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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGAGAAAGAGATTGGAGCAAAATTTGAGGAGGACCTTGATGCAATGCTTCCAAAGTGTGATGTGATTGTTATCAACACCCCTCTCACTGAGCAGACAAGgtatacttttaaatttaacatctcagtcaatcagaaaaattattttagacttgaaatctcaagccacttataattttcaaaattattatcatgagaagtgcattatcagtattattcatatcacaaggaataaattgtttgatcatgttccagagatgagtagtaaccaaagatttctgtgattcag

Basic information

species Glycine max
transcript GLYMA19G01210.2
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G01210.2 (Glycine max), 5'ss of exon 4
lower sequence: LOC_Os06g29180.1 (Oryza sativa), 5'ss of exon 3
TGGAGAAAGAGATTGGAGCAAAATTTGAGGAGGACCTTGATGCAATGCTTCCAAAGTGTGATGTGATTGTTATCAACACCCCTCTCACTGAGCAGACAAGgtatacttttaaatttaacatctcagtcaatcagaaaaattattttagacttgaaatctcaagccacttataattttcaaaattattatcatgagaagtgcattatcagtattattcatatcacaaggaataaattgtttgatcatgttccagagatgagtagtaaccaaagatttctgtgattcag
| |||||||| ||||| || |||| ||| ||||| || ||||| |||||||||||||||||||| ||||| ||||| || ||||| || ||| | |||||||    |  | |   |   ||    ||   |   ||||    |  || || |   |  || |   |  |  | |||  |  ||| || || | ||                                                                                            
TTGAGAAAGAAATTGGGGCCAAATATGAAGAGGATCTCGATGCTATGCTTCCAAAGTGTGATGTCATTGTGATCAATACACCTCTTACAGAGAAAACAAGgt----tcctgatgatcgtattcttgtttgttgcaaaa----tcatatacatagtacatctacttatctgaactttgtatgattctt-tcttcag--------------------------------------------------------------------------------------------

upper sequence: GLYMA19G01210.2 (Glycine max), 5'ss of exon 4
lower sequence: LOC_Os06g29220.1 (Oryza sativa), 5'ss of exon 4
TGGAGAAAGAGATTGGAGCAAAATTTGAGGAGGACCTTGATGCAATGCTTCCAAAGTGTGATGTGATTGTTATCAACACCCCTCTCACTGAGCAGACAAGgtatacttttaaatttaacatctcagtcaatcagaaaaattattttagacttgaaatctcaagccacttataattttcaaaattattatcatgagaagtgcattatcagtattattcatatcacaaggaataaattgtttgatcatgttccagagatgagtagtaaccaaagatttctgtgattcag
| ||||| |||||||| || || | ||||||||| || ||||| ||||||||||||||||||||  |||| |||||||  ||||| || ||| | ||||||| ||   |      |  | |    ||  ||      ||   || |   || | |   |   | |   | | | |||  |   | || |  | ||                                                                                            
TTGAGAAGGAGATTGGGGCCAAGTATGAGGAGGATCTCGATGCCATGCTTCCAAAGTGTGATGTCGTTGTGATCAACATGCCTCTTACGGAGAAAACAAGgtttatcgtccttcattgcgttcttgtttattgttccaaaatttctgtgctagcacatt---gtcttatctgaatttgtatgcttttttgttcag--------------------------------------------------------------------------------------------

upper sequence: GLYMA19G01210.2 (Glycine max), 5'ss of exon 4
lower sequence: GRMZM2G049811_T01 (Zea mays), 5'ss of exon 3
TGGAGAAAGAGATTGGAGCAAAATTTGAGGAGGACCTTGATGCAATGCTTCCAAAGTGTGATGTGATTGTTATCAACACCCCTCTCACTGAGCAGACAAGgtatacttttaaatttaacatctcagtcaatcagaaaaattattttagacttgaaatctcaagccacttataattttcaaaattattatcatgagaagtgcattatcagtattattcatatcacaaggaataaattgtttgatcatgttccagagatgagtagtaaccaaagatttctgtgattcag
| |||||||| ||||| || ||||||||||||||||| ||||| |||||||||||||||||||||||||| |||||||| ||||| || ||| | ||||||| |   || |   |  || |  || |     |  |   | |   ||   |   | | |         | |  ||||||                                                                                                            
TTGAGAAAGAAATTGGGGCCAAATTTGAGGAGGACCTGGATGCTATGCTTCCAAAGTGTGATGTGATTGTGATCAACACACCTCTTACGGAGAAAACAAGgtttgtattcatcatgtacctgacatttccaaaatagtttgacaatattttctgagttttgtttgctgtttttttttcag-----------------------------------------------------------------------------------------------------------

upper sequence: GLYMA19G01210.2 (Glycine max), 5'ss of exon 4
lower sequence: GRMZM2G147714_T01 (Zea mays), 5'ss of exon 4
TGGAGAAAGAGATTGGAGCAAAATTTGAGGAGGACCTTGATGCAATGCTTCCAAAGTGTGATGTGATTGTTATCAACACCCCTCTCACTGAGCAGACAAGgtatacttttaaatttaacatctcagtcaatcagaaaaattattttagacttgaaatctcaagccacttataattttcaaaattattatcatgagaagtgcattatcagtattattcatatcacaaggaataaattgtttgatcatgttccagagatgagtagtaaccaaagatttctgtgattcag
| |||||||| ||||| || ||||||||||||||||| ||||| |||||||||||||||||||||||||| |||||||| ||||| || ||| | ||||||| |   || |   |  || |  || |     |  |   | |   ||   |   | | |         | |  ||||||                                                                                                            
TTGAGAAAGAAATTGGGGCCAAATTTGAGGAGGACCTGGATGCTATGCTTCCAAAGTGTGATGTGATTGTGATCAACACACCTCTTACGGAGAAAACAAGgtttgtattcatcatgtacctgacatttccaaaatagtttgacagtattttctgagttttgtttgctgtttttttttcag-----------------------------------------------------------------------------------------------------------

upper sequence: GLYMA19G01210.2 (Glycine max), 5'ss of exon 4
lower sequence: GRMZM2G423972_T02 (Zea mays), 5'ss of exon 2
TGGAGAAAGAGATTGGAGCAAAATTTGAGGAGGACCTTGATGCAATGCTTCCAAAGTGTGATGTGATTGTTATCAACACCCCTCTCACTGAGCAGACAAGgtatacttttaaatttaacatctcagtcaatcagaaaaattattttagacttgaaatctcaagccacttataattttcaaaattattatcatgagaagtgcattatcagtattattcatatcacaaggaataaattgtttgatcatgttccagagatgagtagtaaccaaagatttctgtgattcag
| |||||||| ||||| || ||||||||||||||||| ||||| |||||||||||||||||||||||||| |||||||| ||||| || ||| | ||||||| |   || |   |  || |  || |     |  |   | |   ||   |   | | |       ||  |  ||||||                                                                                                            
TTGAGAAAGAAATTGGGGCCAAATTTGAGGAGGACCTGGATGCTATGCTTCCAAAGTGTGATGTGATTGTGATCAACACACCTCTTACGGAGAAAACAAGgtttgtattcaccatgtacctgacatttccaaaatagtctgacagtattttctgagttttgt-ttgctgttttttttcag-----------------------------------------------------------------------------------------------------------

upper sequence: GLYMA19G01210.2 (Glycine max), 5'ss of exon 4
lower sequence: GRMZM2G362021_T01 (Zea mays), 5'ss of exon 4
TGGAGAAAGAGATTGGAGCAAAATTTGAGGAGGACCTTGATGCAATGCTTCCAAAGTGTGATGTGATTGTTATCAACACCCCTCTCACTGAGCAGACAAGgtatacttttaaatttaacatctcagtcaatcagaaaaattattttagacttgaaatctcaagccacttataattttcaaaattattatcatgagaagtgcattatcagtattattcatatcacaaggaataaattgtttgatcatgttccagagatgagtagtaaccaaagatttctgtgattcag
| |||||||| ||||| || ||||||||||||||||| ||||| |||||||||||||||||||||||||| |||||||| ||||| || ||| | ||||||| |   || |   |  || |  || |     |  |   | |   ||   |   | | |       ||  |  ||||||                                                                                                            
TTGAGAAAGAAATTGGGGCCAAATTTGAGGAGGACCTGGATGCTATGCTTCCAAAGTGTGATGTGATTGTGATCAACACACCTCTTACGGAGAAAACAAGgtttgtattcatcatgtacctgacatttccaaaatagtttgacagtattttctgagttttgt-ttgctgttttttttcag-----------------------------------------------------------------------------------------------------------

upper sequence: GLYMA19G01210.2 (Glycine max), 5'ss of exon 4
lower sequence: GRMZM2G124919_T01 (Zea mays), 5'ss of exon 4
TGGAGAAAGAGATTGGAGCAAAATTTGAGGAGGACCTTGATGCAATGCTTCCAAAGTGTGATGTGATTGTTATCAACACCCCTCTCACTGAGCAGACAAGgtatacttttaaatttaacatctcagtcaatcagaaaaattattttagacttgaaatctcaagccacttataattttcaaaattattatcatgagaagtgcattatcagtattattcatatcacaaggaataaattgtttgatcatgttccagagatgagtagtaaccaaagatttctgtgattcag
| |||||||| ||||| |  ||||||||||||||||| ||||| |||||||||||||||||||||||||| |||||||| ||||| || ||| | ||||||| |   || |   |  || |  || |     |  |   | |   ||   |   | | |         | |  ||||||                                                                                                            
TTGAGAAAGAAATTGGGGTCAAATTTGAGGAGGACCTGGATGCTATGCTTCCAAAGTGTGATGTGATTGTGATCAACACACCTCTTACGGAGAAAACAAGgtttgtattcatcatgtacctgacatttccaaaatagtttgacagtattttctgagttttgtttgctgtttttttttcag-----------------------------------------------------------------------------------------------------------

upper sequence: GLYMA19G01210.2 (Glycine max), 5'ss of exon 4
lower sequence: GRMZM2G418005_T01 (Zea mays), 5'ss of exon 2
TGGAGAAAGAGATTGGAGCAAAATTTGAGGAGGACCTTGATGCAATGCTTCCAAAGTGTGATGTGATTGTTATCAACACCCCTCTCACTGAGCAGACAAGgtatacttttaaatttaacatctcagtcaatcagaaaaattattttagacttgaaatctcaagccacttataattttcaaaattattatcatgagaagtgcattatcagtattattcatatcacaaggaataaattgtttgatcatgttccagagatgagtagtaaccaaagatttctgtgattcag
| |||||||| ||||| || ||||||||||||||||| ||||| ||||||||||||| |||||||||||| |||||||| ||||| || ||| | ||||||| |   || |   |  || |  || |     |  |   | |   ||   |   | | |       ||  |  ||||||                                                                                                            
TTGAGAAAGAAATTGGGGCCAAATTTGAGGAGGACCTGGATGCTATGCTTCCAAAGTTTGATGTGATTGTGATCAACACACCTCTTACGGAGAAAACAAGgtttgtattcatcatgtacctgacatttccaaaatagtttgacagtattttctgagttttgt-ttgctgttttttttcag-----------------------------------------------------------------------------------------------------------

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|42722748|gb|CK768647.1|CK768647
EST:     CCAAAGTGTGATGTGATTGTTATCAACACCCCTCTCACTGAGCAGACAAG                         GGGATTGTTTGACAAANATAGAATTGCTAAGTGCAAGAAAGGTGTCTTGAT
genomic: CCAAAGTGTGATGTGATTGTTATCAACACCCCTCTCACTGAGCAGACAAGgtatactttt ... tgtgattcagGGGATTGTTTGACAAAAATAGAATTGCTAAGTGCAAGAAAGGTGTCTTGAT
EST: gi|13478163|gb|BG507754.1|BG507754
EST:     CCAAAGTGTGATGTGATTGTTATCAACACCCCTCTCACTGAGCAGACAAG                         GGGATTGTTTGACAAAAATAGAATTGCTAAGTGCAAGAAAGGTGTCTTGAT
genomic: CCAAAGTGTGATGTGATTGTTATCAACACCCCTCTCACTGAGCAGACAAGgtatactttt ... tgtgattcagGGGATTGTTTGACAAAAATAGAATTGCTAAGTGCAAGAAAGGTGTCTTGAT
EST: gi|7232402|gb|AW567758.1|AW567758
EST:     CCAAAGTGTGATGTGATTGTTATCAACACCCCTCTCACTGAGCAGACAAG                         GGGATTGTTTGAC
genomic: CCAAAGTGTGATGTGATTGTTATCAACACCCCTCTCACTGAGCAGACAAGgtatactttt ... tgtgattcagGGGATTGTTTGAC
EST: gi|9986235|gb|BE660343.1|BE660343
EST:     CAAAGTGTGATGTGATTGTTATCAACACCCCTCTCACTGAGCATGACANG                         GGGATTGTTTGACAAAAATAGAATTGCTAAGTGCAAGAAANGTGTCTTGA
genomic: CAAAGTGTGATGTGATTGTTATCAACACCCCTCTCACTGAGCA-GACAAGgtatactttt ... tgtgattcagGGGATTGTTTGACAAAAATAGAATTGCTAAGTGCAAGAAAGGTGTCTTGA
EST: gi|11687585|gb|BF595261.1|BF595261
EST:     CCAAAGTGTGATGTGATTGTTATCAACACCCCTCTCACTGAGCAGACAAG                         GGGATTGTTTGACAAAAATAGAATTGCTAAGTGCAAGAAAAGTGTCTTGAT
genomic: CCAAAGTGTGATGTGATTGTTATCAACACCCCTCTCACTGAGCAGACAAGgtatactttt ... tgtgattcagGGGATTGTTTGACAAAAATAGAATTGCTAAGTGCAAGAAAGGTGTCTTGAT
EST: gi|8285757|gb|BE023316.1|BE023316
EST:     CCAAAGTGTGATGTGATTGTTATCAACACCCCTCTCACTGAGCAGACAAG                         GGGATTGTTTGACAAAAATAGAATTGCTAANTGCCAGAAAGGTGTCTTGAT
genomic: CCAAAGTGTGATGTGATTGTTATCAACACCCCTCTCACTGAGCAGACAAGgtatactttt ... tgtgattcagGGGATTGTTTGACAAAAATAGAATTGCTAAGTGCAAGAAAGGTGTCTTGAT
EST: gi|42722674|gb|CK768573.1|CK768573
EST:     CCAAAGTGTGATGTGATTGTTATCAACACCCCTCTCACTGAGCAGACAAG                         GGGATTGTTTGACAAAAATAGAATTGCTAAGTGCAAGAAAGGTGTCTTGAT
genomic: CCAAAGTGTGATGTGATTGTTATCAACACCCCTCTCACTGAGCAGACAAGgtatactttt ... tgtgattcagGGGATTGTTTGACAAAAATAGAATTGCTAAGTGCAAGAAAGGTGTCTTGAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGGAGAAAGAGATTGGAGCAAAATTTGAGGAGGACCTTGATGCAATGCTTCCAAAGTGTGATGTGATTGTTATCAACACCCCTCTCACTGAGCAGACAAGgtatacttttaaatttaacatctcagtcaatcagaaaaattattttagacttgaaatctcaagccacttataattttcaaaattattatcatgagaagtgcattatcagtattattcatatcacaaggaataaattgtttgatcatgttccagagatgagtagtaaccaaagatttctgtgattcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG