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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...actttttttcttctttgctttcttgatggtatttgtggattataaataaagtattttcattacctcacatcttgtatattttatatttttcttcatgcagAAGTCCCCTTCTGAGTGTATATGCTGACATGTCAGTAACTTGCAAG

Basic information

species Glycine max
transcript GLYMA18G00720.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G00720.2 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os03g08570.1 (Oryza sativa), 3'ss of exon 11
--------------------------------------------------------------------------------------actttttttcttctttgctttcttgatggtatttgtggattataaataaagtattt-tcattacctcacatcttgtatattttatatt----------tttcttcatgcagAAGTCCCCTTCTGAGTGTATATGCTGACATGTCAGTAACTTGCAAG
                                                                                      ||  ||| | ||       ||    |   | | |   |||| |  ||| | | ||  | | ||||  | ||| | | |    | ||||            | ||| | ||| ||| | ||| | ||||| ||||| |||||||||||||||||||||
gtgtctcttctaattcctcatcagttttgctgtcctttcactgcctcatgcatttgctctgtgctatgactggtttatgaactaaaacgatttgtattgcccaaattgggcacattctatcctgattttgtatacattcttgattaataccaaatatcatatgtcccatgtattgatcttgttcccttttctttcagGAGTTCACTTTTAAGTGTTTATGCGGACATGTCAGTAACTTGCAAG

upper sequence: GLYMA18G00720.2 (Glycine max), 3'ss of exon 6
lower sequence: Vv09s0002g00100.t01 (Vitis vinifera), 3'ss of exon 11
actttttttcttctttgctttcttgatggtatttgtggattataaataaagt--attttcattacctcacatcttgtatattttatatttttcttcatgcagAAGTCCCCTTCTGAGTGTATATGCTGACATGTCAGTAACTTGCAAG
  | |||| ||||       | ||  |    |       || | | |   |   |||||  |||| ||| || |  | | || | | |||  |  ||||||||||||||||||||||||| |||||||||||||| ||||| || |||
tttcttttgcttccaaatcatatttctttagtccagtatttgtcattgttgctgatttttcttac-tcagatttgatgttttgttt-tttccccccatgcagAAGTCCCCTTCTGAGTGTGTATGCTGACATGTCCGTAACATGTAAG
















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|151400218|gb|EV270032.1|EV270032
EST:     GTTTGACAGAAAACTGAAGAACACATATGATCACCTTCTCTTTAGCAG                         AAGTCCCCTTCTGAGTGTATATGCTGACATGTCAGTAACTTGCAAG
genomic: GTTTGACAGAAAACTGAAGAACACATATGATCACCTTCTCTTTAGCAGgtcttcctca ... cttcatgcagAAGTCCCCTTCTGAGTGTATATGCTGACATGTCAGTAACTTGCAAG
EST: gi|192309608|gb|FK002888.1|FK002888
EST:     GATCACCTTCTCTTTAGCAG                         AAGTCCCCTTCTGAGTGTATATGCTAACATGTCAGTAACTTGCAAG
genomic: GATCACCTTCTCTTTAGCAGgtcttcctca ... cttcatgcagAAGTCCCCTTCTGAGTGTATATGCTGACATGTCAGTAACTTGCAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ataaagtattttcattacctcacatcttgtatattttatatttttcttcatgcagAAGTCCCCTTCTGAGTGTATATGCTGACATGTCAGTAACTTGCAAG
                acctcac  putative branch site (score: 3)
                                 ttttatatttttcttc  putative PPT
                       atcttgtatattttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
actttttttcttctttgctttcttgatggtatttgtggattataaataaagtattttcattacctcacatcttgtatattttatatttttcttcatgcagAAGTCCCCTTCTGAGTGTATATGCTGACATGTCAGTAACTTGCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - -tgctttc
- - - - - - - - - - - - gatggta
- - - - - - - - - - - - - - - - - - - - - -aaataaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cctcaca