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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atgcttacttcataacttgtaccaaataatatgtaccatttatattgcttgggagaatgtatggaaattgactctttgatgccatgttttccttgaacagATACAAAAATGCCAAAAGTAAAGACAAATCGTGTTAAATACCCAGAGGGCTGGGAATTAATTGAGCCTACACTCCGTGAACTTCAAGCAAAGATGAGGGA

Basic information

species Glycine max
transcript GLYMA08G11450.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G11450.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv05s0020g01520.t01 (Vitis vinifera), 3'ss of exon 1
atgcttacttcataacttgtaccaaataatatgtaccattt--atattgcttgggagaatgtatggaaattgactctttgatgccatgttttc--cttgaaca--gATACAAAAATGCCAAAAGTAAAGACAAATCGTGTTAAATACCCAGAGGGCTGGGAATTAATTGAGCCTACACTCCGTGAACTTCAAGCAAAGATGAGGGA--
         |  |||    |   ||||  || | |  ||||  | |  || |  |  ||  | |   |  |  ||  |  ||   || ||  |   ||||       || || |||||| || || |||||||| ||||| || |||||||||||||||||||| || ||||| || || |||||||| |||| ||||||||| ||  
---------tattaaggaattaaaaattttaggaattatttggacaaagcctacgt-aacctgtatcaggtttcttatcaatcttattttaccaatttgattgtcattagAATAATGCCGAAGGTGAAGACAAACCGTGTCAAGTACCCAGAGGGCTGGGAATTGATAGAGCCCACTCTTCGTGAACTACAAGGAAAGATGAGAGAAG
















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|298170809|gb|HO015785.1|HO015785
EST:     AATCGAGTCACAGACTAGAGCTAAATCAGCATAGAG                         ATACAAAAATGCCAAAAGTAAAGACAAATCGTGTTAAATACCCAGAGGGCT
genomic: AATCGAGTCACAGACTAGAGCTAAATCAGCATAGAGgtacgcgtca ... ccttgaacagATACAAAAATGCCAAAAGTAAAGACAAATCGTGTTAAATACCCAGAGGGCT
EST: gi|151400058|gb|EV269872.1|EV269872
EST:     AATCGAGTCACAGACTAGAGCTAAATCAGCATAGAG                         ATACAAAAATGCCAAAAGTAAAGACAAATCGTGTTAAATACCCAGAGGGCT
genomic: AATCGAGTCACAGACTAGAGCTAAATCAGCATAGAGgtacgcgtca ... ccttgaacagATACAAAAATGCCAAAAGTAAAGACAAATCGTGTTAAATACCCAGAGGGCT
EST: gi|298191433|gb|HO038912.1|HO038912
EST:     AATCGAGTCACAGACTAGAGCTAAATCAGCATAGAG                         ATACAAAAATGCCAAAAGTAAAGACAAATCGTGTTAAATACCCAGAGGGCT
genomic: AATCGAGTCACAGACTAGAGCTAAATCAGCATAGAGgtacgcgtca ... ccttgaacagATACAAAAATGCCAAAAGTAAAGACAAATCGTGTTAAATACCCAGAGGGCT
EST: gi|15815296|gb|BI787571.1|BI787571
EST:     AATCGAGTCACAGACTAGAGCTAAATCAGCATAGAG                         ATACAAAAATGCCAAAAGTAAAGACAAATCGTGTTAAATACCCAGAGGGCT
genomic: AATCGAGTCACAGACTAGAGCTAAATCAGCATAGAGgtacgcgtca ... ccttgaacagATACAAAAATGCCAAAAGTAAAGACAAATCGTGTTAAATACCCAGAGGGCT
EST: gi|192332719|gb|FK025376.1|FK025376
EST:     GAATCGAGTCACAGACTAGAGCTAAATCAGCATAGAG                         ATACAAAAATGCCAAAAGTAAAGACAAATCGTGTTAAATACCCAGAGGGCT
genomic: GAATCGAGTCACAGACTAGAGCTAAATCAGCATAGAGgtacgcgtca ... ccttgaacagATACAAAAATGCCAAAAGTAAAGACAAATCGTGTTAAATACCCAGAGGGCT
EST: gi|298190003|gb|HO032124.1|HO032124
EST:     AATCGAGTCACAGACTAGAGCTAAATCAGCATAGAG                         ATACAAAAATGCCAAAAGTAAAGACAAATCGTGTTAAATACCCAGAGGGCT
genomic: AATCGAGTCACAGACTAGAGCTAAATCAGCATAGAGgtacgcgtca ... ccttgaacagATACAAAAATGCCAAAAGTAAAGACAAATCGTGTTAAATACCCAGAGGGCT
EST: gi|192328777|gb|FK023221.1|FK023221
EST:     AATCGAGTCACAGACTAGAGCTAAATCAGCATAGAG                         ATACAAAAATGCCAAAAGTAAAGACAAATCGTGTTAAATACCCAGAGGGCT
genomic: AATCGAGTCACAGACTAGAGCTAAATCAGCATAGAGgtacgcgtca ... ccttgaacagATACAAAAATGCCAAAAGTAAAGACAAATCGTGTTAAATACCCAGAGGGCT
EST: gi|208176730|gb|GD975157.1|GD975157
EST:     AGCTAAATCAGCATAGAG                         ATACAAAAATGCCAAAAGTAAAGACAAATCGTGTTAAATACCCAGAGGGCT
genomic: AGCTAAATCAGCATAGAGgtacgcgtca ... ccttgaacagATACAAAAATGCCAAAAGTAAAGACAAATCGTGTTAAATACCCAGAGGGCT
EST: gi|192326862|gb|FK015119.1|FK015119
EST:     AATCGAGTCACAGACTAGAGCTAAATCAGCATAGAG                         ATACAAAAATGCCAAAAGTAAAGACAAATCGTGTTAAATACCCAGAGGGCT
genomic: AATCGAGTCACAGACTAGAGCTAAATCAGCATAGAGgtacgcgtca ... ccttgaacagATACAAAAATGCCAAAAGTAAAGACAAATCGTGTTAAATACCCAGAGGGCT
EST: gi|192333383|gb|FK024360.1|FK024360
EST:     AGAATCGAGTCACAGACTAGAGCTAAATCAGCATAGAG                         ATACAAAAATGCCAAAAGTAAAGACAAATCGTGTTAAATACCCAGAGGGCT
genomic: AGAATCGAGTCACAGACTAGAGCTAAATCAGCATAGAGgtacgcgtca ... ccttgaacagATACAAAAATGCCAAAAGTAAAGACAAATCGTGTTAAATACCCAGAGGGCT
EST: gi|193520782|gb|FK482889.1|FK482889
EST:     AATCGAGTCACAGACTAGAGCTAAATCAGCATAGAG                         ATACAAAAATGCCAAAAGTAAAGACAAATCGTGTTAAATACCCAGAGGGCT
genomic: AATCGAGTCACAGACTAGAGCTAAATCAGCATAGAGgtacgcgtca ... ccttgaacagATACAAAAATGCCAAAAGTAAAGACAAATCGTGTTAAATACCCAGAGGGCT
EST: gi|298195326|gb|HO039157.1|HO039157
EST:     AATCGAGTCACAGACTAGAGCTAAATCAGCATAGAG                         ATACAAAAATGCCAAAAGTAAAGACAAATCGTGTTAAATACCCAGAGGGCC
genomic: AATCGAGTCACAGACTAGAGCTAAATCAGCATAGAGgtacgcgtca ... ccttgaacagATACAAAAATGCCAAAAGTAAAGACAAATCGTGTTAAATACCCAGAGGGCT
EST: gi|21888083|gb|BQ741296.1|BQ741296
EST:     AATCGAGTCACAGACTAGAGCTAAATCAGCATAGAG                         ATACAAAAATGCCAAAAGTAAAGACAAATCGTGTTAAATACCCAGAGGGCT
genomic: AATCGAGTCACAGACTAGAGCTAAATCAGCATAGAGgtacgcgtca ... ccttgaacagATACAAAAATGCCAAAAGTAAAGACAAATCGTGTTAAATACCCAGAGGGCT
EST: gi|298174700|gb|HO014731.1|HO014731
EST:     AATCGAGTCACAGACTAGAGCTAAATCAGCATAGAG                         ATACAAAAATGCCAAAAGTAAAGACAAATCGTGTTAAATACCCAGAGGGCT
genomic: AATCGAGTCACAGACTAGAGCTAAATCAGCATAGAGgtacgcgtca ... ccttgaacagATACAAAAATGCCAAAAGTAAAGACAAATCGTGTTAAATACCCAGAGGGCT
EST: gi|151393942|gb|EV263813.1|EV263813
EST:     AATCGAGTCACAGACTAGAGCTAAATCAGCATAGAG                         ATACAAAAATGCCAAAAGTAAAGACAAATCGTGTTAAATACCCAGAGGGCT
genomic: AATCGAGTCACAGACTAGAGCTAAATCAGCATAGAGgtacgcgtca ... ccttgaacagATACAAAAATGCCAAAAGTAAAGACAAATCGTGTTAAATACCCAGAGGGCT
EST: gi|298187336|gb|HO034485.1|HO034485
EST:     AATCGAGTCACAGACTAGAGCTAAATCAGCATAGAG                         ATACAAAAATGCCAAAAGTAAAGACAAATCGTGTTAAATACCCAGAGGGCT
genomic: AATCGAGTCACAGACTAGAGCTAAATCAGCATAGAGgtacgcgtca ... ccttgaacagATACAAAAATGCCAAAAGTAAAGACAAATCGTGTTAAATACCCAGAGGGCT
EST: gi|151398055|gb|EV267933.1|EV267933
EST:     AATCGAGTCACAGACTAGAGCTAAATCAGCATAGAG                         ATACAAAAATGCCAAAAGTAAAGACAAATCGTGCTAAATACCCAGAGGGCT
genomic: AATCGAGTCACAGACTAGAGCTAAATCAGCATAGAGgtacgcgtca ... ccttgaacagATACAAAAATGCCAAAAGTAAAGACAAATCGTGTTAAATACCCAGAGGGCT
EST: gi|193670504|gb|FK610374.1|FK610374
EST:     AATCGAGTCACAGACTAGAGCTAAATCAGCATAGAG                         ATACAAAAATGCCAAAAGTAAAGACAAATCGTGTTAAATACCCAGAGGGCT
genomic: AATCGAGTCACAGACTAGAGCTAAATCAGCATAGAGgtacgcgtca ... ccttgaacagATACAAAAATGCCAAAAGTAAAGACAAATCGTGTTAAATACCCAGAGGGCT
EST: gi|298179222|gb|HO027693.1|HO027693
EST:     AATCGAGTCACAGACTAGAGCTAAATCAGCATAGAG                         ATACAAAAATGCCAAAAGTAAAGACAAATCGTGTTAAATACCCAGAGGGCT
genomic: AATCGAGTCACAGACTAGAGCTAAATCAGCATAGAGgtacgcgtca ... ccttgaacagATACAAAAATGCCAAAAGTAAAGACAAATCGTGTTAAATACCCAGAGGGCT
EST: gi|192325336|gb|FK018337.1|FK018337
EST:     AATCGAGTCACAGACTAGAGCTAAATCAGCATAGAG                         ATACAAAAATGCCAAAAGTAAAGACAAATCGTGTTAAATACCCAGAGGGCT
genomic: AATCGAGTCACAGACTAGAGCTAAATCAGCATAGAGgtacgcgtca ... ccttgaacagATACAAAAATGCCAAAAGTAAAGACAAATCGTGTTAAATACCCAGAGGGCT
EST: gi|192322389|gb|FK014870.1|FK014870
EST:     AATCGAGTCACAGACTAGAGCTAAATCAGCATAGAG                         ATACAAAAATGCCAAAAGTAAAGACAAATCGTGTTAAATACCCAGAGGGCT
genomic: AATCGAGTCACAGACTAGAGCTAAATCAGCATAGAGgtacgcgtca ... ccttgaacagATACAAAAATGCCAAAAGTAAAGACAAATCGTGTTAAATACCCAGAGGGCT
EST: gi|15664938|gb|BI702309.1|BI702309
EST:     AATCGAGTCACAGACTAGAGCTAAATCAGCATAGAG                         ATACAAAAATGCCAAAAGTAAAGACAAATCGTGTTAAATACCCAGAGGGCT
genomic: AATCGAGTCACAGACTAGAGCTAAATCAGCATAGAGgtacgcgtca ... ccttgaacagATACAAAAATGCCAAAAGTAAAGACAAATCGTGTTAAATACCCAGAGGGCT
EST: gi|208032269|gb|GD832239.1|GD832239
EST:     ACTAGAGCTAAATCAGCATAGAG                         ATACAAAAATGCCAAAAGTAAAGACAAATCGTGTTAAATACCCAGAGGGCT
genomic: ACTAGAGCTAAATCAGCATAGAGgtacgcgtca ... ccttgaacagATACAAAAATGCCAAAAGTAAAGACAAATCGTGTTAAATACCCAGAGGGCT
EST: gi|192332718|gb|FK025375.1|FK025375
EST:     AATCGAGTCACAGACTAGAGCTAAATCAGCATAGAG                         ATACAAAAATGCCAAAAGTAAAGACAAATCGTGTTAAATACCCAGAGGGCT
genomic: AATCGAGTCACAGACTAGAGCTAAATCAGCATAGAGgtacgcgtca ... ccttgaacagATACAAAAATGCCAAAAGTAAAGACAAATCGTGTTAAATACCCAGAGGGCT
EST: gi|193438011|gb|FK403136.1|FK403136
EST:     AATCGAGTCACAGACTAGAGCTAAATCAGCATAGAG                         ATACAAAAATGCCAAAAGTAAAGACAAATCGTGTTAAATACCCAGAGGGCT
genomic: AATCGAGTCACAGACTAGAGCTAAATCAGCATAGAGgtacgcgtca ... ccttgaacagATACAAAAATGCCAAAAGTAAAGACAAATCGTGTTAAATACCCAGAGGGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcttgggagaatgtatggaaattgactctttgatgccatgttttccttgaacagATACAAAAATGCCAAAAGTAAAGACAAATCGTGTTAAATACCCAGAGGGCTGGGAATTAATTGAGCCTACACTCCGTGAACTTCAAGCAAAGATGAGGGA
                                       tgttttcctt  CT-rich tract
          aatgtat  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atgcttacttcataacttgtaccaaataatatgtaccatttatattgcttgggagaatgtatggaaattgactctttgatgccatgttttccttgaacagATACAAAAATGCCAAAAGTAAAGACAAATCGTGTTAAATACCCAGAGGGCTGGGAATTAATTGAGCCTACACTCCGTGAACTTCAAGCAAAGATGAGGGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG