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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ccttattcttctataatatgctttcaacttagacaaacaaaagttctgaataagtaaccaattgactgacattttttaatattggatttttgtctggacaGATGGATCAGATACTTGCTGCATACAGGAAGTCATCAAAGCAATGGTCATCCACATTGAACAAACTTGCACAA

Basic information

species Glycine max
transcript GLYMA18G06300.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G06300.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv07s0151g00550.t01 (Vitis vinifera), 3'ss of exon 5
-----------ccttattcttctataatatgctttcaacttagacaaacaaaagttc-tgaataagtaaccaattgactgacattttttaatattggatttttgtctggacaGATGGATCAGATACTTGCTGCATACAGGAAGTCATCAAAGCAATGGTCATCCACATTGAACAAACTTGCACAA-
            || |||  |    || |    |||     | | ||| | |   || | || ||| | | |||    || |||  |||   |||          ||| |||||||||||  ||||||||||||||  ||||||| ||||| || ||||||||||||||||| || || || ||| 
atgctcggaaaactaatttattgggaagaaatgttc--tccacataaatagagcctcataaaaaagaagctaatc--ttgtcatggtttggcatt---------cctgcacagATGGATCGCATACTTGCTGCATATCGGAAGTCCTCAAAACAGTGGTCATCCACATTGAATAAGCTAGCTCAAG
















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|31465914|gb|CD407942.1|CD407942
EST:     TATGTTCTGGAAAGAGCTCTTATTTCAATGCATTCGTCATGTGGGAATGT                         GATGGATCAGATACTTGCTGCATACAGGAAGTCATCAAAGCAATGGTCATC
genomic: TATGTTCTGGAAAGAGCTCTTATTTCAATGCATTCGTCATGTGGGAATGTggtaagcaaa ... tgtctggacaGATGGATCAGATACTTGCTGCATACAGGAAGTCATCAAAGCAATGGTCATC
EST: gi|151412911|gb|EV282723.1|EV282723
EST:     TATGTTCTGGAAAGAGCTCTTATTTCAATGCATTCGTCATGTGGGAACGT                         GATGGATCAGATACTTGCTGCATACAGGAAGTCATCAAAGCAATGGTCATC
genomic: TATGTTCTGGAAAGAGCTCTTATTTCAATGCATTCGTCATGTGGGAATGTggtaagcaaa ... tgtctggacaGATGGATCAGATACTTGCTGCATACAGGAAGTCATCAAAGCAATGGTCATC
EST: gi|209704846|gb|BW661676.1|BW661676
EST:     TATGTTCTGGAAAGAGCTCTTATTTCAATGCATTCGTCATGTGGGAATGT                         GATGGATCAGATACTTGCTGCATACAGGAAGTCATCAAAGCAATGGTCATC
genomic: TATGTTCTGGAAAGAGCTCTTATTTCAATGCATTCGTCATGTGGGAATGTggtaagcaaa ... tgtctggacaGATGGATCAGATACTTGCTGCATACAGGAAGTCATCAAAGCAATGGTCATC
EST: gi|58023446|gb|CX710187.1|CX710187
EST:     TATGTTCTGGAAAGAGCTCTTATTTCAATGCATTCGTCATGTGGGAATGT                         GATGGATCAGATACTTGCTGCATACAGGAAGTCATCAAAGCAATGGTCATC
genomic: TATGTTCTGGAAAGAGCTCTTATTTCAATGCATTCGTCATGTGGGAATGTggtaagcaaa ... tgtctggacaGATGGATCAGATACTTGCTGCATACAGGAAGTCATCAAAGCAATGGTCATC
EST: gi|192332715|gb|FK025372.1|FK025372
EST:     TATGTTCTGGAAAGAGCTCTTATTTCAATGCATTCGTCATGTGGGAATGT                         GATGGATCAGATACTTGCTGCATACAGGAAGTCATCAAAGCAATGGTCATC
genomic: TATGTTCTGGAAAGAGCTCTTATTTCAATGCATTCGTCATGTGGGAATGTggtaagcaaa ... tgtctggacaGATGGATCAGATACTTGCTGCATACAGGAAGTCATCAAAGCAATGGTCATC
EST: gi|209727248|gb|BW663309.1|BW663309
EST:     TATGTTCTGGAAAGAGCTCTTATTTCAATGCATTCGTCATGTGGGAATGT                         GATGGATCAGATACTTGCTGCATACAGGAAGTCATCAAAGCAATGGTCATC
genomic: TATGTTCTGGAAAGAGCTCTTATTTCAATGCATTCGTCATGTGGGAATGTggtaagcaaa ... tgtctggacaGATGGATCAGATACTTGCTGCATACAGGAAGTCATCAAAGCAATGGTCATC
EST: gi|58025042|gb|CX711783.1|CX711783
EST:     TATGTTCTGGAAAGAGCTCTTATTTCAATGCATTCGTCATGTGGGAATGT                         GATGGATCAGATACTTGCTGCATACAGGAAGTCATCAAAGCAATGGTCATC
genomic: TATGTTCTGGAAAGAGCTCTTATTTCAATGCATTCGTCATGTGGGAATGTggtaagcaaa ... tgtctggacaGATGGATCAGATACTTGCTGCATACAGGAAGTCATCAAAGCAATGGTCATC
EST: gi|192296716|gb|FG991284.1|FG991284
EST:     TATGTTCTGGAAAGAGCTCTTATTTCAATGCATTCGTCATGTGGGAATGT                         GATGGATCAGATACTTGCTGCATACAGGAAGTCATCAAAGCAATGGTCATC
genomic: TATGTTCTGGAAAGAGCTCTTATTTCAATGCATTCGTCATGTGGGAATGTggtaagcaaa ... tgtctggacaGATGGATCAGATACTTGCTGCATACAGGAAGTCATCAAAGCAATGGTCATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgaataagtaaccaattgactgacattttttaatattggatttttgtctggacaGATGGATCAGATACTTGCTGCATACAGGAAGTCATCAAAGCAATGGTCATCCACATTGAACAAACTTGCACAA
                                         tttttgtct  CT-rich tract
                       acattttttaatattg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ccttattcttctataatatgctttcaacttagacaaacaaaagttctgaataagtaaccaattgactgacattttttaatattggatttttgtctggacaGATGGATCAGATACTTGCTGCATACAGGAAGTCATCAAAGCAATGGTCATCCACATTGAACAAACTTGCACAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - tgctttc
- - - - - - - - - - - - - - - - - aaacaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttgactg