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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcaacactttctcaagtatcttcaacactaggaaatatattgcaattctgttacttctttttataagctcataagttagttttttctctctgattccttcatcaatttctaaacatttaagGAAGAGATGGAGGAAGCTATCAAGCAGCTAAGGAAGAGTCTAACTTTTAAAGCAAGCCCTATGCCAAGCTTTTACCATGAAGGGCCTCCTCCTAAGGTTG

Basic information

species Glycine max
transcript GLYMA20G34780.4
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G34780.4 (Glycine max), 3'ss of exon 6
lower sequence: AT3G23090.2 (Arabidopsis thaliana), 3'ss of exon 5
gtgcaacactttctcaagtatcttcaacactaggaaatatattgcaattctgttacttctttttataagctcataagttagttttttctctctgattcctt-catcaatttctaaacatttaa-gGAAGAGATGGAGGAAGCTATCAAGCAGCTAAGGAAGAGTCTAACTTTTAAAGCAAGCCCTATGCCAAGCTTTTACCATGAAGGGCCTCCTCCTAAGGTTG
                           || |     |||  |||     ||   | || ||||  || | |  |  |  |  || |||||  |   |   |    |   | || ||||| ||| |||||  |  || | |||| | |  ||  |||| || ||| | |  |||||||||| ||| |||||||  ||||| |||||||||||||| || |||||||
-------------------------tgcattttcctatactttgtgtagctagcaatttttttcctatgtttttttgacatattgttctccttctctttgtatgcccggtactcaacatctaaagGAAGCAACCGAAGCAGCTTTAAGACAATTAAGAAAAAGTTTGAGGTTTAAAGCAAACCCAATGCCAAAATTTTATCATGAAGGGCCTCCCCCAAAGGTTG
















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|15199929|gb|BI424081.1|BI424081
EST:     AGCAGCAAGCAATGGAAGCTGAGAAGAATCAAAGTGAAGCTAGGACCAAG                         GAAGAGATGGAGGAAGCTATC
genomic: AGCAGCAAGCAATGGAAGCTGAGAAGAATCAAAGTGAAGCTAGGACCAAGgtgcaacact ... aacatttaagGAAGAGATGGAGGAAGCTATC
EST: gi|193703750|gb|FK634722.1|FK634722
EST:     AGCAGCAAGCAATGGAAGCTGAGAAGAATCAAAGTGAAGCTAGGACCAAG                         GAAGAGATGGAGGAAGCTATCAAGCAGCTAAGGAAGAGTCTAACTTTTAAA
genomic: AGCAGCAAGCAATGGAAGCTGAGAAGAATCAAAGTGAAGCTAGGACCAAGgtgcaacact ... aacatttaagGAAGAGATGGAGGAAGCTATCAAGCAGCTAAGGAAGAGTCTAACTTTTAAA
EST: gi|6482098|gb|AW201369.1|AW201369
EST:     AGCAGCAAGCAATGGAAGCTGAGAAGAATCAAAGTGAAGCTAGGACCAAG                         GAAGAGATGGAGGAAGCTATCAAGCAGCTAAGGAAGAGTCTAACTTTTAAA
genomic: AGCAGCAAGCAATGGAAGCTGAGAAGAATCAAAGTGAAGCTAGGACCAAGgtgcaacact ... aacatttaagGAAGAGATGGAGGAAGCTATCAAGCAGCTAAGGAAGAGTCTAACTTTTAAA
EST: gi|10236980|gb|BE805868.1|BE805868
EST:     AGCAGCAAGCAATGGAAGCTGAGAAGAATCAAAGTGAAGCTAGGACCAAG                         GAAGAGATGGAGGAAGCTATCAAGCAGCTAAGGAAGAGTCTAACTTTTAAA
genomic: AGCAGCAAGCAATGGAAGCTGAGAAGAATCAAAGTGAAGCTAGGACCAAGgtgcaacact ... aacatttaagGAAGAGATGGAGGAAGCTATCAAGCAGCTAAGGAAGAGTCTAACTTTTAAA
EST: gi|193649840|gb|FK595451.1|FK595451
EST:     AGCAGCAAGCAATGGAAGCTGAGAAGAATCAAAGTGAAGCTAGGACCAAG                         GAAGAGATGGAGGAAGCTATCAAGCAGCTAAGGAAGAGTCTAACTTTTAAA
genomic: AGCAGCAAGCAATGGAAGCTGAGAAGAATCAAAGTGAAGCTAGGACCAAGgtgcaacact ... aacatttaagGAAGAGATGGAGGAAGCTATCAAGCAGCTAAGGAAGAGTCTAACTTTTAAA
EST: gi|192309425|gb|FK000941.1|FK000941
EST:     GGCAGCAAGCAATGGAAGCTGAGAAGAATCAAAGTGAAGCTAGGACCAAG                         GAAGAGATGGAGGAAGCTATCAAGCAGCTAAGGAAGAGTCTAACTTTTAAA
genomic: AGCAGCAAGCAATGGAAGCTGAGAAGAATCAAAGTGAAGCTAGGACCAAGgtgcaacact ... aacatttaagGAAGAGATGGAGGAAGCTATCAAGCAGCTAAGGAAGAGTCTAACTTTTAAA
EST: gi|17153596|gb|BM143529.1|BM143529
EST:     AGCAGCAAGCAATGGAAGCTGAGAAGAATCAAAGTGAAGCTAGGACCAAG                         GAAGAGATGGAGGAAGCTATCAAGCAGCTAAGGAAGAGTCTAACTTTTAAA
genomic: AGCAGCAAGCAATGGAAGCTGAGAAGAATCAAAGTGAAGCTAGGACCAAGgtgcaacact ... aacatttaagGAAGAGATGGAGGAAGCTATCAAGCAGCTAAGGAAGAGTCTAACTTTTAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctcataagttagttttttctctctgattccttcatcaatttctaaacatttaagGAAGAGATGGAGGAAGCTATCAAGCAGCTAAGGAAGAGTCTAACTTTTAAAGCAAGCCCTATGCCAAGCTTTTACCATGAAGGGCCTCCTCCTAAGGTTG
                                        ttctaaa  putative branch site (score: 2)
                                     aatttctaaacattta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgcaacactttctcaagtatcttcaacactaggaaatatattgcaattctgttacttctttttataagctcataagttagttttttctctctgattccttcatcaatttctaaacatttaagGAAGAGATGGAGGAAGCTATCAAGCAGCTAAGGAAGAGTCTAACTTTTAAAGCAAGCCCTATGCCAAGCTTTTACCATGAAGGGCCTCCTCCTAAGGTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC