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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagacttcattttttcttatacgcctttaaagtgtggatttcacagtttcacttgcacatctagttacacaatgttgctttgatcacagGTTGAACAATTTAAGCGCCTTCTTGGAGTCAAACCAATGCCTAAGAAGGAACTTAGAAGTACACCTGCTATATCTCACCCAAAGACGTTGAAATTGCCAA

Basic information

species Glycine max
transcript GLYMA03G38520.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G38520.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv07s0005g02820.t01 (Vitis vinifera), 3'ss of exon 3
-----------------------gttagacttcattttttcttatacgcctttaa--agtgtggatttcacagtttca---cttgcacatctagttacacaatgttgctttgat-----cacagGTTGAACAATTTAAGCGCCTTCTTGGAGTCAAACCAATGCCTAAGAAGGAACTTAGAAGTACACCTGCTATATCTCACCCAAAGACGTTGAAATTGCCAA
                        | | | |  || |||  || | |    || |  | |||  | |   |||||  |   |  |||  | ||||| |  | |  |  |||  |     |||||||||  ||||||| || ||||||||||||||||||||  | | |||||||  |     ||   ||||  ||| |||| ||||| || || ||  | ||||
gtgagtctactggcaggatcttgttcatattagatctttcatttttcctaattgagcaatgtaaaatattcagttatagggccagcat-tttagttgctaagtcctttttttttggctgcacagGTTGGCCAATTTATGCACCTTCTTGGAGTCAAACCAACACTTCAGAAGGATTTGGAGGGTGTTCCTGTCATAACTCATCCAAAAACTTTAAAGCTTCCAA
















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|192323979|gb|FK015700.1|FK015700
EST:     CCGAGGCAGGATGGGAGGCTGCTATAAATCCTCGTTTCTCCAATTATACA                         GTTGAACAATTTAAGCGCCTTCTTGGAGTCAAACCAATGCCTAAGAAGGAA
genomic: CCGAGGCAGGATGGGAGGCTGCTATAAATCCTCGTTTCTCCAATTATACAgttagacttc ... ttgatcacagGTTGAACAATTTAAGCGCCTTCTTGGAGTCAAACCAATGCCTAAGAAGGAA
EST: gi|192329589|gb|FK021903.1|FK021903
EST:     CCGAGGCAGGATGGGAGGCTGCTATAAATCCTCGTTTCTCCAATTATACA                         GTTGAACAATTTAAGCGCCTTCTTGGAGTCAAACCAATGCCTAAGAAGGAA
genomic: CCGAGGCAGGATGGGAGGCTGCTATAAATCCTCGTTTCTCCAATTATACAgttagacttc ... ttgatcacagGTTGAACAATTTAAGCGCCTTCTTGGAGTCAAACCAATGCCTAAGAAGGAA
EST: gi|151398613|gb|EV268484.1|EV268484
EST:     CCGAGGCAGGATGGGAGGCTGCTATAAATCCTCGTTTCTCCAATTATACA                         GTTGAACAATTTAAGCGCCTTCTTGGAGTCAAACCAATGCCTAAGAAGGAA
genomic: CCGAGGCAGGATGGGAGGCTGCTATAAATCCTCGTTTCTCCAATTATACAgttagacttc ... ttgatcacagGTTGAACAATTTAAGCGCCTTCTTGGAGTCAAACCAATGCCTAAGAAGGAA
EST: gi|19346536|gb|BM891416.1|BM891416
EST:     CCGAGGCAGGATGGGAGGCTGCTATAAATCCTCGTTTCTCCAATTATACA                         GTTGAACAATTTAAGCGCCTTCTTGGAGTCAAACCAATGCCTAAGAAGGAA
genomic: CCGAGGCAGGATGGGAGGCTGCTATAAATCCTCGTTTCTCCAATTATACAgttagacttc ... ttgatcacagGTTGAACAATTTAAGCGCCTTCTTGGAGTCAAACCAATGCCTAAGAAGGAA
EST: gi|120532302|gb|EH260435.1|EH260435
EST:     CCGAGGCAGGATGGGAGGCTGCTATAAATCCTCGTTTCTCCAATTATACA                         GTTGAACAATTTAAGCGCCTTCTTGGAGTCAAACCAATGCCTAAGAAGGAA
genomic: CCGAGGCAGGATGGGAGGCTGCTATAAATCCTCGTTTCTCCAATTATACAgttagacttc ... ttgatcacagGTTGAACAATTTAAGCGCCTTCTTGGAGTCAAACCAATGCCTAAGAAGGAA
EST: gi|6134067|gb|AW132396.1|AW132396
EST:     CCGAGGCAGGATGGGAGGCTGCTATAAATCCTCGTTTCTCCAATTATACA                         GTTGAACAATTTAAGCGCCTTCTTGGAGTCAAACCAATGCCTAAGAAGGAA
genomic: CCGAGGCAGGATGGGAGGCTGCTATAAATCCTCGTTTCTCCAATTATACAgttagacttc ... ttgatcacagGTTGAACAATTTAAGCGCCTTCTTGGAGTCAAACCAATGCCTAAGAAGGAA
EST: gi|18713013|gb|BM522699.1|BM522699
EST:     CCGAGGCAGGATGGGAGGCTGCTATAAATCCTCGTTTCTCCAATTATACA                         GTTGAACAATTTAAGCGCCTTCTTGGAGTCAAACCAATGCCTAAGAAGGAA
genomic: CCGAGGCAGGATGGGAGGCTGCTATAAATCCTCGTTTCTCCAATTATACAgttagacttc ... ttgatcacagGTTGAACAATTTAAGCGCCTTCTTGGAGTCAAACCAATGCCTAAGAAGGAA
EST: gi|192308925|gb|FK002149.1|FK002149
EST:     CCGAGGCAGGATGGGAGGCTGCTATAAATCCTCGTTTCTCCAATTATACA                         GTTGAACAATTTAAGCGCCTTCTTGGAGTCAAACCAATGCCTAAGAAGGAA
genomic: CCGAGGCAGGATGGGAGGCTGCTATAAATCCTCGTTTCTCCAATTATACAgttagacttc ... ttgatcacagGTTGAACAATTTAAGCGCCTTCTTGGAGTCAAACCAATGCCTAAGAAGGAA
EST: gi|151411964|gb|EV281775.1|EV281775
EST:     CCGAGGCAGGATGGGAGGCTGCTATAAATCCTCGTTTCTCCAATTATACA                         GTTGAACAATTTAAGCGCCTTCTTGGAGTCAAACCAATGCCTAAGAAGGAA
genomic: CCGAGGCAGGATGGGAGGCTGCTATAAATCCTCGTTTCTCCAATTATACAgttagacttc ... ttgatcacagGTTGAACAATTTAAGCGCCTTCTTGGAGTCAAACCAATGCCTAAGAAGGAA
EST: gi|105634074|gb|DW247372.1|DW247372
EST:     CCGAGGCAGGATGGGAGGCTGCTATAAATCCTCGTTTCTCCAATTATACA                         GCTGAACAATTTAGGCGCCTTCTTGGAGTCAAACCAATGCCTAAGAAGGAA
genomic: CCGAGGCAGGATGGGAGGCTGCTATAAATCCTCGTTTCTCCAATTATACAgttagacttc ... ttgatcacagGTTGAACAATTTAAGCGCCTTCTTGGAGTCAAACCAATGCCTAAGAAGGAA
EST: gi|207761165|gb|GD733298.1|GD733298
EST:     CCGAGGCAGGATGGGAGGCTGCTATAAATCCTCGTTTCTCCAATTATACA                         GTTGAACAATTTAAGCGCCTTCTTGGAGTCAAACCAATGCCTAAGAAGGAA
genomic: CCGAGGCAGGATGGGAGGCTGCTATAAATCCTCGTTTCTCCAATTATACAgttagacttc ... ttgatcacagGTTGAACAATTTAAGCGCCTTCTTGGAGTCAAACCAATGCCTAAGAAGGAA
EST: gi|10238899|gb|BE807795.1|BE807795
EST:     CCGAGGCAGGATGGGAGGCTGCTATAAATCCTCGTTTCTCCAATTATACA                         GTTGAACAATTTAAGCGCCTTCTTGGAGTCAAACCAATGCCTAAGAAGGAA
genomic: CCGAGGCAGGATGGGAGGCTGCTATAAATCCTCGTTTCTCCAATTATACAgttagacttc ... ttgatcacagGTTGAACAATTTAAGCGCCTTCTTGGAGTCAAACCAATGCCTAAGAAGGAA
EST: gi|9986530|gb|BE660638.1|BE660638
EST:     CCGAGGCAGGATGGGAGGCTGCTATAAATCCTCGTTTCTCCAATTATACA                         GTTGAACAATTTAAGCGCCTTCTTGGAGTCAAACCAATGCCTAAGAAGGAA
genomic: CCGAGGCAGGATGGGAGGCTGCTATAAATCCTCGTTTCTCCAATTATACAgttagacttc ... ttgatcacagGTTGAACAATTTAAGCGCCTTCTTGGAGTCAAACCAATGCCTAAGAAGGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggatttcacagtttcacttgcacatctagttacacaatgttgctttgatcacagGTTGAACAATTTAAGCGCCTTCTTGGAGTCAAACCAATGCCTAAGAAGGAACTTAGAAGTACACCTGCTATATCTCACCCAAAGACGTTGAAATTGCCAA
                                           ctttgat  putative branch site (score: 5)
                                        ttgcttt  CT-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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagacttcattttttcttatacgcctttaaagtgtggatttcacagtttcacttgcacatctagttacacaatgttgctttgatcacagGTTGAACAATTTAAGCGCCTTCTTGGAGTCAAACCAATGCCTAAGAAGGAACTTAGAAGTACACCTGCTATATCTCACCCAAAGACGTTGAAATTGCCAA

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