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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttatctggctaatgtgaacttcaccttccttcatcattttagtttcatacatactcaactctaatattttaacttgttttgcgtgtactactgaatccagATCTTAATGTGCTGAATGAATATCAGCAGATTCAATCTTTTTCTGCATTCAACAGTATCTTCAATAATACAGGACTGTTTGGCATTTATGCAAGCACT

Basic information

species Glycine max
transcript GLYMA08G21380.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G21380.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv10s0003g03230.t01 (Vitis vinifera), 3'ss of exon 6
------------------------------------------------------------------------------ttatctggctaatgtgaacttc-accttccttcatcatt-ttagtttcatacatactc----aactctaatat-tttaacttgttttgcgtgtac-tactgaatccagATCTTAATGTGCTGAATGAATATCAGCAGATTCAATCTTTTTCTGCATTCAACAGTATCTTCAATAATACAGGACTGTTTGGCATTTATGCAAGCACT
                                                                               | | | |||  |  ||  | |    ||  | ||| | | ||  ||   || ||| |     |  |||  ||  ||||||| | ||        | |  ||||  ||||||||  |||  ||||||| ||||| ||  |||||||||| ||||||||||||| ||||||||| |||||  || | |||||||||||||| ||||||
gtaagttttacatatggctactggttttcttgtagcttaccttgatcatttgggttattgttatttattattgttggactttatagctgcttggatttcctgtgttgttgcattaatgttgattgagtatatatttctaaatttctgctaagtttaactcgcttgtttcacccattttgaacacagATCTTCGTGTCTTGAATGAGTATCAACAACTTCAATCTTTCTCTGCATTCAACAATATCTTCAACAATACTAGAATTTTTGGCATTTATGCTAGCACT

upper sequence: GLYMA08G21380.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv09s0002g03200.t01 (Vitis vinifera), 3'ss of exon 7
------------------------------------------------------------------------------ttatctggctaatgtgaacttcaccttccttcatcatt-ttagtttcatacatactc----aactctaatat-tttaacttgttttgcgtgtac-tactgaatccagATCTTAATGTGCTGAATGAATATCAGCAGATTCAATCTTTTTCTGCATTCAACAGTATCTTCAATAATACAGGACTGTTTGGCATTTATGCAAGCACT
                                                                               | | | |||  |  ||        ||  | ||| | | ||   |   || ||| |     |  |||  ||  ||||||| ||||        | |  ||||  ||||||||  |||  ||||||| ||||| ||| |||||||||| ||||||||||||| ||||||||| ||||| ||| | |||||||||||||| ||||||
gtaagttttacatatggctactggttttcttgtagcttaccttgatcatttgggttatggttatttattattgttggactttatagctgcttggattcctgtgttgttgcattaatgttgactgagtatatatttctaaatttctgctaagtttaactcgtttgtttaacccattttgaacacagATCTTCGTGTCTTGAATGAGTATCAACAGCTTCAATCTTTCTCTGCATTCAACAATATCTTCAACAATACTGGAATTTTTGGCATTTATGCTAGCACT
















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|17023865|gb|BM094899.1|BM094899
EST:     TGGGTCATTCTCAGCAGGGGGGCCTGGAAAAGGGATGCACTCAAGGCTAT                         ATCTTAATGTGCTGAATGAATATCAGCAGATTCAATCTTTTTCTGCATTCA
genomic: TGGGTCATTCTCAGCAGGGGGGCCTGGAAAAGGGATGCACTCAAGGCTATgtatgtttta ... ctgaatccagATCTTAATGTGCTGAATGAATATCAGCAGATTCAATCTTTTTCTGCATTCA
EST: gi|13562687|gb|BG550907.1|BG550907
EST:     GGGTCATTCTCAGCATTGGTGGCCTGGAAAAGGGATGCACTCAAGGCTAT                         ATCTTAATGTGCTGAATGAATATCAGCAGATTCAATCTTTTTCTGCATTCA
genomic: GGGTCATTCTCAGCAGGGG-GGCCTGGAAAAGGGATGCACTCAAGGCTATgtatgtttta ... ctgaatccagATCTTAATGTGCTGAATGAATATCAGCAGATTCAATCTTTTTCTGCATTCA
EST: gi|18732951|gb|BM527341.1|BM527341
EST:     GGAAAAGGGATGCACTCAAGGCTAT                         ATCTTAATGTGCTGAATGAATATCAGCAGATTCAATCTTTTTCTGCATTCA
genomic: GGAAAAGGGATGCACTCAAGGCTATgtatgtttta ... ctgaatccagATCTTAATGTGCTGAATGAATATCAGCAGATTCAATCTTTTTCTGCATTCA
EST: gi|38192388|gb|CF921594.1|CF921594
EST:     TGGGTCATTCTCAGCAGGGGGGCCTGGAAAAGGGATGCACTCAAGGCTAT                         ATCTTAATGTGCTGAATGAATATCAGCAGATTCAATCTTTTTCTGCATTCA
genomic: TGGGTCATTCTCAGCAGGGGGGCCTGGAAAAGGGATGCACTCAAGGCTATgtatgtttta ... ctgaatccagATCTTAATGTGCTGAATGAATATCAGCAGATTCAATCTTTTTCTGCATTCA
EST: gi|38193674|gb|CF922880.1|CF922880
EST:     TGGGTCATTCTCAGCAGGGGGGCCTGGAAAAGGGATGCACTCAAGGCTAT                         ATCTTAATGTGCTGAATGAATATCAGCAGATTCAATCTTTTTCTGCATTCA
genomic: TGGGTCATTCTCAGCAGGGGGGCCTGGAAAAGGGATGCACTCAAGGCTATgtatgtttta ... ctgaatccagATCTTAATGTGCTGAATGAATATCAGCAGATTCAATCTTTTTCTGCATTCA
EST: gi|10233365|gb|BE802253.1|BE802253
EST:     CTCAGCAGGGGGGCCTGGAAAAGGGATGCACTCAAGGCTAT                         ATCTTAATGTGCTGAATGAATATCAGCAGATTCAATCTTTTTCTGCATTCA
genomic: CTCAGCAGGGGGGCCTGGAAAAGGGATGCACTCAAGGCTATgtatgtttta ... ctgaatccagATCTTAATGTGCTGAATGAATATCAGCAGATTCAATCTTTTTCTGCATTCA
EST: gi|8282640|gb|BE020201.1|BE020201
EST:     TGGGTCATTCTCAGCAGGGGGGCCTGGAAAAGGGATGCACTCAAGGCTAT                         ATCTTAATGTGCTGAATGAATATCAGCAGATTCAATCTTTTTCTGCATTCA
genomic: TGGGTCATTCTCAGCAGGGGGGCCTGGAAAAGGGATGCACTCAAGGCTATgtatgtttta ... ctgaatccagATCTTAATGTGCTGAATGAATATCAGCAGATTCAATCTTTTTCTGCATTCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catacatactcaactctaatattttaacttgttttgcgtgtactactgaatccagATCTTAATGTGCTGAATGAATATCAGCAGATTCAATCTTTTTCTGCATTCAACAGTATCTTCAATAATACAGGACTGTTTGGCATTTATGCAAGCACT
                     ttttaac  putative branch site (score: 2)
              tctaatattttaactt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttatctggctaatgtgaacttcaccttccttcatcattttagtttcatacatactcaactctaatattttaacttgttttgcgtgtactactgaatccagATCTTAATGTGCTGAATGAATATCAGCAGATTCAATCTTTTTCTGCATTCAACAGTATCTTCAATAATACAGGACTGTTTGGCATTTATGCAAGCACT

- - - -gctaatg
- - - - - - - - - - - -ccttcct
- - - - - - - - - - - - - - - - - - - - - - - - -catactc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcgtgta