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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACAGAGAAAATAGAGTTGGAAACTACTGTAGTGGATGAAACAAAGGAACGTGAATCATACTGTGGACAAGGAAATAGAAGGTTTAGTGgtgagtattaattgtccattgtcatgtcttttgccttgaattaccattaaaatctgtacctgcaaaggaagtcaatatgaattccgttttagattgtcgt...

Basic information

species Glycine max
transcript GLYMA18G01590.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G01590.1 (Glycine max), 5'ss of exon 3
lower sequence: AT1G13170.1 (Arabidopsis thaliana), 5'ss of exon 3
ACAGAGAAAATAGAGTTGGAAACTACTGTAGTGGATGAAACAAAGGAACGTGAATCATACTGTGGACAAGGAAATAGAAGGTTTAGTGgtgagt---atta-attgtccattgtcatgtcttt-tgc---cttgaattaccattaaaatctgtacctgcaaaggaagtcaatatgaattccgttttagattgtcgt----------------------------------------------------
|| |||||||||||| ||||| |||| || || |||||||||||||| | ||| || | ||||||||| ||||   || | |||||||||||||   |||| ||||            | ||| |||   ||| |  |     | |  ||  ||  |  ||    |      | || |   | | |   |  | ||                                                    
ACTGAGAAAATAGAGCTGGAAGCTACCGTCGTTGATGAAACAAAGGAGCATGACTCTTGCTGTGGACAGGGAA---GACGATTTAGTGgtgagttacattacattgcttgcaactgcatgtttgtgcatcctttatgtgtatattagctcactaattttaattatatatggaacgattggaggtctgagtgattgtaatttcttccttactcagttgagacagttttaacatcattgttctcctacag

upper sequence: GLYMA18G01590.1 (Glycine max), 5'ss of exon 3
lower sequence: Vv01s0137g00290.t01 (Vitis vinifera), 5'ss of exon 3
ACAGAGAAAATAGAGTTGGAAACTACTGTAGTGGATGAAACAAAGGAACGTGAATCATACTGTGGACAAGGAAATAGAAGGTTTAGTGgtgagtattaattgtc-cattgtcatgtctttt----gccttgaattaccattaaaatctgtacctgcaaaggaagtcaatatgaattccgttttagattgtcgt
||||||||||||||  |||||||||||||||||||||||||||||||||| || ||||||||||| |||||||||||||| || |||||| ||||    || || || |  ||||  || |    |  ||   | | |||  |  | |||| |  || ||  || |  |||         |||  ||  |   
ACAGAGAAAATAGAACTGGAAACTACTGTAGTGGATGAAACAAAGGAACGGGAGTCATACTGTGGCCAAGGAAATAGAAGATTCAGTGgttagtaaatcttttctcactaccatgatttattaatgtttttgttgaacat--atttttgtaacaccagagctagcctgtattttgaataatttgaatatt---
















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|208143256|gb|GD941070.1|GD941070
EST:     GAAATAGAAGGTTTAGTG                         ATTTCTATTCAGTCATGTCTGAGGGCAGTGTTACTGATTCAGTGGCGGATA
genomic: GAAATAGAAGGTTTAGTGgtgagtatta ... catgtctcagATTTCTATTCAGTCATGTCAGAGGGCAGTGTTACTGATTCAGTGGCGGATA
EST: gi|193692216|gb|FK631087.1|FK631087
EST:     AACAAAGGAACGTGAATCATACTGTGGACAAGGAAATAGAAGGTTTAGTG                         ATTTCTATTCCGTCATGTCGGAGGGCAGTGCTACTGAT
genomic: AACAAAGGAACGTGAATCATACTGTGGACAAGGAAATAGAAGGTTTAGTGgtgagtatta ... catgtctcagATTTCTATTCAGTCATGTCAGAGGGCAGTGTTACTGAT
EST: gi|207687879|gb|GD668102.1|GD668102
EST:     AACGTGAATCATACTGTGGACAAGGAAATAGAAGGTTTAGTG                         ATTTCTATTCAGTCATGTCAGAGGGCAGTGTTACTGATTCAGTGGCGGGTA
genomic: AACGTGAATCATACTGTGGACAAGGAAATAGAAGGTTTAGTGgtgagtatta ... catgtctcagATTTCTATTCAGTCATGTCAGAGGGCAGTGTTACTGATTCAGTGGCGGATA
EST: gi|208121253|gb|GD917114.1|GD917114
EST:     AACAAAGGAACGTGAATCATACTGTGGACAAGGAAATAGAAGGTTTAGTG                         ATTTCTATTCAGTCATGTCAGAGGGCAGTGTT
genomic: AACAAAGGAACGTGAATCATACTGTGGACAAGGAAATAGAAGGTTTAGTGgtgagtatta ... catgtctcagATTTCTATTCAGTCATGTCAGAGGGCAGTGTT
EST: gi|207823754|gb|GD797103.1|GD797103
EST:     GAAATAGAAGGTTTAGTG                         ATTTTCTTATTTCAGTCATGTCTGAGGGCAGTGTTACTGATTCAGTGGCGG
genomic: GAAATAGAAGGTTTAGTGgtgagtatta ... catgtctcagA-TTTC-TA-TTCAGTCATGTCAGAGGGCAGTGTTACTGATTCAGTGGCGG
EST: gi|207702476|gb|GD684254.1|GD684254
EST:     GAAGGTTTAGTG                         ATTTCTATTCAGTCATGTCAGAGGGCAGTGTTACTGATTCAGTGGCGGATA
genomic: GAAGGTTTAGTGgtgagtatta ... catgtctcagATTTCTATTCAGTCATGTCAGAGGGCAGTGTTACTGATTCAGTGGCGGATA
EST: gi|193490939|gb|FK454692.1|FK454692
EST:     AACAAAGGAACGTGAATCATACTGTGGACAAGGAAATAGAAGGTTTAGTG                         ATTTCTATTCAGTCA
genomic: AACAAAGGAACGTGAATCATACTGTGGACAAGGAAATAGAAGGTTTAGTGgtgagtatta ... catgtctcagATTTCTATTCAGTCA
EST: gi|193625662|gb|FK577902.1|FK577902
EST:     AACAAAGGAACGTGAATCATACTGTGGACAAGGAAATAGAAGGTTTAGTG                         ATTTCTATTCAGTCATGTCAGAGGGCAGTGTTACTGATTCAGTGGCGG
genomic: AACAAAGGAACGTGAATCATACTGTGGACAAGGAAATAGAAGGTTTAGTGgtgagtatta ... catgtctcagATTTCTATTCAGTCATGTCAGAGGGCAGTGTTACTGATTCAGTGGCGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACAGAGAAAATAGAGTTGGAAACTACTGTAGTGGATGAAACAAAGGAACGTGAATCATACTGTGGACAAGGAAATAGAAGGTTTAGTGgtgagtattaattgtccattgtcatgtcttttgccttgaattaccattaaaatctgtacctgcaaaggaagtcaatatgaattccgttttagattgtcgt

- - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA