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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattggttactgctctgattatgtatcacttttttttcctggttgccatttagctgagattattttccgttttatttgttatcagGTCTTAAATGAATGTGTGGAAGCTGAGAACTGGCTCAGGGAGAAAAAACAGCATCAGGACTCGCTTCCAAAATATGCCACCCCTGTACTTTTGTCAGCTG

Basic information

species Glycine max
transcript GLYMA13G43630.2
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G43630.2 (Glycine max), 3'ss of exon 8
lower sequence: Vv09s0002g04680.t01 (Vitis vinifera), 3'ss of exon 7
----------------------------------------------------------------------gtaattggttactgctctgattatgtatcacttttttttcctggttgccatttagctgagattattttccgttttatttgttatcagGTCTTAAATGAATGTGTGGAAGCTGAGAACTGGCTCAGGGAGAAAAAACAGCATCAGGACTCGCTTCCAAAATATGCCACCCCTGTACTTTTGTCAGCTG
                                                                       ||| ||   |       |   |  |   |  | |      | |   |  |||   | | |||  |||    ||| ||| || | ||||||| | ||| ||||||||||| |||  |||| | ||||||||||| ||||| |||||||| ||||| ||| |||||||||| || ||  |||| || |
gtaatagattctgtattgtttgtaaattgattattcttcaaaatgctcccctagcctctgaaccaccaatataaatgcaaaggatgaaggaaagtttgaaaatatccaattttggaacatttttttttatatt--tttaaaatttttttattgt-agGTCTTGAGTGAGTGTGTGGAAGCAGAGGCCTGGTTAAGGGAGAAAAAGCAGCAGCAGGACTCACTTCCCAAACATGCCACCCCAGTCCTCCTGTCCGCCG
















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|254322029|gb|GR837443.1|GR837443
EST:     TGTCAAATGATCCCAAGTTTGATCACATTGACATCAATGAGAAACAAAAG                         GTCTTAAATGAATGTGTGGAAGCTGAGAACTGGCTCAGGGAGAAAAAACAG
genomic: TGTCAAATGATCCCAAGTTTGATCACATTGACATCAATGAGAAACAAAAGgtaattggtt ... ttgttatcagGTCTTAAATGAATGTGTGGAAGCTGAGAACTGGCTCAGGGAGAAAAAACAG
EST: gi|192294395|gb|FG987324.1|FG987324
EST:     TGTCAAATGATCCCAAGTTTGATCACATTGACATCAATGAGAAACAAAAG                         GTCTTAAATGAATGTGTGGAAGCTGAGAACTGGCTCAGGGAGAAAAAACAG
genomic: TGTCAAATGATCCCAAGTTTGATCACATTGACATCAATGAGAAACAAAAGgtaattggtt ... ttgttatcagGTCTTAAATGAATGTGTGGAAGCTGAGAACTGGCTCAGGGAGAAAAAACAG
EST: gi|207834617|gb|GD805482.1|GD805482
EST:     TGTCAAATGATCCCAAGTTTGATCACATTGACATCAATGAGAAACAAAAG                         GTCTTAAATGAATGTGTGGAAGCTGAGAACTGGCTCAGGGAGAAAAAACAG
genomic: TGTCAAATGATCCCAAGTTTGATCACATTGACATCAATGAGAAACAAAAGgtaattggtt ... ttgttatcagGTCTTAAATGAATGTGTGGAAGCTGAGAACTGGCTCAGGGAGAAAAAACAG
EST: gi|207735431|gb|GD710274.1|GD710274
EST:     TGTCAAATGATCCCAAGTTTGATCACATTGACATCAATGAGAAACAAAAG                         GTCTTAAATGAATGTGTGGAAGCTGAGAACTGGCTCAGGGAGAAAAAACAG
genomic: TGTCAAATGATCCCAAGTTTGATCACATTGACATCAATGAGAAACAAAAGgtaattggtt ... ttgttatcagGTCTTAAATGAATGTGTGGAAGCTGAGAACTGGCTCAGGGAGAAAAAACAG
EST: gi|11117948|gb|BF219541.1|BF219541
EST:     TGTCAAATGATCCCAAGTTTGNNNNNATTGACATCAATGAGANNNAAAAG                         GTCTTAAATGAATGTGTNNNAGCTGAGAACTGGCTCAGGGAGAAAAAACAG
genomic: TGTCAAATGATCCCAAGTTTGATCACATTGACATCAATGAGAAACAAAAGgtaattggtt ... ttgttatcagGTCTTAAATGAATGTGTGGAAGCTGAGAACTGGCTCAGGGAGAAAAAACAG
EST: gi|23730841|gb|BU763524.1|BU763524
EST:     TGTCAAATGATCCCAAGTTTGATCACATTGACATCAATGAGAAACAAAAG                         GTCTTAAATGAATGTGTGGAAGCTGAGAACTGGCTCAGGGAGAAAAAACAG
genomic: TGTCAAATGATCCCAAGTTTGATCACATTGACATCAATGAGAAACAAAAGgtaattggtt ... ttgttatcagGTCTTAAATGAATGTGTGGAAGCTGAGAACTGGCTCAGGGAGAAAAAACAG
EST: gi|11687354|gb|BF595030.1|BF595030
EST:     TGTCAAATGATCCCAAGTTTGATCACATTGACATCAATGAGAAACAAAAG                         GTCTTAAATGAATGTGTGGAAGCTGAGAACTGGCTCAGGGAGAAAAAACAG
genomic: TGTCAAATGATCCCAAGTTTGATCACATTGACATCAATGAGAAACAAAAGgtaattggtt ... ttgttatcagGTCTTAAATGAATGTGTGGAAGCTGAGAACTGGCTCAGGGAGAAAAAACAG
EST: gi|6094746|gb|AW119475.1|AW119475
EST:     TGTCAAATGATCCCAAGTTTGATCACATTGACATCAATGAGAAACAAAAG                         GTCTTAAATGAATGTGTGGAAGCTGAGAACTGGCTCAGGGAGAAAAAACAG
genomic: TGTCAAATGATCCCAAGTTTGATCACATTGACATCAATGAGAAACAAAAGgtaattggtt ... ttgttatcagGTCTTAAATGAATGTGTGGAAGCTGAGAACTGGCTCAGGGAGAAAAAACAG
EST: gi|298183420|gb|HO028633.1|HO028633
EST:     TGTCAAATGATCCCAAGTTTGATCACATTGACATCAATGAGAAACAAAAG                         GTCTTAAATGAATGTGTGGAAGCTGAGAACTGGCTCAGGGAGAAAAAACAG
genomic: TGTCAAATGATCCCAAGTTTGATCACATTGACATCAATGAGAAACAAAAGgtaattggtt ... ttgttatcagGTCTTAAATGAATGTGTGGAAGCTGAGAACTGGCTCAGGGAGAAAAAACAG
EST: gi|192301840|gb|FG997698.1|FG997698
EST:     TGTCAAATGATCCCAAGTTTGATCACATTGACATCAATGAGAAACAAAAG                         GTCTTAAATGAATGTGTGGAAGCTGAGAACTGGCTCAGGGAGAAAAAACAG
genomic: TGTCAAATGATCCCAAGTTTGATCACATTGACATCAATGAGAAACAAAAGgtaattggtt ... ttgttatcagGTCTTAAATGAATGTGTGGAAGCTGAGAACTGGCTCAGGGAGAAAAAACAG
EST: gi|254322030|gb|GR837444.1|GR837444
EST:     TGTCAAATGATCCCAAGTTTGATCACATTGACATCAATGAGAAACAAAAG                         GTCTTAAATGAATGTGTGGAAGCTGAGAACTGGCTCAGGGAGAAAAAACAG
genomic: TGTCAAATGATCCCAAGTTTGATCACATTGACATCAATGAGAAACAAAAGgtaattggtt ... ttgttatcagGTCTTAAATGAATGTGTGGAAGCTGAGAACTGGCTCAGGGAGAAAAAACAG
EST: gi|298166695|gb|HO010134.1|HO010134
EST:     TGTCAAATGATCCCAAGTTTGATCACATTGACATCAATGAGAAACAAAAG                         GTCTTAAATGAATGTGTGGAAGCTGAGAACTGGCTCAGGGAGAAAAAACAG
genomic: TGTCAAATGATCCCAAGTTTGATCACATTGACATCAATGAGAAACAAAAGgtaattggtt ... ttgttatcagGTCTTAAATGAATGTGTGGAAGCTGAGAACTGGCTCAGGGAGAAAAAACAG
EST: gi|298169033|gb|HO020393.1|HO020393
EST:     GTTTGATCACATTGACATCAATGAGAAACAAAAG                         GTCTTAAATGAATGTGTGGAAGCTGAGAACTGGCTCAGGGAGAAAAAACAG
genomic: GTTTGATCACATTGACATCAATGAGAAACAAAAGgtaattggtt ... ttgttatcagGTCTTAAATGAATGTGTGGAAGCTGAGAACTGGCTCAGGGAGAAAAAACAG
EST: gi|22931443|gb|BU548582.1|BU548582
EST:     TGTCAAATGATCCCAAGTTTGATCACATTGACATCAATGAGAAACAAAAN                         NNCTTAAATGAATGTGTGGAAGCTGAGAACTGGCTCAGGGAGAAAAAACAG
genomic: TGTCAAATGATCCCAAGTTTGATCACATTGACATCAATGAGAAACAAAAGgtaattggtt ... ttgttatcagGTCTTAAATGAATGTGTGGAAGCTGAGAACTGGCTCAGGGAGAAAAAACAG
EST: gi|8827941|gb|BE211671.1|BE211671
EST:     TGTCAAATGATCCCAAGTTTGATCACATTGACATCAATGAGAAACAAAAG                         GTCTTAAATGAATGTGTGGAAGCTGAGAACTGGCTCAGGGAGAAAAAACAG
genomic: TGTCAAATGATCCCAAGTTTGATCACATTGACATCAATGAGAAACAAAAGgtaattggtt ... ttgttatcagGTCTTAAATGAATGTGTGGAAGCTGAGAACTGGCTCAGGGAGAAAAAACAG
EST: gi|192301841|gb|FG997699.1|FG997699
EST:     CCCAAGTTTGATCACATTGACATCAATGAGAAACAAAAG                         GTCTTAAATGAATGTGTGGAAGCTGAGAACTGGCTCAGGGAGAAAAAACAG
genomic: CCCAAGTTTGATCACATTGACATCAATGAGAAACAAAAGgtaattggtt ... ttgttatcagGTCTTAAATGAATGTGTGGAAGCTGAGAACTGGCTCAGGGAGAAAAAACAG
EST: gi|6963487|gb|AW432180.1|AW432180
EST:     TGTCAAATGATCCCAAGTTTGATCACATTGACATCAATGAGAAACAAAAG                         GTCTTAAATGAATGTGTGGAAGCTGAGAACTGGCTCAGGGAGAAAAAACAG
genomic: TGTCAAATGATCCCAAGTTTGATCACATTGACATCAATGAGAAACAAAAGgtaattggtt ... ttgttatcagGTCTTAAATGAATGTGTGGAAGCTGAGAACTGGCTCAGGGAGAAAAAACAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttttttcctggttgccatttagctgagattattttccgttttatttgttatcagGTCTTAAATGAATGTGTGGAAGCTGAGAACTGGCTCAGGGAGAAAAAACAGCATCAGGACTCGCTTCCAAAATATGCCACCCCTGTACTTTTGTCAGCTG
                                ttttccgttttattt  CT-rich tract
                                       ttttatttgttatca  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
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaattggttactgctctgattatgtatcacttttttttcctggttgccatttagctgagattattttccgttttatttgttatcagGTCTTAAATGAATGTGTGGAAGCTGAGAACTGGCTCAGGGAGAAAAAACAGCATCAGGACTCGCTTCCAAAATATGCCACCCCTGTACTTTTGTCAGCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG