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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctcaagtgtggtttactttgatgtctctttctattttgtacgctttaatctcatctcatcagtttcccgcttcacacacaacacgtgcaactgatgacagTTTGTTGGAGAGTTAGCTCGGGTAGCAGCACCAGGTGCCACTATAATAATAGTAACATGGTGCCACAGGGATCTTGGCCCTGACGAACAATCCTTACATC

Basic information

species Glycine max
transcript GLYMA12G01690.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G01690.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv16s0039g01410.t01 (Vitis vinifera), 3'ss of exon 3
-------------------------------------------------------ctcaagtgtggtttact---ttgatgtctctttctattttgtacgctttaatctcatctcatcagtttcccgcttcacac-acaacacgtgcaactgatgac------agTTTGTTGGAGAGTTAGCTCGGGTAGCAGCACCAGGTGCCACTATAATAATAGTAACATGGTGCCACAGGGATCTTGGCCCTGACGAACAATCCTTACATC
                                                        |  | | || || | |      ||  || |   || |||  | | | |  | |    |  |  |  |   |  | |    |    || ||    || || |      |||||||| | ||||| ||||| || | ||| ||||||| ||| |||||| | |||||||||||||| ||||||||   ||||   ||| |||||||| | |
gtggattcttctcactttcactctcacactttgtattttgatcatattacattccttggattttgattcattgaacaaatacctatgcttaattttcatgttattgtattggttgctgtggatgttgacttatgttattctacttgattttgttggctttgtcagTTTGTTAGTGAGTTGGCTCGAGTTGTAGCCCCAGGTGGCACAATAATACTTGTAACATGGTGCCATAGGGATCTCTCCCCTTCTGAAGAATCCTTAAAGC
















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|20498613|gb|BQ273543.1|BQ273543
EST:     ATCTGGTGTGGTCCATGGAGAGTGGAGAGCATATGCCTGACAAAGCTAAG                         TTTGTTGGAGAGTTAGCTCGGGTAGCAGCACCAGGTGCCACTATAATAATA
genomic: ATCTGGTGTGGTCCATGGAGAGTGGAGAGCATATGCCTGACAAAGCTAAGgttttaattt ... ctgatgacagTTTGTTGGAGAGTTAGCTCGGGTAGCAGCACCAGGTGCCACTATAATAATA
EST: gi|58023022|gb|CX709763.1|CX709763
EST:     TGGTGTGGTCCATGGAGAGTGGAGAGCATATGCCTGACAAAGCTAAG                         -TTGTTGGAGAGTTAGCTCGGGTAGCAGCACCAGGTGCCACTATAATAATA
genomic: TGGTGTGGTCCATGGAGAGTGGAGAGCATATGCCTGACAAAGCTAAGgttttaattt ... ctgatgacagTTTGTTGGAGAGTTAGCTCGGGTAGCAGCACCAGGTGCCACTATAATAATA
EST: gi|17023756|gb|BM094790.1|BM094790
EST:     GGAGAGCATATGCCTGACAAAGCTAAG                         TTTGTTGGAGAGTTAGCTCGGGTAGCAGCACCAGGTGCCACTATAATAATA
genomic: GGAGAGCATATGCCTGACAAAGCTAAGgttttaattt ... ctgatgacagTTTGTTGGAGAGTTAGCTCGGGTAGCAGCACCAGGTGCCACTATAATAATA
EST: gi|21994774|gb|BQ786302.1|BQ786302
EST:     ATCTGGTGTGGTCCATGGAGAGTGGAGAGCATATGCCTGACAAAGCTAAG                         TTTGTTGGAGAGTTAGCTCGGGTAGCAGCACCAGGTGCCACTATAATAATA
genomic: ATCTGGTGTGGTCCATGGAGAGTGGAGAGCATATGCCTGACAAAGCTAAGgttttaattt ... ctgatgacagTTTGTTGGAGAGTTAGCTCGGGTAGCAGCACCAGGTGCCACTATAATAATA
EST: gi|57574459|gb|CX547434.1|CX547434
EST:     ATCTGGTGTGGTCCATGGAGAGTGGAGAGCATATGCCTGACAAAGCTAAG                         TTTGTTGGAGAGTTAGCTCGGGTAGCAGCACCAGGTGCCACTATAATAATA
genomic: ATCTGGTGTGGTCCATGGAGAGTGGAGAGCATATGCCTGACAAAGCTAAGgttttaattt ... ctgatgacagTTTGTTGGAGAGTTAGCTCGGGTAGCAGCACCAGGTGCCACTATAATAATA
EST: gi|18733793|gb|BM527813.1|BM527813
EST:     ATCTGGTGTGGTCCATGGAGAGTGGAGAGCATATGCCTGACAAAGCTAAG                         TTTGTTGGAGAGTTAGCTCGGGTAGCAGCACCAGGTGCCACTATAATAATA
genomic: ATCTGGTGTGGTCCATGGAGAGTGGAGAGCATATGCCTGACAAAGCTAAGgttttaattt ... ctgatgacagTTTGTTGGAGAGTTAGCTCGGGTAGCAGCACCAGGTGCCACTATAATAATA
EST: gi|151394148|gb|EV264019.1|EV264019
EST:     ATCTGGTGTGGTCCATGGAGAGTGGAGAGCATATGCCTGACAAAGCTAAG                         TTTGTTGGAGAGTTAGCTCGGGTAGCAGCACCAGGTGCCACTATAATAATA
genomic: ATCTGGTGTGGTCCATGGAGAGTGGAGAGCATATGCCTGACAAAGCTAAGgttttaattt ... ctgatgacagTTTGTTGGAGAGTTAGCTCGGGTAGCAGCACCAGGTGCCACTATAATAATA
EST: gi|20498372|gb|BQ273302.1|BQ273302
EST:     ATCTGGTGTGGTCCATGGAGAGTGGAGAGCATATGCCTGACAAAGCTAAG                         TTTGTTGGAGAGTTAGCTCGGGTAGCAGCACCAGGTGCCACTATAATAATA
genomic: ATCTGGTGTGGTCCATGGAGAGTGGAGAGCATATGCCTGACAAAGCTAAGgttttaattt ... ctgatgacagTTTGTTGGAGAGTTAGCTCGGGTAGCAGCACCAGGTGCCACTATAATAATA
EST: gi|120493216|gb|EH221383.1|EH221383
EST:     ATCTGGTGTGGTCCATGGAGAGTGGAGAGCATATGCCTGACAAAGCTAAG                         TTTGTTGGAGAGTTAGCTCGGGTAGCAGCACCAGGTGCCACTATAATAATA
genomic: ATCTGGTGTGGTCCATGGAGAGTGGAGAGCATATGCCTGACAAAGCTAAGgttttaattt ... ctgatgacagTTTGTTGGAGAGTTAGCTCGGGTAGCAGCACCAGGTGCCACTATAATAATA
EST: gi|120494419|gb|EH222586.1|EH222586
EST:     ATCTGGTGTGGTCCATGGAGAGTGGAGAGCATATGCCTGACAAAGCTAAG                         TTTGTTGGAGAGTTAGCTCGGGTAGCAGCACCAGGTGCCACTATAATAATA
genomic: ATCTGGTGTGGTCCATGGAGAGTGGAGAGCATATGCCTGACAAAGCTAAGgttttaattt ... ctgatgacagTTTGTTGGAGAGTTAGCTCGGGTAGCAGCACCAGGTGCCACTATAATAATA
EST: gi|254344754|gb|GR855518.1|GR855518
EST:     ATCTGGTGTGGTCCATGGAGAGTGGAGAGCATATGCCTGACAAAGCTAAG                         TTTGTTGGAGAGTTAGCTCGGGTAGCAGCACCACGTGCCACTATAATAATA
genomic: ATCTGGTGTGGTCCATGGAGAGTGGAGAGCATATGCCTGACAAAGCTAAGgttttaattt ... ctgatgacagTTTGTTGGAGAGTTAGCTCGGGTAGCAGCACCAGGTGCCACTATAATAATA
EST: gi|15000769|gb|BI321583.1|BI321583
EST:     ATCTGGTGTGGTCCATGGAGAGTGGAGAGCATATGCCTGACAAAGCTAAG                         TTTGTTGGAGAGTTAGCTCGGGTAGCAGCACCAGGTGCCACTATAATAATA
genomic: ATCTGGTGTGGTCCATGGAGAGTGGAGAGCATATGCCTGACAAAGCTAAGgttttaattt ... ctgatgacagTTTGTTGGAGAGTTAGCTCGGGTAGCAGCACCAGGTGCCACTATAATAATA
EST: gi|120495732|gb|EH223899.1|EH223899
EST:     ATCTGGTGTGGTCCATGGAGAGTGGAGAGCATATGCCTGACAAAGCTAAG                         TTTGTTGGAGAGTTAGCTCGGGTAGCAGCACCAGGTGCCACTATAATAATA
genomic: ATCTGGTGTGGTCCATGGAGAGTGGAGAGCATATGCCTGACAAAGCTAAGgttttaattt ... ctgatgacagTTTGTTGGAGAGTTAGCTCGGGTAGCAGCACCAGGTGCCACTATAATAATA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taatctcatctcatcagtttcccgcttcacacacaacacgtgcaactgatgacagTTTGTTGGAGAGTTAGCTCGGGTAGCAGCACCAGGTGCCACTATAATAATAGTAACATGGTGCCACAGGGATCTTGGCCCTGACGAACAATCCTTACATC
                                           aactgat  putative branch site (score: 3)
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctcaagtgtggtttactttgatgtctctttctattttgtacgctttaatctcatctcatcagtttcccgcttcacacacaacacgtgcaactgatgacagTTTGTTGGAGAGTTAGCTCGGGTAGCAGCACCAGGTGCCACTATAATAATAGTAACATGGTGCCACAGGGATCTTGGCCCTGACGAACAATCCTTACATC

- -aagtgtg
- - - - - - - - - tgatgtc
- - - - - - - - - - - - - - - - - - tgtacgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -acacaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cacgtgc