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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatttttggttgtatatcttgatttaaaacctgatgtgcctttactgatcatgctctgtgtgtttattgccttttatagGAGTAATGTTGACAAAAGAGAGGCACTTGAGAACTTAGATCTCATTCTCCTGTGTCTTGACGAGATTGTTGATGGAGG

Basic information

species Glycine max
transcript GLYMA08G20370.3
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G20370.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv09s0002g01710.t01 (Vitis vinifera), 3'ss of exon 3
-----------gtatttttggttgt-atatcttgatttaaaacctgatgtgcctttactgatcatgctctgtgtgtt---------tattgccttttatagGAGTAATGTTGACAAAAGAGAGGCACTTGAGAACTTAGATCTCATTCTCCTGTGTCTTGACGAGATTGTTGATGGAGG
            ||  | | |   | || ||||||||| |   ||||||  |  | | ||||  | || ||     |         ||     |||  |||||  ||  ||||||| || ||||||||||||||||| |||||||||||||| || ||||| |||||||||||||||||
gtattgtaatcataactctagccttcatttcttgatttcatctctgatgatctgtaattgatgcttctttgccacctaaaacatcatacccattttgttagGAACAACATTGACAAGAGGGAGGCACTTGAGAACTTGGATCTCATTCTCCTATGCCTTGATGAGATTGTTGATGGAGG
















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|31560978|gb|CD486816.1|CD486816
EST:     CTAGCATCAGTTCTTCAAGGTTTCTTTGATGCAGTCACCCTTCTGTTGAG                         GAGTAATGTTGACAAAAGAGAGGCACTTGAGAACTTAGATCTCATTCTCCT
genomic: CTAGCATCAGTTCTTCAAGGTTTCTTTGATGCAGTCACCCTTCTGTTGAGgtatttttgg ... ccttttatagGAGTAATGTTGACAAAAGAGAGGCACTTGAGAACTTAGATCTCATTCTCCT
EST: gi|21256834|gb|BQ453722.1|BQ453722
EST:     CTAGCATCAGTTCTTCAAGGTTTCTTTGATGCAGTCACCCTTCTGTTGAG                         GAGTAATGTTGACAAAAGAGAGGCACTTGAGAACTTAGATCTCATTCTCCT
genomic: CTAGCATCAGTTCTTCAAGGTTTCTTTGATGCAGTCACCCTTCTGTTGAGgtatttttgg ... ccttttatagGAGTAATGTTGACAAAAGAGAGGCACTTGAGAACTTAGATCTCATTCTCCT
EST: gi|19937410|gb|BQ081279.1|BQ081279
EST:     GTTTCTTTGATGCAGTCACCCTTCTGTTGAG                         GAGTAATGTTGACAAAAGAGAGGCACTTGAGAACTTAGATCTCATTCTCCT
genomic: GTTTCTTTGATGCAGTCACCCTTCTGTTGAGgtatttttgg ... ccttttatagGAGTAATGTTGACAAAAGAGAGGCACTTGAGAACTTAGATCTCATTCTCCT
EST: gi|7285995|gb|AW598482.1|AW598482
EST:     CTAGCATCAGTTCTTCAAGGTTTCTTTGATGCAGTCACCCTTCTGTTGAG                         GAGTAATGTTGACAAAAGAGAGGCACTTGAGAACTTAGATCTCATTCTCCT
genomic: CTAGCATCAGTTCTTCAAGGTTTCTTTGATGCAGTCACCCTTCTGTTGAGgtatttttgg ... ccttttatagGAGTAATGTTGACAAAAGAGAGGCACTTGAGAACTTAGATCTCATTCTCCT
EST: gi|31470945|gb|CD412973.1|CD412973
EST:     CTAGCATCAGTTCTTCAAGGTTTCTTTGATGCAGTCACCCTTCTGTTGAG                         GAGTAATGTTGACAAAAGAGAGGCACTTGAGAACTTAGATCTCATTCTCCT
genomic: CTAGCATCAGTTCTTCAAGGTTTCTTTGATGCAGTCACCCTTCTGTTGAGgtatttttgg ... ccttttatagGAGTAATGTTGACAAAAGAGAGGCACTTGAGAACTTAGATCTCATTCTCCT
EST: gi|8404161|gb|BE059795.1|BE059795
EST:     AAGGTTTCTTTGATGCAGTCACCCTTCTGTTGAG                         GAGTAATGTTGACAAAAGAGAGGCACTTGAGAACTTAGATCTCATTCTCCT
genomic: AAGGTTTCTTTGATGCAGTCACCCTTCTGTTGAGgtatttttgg ... ccttttatagGAGTAATGTTGACAAAAGAGAGGCACTTGAGAACTTAGATCTCATTCTCCT
EST: gi|31305637|gb|CD390840.1|CD390840
EST:     CTAGCATCAGTTCTTCAAGGTTTCTTTGATGCAGTCACCCTTCTGTTGAG                         GAGTAATGTTGACAAAAGAGAGGCACTTGAGAACTTAGATCTCATTCTCCT
genomic: CTAGCATCAGTTCTTCAAGGTTTCTTTGATGCAGTCACCCTTCTGTTGAGgtatttttgg ... ccttttatagGAGTAATGTTGACAAAAGAGAGGCACTTGAGAACTTAGATCTCATTCTCCT
EST: gi|7029699|gb|AW459482.1|AW459482
EST:     AGGTTTCTTTGATGCAGTCACCCTTCTGTTGAG                         GAGTAATGTTGACAAAAGAGAGGCACTTGAGAACTTAGATCTCATTCTCCT
genomic: AGGTTTCTTTGATGCAGTCACCCTTCTGTTGAGgtatttttgg ... ccttttatagGAGTAATGTTGACAAAAGAGAGGCACTTGAGAACTTAGATCTCATTCTCCT
EST: gi|193376778|gb|FK340973.1|FK340973
EST:     CTAGCATCAGTTCTTCAAGGTTTCTTTGATGCAGTCACCCTTCTGTTGAG                         GAGTAATGTTGACAAAAGAGAGGCACTTGAGAACTTAGATCTCATTCTCCT
genomic: CTAGCATCAGTTCTTCAAGGTTTCTTTGATGCAGTCACCCTTCTGTTGAGgtatttttgg ... ccttttatagGAGTAATGTTGACAAAAGAGAGGCACTTGAGAACTTAGATCTCATTCTCCT
EST: gi|151410805|gb|EV280620.1|EV280620
EST:     CTAGCATCAGTTCTTCAAGGTTTCTTTGATGCAGTCACCCTTCTGTTGAG                         GAGTAATGTTGACAAAAGAGAGGCACTTGAGAACTTAGATCTCATTCTCCT
genomic: CTAGCATCAGTTCTTCAAGGTTTCTTTGATGCAGTCACCCTTCTGTTGAGgtatttttgg ... ccttttatagGAGTAATGTTGACAAAAGAGAGGCACTTGAGAACTTAGATCTCATTCTCCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taaaacctgatgtgcctttactgatcatgctctgtgtgtttattgccttttatagGAGTAATGTTGACAAAAGAGAGGCACTTGAGAACTTAGATCTCATTCTCCTGTGTCTTGACGAGATTGTTGATGGAGG
                  tactgat  putative branch site (score: 2)
                                          ttgcctttt  putative PPT
                                               ttttata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatttttggttgtatatcttgatttaaaacctgatgtgcctttactgatcatgctctgtgtgtttattgccttttatagGAGTAATGTTGACAAAAGAGAGGCACTTGAGAACTTAGATCTCATTCTCCTGTGTCTTGACGAGATTGTTGATGGAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG