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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCCCATTTCATGAAGGAAGAGGAGGAGCAGATGAAACTTCAAAAACAAGAAGCATTGCAACTGCTTAAGAAGAAGGAGAAAACTGAAAATATAATCAAGgttttttcttctctatcaattgttctagtccttttgttttacattccagtactttagttgatgctaatccacccaagcaatgttgcag

Basic information

species Glycine max
transcript GLYMA08G02550.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G02550.1 (Glycine max), 5'ss of exon 6
lower sequence: AT4G23800.2 (Arabidopsis thaliana), 5'ss of exon 5
TGCCCATTTCATGAAGGAAGAGGAGGAGCAGATGAAACTTCAAAAACAAGAAGCATTGCAACTGCTTAAGAAGAAGGAGAAAACTGAAAATATAATCAAGgttttttcttctctatcaattgttctagtccttttgttttacattccagtactttagttgatgctaatccacccaagcaa-tgttgcag------------------
      |   | ||| ||||| ||||| |   ||||||| || |||||||||||  | ||| ||||||||||||||||||||||||| ||| | ||||||||  |  || |||| ||| |    ||   |         |  ||| ||   |      | |    |    |   |      | ||||||                  
CCTGAGTCAGAAGAAAGAAGAAGAGGAACTCTTGAAACTCCACAAACAAGAAGCTCTTCAAATGCTTAAGAAGAAGGAGAAAACTGATAATCTGATCAAGgtaataact-ctctctcactcacacttaactcaccaaggtctatttcaactcagagactcacaggatcataattatttgtctcttgcagaaggagaaggcgaccaag

upper sequence: GLYMA08G02550.1 (Glycine max), 5'ss of exon 6
lower sequence: AT4G11080.1 (Arabidopsis thaliana), 5'ss of exon 5
TGCCCATTTCATGAAGGAAGAGGAGGAGCAGATGAAACTTCAAAAACAAGAAGCATTGCAACTGCTTAAGAAGAAGGAGAAAACTGAAAATATAATCAAGgtt--ttttcttctctatcaattgttctagtccttttgttttacattccagtactttagttgatgctaatccacccaagcaatgttgcag
          | ||| ||||| || ||    |||||||| || |||||||||||  | ||||| || ||||||||||||||||| || ||||| || ||||||  | | ||   ||  || |   |  ||   |||||   || |   |||||  | |    |  |   |   |        | ||||||
AATGAGCCAGAAGAAAGAAGAAGAAGAATTCATGAAACTCCATAAACAAGAAGCTCTCCAACTTCTCAAGAAGAAGGAGAAAACCGACAATATCATAAAGgttaatatactaaactcacagtgcattgagctattttgggatataagtcagtaactaacacaacacatgttttctt------tcttgcag

upper sequence: GLYMA08G02550.1 (Glycine max), 5'ss of exon 6
lower sequence: AT4G23800.1 (Arabidopsis thaliana), 5'ss of exon 5
TGCCCATTTCATGAAGGAAGAGGAGGAGCAGATGAAACTTCAAAAACAAGAAGCATTGCAACTGCTTAAGAAGAAGGAGAAAACTGAAAATATAATCAAGgttttttcttctctatcaattgttctagtccttttgttttacattccagtactttagttgatgctaatccacccaagcaa-tgttgcag
      |   | ||| ||||| ||||| |   ||||||| || |||||||||||  | ||| ||||||||||||||||||||||||| ||| | ||||||||  |  || |||| ||| |    ||   |         |  ||| ||   |      | |    |    |   |      | ||||||
CCTGAGTCAGAAGAAAGAAGAAGAGGAACTCTTGAAACTCCACAAACAAGAAGCTCTTCAAATGCTTAAGAAGAAGGAGAAAACTGATAATCTGATCAAGgtaataact-ctctctcactcacacttaactcaccaaggtctatttcaactcagagactcacaggatcataattatttgtctcttgcag

upper sequence: GLYMA08G02550.1 (Glycine max), 5'ss of exon 6
lower sequence: Vv02s0025g01220.t01 (Vitis vinifera), 5'ss of exon 6
TGCCCATTTCATGAAGGAAGAGGAGGAGCAGATGAAACTTCAAAAACAAGAAGCATTGCAACTGCTTAAGAAGAAGGAGAAAACTGAAAATATAATCAAGgttttttcttctctatca--attgttctagtccttttgttttacattccagtactttagttgatgctaatccacccaagcaatgttgcag
||   || ||| ||||| ||||||||||||||||||| | || ||||| |||||||| |||||||| |||||||| || ||||| |||||||||||||||||| || |  |  | |||  ||   | |     | |||||     || ||  ||||     |  |||||||         ||| | |   
TGAAGATCTCAAGAAGGGAGAGGAGGAGCAGATGAAAATCCAGAAACATGAAGCATTACAACTGCTCAAGAAGAAAGAAAAAACCGAAAATATAATCAAGgttctt-caacgttgtcaccataaatttgtgggtattgtt---ggtttcaaaacttattcagcagctaatctgtggtttgaatatag---

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|208285783|gb|GE087381.1|GE087381
EST:     AAGCATTGCAACTGCTTAAGAAGAAGGAGAAAACTGAAAATATAATCAAG                         AAAACGAA-CAGAACCG
genomic: AAGCATTGCAACTGCTTAAGAAGAAGGAGAAAACTGAAAATATAATCAAGgttttttctt ... aatgttgcagAAAACAAAACAGAACCG
EST: gi|193621118|gb|FK570410.1|FK570410
EST:     AGCATTGCAAACTGCTTAAGAAGAAGGAGAAA-CTGAAAATATAATCAAG                         AAAACAAAACAGAACCG
genomic: AGCATTGCAA-CTGCTTAAGAAGAAGGAGAAAACTGAAAATATAATCAAGgttttttctt ... aatgttgcagAAAACAAAACAGAACCG
EST: gi|208241159|gb|GE041837.1|GE041837
EST:     AAGCATTGCAACTGCTTAAGAAGAAGGAGAAAACTGAAAATATAATCAAG                         AAAACAAAACAG
genomic: AAGCATTGCAACTGCTTAAGAAGAAGGAGAAAACTGAAAATATAATCAAGgttttttctt ... aatgttgcagAAAACAAAACAG
EST: gi|193412757|gb|FK378646.1|FK378646
EST:     AAGCATTGCAACTGCTTAAGAAGAAGGAGAAAACTGAAAATATAATCAAG                         AAAACAAAACAGAACCGCCAG
genomic: AAGCATTGCAACTGCTTAAGAAGAAGGAGAAAACTGAAAATATAATCAAGgttttttctt ... aatgttgcagAAAACAAAACAGAACCGCCAG
EST: gi|208055455|gb|GD853248.1|GD853248
EST:     AAGCATTGCAACTGCTTAAGAAGAAGGNGAAAACTGAAAATATAATCAAG                         AAAACAAAACAGAACCGCCAGAAGAA
genomic: AAGCATTGCAACTGCTTAAGAAGAAGGAGAAAACTGAAAATATAATCAAGgttttttctt ... aatgttgcagAAAACAAAACAGAACCGCCAGAAGAA
EST: gi|207713118|gb|GD694666.1|GD694666
EST:     GCATTGCAACTGACTTAAAGAAGAAGGAGAAAACTGAAAATATAATCAAG                         AAAACAAAACAGAACCGCC
genomic: GCATTGCAACTG-CTTAA-GAAGAAGGAGAAAACTGAAAATATAATCAAGgttttttctt ... aatgttgcagAAAACAAAACAGAACCGCC
EST: gi|207772050|gb|GD743511.1|GD743511
EST:     AAGCATTGCAACTGCTTAAGAAGAAGGAGAAAACTGAAAATATAATCAAG                         AAA-CAAAACA
genomic: AAGCATTGCAACTGCTTAAGAAGAAGGAGAAAACTGAAAATATAATCAAGgttttttctt ... aatgttgcagAAAACAAAACA
EST: gi|193579812|gb|FK536413.1|FK536413
EST:     AAGCATTGCAACTGCTTAAGAAGAAGGAGAAAACTGAAAATATAATCAAG                         AAAACAAAACNGAACCGCC
genomic: AAGCATTGCAACTGCTTAAGAAGAAGGAGAAAACTGAAAATATAATCAAGgttttttctt ... aatgttgcagAAAACAAAACAGAACCGCC
EST: gi|193655124|gb|FK598752.1|FK598752
EST:     AAGCATTGCAACTGCTTAAGAAGAAGGAGAAAACTGAAAATATAATCAAG                         AAAACAAAACAGAACCGCCAGAAGAAGGAACAGAACAAGGAT
genomic: AAGCATTGCAACTGCTTAAGAAGAAGGAGAAAACTGAAAATATAATCAAGgttttttctt ... aatgttgcagAAAACAAAACAGAACCGCCAGAAGAAGAAACAGAACAAGGAT
EST: gi|193600843|gb|FK550380.1|FK550380
EST:     AAGCATTGCAACTGCTTAAGAAGAAGGAGAAAACTGAAAATATAATCAAG                         AAAACAAAACAGAACCGCC
genomic: AAGCATTGCAACTGCTTAAGAAGAAGGAGAAAACTGAAAATATAATCAAGgttttttctt ... aatgttgcagAAAACAAAACAGAACCGCC
EST: gi|208272816|gb|GE072286.1|GE072286
EST:     AAGCATTGCAACTGCTTAAGAAGAAGGAGAAAACTGAAAATATAATCAAG                         AAAACAAAACAGAACCGCCAGAAG
genomic: AAGCATTGCAACTGCTTAAGAAGAAGGAGAAAACTGAAAATATAATCAAGgttttttctt ... aatgttgcagAAAACAAAACAGAACCGCCAGAAG
EST: gi|208037422|gb|GD835323.1|GD835323
EST:     AAGCATTGCAACTGCTTAAGAAGAAGGAGAAAACTGAAAATATAATCAAG                         AAAACAAAACAGAACCG
genomic: AAGCATTGCAACTGCTTAAGAAGAAGGAGAAAACTGAAAATATAATCAAGgttttttctt ... aatgttgcagAAAACAAAACAGAACCG
EST: gi|193470278|gb|FK438865.1|FK438865
EST:     AAGCATTGCAACTGCTTAAGAAGAAGGAGAAAACTGAAAATATAATCAAG                         AAAACAAAACAGAA
genomic: AAGCATTGCAACTGCTTAAGAAGAAGGAGAAAACTGAAAATATAATCAAGgttttttctt ... aatgttgcagAAAACAAAACAGAA
EST: gi|208229004|gb|GE024326.1|GE024326
EST:     AAGCATTGCAACTGCTTAAGAAGAAGGAGAAAACTGAAAATATAATCAAG                         AAAACAAAACAGAACCGCC
genomic: AAGCATTGCAACTGCTTAAGAAGAAGGAGAAAACTGAAAATATAATCAAGgttttttctt ... aatgttgcagAAAACAAAACAGAACCGCC
EST: gi|193529626|gb|FK484859.1|FK484859
EST:     CTGAAAGTATAATCAAG                         AAAACAAAACAGAACCGCCAGAAGAAGAAACAGAACAAGGATGACAAGAAT
genomic: CTGAAAATATAATCAAGgttttttctt ... aatgttgcagAAAACAAAACAGAACCGCCAGAAGAAGAAACAGAACAAGGATGACAAGAAT
EST: gi|208162493|gb|GD963182.1|GD963182
EST:     AATATAATCAAG                         AAAACAAAACAGAACCGCCAGAAGAAGAAACAGAACAAGGATGACAAGAAT
genomic: AATATAATCAAGgttttttctt ... aatgttgcagAAAACAAAACAGAACCGCCAGAAGAAGAAACAGAACAAGGATGACAAGAAT
EST: gi|208290186|gb|GE082278.1|GE082278
EST:     AGCATTGCAACTGCTTAAGAAGAAGGAGAAAACTGAAAATATAATACAAG                         AAAACAAAACAG
genomic: AGCATTGCAACTGCTTAAGAAGAAGGAGAAAACTGAAAATATAAT-CAAGgttttttctt ... aatgttgcagAAAACAAAACAG
EST: gi|207778684|gb|GD749429.1|GD749429
EST:     AAGCATTGCAACTGCTTAAGAAGAAGGAGAAAACTGAAAATATAATCAAG                         AAAACAAAACAG
genomic: AAGCATTGCAACTGCTTAAGAAGAAGGAGAAAACTGAAAATATAATCAAGgttttttctt ... aatgttgcagAAAACAAAACAG
EST: gi|208023000|gb|GD821010.1|GD821010
EST:     AAGCATTGCAACTGCTTAAGAAGAAGGAGAAAACTGAAAATATAATCAAG                         AAAACAAA-CAGAACCGCC
genomic: AAGCATTGCAACTGCTTAAGAAGAAGGAGAAAACTGAAAATATAATCAAGgttttttctt ... aatgttgcagAAAACAAAACAGAACCGCC
EST: gi|208173057|gb|GD967588.1|GD967588
EST:     AACTGAAAATATAATTCAAG                         AAAACAAAACAGAACCGCCAGAAGAAGAAACAGAACAAGGATGACAAGAA
genomic: AACTGAAAATATAA-TCAAGgttttttctt ... aatgttgcagAAAACAAAACAGAACCGCCAGAAGAAGAAACAGAACAAGGATGACAAGAA
EST: gi|208228809|gb|GE024229.1|GE024229
EST:     AAGCATTGCAACTGCTTAAGAAGAAGGAGAAAACTGAAAATATAATCAAG                         AAAACAAAACAGAACCGCCAGAAGAA
genomic: AAGCATTGCAACTGCTTAAGAAGAAGGAGAAAACTGAAAATATAATCAAGgttttttctt ... aatgttgcagAAAACAAAACAGAACCGCCAGAAGAA
EST: gi|207772279|gb|GD746484.1|GD746484
EST:     AAGCATTGCAACTGCTTAAGAAGAAGGAGAAAACTGAAAATATAATCAAG                         AAAACAAAACAGAACCG
genomic: AAGCATTGCAACTGCTTAAGAAGAAGGAGAAAACTGAAAATATAATCAAGgttttttctt ... aatgttgcagAAAACAAAACAGAACCG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGCCCATTTCATGAAGGAAGAGGAGGAGCAGATGAAACTTCAAAAACAAGAAGCATTGCAACTGCTTAAGAAGAAGGAGAAAACTGAAAATATAATCAAGgttttttcttctctatcaattgttctagtccttttgttttacattccagtactttagttgatgctaatccacccaagcaatgttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA