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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtgttggtgaaacttttgattttgttttttactattataattcaaatgaatgcaaaggacttgactttgttttgttgtgtactgtcaacttgtttttcagGAACAAAATTGTCAGAAGATTGCAGGAAATATGGTGTTGAAAATACTTGTACCAGTGGTAATACGTTATCGAAAGCTGCATTGAATTATGGACGAGCTCG

Basic information

species Vitis vinifera
transcript Vv03s0038g00460.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv03s0038g00460.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA12G04210.1 (Glycine max), 3'ss of exon 3
gtgtgttggtgaaacttttgattttgttttttactattataattcaaatg-aatgcaaaggacttgact-ttgttttgttgtgtactgtcaacttgtttttcagGAACAAAATTGTCAGAAGATTGCAGGAAATATGGTGTTGAAAATACTTGTACCAGTGGTAATACGTTATCGAAAGCTGCATTGAATTATGGACGAGCTCG
                  | || ||| ||| ||    |   ||  || |    |||| |  |  | | | |||  || || | |||  | | ||| |||  |||||||||| |||||||||||| |||||||||||||||  |||||||| |||||||| ||||||||  | || | ||||||| | | || ||  ||||| | 
-------------gtaagtaatattggtttataaagcttctatataagtttgttgcagaaaatgttattattgaattcttctataccattatcttatttaacagGAACAAAGTTGTCAGAAGATAGCAGGAAATATGGTGCAGAAAATACATGTACCAGCGGTAATACACTGTCTAGAGCTGCACTAAGTTTTGCGCGAGCCCA

upper sequence: Vv03s0038g00460.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA11G11950.3 (Glycine max), 3'ss of exon 3
gtgtgttggtgaaacttttgattttgttttttactattataattcaaatgaatgcaaaggacttgactttgttttgttgtgtactgtcaacttgtttttcagGAACAAAATTGTCAGAAGATTGCAGGAAATATGGTGTTGAAAATACTTGTACCAGTGGTAATACGTTATCGAAAGCTGCATTGAATTATGGACGAGCTCG
                      |  | || | |   || ||  | |  |   |||| |  ||   ||| | | |||   |   || | | ||| |||  |||||||||| |||||||||||  |||||||||||||||  |||||||| |||||||||||||||||  | |||| ||||||| | | || ||  | ||| | 
---------------------gtaaggttatgaagcttctatataactttgttgcagaaaac---actat-tattgaactcctctat-atcttatttaacagGAACAAAGTTGTCAGAAGACAGCAGGAAATATGGTGCAGAAAATACATGTACCAGTGGTAATACACTGTCGAGAGCTGCACTAAGTTTTGCGCAAGCCCA

upper sequence: Vv03s0038g00460.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA06G01120.2 (Glycine max), 3'ss of exon 3
----gtgtgttggtgaaacttttgattttgttttttactattataattcaaatgaatgcaaaggacttgactttgttttgttgt-gtactgtca-acttgtttttcagGAACAAAATTGTCAGAAGATTGCAGGAAATATGGTGTTGAAAATACTTGTACCAGTGGTAATACGTTATCGAAAGCTGCATTGAATTATGGACGAGCTCG
     |||  | | ||   | |  ||   ||||  |  || | ||||   |||       |  | ||    |  || ||||| | | | || || ||||||||  |||||||||| || ||||||||| |||||||||||||||  || ||||| ||||||||||||| ||| ||||| | ||||||  | ||||||| ||| || ||
ccccctgtaatagagattttctccatga-gtttgatcttagtttaatcttaat-------accggctcttatcagtattgttattgaattgccatacttgtttaacagGAACAAAGTTATCAGAAGATAGCAGGAAATATGGTGCAGATAATACATGTACCAGTGGTAGTACTTTATCAAGAGCTGCGCTAAATTATGCACGTGCCCG

upper sequence: Vv03s0038g00460.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA04G01100.2 (Glycine max), 3'ss of exon 3
gtgtgttggtgaaacttttgattttgttttttactattataattcaaatgaatgcaaaggacttgacttt----gttttgttgt-gtactgtcaacttgtttttcagGAACAAAATTGTCAGAAGATTGCAGGAAATATGGTGTTGAAAATACTTGTACCAGTGGTAATACGTTATCGAAAGCTGCATTGAATTATGGACGAGCTCG
      |  ||  |  | | ||||   |||  || | | | ||   | |  |  |  |  ||  |   ||    || ||||| | | | |  ||  || |||  |||||||||| || |||||||||  ||||||||||||||  || ||||| ||||||||||||| ||| ||||| | ||||||  | ||||||| ||  || ||
------ttctggtatatgt-atttccatttccacgagtttgatcttagtttaatcttaataccagctcttttcggtattgttattgaattaccatgttatttaacagGAACAAAGTTATCAGAAGATAACAGGAAATATGGTGCAGATAATACGTGTACCAGTGGTAGTACATTATCAAGAGCTGCGCTAAATTATGCACATGCCCG

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|351024745|gb|FQ430570.1|FQ430570
EST:     TCGTGGTGTAGAAGGTTTTATCGTTACTGGGTCCAAACAAGTTGAAATAG                         GAACAAAATTGTCAGAAGATTGCAGGAAATATGGTGTTGAAAATACTTGTA
genomic: TCGTGGTGTAGAAGGTTTTATCGTTACTGGGTCCAAACAAGTTGAAATAGgtgtgttggt ... tgtttttcagGAACAAAATTGTCAGAAGATTGCAGGAAATATGGTGTTGAAAATACTTGTA
EST: gi|351035615|gb|FQ463460.1|FQ463460
EST:     TCGTGGTGTAGAAGGTTTTATCGTTACTGGGTCCAAACAAGTTGAAATAG                         GAACAAAATTGTCAGAAGATTGCAGGAAATATGGTGTTGAAAATACTTGTA
genomic: TCGTGGTGTAGAAGGTTTTATCGTTACTGGGTCCAAACAAGTTGAAATAGgtgtgttggt ... tgtttttcagGAACAAAATTGTCAGAAGATTGCAGGAAATATGGTGTTGAAAATACTTGTA
EST: gi|349826387|gb|FQ417884.1|FQ417884
EST:     TCGTGGTGTAGAAGGTTTTATCGTTACTGGGTCCAAACAAGTTGAAATAG                         GAACAAAATTGTCAGAAGATTGCAGGAAATATGGTGTTGAAAATACTTGTA
genomic: TCGTGGTGTAGAAGGTTTTATCGTTACTGGGTCCAAACAAGTTGAAATAGgtgtgttggt ... tgtttttcagGAACAAAATTGTCAGAAGATTGCAGGAAATATGGTGTTGAAAATACTTGTA
EST: gi|351023475|gb|FQ432858.1|FQ432858
EST:     TCGTGGTGTAGAAGGTTTTATCGTTACTGGGTCCAAACAAGTTGAAATAG                         GAACAAAATTGTCAGAAGATTGCAGGAAATATGGTGTTGAAAATACTTGTA
genomic: TCGTGGTGTAGAAGGTTTTATCGTTACTGGGTCCAAACAAGTTGAAATAGgtgtgttggt ... tgtttttcagGAACAAAATTGTCAGAAGATTGCAGGAAATATGGTGTTGAAAATACTTGTA
EST: gi|351040290|gb|FQ425376.1|FQ425376
EST:     TCGTGGTGTAGAAGGTTTTATCGTTACTGGGTCCAAACAAGTTGAAATAG                         GAACAAAATTGTCAGAAGATTGCAGGAAATATGGTGTTGAAAATACTTGTA
genomic: TCGTGGTGTAGAAGGTTTTATCGTTACTGGGTCCAAACAAGTTGAAATAGgtgtgttggt ... tgtttttcagGAACAAAATTGTCAGAAGATTGCAGGAAATATGGTGTTGAAAATACTTGTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgaatgcaaaggacttgactttgttttgttgtgtactgtcaacttgtttttcagGAACAAAATTGTCAGAAGATTGCAGGAAATATGGTGTTGAAAATACTTGTACCAGTGGTAATACGTTATCGAAAGCTGCATTGAATTATGGACGAGCTCG
             acttgac  putative branch site (score: 4)
                                           cttgtttttc  putative PPT
                    tttgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgtgttggtgaaacttttgattttgttttttactattataattcaaatgaatgcaaaggacttgactttgttttgttgtgtactgtcaacttgtttttcagGAACAAAATTGTCAGAAGATTGCAGGAAATATGGTGTTGAAAATACTTGTACCAGTGGTAATACGTTATCGAAAGCTGCATTGAATTATGGACGAGCTCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC