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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtgttgttttactcttcctcaatagaatagtgttagttgatttgtacattgctctggattcttgttatttatcactaaattggctgctttcttgttgcagTCATTGTTGTGTGATCCAAACCCAAATTCACCAGCAAATTCTGAAGCTGCTCGGATGTTCAGCGAAAACAAGCGCGAATACAACAGAAAAGTACGCGAGA

Basic information

species Glycine max
transcript GLYMA08G40860.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G40860.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os05g08960.1 (Oryza sativa), 3'ss of exon 5
gtgttgttttactcttcctcaatagaatagtgttagttgatttgtacattgctctggattcttgttatttatcactaa-attggctgcttt---cttgttgcagTCATTGTTGTGTGATCCAAACCCAAATTCACCAGCAAATTCTGAAGCTGCTCGGATGTTCAGCGAAAACAAGCGCGAATACAACAGAAAAGTACGCGAGA
       |  |   ||| |  |   || |   | |  |  |     || |    | |||| |   | || |  |||   |||  |||||||    |  || |||||  || | || |||||||||||||||||||| || || ||||||||||| ||  | ||||| || |||||||| ||||||||| ||||||| || ||||
---acaatgcatatttcatggactcaagacattgacatattacaggcaatttcattgatt-taactgttcagtacttctatttcctgctttgtattatttccagTCGCTGCTTTGCGATCCAAACCCAAATTCACCTGCCAACTCTGAAGCTGCCCGCCTATTCAGTGAGAACAAGCGGGAATACAACCGAAAAGTTCGTGAGA

upper sequence: GLYMA08G40860.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os05g08960.2 (Oryza sativa), 3'ss of exon 5
gtgttgttttactcttcctcaatagaatagtgttagttgatttgtacattgctctggattcttgttatttatcactaaattggctgctttcttgttgcagTCATTGTTGTGTGATCCAAACCCAAATTCACCAGCAAATTCTGAAGCTGCTCGGATGTTCAGCGAAAACAAGCGCGAATACAACAGAAAAGTACGCGAGA----------------------------------------------
                                            | ||||| | |   |  |   || || |   |      |||   |  |  || |||||  || | || |||||||||||||||||||| || || ||||||||||| ||  | ||||| || |||||||| ||||||||| ||||||| || ||||                                              
-------------------------------------------tttcattgatttaactgttcagtacttctattt---cctgctttgtattatttccagtcgctgctttgcgatccaaacccaaattcacctgccaactctgaagCTGCCCGCCTATTCAGTGAGAACAAGCGGGAATACAACCGAAAAGTTCGTGAGATAGTGGAGCAGAGCTGGACCGCGGACTGATCCACTCCATCTAACCA

upper sequence: GLYMA08G40860.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G110983_T03 (Zea mays), 3'ss of exon 3
--gtgttgttttactcttcctcaatagaatagtgttagttgatttgtacattgctctggattcttgttatttatcactaaattg-gctgctttcttgttgcagTCATTGTTGTGTGATCCAAACCCAAATTCACCAGCAAATTCTGAAGCTGCTCGGATGTTCAGCGAAAACAAGCGCGAATACAACAGAAAAGTACGCGAGA
     | | | |  | |   | | ||  ||  | |||    || ||| |  || |    |   |   | | | | |||||  || | |   | |   ||||||||||||||||| ||||||||||| ||||| || || || |||||||| || || ||||||||||| |||||||| || |||||| | ||||| || ||| 
tgccatcgctgt-ttatgaattattatgatgttcttaaaccatctgtgc--tgatggctacagtgcgtgtgtgtgactaacctgaggtttgtgccatttgcagTCATTGTTGTGCGATCCAAACCCGAATTCGCCCGCTAACTCTGAAGCCGCCCGCATGTTCAGCGAGAACAAGCGAGAGTACAACCGCAAAGTTCGGGAGG

upper sequence: GLYMA08G40860.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv01s0026g01770.t01 (Vitis vinifera), 3'ss of exon 6
gtgttgttttactcttcctcaatagaatagtgttagttgatttgtacattgctctg-gattcttgttatttatcactaaattggctgctttctt--gttgcagTCATTGTTGTGTGATCCAAACCCAAATTCACCAGCAAATTCTGAAGCTGCTCGGATGTTCAGCGAAAACAAGCGCGAATACAACAGAAAAGTACGCGAGA
    | ||  | |      ||||  |  |  | |  ||    ||||  ||||| || ||   ||   |||  | | ||  ||| || | |  |    ||||||||  || | ||||| ||||||||||| || || |||||||| ||||| || |||||||| || || |||||||| ||||||||||||| ||| || ||||
---attttggattaaagaacaatttataatggctttttatagtgtagcttgctttgtgagaatttggattgctaattatgttgccttcctcttatgattgcagTCGCTGCTTTGTGACCCAAACCCAAACTCTCCTGCAAATTCAGAAGCAGCACGGATGTTTAGTGAGAACAAGCGTGAATACAACAGAAGAGTGCGTGAGA

upper sequence: GLYMA08G40860.1 (Glycine max), 3'ss of exon 5
lower sequence: PP1S219_106V6.1 (Physcomitrella patens), 3'ss of exon 4
----gtgttgttttactcttcctcaatagaatagtgttagttgatttgtacattgctctggattcttgttatttatcactaaattggctgctttcttgttgcagTCATTGTTGTGTGATCCAAACCCAAATTCACCAGCAAATTCTGAAGCTGCTCGGATGTTCAGCGAAAACAAGCGCGAATACAACAGAAAAGTACGCGAGA
    | || | |    ||||| |||   |  |   |           | |   ||     ||| | ||  |  | |  ||  |     ||  ||  || ||||||| ||| | || || |||||||| |||||||||||||| || || |||||||| |||| |||||| |||  ||| ||||| ||| | |  ||||||||||
gcgagagtggatggcttcttcttcagc-gtgtgcagccgaacacagcg-atgatgacgacgatgcgtgaaagctgtttctctaacacgtggctt--tggtgcagTCTTTGCTATGCGACCCAAACCCGAATTCACCAGCAAACTCGGAGGCTGCTCGCATGTACAGCGAGAACCGGCGTGAATATAACCGGAGGGTACGCGAGA

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|48575511|gb|CO036440.1|CO036440
EST:     ATCAGTGGAGCCCTATATATGATGTAGCTGCAATTCTTACCTCAATCCAG                         TCATTGTTGTGTGATCCAAACCCAAATTCACCAGCAAATTCTGAAGCTGCT
genomic: ATCAGTGGAGCCCTATATATGATGTAGCTGCAATTCTTACCTCAATCCAGgtaattgtga ... cttgttgcagTCATTGTTGTGTGATCCAAACCCAAATTCACCAGCAAATTCTGAAGCTGCT
EST: gi|192333434|gb|FK023963.1|FK023963
EST:     ATCAGTGGAGCCCTATATATGATGTAGCTGCAATTCTTACCTCAATCCAG                         TCATTGTTGTGTGATCCAAACCCAAATTCACCAGCAAATTCTGAAGCTGCT
genomic: ATCAGTGGAGCCCTATATATGATGTAGCTGCAATTCTTACCTCAATCCAGgtaattgtga ... cttgttgcagTCATTGTTGTGTGATCCAAACCCAAATTCACCAGCAAATTCTGAAGCTGCT
EST: gi|10233426|gb|BE802314.1|BE802314
EST:     ATCAGTGGAGCCCTATATATGATGTAGCTGCAATTCTTACCTCAATCCAG                         TCATTGTTGTGTGATCCAAACCCAAATTCACCAGCAAATTCTGAAGCTGCT
genomic: ATCAGTGGAGCCCTATATATGATGTAGCTGCAATTCTTACCTCAATCCAGgtaattgtga ... cttgttgcagTCATTGTTGTGTGATCCAAACCCAAATTCACCAGCAAATTCTGAAGCTGCT
EST: gi|6667965|gb|AW279416.1|AW279416
EST:     TGATGTAGCTGCAATTCTTACCTCAATCCAG                         TCATTGTTGTGTGATCCAAACCCAAATTCACCAGCAAATTCTGAAGCTGCT
genomic: TGATGTAGCTGCAATTCTTACCTCAATCCAGgtaattgtga ... cttgttgcagTCATTGTTGTGTGATCCAAACCCAAATTCACCAGCAAATTCTGAAGCTGCT
EST: gi|192297623|gb|FG989571.1|FG989571
EST:     ATCAGTGGAGCCCTATATATGATGTAGCTGCAATTCTTACCTCAATCCAG                         TCATTGTTGTGTGATCCAAACCCAAATTCACCAGCAAATTCTGAAGCTGCT
genomic: ATCAGTGGAGCCCTATATATGATGTAGCTGCAATTCTTACCTCAATCCAGgtaattgtga ... cttgttgcagTCATTGTTGTGTGATCCAAACCCAAATTCACCAGCAAATTCTGAAGCTGCT
EST: gi|10254514|gb|BE822280.1|BE822280
EST:     ATGATGTAGCTGCAATTCTTACCTCAATCCAG                         TCATTGTTGTGTGATCCAAACCCAAATTCACCAGCAAATTCTGAAGCTGCT
genomic: ATGATGTAGCTGCAATTCTTACCTCAATCCAGgtaattgtga ... cttgttgcagTCATTGTTGTGTGATCCAAACCCAAATTCACCAGCAAATTCTGAAGCTGCT
EST: gi|192306185|gb|FG995035.1|FG995035
EST:     ATCAGTGGAGCCCTATATATGATGTAGCTGCAATTCTTACCTCAATCCAG                         TCATTGTTGTGTGATCCAAACCCAAATTCACCAGCAAATTCTGAAGCTGCT
genomic: ATCAGTGGAGCCCTATATATGATGTAGCTGCAATTCTTACCTCAATCCAGgtaattgtga ... cttgttgcagTCATTGTTGTGTGATCCAAACCCAAATTCACCAGCAAATTCTGAAGCTGCT
EST: gi|192306775|gb|FG998142.1|FG998142
EST:     ATCAGTGGAGCCCTATATATGATGTAGCTGCAATTCTTACCTCAATCCAG                         TCATTGTTGTGTGATCCAAACCCAAATTCACCAGCAAATTCTGAAGCTGCT
genomic: ATCAGTGGAGCCCTATATATGATGTAGCTGCAATTCTTACCTCAATCCAGgtaattgtga ... cttgttgcagTCATTGTTGTGTGATCCAAACCCAAATTCACCAGCAAATTCTGAAGCTGCT
EST: gi|209721200|gb|BW665731.1|BW665731
EST:     ATCAGTGGAGCCCTATATATGATGTAGCTGCAATTCTTACCTCAATCCAG                         TCATTGTTGTGTGATCCAAACCCAAATTCACCAGCAAATTCTGAAGCTGCT
genomic: ATCAGTGGAGCCCTATATATGATGTAGCTGCAATTCTTACCTCAATCCAGgtaattgtga ... cttgttgcagTCATTGTTGTGTGATCCAAACCCAAATTCACCAGCAAATTCTGAAGCTGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acattgctctggattcttgttatttatcactaaattggctgctttcttgttgcagTCATTGTTGTGTGATCCAAACCCAAATTCACCAGCAAATTCTGAAGCTGCTCGGATGTTCAGCGAAAACAAGCGCGAATACAACAGAAAAGTACGCGAGA
                           cactaaa  putative branch site (score: 2)
                                      ctgctttctt  putative PPT
                   ttatttatcactaaat  TA-rich tract