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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tggaaaaaagggtcaagccattggccaagggtaatgattttatgcattatttaacaaatttcaaatgtgaactaataaggatgttgttgatgttttgtagGTATGGGCATCTTTGTTATTGTATCGCCAAATATTGGATGAGATAGAAGCTAATGATTACAACAATTTCACCAGGAGGGCTTATGTGAGCAAAGCCAAGA

Basic information

species Glycine max
transcript GLYMA02G40720.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G40720.1 (Glycine max), 3'ss of exon 6
lower sequence: AT5G17230.1 (Arabidopsis thaliana), 3'ss of exon 6
tggaaaaaagggtcaagccattggccaagggtaatgattttatgca-ttatttaacaaatttcaaatgtgaactaataaggatgttgttgatgttttgtagGTATGGGCATCTTTGTTATTGTATCGCCAAATATTGGATGAGATAGAAGCTAATGATTACAACAATTTCACCAGGAGGGCTTATGTGAGCAAAGCCAAGA
  | ||        ||  || |   ||   | ||   |    |  | ||||||        || | | | | |     ||||  | | ||   | ||  |||||||||| || ||| |||||||  |   |||| |||| ||||| ||||| ||||||||||||||||| || | ||| ||||||||| | |||| |||||
--gtaagtgtctctaaaacactcttcagccgcaagtttaccgtttacttatttcttttggatcgattttaaccc--cgaggacttggctgcaatgtttcagGTATGGGCTTCATTGCTATTGTACAGGAGAATACTGGACGAGATTGAAGCGAATGATTACAACAATTTTACTAAGAGAGCTTATGTGGGGAAAGTCAAGA

upper sequence: GLYMA02G40720.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv04s0079g00680.t01 (Vitis vinifera), 3'ss of exon 6
tggaaaaaagggtcaagccattggccaagggta-atgattttatgcattatttaacaaatttcaaatgtgaactaataagga-tgttgttgatgttttgtagGTATGGGCATCTTTGTTATTGTATCGCCAAATATTGGATGAGATAGAAGCTAATGATTACAACAATTTCACCAGGAGGGCTTATGTGAGCAAAGCCAAGA
||  |  ||   |      |||  |   ||||  || |||     ||    ||  |  || |    | || | |  |  ||| |||  | ||||||  | ||||||||||||||||  | |||||||| |||||| |||||||||| |||||||| ||||||||||| ||||| ||||| ||||||||||||||||| ||||
tgtcaggaaaatttctataattttcattgggttcattattagcaacagatgtttcctgatgtatgttttggaatgttttggaatgtcttggatgtt--gcagGTATGGGCATCTTTTCTGTTGTATCGGCAAATACTGGATGAGATTGAAGCTAACGATTACAACAACTTCACTAGGAGAGCTTATGTGAGCAAAGCTAAGA
















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|120532320|gb|EH260453.1|EH260453
EST:     ATGAGGCAGAAAAGGGAGTGA-CGAGCTTAATGAAGCTAGCAGATGGCCG                         GTATGGGCATCTTTGTTATTGTATCGCCAAATATTGGATGAGATAGAAGCT
genomic: ATGAGGCAGAAAAGGGAGTGACCGAGCTTAATGAAGCTAGCAGATGGCCGgtaagaaatt ... tgttttgtagGTATGGGCATCTTTGTTATTGTATCGCCAAATATTGGATGAGATAGAAGCT
EST: gi|5761334|gb|AI966693.1|AI966693
EST:     ATGAGGCAGAAAAGGGAGTGACCGAGCTTAATGAAGCTAGCAGATGGCCG                         GTATGGGCATCTTTGTTATTGTATCGCCAAATATTGGATGAGATAGAAGCT
genomic: ATGAGGCAGAAAAGGGAGTGACCGAGCTTAATGAAGCTAGCAGATGGCCGgtaagaaatt ... tgttttgtagGTATGGGCATCTTTGTTATTGTATCGCCAAATATTGGATGAGATAGAAGCT
EST: gi|12774776|gb|BG239724.1|BG239724
EST:     ATGAGGCAGAAAAGGGAGTGACCGAGCTTAATGAAGCTAGCAGATGGCCG                         GTATGGGCATCTTTGTTATTGTATCGCCAAATATTGGATGAGATAGAAGCT
genomic: ATGAGGCAGAAAAGGGAGTGACCGAGCTTAATGAAGCTAGCAGATGGCCGgtaagaaatt ... tgttttgtagGTATGGGCATCTTTGTTATTGTATCGCCAAATATTGGATGAGATAGAAGCT
EST: gi|18040161|gb|BM308455.1|BM308455
EST:     ATGAGGCAGAAAAGGGAGTGACCGAGCTTAATGAAGCTAGCAGATGGCCG                         GTATGGGCATCTTTGTTATTGTATCGCCAAATATTGGATGAGATAGAAGCT
genomic: ATGAGGCAGAAAAGGGAGTGACCGAGCTTAATGAAGCTAGCAGATGGCCGgtaagaaatt ... tgttttgtagGTATGGGCATCTTTGTTATTGTATCGCCAAATATTGGATGAGATAGAAGCT
EST: gi|7284145|gb|AW596743.1|AW596743
EST:     ATGAGGCAGAAAAGGGAGTGACCGAGCTTAATGAAGCTAGCAGATGGCCG                         GTATGGGCATCTTTGTTATTGTATCGCCAAATATTGGATGAGATAGAAGCT
genomic: ATGAGGCAGAAAAGGGAGTGACCGAGCTTAATGAAGCTAGCAGATGGCCGgtaagaaatt ... tgttttgtagGTATGGGCATCTTTGTTATTGTATCGCCAAATATTGGATGAGATAGAAGCT
EST: gi|193566537|gb|FK522482.1|FK522482
EST:     ATGAAGCTAGCAGATGGCCG                         GTATGGGCATCTTTGTTATTGTATCGCCAAATATTGGATGAGATAGAAGCT
genomic: ATGAAGCTAGCAGATGGCCGgtaagaaatt ... tgttttgtagGTATGGGCATCTTTGTTATTGTATCGCCAAATATTGGATGAGATAGAAGCT
EST: gi|208048168|gb|GD848793.1|GD848793
EST:     ATGAGGCAGAAAAGGGAGTGACCGAGCTTAATGAAGCTAGCAGATGGCCG                         GTATGGGCATCTTTGTTATTGTATCGCCAAATATTGGATGAGATAGAAGCT
genomic: ATGAGGCAGAAAAGGGAGTGACCGAGCTTAATGAAGCTAGCAGATGGCCGgtaagaaatt ... tgttttgtagGTATGGGCATCTTTGTTATTGTATCGCCAAATATTGGATGAGATAGAAGCT
EST: gi|193554463|gb|FK511380.1|FK511380
EST:     ATGAAGCTAGCAGATGGCCG                         GTATGGGCATCTTTGTTATTGTATCG
genomic: ATGAAGCTAGCAGATGGCCGgtaagaaatt ... tgttttgtagGTATGGGCATCTTTGTTATTGTATCG
EST: gi|193378555|gb|FK343804.1|FK343804
EST:     ATGAGGCAGAAAAGGGAGTGACCGAGCTTAATGAAGCTAGCAGATGGCCG                         GTATGGGCATCTTTGTTATTGTATCGCCAAATATTGGATGAGATAGAAGCT
genomic: ATGAGGCAGAAAAGGGAGTGACCGAGCTTAATGAAGCTAGCAGATGGCCGgtaagaaatt ... tgttttgtagGTATGGGCATCTTTGTTATTGTATCGCCAAATATTGGATGAGATAGAAGCT
EST: gi|120533005|gb|EH261138.1|EH261138
EST:     ATGAGGCAGAAAAGGGAGTGACCGAGCTTAATGAAGCTAGCAGATGGCCG                         GTATGGGCATCTTTGTTATTGTATCGCCAAATATTGGATGAGATAGAAGCT
genomic: ATGAGGCAGAAAAGGGAGTGACCGAGCTTAATGAAGCTAGCAGATGGCCGgtaagaaatt ... tgttttgtagGTATGGGCATCTTTGTTATTGTATCGCCAAATATTGGATGAGATAGAAGCT
EST: gi|13482477|gb|BG511820.1|BG511820
EST:     ATGAGGCAGAAAAGGGAGTGACCGAGCTTAATGAAGCTAGCAGATGGCCG                         GTATGGGCATCTTTGTTATTGTATCGCCAAATATTGGATGAGATAGAAGCT
genomic: ATGAGGCAGAAAAGGGAGTGACCGAGCTTAATGAAGCTAGCAGATGGCCGgtaagaaatt ... tgttttgtagGTATGGGCATCTTTGTTATTGTATCGCCAAATATTGGATGAGATAGAAGCT
EST: gi|193558438|gb|FK515299.1|FK515299
EST:     ATGAAGCTAGCAGATGGCCG                         GTATGGGTCATCTTTGTTATTGTATCGCCAAATATTGGATGAGATAGAAGC
genomic: ATGAAGCTAGCAGATGGCCGgtaagaaatt ... tgttttgtagGTATGGG-CATCTTTGTTATTGTATCGCCAAATATTGGATGAGATAGAAGC
EST: gi|31455984|gb|CD398012.1|CD398012
EST:     ATGAGGCAGAAAAGGGAGTGACCGAGCTTAATGAAGCTAGCAGATGGCCG                         GTATGGGCATCTTTGTTATTGTATCGCCAAATATTGGATGAGATAGAAGCT
genomic: ATGAGGCAGAAAAGGGAGTGACCGAGCTTAATGAAGCTAGCAGATGGCCGgtaagaaatt ... tgttttgtagGTATGGGCATCTTTGTTATTGTATCGCCAAATATTGGATGAGATAGAAGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attatttaacaaatttcaaatgtgaactaataaggatgttgttgatgttttgtagGTATGGGCATCTTTGTTATTGTATCGCCAAATATTGGATGAGATAGAAGCTAATGATTACAACAATTTCACCAGGAGGGCTTATGTGAGCAAAGCCAAGA
     ttaacaaatttcaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tggaaaaaagggtcaagccattggccaagggtaatgattttatgcattatttaacaaatttcaaatgtgaactaataaggatgttgttgatgttttgtagGTATGGGCATCTTTGTTATTGTATCGCCAAATATTGGATGAGATAGAAGCTAATGATTACAACAATTTCACCAGGAGGGCTTATGTGAGCAAAGCCAAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- gaaaaaa
- - - - - - -caagcca
- - - - - - - - - - - - - - - - - - - - - tgcatta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtgaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gttgttg