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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gcatggttcattttactctttttctagttaagttaaatatttaggggatgtaaccttccatttcatgtctgtaattttgctcagtaggatatgcaagctttttctcatacatataccacggattggatgcttgtcttctgtgtagagataatttacttgatactctgattatcagGGAGGGAAAATCCTAACCGGTGGATCTGTATTAGAGTCGGGAGGAAATTTTGTACAACCAACAATTGTTGAGATTTCTCCAGATGCTCCTGTAGTTAAAG

Basic information

species Glycine max
transcript GLYMA09G08150.2
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G08150.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv11s0016g00900.t01 (Vitis vinifera), 3'ss of exon 10
gcatggttcattttactctttttctagttaagttaaatatttaggggatgtaaccttccatttcatgtctgtaattttgctcagtaggatatgcaagctttttctcatacatataccacggattggatgcttgtcttctgtgtagagataatttacttgatactctgattat-cagGGAGGGAAAATCCTAACCGGTGGATCTGTATTAGAGTCGGGAGGAAATTTTGTACAACCAACAATTGTTGAGATTTCTCCAGATGCTCCTGTAGTTAAAG
                                                                            |  |  ||  |  |     |  ||||  |   |  |||   ||      |  | || | |  || ||   | |||| ||     | |   |   || |||||||| || || || |  ||||| ||     |||| || |  ||||||||||| || |||||||| ||||||||||||||| ||||  |||||||||| |
---------------------------------------------------------------------------atctcaaagctgcttggattaatttttgatagaatttattttaccagaatgtcgttt-tttcttgggttttgttaatctaaactcttccaaggacattcagGGAGGAAATATTCTGATTGGTGGGTCCACTGTAGAATCTGAGGGAAATTTTGTGCAGCCAACAATCGTTGAGATTTCTCCAAATGCCTCTGTAGTTAAGG
















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|193671020|gb|FK608298.1|FK608298
EST:     GTGCTTCAGTAGAAAACTTTCAGAAGGGTATTTCAGTCATAAAATCTCAG                         GGAGGGAAAATCCTAACCGGTGGATCTGTATTAGAGTCGGGAGGAAATTTT
genomic: GTACTTCAGTAGAAAACTTTCAGAAGGGTATTTCAGTCATAAAATCTCAGgcatggttca ... tgattatcagGGAGGGAAAATCCTAACCGGTGGATCTGTATTAGAGTCGGGAGGAAATTTT
EST: gi|58019812|gb|CX706554.1|CX706554
EST:     GTACTTCAGTAGAAAACTTTCAGAAGGGTATTTCAGTCATAAAATCTCAG                         GGAGGGAAAATCCTAACCGGTGGATCTGTATTAGAGTCGGGAGGAAATTTT
genomic: GTACTTCAGTAGAAAACTTTCAGAAGGGTATTTCAGTCATAAAATCTCAGgcatggttca ... tgattatcagGGAGGGAAAATCCTAACCGGTGGATCTGTATTAGAGTCGGGAGGAAATTTT
EST: gi|57575444|gb|CX548419.1|CX548419
EST:     GTACTTCAGTAGAAAACTTTCAGAAGGGTATTTCAGTCATAAAATCTCAG                         GGAGGGAAAATCCTAACCGGTGGATCTGTATTAGAGTCGGGAGGAAATTTT
genomic: GTACTTCAGTAGAAAACTTTCAGAAGGGTATTTCAGTCATAAAATCTCAGgcatggttca ... tgattatcagGGAGGGAAAATCCTAACCGGTGGATCTGTATTAGAGTCGGGAGGAAATTTT
EST: gi|193541518|gb|FK499200.1|FK499200
EST:     GTGCTTCAGTAGAAAACTTTCAGAAGGGTATTTCAGTCATAAAATCTCAG                         GGAGGGAAAATCCTAACCGGTGGATCTGTATTAGAGTCGGGAGGAAATTTT
genomic: GTACTTCAGTAGAAAACTTTCAGAAGGGTATTTCAGTCATAAAATCTCAGgcatggttca ... tgattatcagGGAGGGAAAATCCTAACCGGTGGATCTGTATTAGAGTCGGGAGGAAATTTT
EST: gi|193630538|gb|FK580885.1|FK580885
EST:     GTACTTCAGTAGAAAACTTTCAGAAGGGTATTTCAGTCATAAAATCTCAG                         GGAGGGAAAATCCTAACCGGTGGATCTGTATTAGAGTCGGGAGGAAATTTT
genomic: GTACTTCAGTAGAAAACTTTCAGAAGGGTATTTCAGTCATAAAATCTCAGgcatggttca ... tgattatcagGGAGGGAAAATCCTAACCGGTGGATCTGTATTAGAGTCGGGAGGAAATTTT
EST: gi|254336948|gb|GR843127.1|GR843127
EST:     ATTTCAGTCATAAAATCTCAG                         GGAGGGAAAATCCTAACCGGTGGATCTGTATTAGAGTCGGGAGGAAATTTT
genomic: ATTTCAGTCATAAAATCTCAGgcatggttca ... tgattatcagGGAGGGAAAATCCTAACCGGTGGATCTGTATTAGAGTCGGGAGGAAATTTT
EST: gi|254336949|gb|GR843128.1|GR843128
EST:     ATTTCAGTCATAAAATCTCAG                         GGAGGGAAAAT-CTAACCGGTGGATCTGTATTAGAGTCGGGAGGAAATTTT
genomic: ATTTCAGTCATAAAATCTCAGgcatggttca ... tgattatcagGGAGGGAAAATCCTAACCGGTGGATCTGTATTAGAGTCGGGAGGAAATTTT
EST: gi|19452651|gb|BM954061.1|BM954061
EST:     GTACTTCAGTAGAAAACTTTCAGAAGGGTATTTCAGTCATAAAATCTCAG                         GGAGGGAAAATCCTAACCGGTGGATCTGTATTAGAGTCGGGAGGAAATTTT
genomic: GTACTTCAGTAGAAAACTTTCAGAAGGGTATTTCAGTCATAAAATCTCAGgcatggttca ... tgattatcagGGAGGGAAAATCCTAACCGGTGGATCTGTATTAGAGTCGGGAGGAAATTTT
EST: gi|58022682|gb|CX709423.1|CX709423
EST:     GTAGTTCAGTAGAAAACTTTCAGAAGGGTATTTCAGTCATAAAATCTCAG                         GGAGGGAAAATCCTAACCGGTGGATCTGTATTAGAGTCGGGAGGAAATTTT
genomic: GTACTTCAGTAGAAAACTTTCAGAAGGGTATTTCAGTCATAAAATCTCAGgcatggttca ... tgattatcagGGAGGGAAAATCCTAACCGGTGGATCTGTATTAGAGTCGGGAGGAAATTTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gattggatgcttgtcttctgtgtagagataatttacttgatactctgattatcagGGAGGGAAAATCCTAACCGGTGGATCTGTATTAGAGTCGGGAGGAAATTTTGTACAACCAACAATTGTTGAGATTTCTCCAGATGCTCCTGTAGTTAAAG
                                          ctctgat  putative branch site (score: 4)
                           ataatttacttgata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcatggttcattttactctttttctagttaagttaaatatttaggggatgtaaccttccatttcatgtctgtaattttgctcagtaggatatgcaagctttttctcatacatataccacggattggatgcttgtcttctgtgtagagataatttacttgatactctgattatcagGGAGGGAAAATCCTAACCGGTGGATCTGTATTAGAGTCGGGAGGAAATTTTGTACAACCAACAATTGTTGAGATTTCTCCAGATGCTCCTGTAGTTAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG