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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGAGACTTCTTTCGGCGATGATATGTGAATACCTTGACTGGGCGCAGCTCAGTCATACGCTAAAAGTTTATCTTCCGGAATGTAATTTGgtaattaatgaatccttgtttttatttttccgtagtatctgcgttcctgttggctgttgctttctgttatttttttttcccgtcgtgaggcatttggctgaataaacatttttgcag

Basic information

species Glycine max
transcript GLYMA20G38790.3
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G38790.2 (Glycine max), 5'ss of exon 3
lower sequence: LOC_Os12g01170.1 (Oryza sativa), 5'ss of exon 3
GGAGACTTCTTTCGGCGATGATATGTGAATACCTTGACTGGGCGCAGCTCAGTCATACGCTAAAAGTTTATCTTCCGGAATGTAATTTGgtaattaatgaatccttgtttttatttttccgtag-tatctgcgttcctgttggctgttgctttctgttatttttttttcccgtcgtgaggcatttggctgaataaacatttttgcag
| ||  |  |  | ||  |  || |||||||| | || ||||| ||||| ||||| ||| | ||||||||||| || ||||||||| ||||||    |       | |  | | | ||   | | ||| | |           ||| |  |  ||| ||||  || ||  |    ||  |||||||  | ||| |            
GTAGGTTATTAACAGCACTTGTAAGTGAATACTTGGAGTGGGCCCAGCTAAGTCACACGATGAAAGTTTATCTGCCTGAATGTAATCTGgtaacagtttgccatatctcataaatcttggatggatatgtccaaaatcaacatctgctaatg-ctgctattgattgttggc----tgttgcatttg--taaatcag-----------

upper sequence: GLYMA20G38790.2 (Glycine max), 5'ss of exon 3
lower sequence: Vv13s0067g03320.t01 (Vitis vinifera), 5'ss of exon 3
GGAGACTTCTTTCGGCGATGATATGTGAATACCTTGACTGGGCGCAGCTCAGTCATACGCTAAAAGTTTATCTTCCGGAATGTAATTTGgtaattaatga-atccttgtttttatttttccgtagtatctgcgttcctgttggctgttgctttctgttatttttttttcccgtcgtgaggcat-ttggctgaataaacat-ttttgcag--------------------
| ||  | ||  | ||  | |||||||||||| | |||||||| ||  | |  || ||   |||||||||| ||||||||||||||||||||||   ||| ||  |   | || || |    |  | |     ||| | || ||  ||  |||     | | | |||     || |    ||| ||  ||||  |  ||  ||||                        
GAAGGTTGCTAGCTGCACTAATATGTGAATACTTGGACTGGGCACAATTGAACCACACATCAAAAGTTTATATTCCGGAATGTAATTTGgtaatctgtgacattttgactatttttctgttttcttcttcttcttcttttttgcaattagttttaaccactctgtttaattatccttttacatatttactgatgagtcaagttttattttttattttttcaaaatgcag
















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|298186320|gb|HO036953.1|HO036953
EST:     GGGCGCAGCTCAGTCATACGCTAAAAGTTTATCTTCCGGAATGTAATTTG                         GAGAAAGATTTTTGGAAGACAGAGCTTAAGGAGTTTAGTGCCAAAAGTGGA
genomic: GGGCGCAGCTCAGTCATACGCTAAAAGTTTATCTTCCGGAATGTAATTTGgtaattaatg ... atttttgcagGAGAAAGATTTTTGGAAGACAGAGCTTAAGGAGTTTAGTGCCAAAAATGGA
EST: gi|208206870|gb|GE004663.1|GE004663
EST:     GGGCGCAGCTCAGTCATACGCTAAAAGTTTATCTTCCGGAATGTAATTTG                         GAGAAAGATTTTTGGAAGACAGAGCTTAAGGAGTTTAGTGCCAAAAATGGA
genomic: GGGCGCAGCTCAGTCATACGCTAAAAGTTTATCTTCCGGAATGTAATTTGgtaattaatg ... atttttgcagGAGAAAGATTTTTGGAAGACAGAGCTTAAGGAGTTTAGTGCCAAAAATGGA
EST: gi|298168800|gb|HO009730.1|HO009730
EST:     GGGCGCAGCTCAGTCATACGCTAAAAGTTTATCTTCCGGGATGTAATTTG                         GAGAAAGATTTTTGGAAGACAGAGCTTAAGGAGTTTAGTGCCAAAAATGGA
genomic: GGGCGCAGCTCAGTCATACGCTAAAAGTTTATCTTCCGGAATGTAATTTGgtaattaatg ... atttttgcagGAGAAAGATTTTTGGAAGACAGAGCTTAAGGAGTTTAGTGCCAAAAATGGA
EST: gi|193338472|gb|FK303399.1|FK303399
EST:     GCAGCTCAGTCATACGCTTAAAAGTTTTATTCTTTCCGGAATGTAATTTG                         GAGAAAGATTTT-GGAAGACAGAGCTTAAGGAGTTTAGTGCCAAAAATGGA
genomic: GCAGCTCAGTCATACGCT-AAAAGTTT-AT-CTT-CCGGAATGTAATTTGgtaattaatg ... atttttgcagGAGAAAGATTTTTGGAAGACAGAGCTTAAGGAGTTTAGTGCCAAAAATGGA
EST: gi|151405233|gb|EV275047.1|EV275047
EST:     GGGCGCAGCTCAGTCATACGCTAAAAGTTTATCTTCCGGAATGTAATTTG                         GAGAAAGATTTTTGGAAGACAGAGCTTAAGGAGTTTAGTGCCAAAAATGGA
genomic: GGGCGCAGCTCAGTCATACGCTAAAAGTTTATCTTCCGGAATGTAATTTGgtaattaatg ... atttttgcagGAGAAAGATTTTTGGAAGACAGAGCTTAAGGAGTTTAGTGCCAAAAATGGA
EST: gi|298191648|gb|HO039127.1|HO039127
EST:     GGGCGCAGCTCAGTCATACGCTAAAAGTTTATCTTCCGGAATGTAATTTG                         GAGAAAGATTTTTGGAAGACAGAGCTTAAGGAGTTTAGTGCCAAAAATGGA
genomic: GGGCGCAGCTCAGTCATACGCTAAAAGTTTATCTTCCGGAATGTAATTTGgtaattaatg ... atttttgcagGAGAAAGATTTTTGGAAGACAGAGCTTAAGGAGTTTAGTGCCAAAAATGGA
EST: gi|208224417|gb|GE021812.1|GE021812
EST:     GGGCGCAGCTCAGTCATACGCTAAAAGTTTATCTTCCGGAATGTAATTTG                         GAGAAAGATTTTTGGAAGACAGAGCTTAAGGAGTTTAGTGCCAAAAATGGA
genomic: GGGCGCAGCTCAGTCATACGCTAAAAGTTTATCTTCCGGAATGTAATTTGgtaattaatg ... atttttgcagGAGAAAGATTTTTGGAAGACAGAGCTTAAGGAGTTTAGTGCCAAAAATGGA
EST: gi|13563206|gb|BG551426.1|BG551426
EST:     GGGCGCAGCTCAGTCATACGCTAAAAGTTTATCTTCCGGAATGTAATTTG                         GAGAAAGATTTTTGGAAGACAGAGCTTAAGGAGTTTAGTACCAAAAATGGA
genomic: GGGCGCAGCTCAGTCATACGCTAAAAGTTTATCTTCCGGAATGTAATTTGgtaattaatg ... atttttgcagGAGAAAGATTTTTGGAAGACAGAGCTTAAGGAGTTTAGTGCCAAAAATGGA
EST: gi|208192634|gb|GD989754.1|GD989754
EST:     GGGCGCAGCTCAGTCATACGCTAAAAGTTTATCTTCCGGAATGTAATTTG                         GAGAAAGATTTTTGGAAGACAGAGCTTAAGGAGTTTAGTGCCAAAAATGGA
genomic: GGGCGCAGCTCAGTCATACGCTAAAAGTTTATCTTCCGGAATGTAATTTGgtaattaatg ... atttttgcagGAGAAAGATTTTTGGAAGACAGAGCTTAAGGAGTTTAGTGCCAAAAATGGA
EST: gi|298198893|gb|HO042256.1|HO042256
EST:     GGGCGCAGCTCAGTCATACGCTAAAAGTTTATCTTCCGGAATGTAATTTG                         GAGAAAGATTTTTGGAAGACAGAGCTTAAGGAGTTTAGTGCCAAAAATGGA
genomic: GGGCGCAGCTCAGTCATACGCTAAAAGTTTATCTTCCGGAATGTAATTTGgtaattaatg ... atttttgcagGAGAAAGATTTTTGGAAGACAGAGCTTAAGGAGTTTAGTGCCAAAAATGGA
EST: gi|193340928|gb|FK307205.1|FK307205
EST:     GGGCGCAGCTCAGTCATACGCTAAAAGTTTATCTTCCGGAATGTAATTTG                         GAGAAAGATTTTTGGAAGACAGAGCTTAAGGAGTTTAGTGCCAAAAATGGA
genomic: GGGCGCAGCTCAGTCATACGCTAAAAGTTTATCTTCCGGAATGTAATTTGgtaattaatg ... atttttgcagGAGAAAGATTTTTGGAAGACAGAGCTTAAGGAGTTTAGTGCCAAAAATGGA
EST: gi|151408547|gb|EV278355.1|EV278355
EST:     GGGCGCAGCTCAGTCATACGCTAAAAGTTTATCTTCCGGAATGTAATTTG                         GAGAAAGATTTTTGGAAGACAGAGCTTAAGGAGTTTAGTGCCAAAAATGGA
genomic: GGGCGCAGCTCAGTCATACGCTAAAAGTTTATCTTCCGGAATGTAATTTGgtaattaatg ... atttttgcagGAGAAAGATTTTTGGAAGACAGAGCTTAAGGAGTTTAGTGCCAAAAATGGA
EST: gi|254329094|gb|GR833466.1|GR833466
EST:     GGGCGCAGCTCAGTCATACGCTAAAAGTTTATCTTCCGGAATGTAATTTG                         GAGAAAGATTTTTGGAAGACAGAGCTTAAGGAGTTTAGTGCCAAAAATGGA
genomic: GGGCGCAGCTCAGTCATACGCTAAAAGTTTATCTTCCGGAATGTAATTTGgtaattaatg ... atttttgcagGAGAAAGATTTTTGGAAGACAGAGCTTAAGGAGTTTAGTGCCAAAAATGGA
EST: gi|192325538|gb|FK018434.1|FK018434
EST:     GGGCGCAGCTCAGTCATACGCTAAAAGTTTATCTTCCGGAATGTAATTTG                         GAGAAAGATTTTTGGAAGACAGAGCTTAAGGAGTTTAGTGCCAAAAATGGA
genomic: GGGCGCAGCTCAGTCATACGCTAAAAGTTTATCTTCCGGAATGTAATTTGgtaattaatg ... atttttgcagGAGAAAGATTTTTGGAAGACAGAGCTTAAGGAGTTTAGTGCCAAAAATGGA
EST: gi|22522110|gb|BU080921.1|BU080921
EST:     GGGCGCAGCTCAGTCATACGCTAAAAGTTTATCTTCCGGAATGTAATTTG                         GAGAAAGATTTTTGGAAGACAGAGCTTAAGGAGTTTAGTGCCAAAAATGGA
genomic: GGGCGCAGCTCAGTCATACGCTAAAAGTTTATCTTCCGGAATGTAATTTGgtaattaatg ... atttttgcagGAGAAAGATTTTTGGAAGACAGAGCTTAAGGAGTTTAGTGCCAAAAATGGA
EST: gi|298199357|gb|HO042720.1|HO042720
EST:     GGGCGCGGCTCAGTCATACGCTAAAAGTTTATCTTCCGGAATGTAATTTG                         GAGAAAGATTTTTGGAAGACAGAGCTTAAGGAGTTTAGTGCCAAAAATGGA
genomic: GGGCGCAGCTCAGTCATACGCTAAAAGTTTATCTTCCGGAATGTAATTTGgtaattaatg ... atttttgcagGAGAAAGATTTTTGGAAGACAGAGCTTAAGGAGTTTAGTGCCAAAAATGGA
EST: gi|298184578|gb|HO029791.1|HO029791
EST:     GGGCGCAGCTCAGTCATACGCTAAAAGTTTATCTTCCGGAATGTAATTTG                         GAGAAAGATTTTTGGAAGACAGAGCTTAAGGAGTTTAGTGCCAAAAATGGA
genomic: GGGCGCAGCTCAGTCATACGCTAAAAGTTTATCTTCCGGAATGTAATTTGgtaattaatg ... atttttgcagGAGAAAGATTTTTGGAAGACAGAGCTTAAGGAGTTTAGTGCCAAAAATGGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGAGACTTCTTTCGGCGATGATATGTGAATACCTTGACTGGGCGCAGCTCAGTCATACGCTAAAAGTTTATCTTCCGGAATGTAATTTGgtaattaatgaatccttgtttttatttttccgtagtatctgcgttcctgttggctgttgctttctgttatttttttttcccgtcgtgaggcatttggctgaataaacatttttgcag

- - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - -  AGCTCA