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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CACTGAAGAGAAACTTGAAGCTGCTGGTAAGAAGAAAGAAGAAGGAAATGTGTTGTTTAAAGCTGGTAAGCATGCAAGAGCTTCCAAAAGATATGAAAAGgtaatctaaaatagattatacatttcactttctacatgttgatgcacctgctgatggtactgaaatcttactgtag

Basic information

species Glycine max
transcript GLYMA08G46090.2
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G46090.2 (Glycine max), 5'ss of exon 9
lower sequence: AT5G48570.1 (Arabidopsis thaliana), 5'ss of exon 9
CACTGAAGAGAAACTTGAAGCTGCTGGTAAGAAGAAAGAAGAAGGAAATGTGTTGTTTAAAGCTGGTAAGCATGCAAGAGCTTCCAAAAGATATGAAAAGgtaatctaaaatagattatacatttcactttctacatgttgatgcacctgctga-----tggtactgaaatcttactgtag
|||  | || |   | |||||||| || ||||||||||||||||| ||||||||||| |||||||| ||  | ||||||||||| || ||||| || | |||  |    | | | |  ||   ||  ||    | |   | |||    || | |     |   |   |  | | | || ||
CACACAGGAAAGGATAGAAGCTGCAGGCAAGAAGAAAGAAGAAGGCAATGTGTTGTTCAAAGCTGGAAAATACGCAAGAGCTTCAAAGAGATACGAGAGGgt--ttgggatttggtcctagtatttgcta--aagaaacttatgtttttgtttagattttaacatcaagttttgattgcag

upper sequence: GLYMA08G46090.2 (Glycine max), 5'ss of exon 9
lower sequence: AT3G25230.1 (Arabidopsis thaliana), 5'ss of exon 9
CACTGAAGAGAAACTTGAAGCTGCTGGTAAGAAGAAAGAAGAAGGAAATGTGTTGTTTAAAGCTGGTAAGCATGCAAGAGCTTCCAAAAGATATGAAAAGgtaatctaaaatagattatacatttcacttt---ctacatgttgatgcacctgctgatggtactgaaatcttactgtag
|||||| |||||  ||||||||||| |||||||||| ||||||||||||     ||||||||  || ||  || |    |||||||| |||||||| |||||| | | | |   | ||   ||| |  | |    || | || ||  || |  || |   |  | || | |      ||
CACTGAGGAGAAGATTGAAGCTGCTAGTAAGAAGAAGGAAGAAGGAAATTCCAAGTTTAAAGGAGGCAAATATTCCCTGGCTTCCAAGAGATATGAGAAGgta-tatgatacgaactacttattgctttatgagttataagtcga-acaacatcttaca-tggttaagtttcttctcag

upper sequence: GLYMA08G46090.2 (Glycine max), 5'ss of exon 9
lower sequence: Vv00s0958g00020.t01 (Vitis vinifera), 5'ss of exon 5
CACTGAAGAGAAACTTGAAGCTGCTGGTAAGAAGAAAGAAGAAGGAAATGTGTTGTTTAAAGCTGGTAAGCATGCAAGAGCTTCCAAAAGATATGAAAAGgtaatctaaaatagattatacatttcactttctacatgttgatgc--acctgctgatggtactgaa---atcttactgtag------------
||||||||||||  |||| |||||||| |||||||| |||||||| |||||| | || || ||||||||  |||||||||| || || |||||||| |||||||  | | ||     |||   ||    |  |   |   | |     ||        || || ||   ||||| || | |            
CACTGAAGAGAAGATTGAGGCTGCTGGCAAGAAGAAGGAAGAAGGCAATGTGCTATTCAAGGCTGGTAAATATGCAAGAGCCTCAAAGAGATATGAGAAGgtaaaatcatatgtggaatatgcttagtctattgattagcggtctctgccattcctctgtcctcaatttatctttcttttggttgcaatgcag

upper sequence: GLYMA08G46090.2 (Glycine max), 5'ss of exon 9
lower sequence: Vv00s0769g00010.t01 (Vitis vinifera), 5'ss of exon 9
CACTGAAGAGAAACTTGAAGCTGCTGGTAAGAAGAAAGAAGAAGGAAATGTGTTGTTTAAAGCTGGTAAGCATGCAAGAGCTTCCAAAAGATATGAAAAGgtaatctaaaatagattatacatttcactttctacatgttgatgc--acctgctgatggtactgaa---atcttactgtag------------
||||||||||||  |||| |||||||| |||||||| |||||||| |||||| | || || ||||||||  |||||||||| || || |||||||| |||||||  | | ||     |||   || |  |  |   |   | |     ||        || || ||   ||||| || | |            
CACTGAAGAGAAGATTGAGGCTGCTGGCAAGAAGAAGGAAGAAGGCAATGTGCTATTCAAGGCTGGTAAATATGCAAGAGCCTCAAAGAGATATGAGAAGgtaaaatcatatgtgggatatgcttaatctattgattagcggtctctgccattcctctgtcctcaatttatctttcttttggttgcaatgcag

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|209724188|gb|BW659722.1|BW659722
EST:     TGTTGTTTAAAGCTGGTAAGCATGCAAGAGCTTCCAAAAGATATGAAAAG                         GCTGTAAAGTACATAGAATATGATTCCTCATTCGGTGAGGAGGAGAAAAAG
genomic: TGTTGTTTAAAGCTGGTAAGCATGCAAGAGCTTCCAAAAGATATGAAAAGgtaatctaaa ... cttactgtagGCTGTAAAGTACATAGAATATGATTCCTCATTCGGTGAGGAGGAGAAAAAG
EST: gi|193717162|gb|FK655588.1|FK655588
EST:     TGTTGTTTAAAGCTGGTAAGCATGCAAGAGCTTCCAAAAGATATGAAAAG                         GCTGTAAAGTACATAGAATATGATTCCTCATTCGGTGAGGAGGAGAAAAAG
genomic: TGTTGTTTAAAGCTGGTAAGCATGCAAGAGCTTCCAAAAGATATGAAAAGgtaatctaaa ... cttactgtagGCTGTAAAGTACATAGAATATGATTCCTCATTCGGTGAGGAGGAGAAAAAG
EST: gi|193331359|gb|FK296739.1|FK296739
EST:     TGTTGTTTAAAGCTGGTAAGCATGCAAGAGCTTCCAAAAGATATGAAAAG                         GCTGTAAAGTACATAGAATATGATTCCTCATTCGGTGAGGAGGAGAAAAAG
genomic: TGTTGTTTAAAGCTGGTAAGCATGCAAGAGCTTCCAAAAGATATGAAAAGgtaatctaaa ... cttactgtagGCTGTAAAGTACATAGAATATGATTCCTCATTCGGTGAGGAGGAGAAAAAG
EST: gi|193665940|gb|FK611327.1|FK611327
EST:     TGTTGTTTAAAGCTGGTAAGCATGCAAGAGCTTCCAAAAGATATGAAAAG                         GCTGTAAAGTACATAGAATATGATTCCTCATTCGGTGAGGAGGAGAAAAAG
genomic: TGTTGTTTAAAGCTGGTAAGCATGCAAGAGCTTCCAAAAGATATGAAAAGgtaatctaaa ... cttactgtagGCTGTAAAGTACATAGAATATGATTCCTCATTCGGTGAGGAGGAGAAAAAG
EST: gi|193386205|gb|FK351665.1|FK351665
EST:     TGTTGTTTAAAGCTGGTAAGCATGCAAGAGCTTCCAAAAGATATGAAAAG                         GCTGTAAAGTACATAGAATATGATTCCTCATTCGGTGAGGAGGAGAAAAAG
genomic: TGTTGTTTAAAGCTGGTAAGCATGCAAGAGCTTCCAAAAGATATGAAAAGgtaatctaaa ... cttactgtagGCTGTAAAGTACATAGAATATGATTCCTCATTCGGTGAGGAGGAGAAAAAG
EST: gi|193429516|gb|FK394464.1|FK394464
EST:     TGTTGTTTAAAGCTGGTAAGCATGCAAGAGCTTCCAAAAGATATGAAAAG                         GCTGTAAAGTACATAGAATATGGTTCCTCATTCGGTGAGGAGGAGAAAAAG
genomic: TGTTGTTTAAAGCTGGTAAGCATGCAAGAGCTTCCAAAAGATATGAAAAGgtaatctaaa ... cttactgtagGCTGTAAAGTACATAGAATATGATTCCTCATTCGGTGAGGAGGAGAAAAAG
EST: gi|208301049|gb|GE098532.1|GE098532
EST:     TGTTGTTTAAAGCTGGTAAGCATGCAAGAGCTTCCAAAGGATATGAAAAG                         GCTGTAAAGTACATAGAATATGATTCCTCATTCGGTGAGG
genomic: TGTTGTTTAAAGCTGGTAAGCATGCAAGAGCTTCCAAAAGATATGAAAAGgtaatctaaa ... cttactgtagGCTGTAAAGTACATAGAATATGATTCCTCATTCGGTGAGG
EST: gi|207808632|gb|GD780577.1|GD780577
EST:     TGTTGTTTAAAGCTGGTAAGCATGCAAGAGCTTCCAAAAGATATGAAAAG                         GCTGTAAAGTACATAGAATATGATTCCTCATTCGGTGAGGAGGAGAAAAAG
genomic: TGTTGTTTAAAGCTGGTAAGCATGCAAGAGCTTCCAAAAGATATGAAAAGgtaatctaaa ... cttactgtagGCTGTAAAGTACATAGAATATGATTCCTCATTCGGTGAGGAGGAGAAAAAG
EST: gi|193566984|gb|FK525085.1|FK525085
EST:     TGTTGTTTAAAGCTGGTAAGCATGCAAGAGCTTCCAAAAGATATGAAAAG                         GCTGTAAAGTACATAGAATATGATTCCTCATTCGGTGAGGAGGAGAAAAAA
genomic: TGTTGTTTAAAGCTGGTAAGCATGCAAGAGCTTCCAAAAGATATGAAAAGgtaatctaaa ... cttactgtagGCTGTAAAGTACATAGAATATGATTCCTCATTCGGTGAGGAGGAGAAAAA-

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CACTGAAGAGAAACTTGAAGCTGCTGGTAAGAAGAAAGAAGAAGGAAATGTGTTGTTTAAAGCTGGTAAGCATGCAAGAGCTTCCAAAAGATATGAAAAGgtaatctaaaatagattatacatttcactttctacatgttgatgcacctgctgatggtactgaaatcttactgtag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT