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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAACATTGCATCTTGTTTTAAGGCTTCGTGGTGGTATTATTGAGCCATCTTTGATGGCACTGGCGAGGAAATATAACCAGGATAAGATGATCTGCCGCAAgtaagtttacacatcctagtattggatcctgttggttcattcataagtaataagaaatattgttcttgtgaagtatagtcaaagtgccaaaaaaacttgt...

Basic information

species Glycine max
transcript GLYMA04G40980.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G40980.1 (Glycine max), 5'ss of exon 3
lower sequence: PP1S330_45V6.1 (Physcomitrella patens), 5'ss of exon 1
CAACATTGCATCTTGTTTTAAGGCTTCGTGGTGGTATTATTGAGCCATCTTTGATGGCACTGGCGAGGAAATATAACCAGGATAAGATGATCTGCCGCAAgtaagtttacacatcctagtattggatcctgttggttca--ttcataagtaataagaaatattgttct-tgtgaagtatagtcaaagtgccaaaaaaacttgt
| || |||||  | ||  |  | || || || |||||||| ||||||||||| |||||||||||  | || || |||||||| |||||||||||||| |||| |||   |    | |   |    |   |    |  ||  |||||  | | |  |   ||  | | | |||| ||| || |  ||     |      | |  
CTACCTTGCACTTGGTGCTCCGTCTGCGGGGCGGTATTATCGAGCCATCTTTAATGGCACTGGCTCGCAAGTACAACCAGGAGAAGATGATCTGCCGGAAgtgagtgctcggcccttttaagctcactattgcagcgcagtttcatgtgaactgtgtcgtacgggtttatgtgtagt-taatagaatcataaggtgggcgt--

upper sequence: GLYMA04G40980.1 (Glycine max), 5'ss of exon 3
lower sequence: PP1S241_60V6.1 (Physcomitrella patens), 5'ss of exon 1
CAACATTGCATCTTGTTTTAAGGCTTCGTGGTGGTATTATTGAGCCATCTTTGATGGCACTGGCGAGGAAATATAACCAGGATAAGATGATCTGCCGCAAgtaagtttacacatcctagtattggatcctgttggttcattcataa-gtaataagaaatattgttcttgtgaagtatagtcaaagtgccaaaaaaacttgt---
| || |||||  | ||  |  | ||||| || ||||| || ||||| ||||||||||| |||||| | || || |||||||| || ||||||||||| |||| |||   | |  |   |||  |  | | | |  || || |  ||   |||  ||  |  | ||  |||    | |        |  |       ||  |   
CCACCTTGCACTTGGTGCTTCGTCTTCGGGGAGGTATCATCGAGCCCTCTTTGATGGCCCTGGCGCGCAAGTACAACCAGGAAAAAATGATCTGCCGGAAgtgagtc--ctctgctctgtagggtttacagct--tttatgcgcaatacaatccgacttcgttttactgtttgttttttctcttctctctcttcttctccttca
















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|57574197|gb|CX547172.1|CX547172
EST:     TTGATGGCACTGGCGAGGAAATATAACCAGGATAAGATGATCTGCCGCAA                         GTGTTATGCCCGTTTACATCCCCGTGCTGTGAACTGCAGGAAAAAGAAGTG
genomic: TTGATGGCACTGGCGAGGAAATATAACCAGGATAAGATGATCTGCCGCAAgtaagtttac ... tgctttgcagGTGTTATGCCCGTTTACATCCCCGTGCTGTGAACTGCAGGAAAAAGAAGTG
EST: gi|151398433|gb|EV268304.1|EV268304
EST:     TTGATGGCACTGGCGAGGAAATATAACCAGGATAAGATGATCTGCCGCAA                         GTGTTATGCCCGTTTACATCCCCGTGCTGTGAACTGCAGGAAAAAGAAGTG
genomic: TTGATGGCACTGGCGAGGAAATATAACCAGGATAAGATGATCTGCCGCAAgtaagtttac ... tgctttgcagGTGTTATGCCCGTTTACATCCCCGTGCTGTGAACTGCAGGAAAAAGAAGTG
EST: gi|13240099|gb|BG359408.1|BG359408
EST:     TTGATGGCACTGGCGAGGAAATATAACCAGGATAAGATGATCTGCCGCAN                         GTGTTATGCCCGTTTACATCCCCGTGCTGTGAACTGCAGGAAAAAGAAGTG
genomic: TTGATGGCACTGGCGAGGAAATATAACCAGGATAAGATGATCTGCCGCAAgtaagtttac ... tgctttgcagGTGTTATGCCCGTTTACATCCCCGTGCTGTGAACTGCAGGAAAAAGAAGTG
EST: gi|208319895|gb|GE116310.1|GE116310
EST:     TTGATGGCACTGGCGAGGAAATATAACCAGGATAAGATGATCTGCCGCAA                         GTGTTATGCCCGTTTACATCCCCGTGCTGTGAACTGCAGGAAAAAGAAGTG
genomic: TTGATGGCACTGGCGAGGAAATATAACCAGGATAAGATGATCTGCCGCAAgtaagtttac ... tgctttgcagGTGTTATGCCCGTTTACATCCCCGTGCTGTGAACTGCAGGAAAAAGAAGTG
EST: gi|213592793|gb|DB981297.1|DB981297
EST:     TTGATGGCACTGGCGAGGAAATATAACCAGGATAAGATGATCTGCCGCAA                         GTGTTATGCCCGTTTACATCCCCGTGCTGTGAACTGCAGGAAAAAGAAGTG
genomic: TTGATGGCACTGGCGAGGAAATATAACCAGGATAAGATGATCTGCCGCAAgtaagtttac ... tgctttgcagGTGTTATGCCCGTTTACATCCCCGTGCTGTGAACTGCAGGAAAAAGAAGTG
EST: gi|151410135|gb|EV279943.1|EV279943
EST:     TTGATGGCACTGGCGAGGAAATATAACCAGGATAAGATGATCTGCCGCAA                         GTGTTATGCCCGTTTACATCCCCGTGCTGTGAACTGCAGGAAAAAGAAGTG
genomic: TTGATGGCACTGGCGAGGAAATATAACCAGGATAAGATGATCTGCCGCAAgtaagtttac ... tgctttgcagGTGTTATGCCCGTTTACATCCCCGTGCTGTGAACTGCAGGAAAAAGAAGTG
EST: gi|18719025|gb|BM523129.1|BM523129
EST:     TTGATGGCACTGGCGAGGAAATATAACCAGGATAAGATGATCTGCCGCAA                         GTGTTATGCCCGTTTACATCCCCGTGCTGTGAACTGCAGGAAAAAGAAGTG
genomic: TTGATGGCACTGGCGAGGAAATATAACCAGGATAAGATGATCTGCCGCAAgtaagtttac ... tgctttgcagGTGTTATGCCCGTTTACATCCCCGTGCTGTGAACTGCAGGAAAAAGAAGTG
EST: gi|192324803|gb|FK016874.1|FK016874
EST:     TTGATGGCACTGGCGAGGAAATATAACCAGGATAAGATGATCTGCCGCAA                         GTGTTATGCCCGTTTACATCCCCGTGCTGTGAACTGCAGGAAAAAGAAGTG
genomic: TTGATGGCACTGGCGAGGAAATATAACCAGGATAAGATGATCTGCCGCAAgtaagtttac ... tgctttgcagGTGTTATGCCCGTTTACATCCCCGTGCTGTGAACTGCAGGAAAAAGAAGTG
EST: gi|213618032|gb|DB963665.1|DB963665
EST:     TTGATGGCACTGGCGAGGAAATATAACCAGGATAAGATGATCTGCCGCAA                         GTGTTATGCCCGTTTACATCCCCGTGCTGTGAACTGCAGGAAAAAGAAGTG
genomic: TTGATGGCACTGGCGAGGAAATATAACCAGGATAAGATGATCTGCCGCAAgtaagtttac ... tgctttgcagGTGTTATGCCCGTTTACATCCCCGTGCTGTGAACTGCAGGAAAAAGAAGTG
EST: gi|192317237|gb|FK009810.1|FK009810
EST:     TTGATGGCACTGGCGAGGAAATATAACCAGGATAAGATGATCTGCCGCAA                         GTGTTATGCCCGTTTACATCCCCGTGCTGTGAACTGCAGGAAAA-GAAGTG
genomic: TTGATGGCACTGGCGAGGAAATATAACCAGGATAAGATGATCTGCCGCAAgtaagtttac ... tgctttgcagGTGTTATGCCCGTTTACATCCCCGTGCTGTGAACTGCAGGAAAAAGAAGTG
EST: gi|21639171|gb|BM140217.1|BM140217
EST:     TTGATGGCACTGGCGAGGAAATATAACCAGGATAAGATGATCTGCCGCAA                         GTGTTATGCCCGTTTACATCCCCGTGCTGTGAACTGCAGGAAAAAGAAGTG
genomic: TTGATGGCACTGGCGAGGAAATATAACCAGGATAAGATGATCTGCCGCAAgtaagtttac ... tgctttgcagGTGTTATGCCCGTTTACATCCCCGTGCTGTGAACTGCAGGAAAAAGAAGTG
EST: gi|58023032|gb|CX709773.1|CX709773
EST:     TTGATGGCACTGGCGAGGAAATATAACCAGGATAAGATGATCTGCCGCAA                         GTGTTATGCCCGTTTACATCCCCGTGCTGTGAACTGCAGGAAAAAGAAGTG
genomic: TTGATGGCACTGGCGAGGAAATATAACCAGGATAAGATGATCTGCCGCAAgtaagtttac ... tgctttgcagGTGTTATGCCCGTTTACATCCCCGTGCTGTGAACTGCAGGAAAAAGAAGTG
EST: gi|208036764|gb|GD833923.1|GD833923
EST:     AGGATAAGACGATCTGCCGCAA                         GTGTTATGCCCGTTTACATCCCCGTGCTGTGAACTGCAGGAAAAAGAAGTG
genomic: AGGATAAGATGATCTGCCGCAAgtaagtttac ... tgctttgcagGTGTTATGCCCGTTTACATCCCCGTGCTGTGAACTGCAGGAAAAAGAAGTG
EST: gi|254318519|gb|GR832687.1|GR832687
EST:     TTGATGGCACTGGCGAGGAAATATAACCAGGATAAGATGATCTGCCGCAA                         GTGTTATGCCCGTTTACATCCCCGTGCTGTGAACTGCAGGAAAAAGAAGTG
genomic: TTGATGGCACTGGCGAGGAAATATAACCAGGATAAGATGATCTGCCGCAAgtaagtttac ... tgctttgcagGTGTTATGCCCGTTTACATCCCCGTGCTGTGAACTGCAGGAAAAAGAAGTG
EST: gi|57574032|gb|CX547007.1|CX547007
EST:     TTGATGGCACTGGCGAGGAAATATAACCAGGATAAGATGATCTGCCGCAA                         GTGTTATGCCCGTTTACATCCCCGTGCTGTGAACTGCAGGAAAAAGAAGTG
genomic: TTGATGGCACTGGCGAGGAAATATAACCAGGATAAGATGATCTGCCGCAAgtaagtttac ... tgctttgcagGTGTTATGCCCGTTTACATCCCCGTGCTGTGAACTGCAGGAAAAAGAAGTG
EST: gi|151412758|gb|EV282570.1|EV282570
EST:     TTGATGGCACTGGCGAGGAAATATAACCAGGATAAGATGATCTGCCGCAA                         GTGTTATGCCCGTTTACATCCCCGTGCTGTGAACTGCAGGAAAAAGAAGTG
genomic: TTGATGGCACTGGCGAGGAAATATAACCAGGATAAGATGATCTGCCGCAAgtaagtttac ... tgctttgcagGTGTTATGCCCGTTTACATCCCCGTGCTGTGAACTGCAGGAAAAAGAAGTG
EST: gi|207820974|gb|GD790893.1|GD790893
EST:     TTGATGGCACTGGCGAGGAAATATAACCAGGATAAGATGATCTGCCGCAA                         GTGTTATGCCCGTTTACATCCCCGTGCTGTGAACTGCAGGAAAAAGAAGTG
genomic: TTGATGGCACTGGCGAGGAAATATAACCAGGATAAGATGATCTGCCGCAAgtaagtttac ... tgctttgcagGTGTTATGCCCGTTTACATCCCCGTGCTGTGAACTGCAGGAAAAAGAAGTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAACATTGCATCTTGTTTTAAGGCTTCGTGGTGGTATTATTGAGCCATCTTTGATGGCACTGGCGAGGAAATATAACCAGGATAAGATGATCTGCCGCAAgtaagtttacacatcctagtattggatcctgttggttcattcataagtaataagaaatattgttcttgtgaagtatagtcaaagtgccaaaaaaacttgt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ataagaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -caaaaaaa