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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATCCTCACAAGTGCTGTTCCACAGATAAAACCTGGGTTTGATCCTACCAAAGGACAAAGACCAGAGTTCTATTTTGATGATGGTGCATATCCTGAGCAGGtactattacagtttctgcattattcttaagtatttttttaaatttatccccctttttattcatattttaatgatttttacatattagg

Basic information

species Glycine max
transcript GLYMA18G39930.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G39930.1 (Glycine max), 5'ss of exon 2
lower sequence: Vv08s0007g00530.t01 (Vitis vinifera), 5'ss of exon 2
-ATCCTCACAAGTGCTGTTCCACAGATAAAACCTGGGTTTGATCCTACCAAAGGACAAAGACCAGAGTTCTATTTTGATGATGGTGCATATCCTGAGCAGGta-ctattacagtttctg-cattattcttaagtatttttttaaatttatccccctttttattcatattttaa--tgatttttacatattagg
 || |||||||||||||| ||   ||| ||||||||||||||||| || ||||| ||||| |||||||| |||||||| || || || | ||||||||||||| ||| |    | ||||   |||   |||   | ||| |    |  ||    |||||   | || ||  ||  |   ||||  || |||| 
AATTCTCACAAGTGCTGTGCCTAGGATGAAACCTGGGTTTGATCCAACTAAAGGTCAAAGGCCAGAGTTTTATTTTGAAGAAGGAGCCTTTCCTGAGCAGgtaactacttagttatctgattttaggattatagaatttctgttgtccatgtttcttttgccttatgttgaaagttttcttttttatgttag-
















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|208333137|gb|GE127414.1|GE127414
EST:     TGCATATCCTGAGCAGG                         TCGACTGGATTGGGCAGAAAAATCAAATAGATGCCG
genomic: TGCATATCCTGAGCAGGtactattaca ... acatattaggTTGACTGGATTGGGCAGAAAAATCAAATAGATGCCG
EST: gi|58019799|gb|CX706541.1|CX706541
EST:     AGGACAAAGACCAGAGTTCTATTTTGATGATGGTGCATATCCTGAGCAGG                         TTGACTGGATTGGGCAGAAAAATCAAATAGATGCCG
genomic: AGGACAAAGACCAGAGTTCTATTTTGATGATGGTGCATATCCTGAGCAGGtactattaca ... acatattaggTTGACTGGATTGGGCAGAAAAATCAAATAGATGCCG
EST: gi|193429904|gb|FK395552.1|FK395552
EST:     AGGACAAAGACCAGAGTTCTATTTTGATGATGGTGCATATCCTGAGCAGG                         TTGACTGGATTGGGCAGAAAAATCAAATAGATGCCG
genomic: AGGACAAAGACCAGAGTTCTATTTTGATGATGGTGCATATCCTGAGCAGGtactattaca ... acatattaggTTGACTGGATTGGGCAGAAAAATCAAATAGATGCCG
EST: gi|213620500|gb|DB957344.1|DB957344
EST:     AGGACAAAGACCAGAGTTCTATTTTGATGATGGTGCATATCCTGAGCAGG                         TTGACTGGATTGGGCAGAAAAATCAAATAGATGCCG
genomic: AGGACAAAGACCAGAGTTCTATTTTGATGATGGTGCATATCCTGAGCAGGtactattaca ... acatattaggTTGACTGGATTGGGCAGAAAAATCAAATAGATGCCG
EST: gi|193333926|gb|FK301314.1|FK301314
EST:     AGGACAAAGACCAGAGTTCTATTTTGATGATGGTGCATATCCTGAGCAGG                         TTGACTGGATTGGGCAGAAAAATCAAATAGATGCCG
genomic: AGGACAAAGACCAGAGTTCTATTTTGATGATGGTGCATATCCTGAGCAGGtactattaca ... acatattaggTTGACTGGATTGGGCAGAAAAATCAAATAGATGCCG
EST: gi|207782942|gb|GD754527.1|GD754527
EST:     AGGACAAAGACCAGAGTTCTATTTTGATGATGGTGCATATCCTGAGCAGG                         TTGACTGGATTGTGCAGAAAAATCAAATAGATGCCG
genomic: AGGACAAAGACCAGAGTTCTATTTTGATGATGGTGCATATCCTGAGCAGGtactattaca ... acatattaggTTGACTGGATTGGGCAGAAAAATCAAATAGATGCCG
EST: gi|193320346|gb|FK283991.1|FK283991
EST:     AGGACAAAGACCAGAGTTCTATTTTGATGATGGTGCATATCCTGAGCAGG                         TTGACTGGATTGGGCAGAAAAATCAAATAGATGCCG
genomic: AGGACAAAGACCAGAGTTCTATTTTGATGATGGTGCATATCCTGAGCAGGtactattaca ... acatattaggTTGACTGGATTGGGCAGAAAAATCAAATAGATGCCG
EST: gi|193436041|gb|FK401157.1|FK401157
EST:     AGGACAAAGACCAGAGTTCTATTTTGATGATGGTGCATATCCTGAGCAGG                         TTGACTGGATTGGGCAGAAAAAATCAAATAGATGCCG
genomic: AGGACAAAGACCAGAGTTCTATTTTGATGATGGTGCATATCCTGAGCAGGtactattaca ... acatattaggTTGACTGGATTGGGCAG-AAAAATCAAATAGATGCCG
EST: gi|151397652|gb|EV267525.1|EV267525
EST:     AGGACAAAGACCAGAGTTCTATTTTGATGATGGTGCATATCCTGAGCAGG                         TTGACTGGATTGGGCAGAAAAATCAAATAGATGCCG
genomic: AGGACAAAGACCAGAGTTCTATTTTGATGATGGTGCATATCCTGAGCAGGtactattaca ... acatattaggTTGACTGGATTGGGCAGAAAAATCAAATAGATGCCG
EST: gi|17023106|gb|BM094140.1|BM094140
EST:     AGGACAAAGACCAGAGTTCTATTTTGATGATGGTGCATATCCTGAGCAGG                         TTGACTGGATTGGGCAGAAAAATCAAATAGATGCCG
genomic: AGGACAAAGACCAGAGTTCTATTTTGATGATGGTGCATATCCTGAGCAGGtactattaca ... acatattaggTTGACTGGATTGGGCAGAAAAATCAAATAGATGCCG
EST: gi|207820378|gb|GD792832.1|GD792832
EST:     AGGACAAAGACCAGAGTTCTATTTTGATGATGGTGCATATCCTGAGCAGG                         TTGACTGGATTGGGCAGAAAAATCAAATAGATGCCG
genomic: AGGACAAAGACCAGAGTTCTATTTTGATGATGGTGCATATCCTGAGCAGGtactattaca ... acatattaggTTGACTGGATTGGGCAGAAAAATCAAATAGATGCCG
EST: gi|298174286|gb|HO017622.1|HO017622
EST:     AGGACAAAGACCAGAGTTCTATTTTGATGATGGTGCATATCCTGAGCAGG                         TTGACTGGATTGGGCAGAAAAATCAAATAGTTGCCG
genomic: AGGACAAAGACCAGAGTTCTATTTTGATGATGGTGCATATCCTGAGCAGGtactattaca ... acatattaggTTGACTGGATTGGGCAGAAAAATCAAATAGATGCCG
EST: gi|193726451|gb|FK661137.1|FK661137
EST:     AGGACAAAGACCAGAGTTCTATTTTGATGATGGTGCATATCCTGAGCAGG                         TTGACTGGATTGGGCAGAAAAATCAAATAGATGCCG
genomic: AGGACAAAGACCAGAGTTCTATTTTGATGATGGTGCATATCCTGAGCAGGtactattaca ... acatattaggTTGACTGGATTGGGCAGAAAAATCAAATAGATGCCG
EST: gi|58022869|gb|CX709610.1|CX709610
EST:     AGGACAAAGACCAGAGTTTTATTTTGATGATGGTGCATATCCTGAGCAGG                         TTGACTGGATTGGGCAGAAAAATCAAATAGATGCCG
genomic: AGGACAAAGACCAGAGTTCTATTTTGATGATGGTGCATATCCTGAGCAGGtactattaca ... acatattaggTTGACTGGATTGGGCAGAAAAATCAAATAGATGCCG
EST: gi|193349121|gb|FK315299.1|FK315299
EST:     AGGACAAAGACCAGAGTTCTATTTTGATGATGGTGCATATCCTGAGCAGG                         TTGACTGGATTGGGCAGAAAAATCAAATAGATGCCG
genomic: AGGACAAAGACCAGAGTTCTATTTTGATGATGGTGCATATCCTGAGCAGGtactattaca ... acatattaggTTGACTGGATTGGGCAGAAAAATCAAATAGATGCCG
EST: gi|193400899|gb|FK368820.1|FK368820
EST:     AGGACAAAGACCAGAGTTCTATTTTGATGATGGTGCATATCCTGAGCAGG                         TTGACTGGATTG
genomic: AGGACAAAGACCAGAGTTCTATTTTGATGATGGTGCATATCCTGAGCAGGtactattaca ... acatattaggTTGACTGGATTG
EST: gi|208073385|gb|GD867302.1|GD867302
EST:     AGGACAAAGACCAGAGTTCTATTTTGATGATGGTGCATATCCTGAGCAGG                         TTGACTGGATTGGGCAGAAAAATCAAATAGATGCCG
genomic: AGGACAAAGACCAGAGTTCTATTTTGATGATGGTGCATATCCTGAGCAGGtactattaca ... acatattaggTTGACTGGATTGGGCAGAAAAATCAAATAGATGCCG
EST: gi|192327079|gb|FK015471.1|FK015471
EST:     AGGACAAAGACCAGAGTTCTATTTTGATGATGGTGCATATCCTGAGCAGG                         TTGACTGGATTGGGCAGAAAAATCAAATAGATGCCG
genomic: AGGACAAAGACCAGAGTTCTATTTTGATGATGGTGCATATCCTGAGCAGGtactattaca ... acatattaggTTGACTGGATTGGGCAGAAAAATCAAATAGATGCCG
EST: gi|58016336|gb|CX703078.1|CX703078
EST:     AGGACAAAGACCAGAGTTCTATTTTGATGATGGTGCATATCCTGAGCAGG                         TTGACTGGATTGGGCAGAAAAATCAAATAGATGCCG
genomic: AGGACAAAGACCAGAGTTCTATTTTGATGATGGTGCATATCCTGAGCAGGtactattaca ... acatattaggTTGACTGGATTGGGCAGAAAAATCAAATAGATGCCG
EST: gi|193415735|gb|FK381437.1|FK381437
EST:     AGGACAAAGACCAGAGTTCTATTTTGATGATGGTGCATATCCTGAGCAGG                         TTGACTGGATTGGGCAGAAAAATCAAATAGATGCCG
genomic: AGGACAAAGACCAGAGTTCTATTTTGATGATGGTGCATATCCTGAGCAGGtactattaca ... acatattaggTTGACTGGATTGGGCAGAAAAATCAAATAGATGCCG
EST: gi|193354431|gb|FK321179.1|FK321179
EST:     AGGACAAAGACCAGAGTTCTATTTTGATGATGGTGCATATCCTGAGCAGG                         TTGACTGGATTGGGCAGAAAAATCAAATAGATGCCG
genomic: AGGACAAAGACCAGAGTTCTATTTTGATGATGGTGCATATCCTGAGCAGGtactattaca ... acatattaggTTGACTGGATTGGGCAGAAAAATCAAATAGATGCCG
EST: gi|193436727|gb|FK399528.1|FK399528
EST:     AGGACAAAGACCAGAGTTCTATTTTGATGATGGTGCATATCCTGAGCAGG                         TTGACTGGATTGGGCAGAAAAATCAAATAGATGCCG
genomic: AGGACAAAGACCAGAGTTCTATTTTGATGATGGTGCATATCCTGAGCAGGtactattaca ... acatattaggTTGACTGGATTGGGCAGAAAAATCAAATAGATGCCG
EST: gi|58019388|gb|CX706130.1|CX706130
EST:     AGGACAAAGACCAGAGTTCTATTTTGATGATGGTGCATATCCTGAGCAGG                         TTGACTGGATTGGGCAGAAAAATCAAATAGATGCCG
genomic: AGGACAAAGACCAGAGTTCTATTTTGATGATGGTGCATATCCTGAGCAGGtactattaca ... acatattaggTTGACTGGATTGGGCAGAAAAATCAAATAGATGCCG
EST: gi|7028397|gb|AW458180.1|AW458180
EST:     AGGACAAAGACCAGAGTTCTATTTTGATGATGGTGCATATCCTGAGCAGG                         TTGACTGGATTGGGCAGAAAAATCAAATAGATGCCG
genomic: AGGACAAAGACCAGAGTTCTATTTTGATGATGGTGCATATCCTGAGCAGGtactattaca ... acatattaggTTGACTGGATTGGGCAGAAAAATCAAATAGATGCCG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATCCTCACAAGTGCTGTTCCACAGATAAAACCTGGGTTTGATCCTACCAAAGGACAAAGACCAGAGTTCTATTTTGATGATGGTGCATATCCTGAGCAGGtactattacagtttctgcattattcttaagtatttttttaaatttatccccctttttattcatattttaatgatttttacatattagg

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