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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacacatcttggagctaacataatcattgcattggccataatttcaatgatctgatattctgatgtaatatgtttctttacccagGTATATCTATAGGCATAGTTACTGCCATTGCAGCTCCAGCAAGTCTAACGGTTGAATTTGAAGGCAATGGTGGCCATGCGGGTGCTGCCCTTATGCCTAA

Basic information

species Glycine max
transcript GLYMA10G32850.2
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G32850.2 (Glycine max), 3'ss of exon 5
lower sequence: AT5G43600.1 (Arabidopsis thaliana), 3'ss of exon 6
gtacacatcttggagctaacata-atcattgcattggccataatttcaatgatctgatattctgatgtaatatgtttctttacc-cagGTATATCTATAGGCATAGTTACTGCCATTGCAGCTCCAGCAAGTCTAACGGTTGAATTTGAAGGCAATGGTGGCCATGCGGGTGCTGCCCTTATGCCTAA
|| |   |     | ||    |   |    | |||     |  ||||  |  |    |||  | |  ||| ||  || || ||| ||||| ||  ||| ||  | || || |||||||| |||||||||||| | | ||| ||||||||||||||||| || ||||| |||||||  ||||||||  |
gtccggttaacttaccttttctgcgtggaagaattttgtgttttttctctctttcattatagtta-ataagatcatttttgaccacagGTTTAGATATCGGTGTTGTAACCGCCATTGCTGCTCCAGCAAGTTTGAAGGTGGAATTTGAAGGCAATGGAGGTCATGCTGGTGCTGTACTTATGCCATA

upper sequence: GLYMA10G32850.2 (Glycine max), 3'ss of exon 5
lower sequence: Vv05s0020g04900.t01 (Vitis vinifera), 3'ss of exon 6
gtacacatcttggagctaacata--atcattgcattggccataa-tttcaatgatctgatattctgatgtaatatgtttctttacccagGTATATCTATAGGCATAGTTACTGCCATTGCAGCTCCAGCAAGTCTAACGGTTGAATTTGAAGGCAATGGTGGCCATGCGGGTGCTGCCCTTATGCCTAA
|||  | ||||   | |  |||   ||  ||      |||| || ||||||   ||  || |  || | ||     | | || |   ||| |||||||| ||||| || ||||||||||| || || |||||| | |  || || |||||||||||||| |||||||||||||||| | | ||||| ||
gtaggcctctttctgttctcattttattcttttcacagccacaactttcaaaattcccatttattggtcta-----tattttgatgtagGAATATCTATTGGCATTGTAACTGCCATTGCTGCCCCTGCAAGTATCAAAGTGGATTTTGAAGGCAATGGAGGCCATGCGGGTGCTGTCTTGATGCCAAA
















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|208067149|gb|GD861317.1|GD861317
EST:     CAAGGACCTATTCTGGAAGATGAAG                         GTATTATCTATAGGCATAGTTACTGCCATTGCAGCTCCAGCAAGTCTAACG
genomic: CAAGGACCTATTCTGGAAGATGAAGgtacacatct ... ctttacccagGTA-TATCTATAGGCATAGTTACTGCCATTGCAGCTCCAGCAAGTCTAACG
EST: gi|207753251|gb|GD725061.1|GD725061
EST:     TGCTTTTGTAGAACTGCACATAGAACAAGGACCTATTCTGGAAGATGAAG                         GTATATCTATAGGCATAGTTACTGCCATTGCAGCTCCAGCAAGTCTAACGG
genomic: TGCTTTTGTAGAACTGCACATAGAACAAGGACCTATTCTGGAAGATGAAGgtacacatct ... ctttacccagGTATATCTATAGGCATAGTTACTGCCATTGCAGCTCCAGCAAGTCTAACGG
EST: gi|14990231|gb|BI315904.1|BI315904
EST:     TGCTTTTGTAGAACTGCACATAGAACAAGGACCTATTCTGGAAGATGAAG                         GTATATCTATAGGCATAGTTACTGCCATTGCAGCTCCAGCAAGTCTAACGG
genomic: TGCTTTTGTAGAACTGCACATAGAACAAGGACCTATTCTGGAAGATGAAGgtacacatct ... ctttacccagGTATATCTATAGGCATAGTTACTGCCATTGCAGCTCCAGCAAGTCTAACGG
EST: gi|14011696|gb|BG726618.1|BG726618
EST:     TGCTTTTGTAGAACTGCACATAGAACAAGGACCTATTCTGGAAGATGAAG                         GTATATCTATAGGCATAGTTACTGCCATTGCAGCTCCAGCAAGTCTAACGG
genomic: TGCTTTTGTAGAACTGCACATAGAACAAGGACCTATTCTGGAAGATGAAGgtacacatct ... ctttacccagGTATATCTATAGGCATAGTTACTGCCATTGCAGCTCCAGCAAGTCTAACGG
EST: gi|193332291|gb|FK298609.1|FK298609
EST:     TGCTTTTGTAGAACTGCACATAGAACAAGGACCTATTCTGGAAGATGAAG                         GTATATCTATAGGCATAGTTACTGCCATTGCAGCTCCAGCAAGTCTAACGG
genomic: TGCTTTTGTAGAACTGCACATAGAACAAGGACCTATTCTGGAAGATGAAGgtacacatct ... ctttacccagGTATATCTATAGGCATAGTTACTGCCATTGCAGCTCCAGCAAGTCTAACGG
EST: gi|6667618|gb|AW279069.1|AW279069
EST:     CACATAGAACAAGGACCTATTCTGGAAGATGAAG                         GTATATCTATAGGCATAGTTACTGCCATTGCAGCTCCAGCAAGTCTAACGG
genomic: CACATAGAACAAGGACCTATTCTGGAAGATGAAGgtacacatct ... ctttacccagGTATATCTATAGGCATAGTTACTGCCATTGCAGCTCCAGCAAGTCTAACGG
EST: gi|192306703|gb|FG998857.1|FG998857
EST:     TGCTTTTGTAGAACTGCACATAGAACAAGGACCTATTCTGGAAGATGAAG                         GTATATCTATAGGCATAGTTACTGCCATTGCAGCTCCAGCAAGTCTAACGG
genomic: TGCTTTTGTAGAACTGCACATAGAACAAGGACCTATTCTGGAAGATGAAGgtacacatct ... ctttacccagGTATATCTATAGGCATAGTTACTGCCATTGCAGCTCCAGCAAGTCTAACGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attggccataatttcaatgatctgatattctgatgtaatatgtttctttacccagGTATATCTATAGGCATAGTTACTGCCATTGCAGCTCCAGCAAGTCTAACGGTTGAATTTGAAGGCAATGGTGGCCATGCGGGTGCTGCCCTTATGCCTAA
                           ttctgat  putative branch site (score: 3)
                                          tttctttaccc  putative PPT
                                   taatatgtttcttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacacatcttggagctaacataatcattgcattggccataatttcaatgatctgatattctgatgtaatatgtttctttacccagGTATATCTATAGGCATAGTTACTGCCATTGCAGCTCCAGCAAGTCTAACGGTTGAATTTGAAGGCAATGGTGGCCATGCGGGTGCTGCCCTTATGCCTAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC