss of exon 1
gtttggtttttgtaattttgaatttcgaatttcaatttgagtgcataatcgttggttccgtgatttcgttttatacagtttgaaattttcgtt-tgtggtttctgatttacgagatctggtttcagatctgcaatacctgtgcttgtgcgtttgatttttgaattggtatggtttttttgttgtttttttttcagATGTGTTTCGATTGCAATGCGAAGAACCCTACCTGGGCGTCCGTCACGTATGGGATCTTTCTCTGCATCGATTGCTCCGCCGTACACCGCAGTCTCGGCG
                                                                                          ||  |||      || | |||   ||||           |   ||  |   | | ||   |  ||| |   |  |       || | ||    | |||||| ||||| ||||| |||||||||||||||||||| || ||||| ||||| || || |||||||||||||||||||||||||| || || || || ||||| ||||
------------------------------------------------------------------------------------------gtaatgttaacgatgttctacagaatctatagattcgattaagatctcgaagttcgtcgatcagatctgacagatttaggatttatctttgaatattttttgcagATTTGTTTTGATTGCAATGCGAAGAACCCAACATGGGCTTCCGTTACTTACGGGATCTTTCTCTGCATCGATTGCTCAGCTGTTCATCGGAGTCTTGGCG

upper sequence: GLYMA08G36700.2 (Glycine max), 3'ss of exon 1
lower sequence: Vv02s0012g01330.t01 (Vitis vinifera), 3'ss of exon 1
gtttggtttttgtaattttgaatttcgaatttcaatttgagtgcataatcgttggttccgtgatttcgttttatacagtttgaaattttcgtttgtggtttctgatttacgagatctggtttcagatctgcaatacctgtgcttgtgcgtttgatttttgaattggtatggtttttttgttgtttttttttcagATGTGTTTCGATTGCAATGCGAAGAACCCTACCTGGGCGTCCGTCACGTATGGGATCTTTCTCTGCATCGATTGCTCCGCCGTACACCGCAGTCTCGGCG
                        ||   | |  | |  | | | |    ||   ||      |||  |||| |    |||   ||||| |||| ||||||    ||   ||||||||||| |||||||| |        | ||  ||| |||  | | |  ||  |||   ||| ||  | |||  |||| |||||||||| ||||| |||||||||||||| || |||||||||||||||||||||||||| ||||||||||| ||||||||||| ||  | ||||| || |
-----------------------gtctgttctttactgaatttcttcgcggtatttttaaatgttttcttttgt----tttt--attttggtttttggttttctgttcttgagatctggtt-cagatctgga--------ggtttcgcgattggatctcggttttttat---tttgtttctttttggtttttagATGTGTTTTGATTGTAATGCGAAGAACCCGACTTGGGCGTCCGTCACGTATGGGATCTTCCTCTGCATCGACTGCTCCGCCGTGCATAGGAGTCTTGGGG

upper sequence: GLYMA08G36700.2 (Glycine max), 3'ss of exon 1
lower sequence: PP1S795_4V6.1 (Physcomitrella patens), 3'ss of exon 1
gtttggtttttgtaattttgaatttcgaatttcaatttgagtgcataatcgttggttccgtgatttcgttttatacagtttgaaattttcgtttgtggtttctgatttacgagatctggtttcagatctgcaatacctgtgcttgtgcgtttgatttttgaattggt-atggtttttttgttgtttttttttcagATGTGTTTCGATTGCAATGCGAAGAACCCTACCTGGGCGTCCGTCACGTATGGGATCTTTCTCTGCATCGATTGCTCCGCCGTACACCGCAGTCTCGGCG
                                                                                          |  |   | ||    |   |   |  || |  ||    |   ||    | |  ||| || ||  ||  | ||||  | | |  |  |   |||  |      |||||||||||||| |||||| ||||||| || || |||||||| || ||||||||  | ||  | ||| | || || || ||  |||| || |||||||| |
------------------------------------------------------------------------------------------gagtactgctttgcttgcgcacaaaatgctagcatgagtttgattgtggagtgtgttcggttttttactaaattcttcacgagtcgtcgattggatg-----cagATGTGTTTCGACTGCAATTCGAAGAATCCCACTTGGGCGTCAGTGACGTATGGAGTGTTCATATGCCTGGACTGTTCAGCTCTACATCGTAGTCTCGGTG

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|18735589|gb|BM528850.1|BM528850
EST:     CCGACAAGAACACCGTGTTCAGAAAGCTCAAGGCGAAGTCTGAAAATAAG                         ATGTGTTTCGATTGCAATGCGAAGAACCCTACCTGGGCGTCCGTCACGTAT
genomic: CCGACAAGAACACCGTGTTCAGAAAGCTCAAGGCGAAGTCTGAAAATAAGgtttggtttt ... tttttttcagATGTGTTTCGATTGCAATGCGAAGAACCCTACCTGGGCGTCCGTCACGTAT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcttgtgcgtttgatttttgaattggtatggtttttttgttgtttttttttcagATGTGTTTCGATTGCAATGCGAAGAACCCTACCTGGGCGTCCGTCACGTATGGGATCTTTCTCTGCATCGATTGCTCCGCCGTACACCGCAGTCTCGGCG
         gtttgat  putative branch site (score: 5)
                                tttttttgttgttttt  putative PPT
                                tttttttgttgttttt  TA-rich tract