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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaactctcatgacctggagcaacatcttctagttcattttaaaagtcatacttacccaatgaaccgatctatgtctatagGTCTATTATCTTTACTAATGGGACTGAAGAGTTGAGACTGGCTGCTGTCAGCAAAGAAAGAGAACAAACTGTGTCAAAGAGCAGTATTGTGACTACTCAA

Basic information

species Vitis vinifera
transcript Vv04s0023g03200.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0023g03200.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA16G24130.1 (Glycine max), 3'ss of exon 2
-----------------gtaactctcatgacctggagcaacatcttctagttcattttaaaagtcatacttacccaatgaaccg-atctatgtct--atagGTCTATTATCTTTACTAATGGGACTGAAGAGTTGAGACTGGCTGCTGTCAGCAAAGAAAGAGAACAAACTGTGTCAAAGAGCAGTATTGTGACTACTCAA
                 |  |  | ||    || | |    | || |   | || | | |   | |    ||   | | |||   | |||| |      || |||||||| |||  |||||| || ||||| |  ||| ||||||||||||||||||||   ||||||||  ||||||  ||||| ||||||||||| |||
gtaggaggagcactgttgccaaccacaatttcttgtgatctacctccatatccagtctcatgctgagtgctatttacttaactatacctatattctggcagATCTATTATTTTTGTTAATGGAACCGAAGAATCAAGAATGGCTGCTGTCAGCAAAGAACAGGAACAAACCCTGTCAAGAAGCAGCATTGTGACTACACAA

upper sequence: Vv04s0023g03200.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA02G05550.1 (Glycine max), 3'ss of exon 2
------gtaactctcatgacctggagcaacatcttctagt------tcattttaaaagtcatacttacc-caatgaaccgatctatgtctata--------gGTCTATTATCTTTACTAATGGGACTGAAGAGTTGAGACTGGCTGCTGTCAGCAAAGAAAGAGAACAAACTGTGTCAAAGAGCAGTATTGTGACTACTCAA
      | | | || ||| ||     |||  |||| |  |      |||| |  |   |||| || ||  | ||| || || ||||  |||||        | |||||||| |||  |||||| || ||||| |  ||| ||||||||||||||||||||   ||||||||   |||||  ||||| |||||||||||||||
gtaggaggagcactgatg-ccaaccacaatttcttgtgatcttccttcatatccagcctcatgctgactgctatgtactgaactatacctatatgctggcagATCTATTATTTTTGTTAATGGAACCGAAGAATCAAGAATGGCTGCTGTCAGCAAAGAACAGGAACAAACCAGGTCAAGAAGCAGCATTGTGACTACTCAA
















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|77582988|gb|DV220511.1|DV220511
EST:     GATTCTAGGCAGGTATTTGGGCAAGGCCCTGATGTGGGTAACCAATATAG                         GTCTATTATCTTTACTAATGGGACTGAAGAGTTGAGACTGGCTGCTGTCAG
genomic: GATTCTAGGCAGGTATTTGGGCAAGGCCCTGATGTGGGTAACCAATATAGgtaactctca ... atgtctatagGTCTATTATCTTTACTAATGGGACTGAAGAGTTGAGACTGGCTGCTGTCAG
EST: gi|110719878|gb|EE095384.1|EE095384
EST:     GATTCTAGGCAGGTATTTGGGCAAGGCCCTGATGTGGGTAACCAATATAG                         GTCTATTATCTTTACTAATGGGACTGAAGAGTTGAGACTGGCTGCTGTCAG
genomic: GATTCTAGGCAGGTATTTGGGCAAGGCCCTGATGTGGGTAACCAATATAGgtaactctca ... atgtctatagGTCTATTATCTTTACTAATGGGACTGAAGAGTTGAGACTGGCTGCTGTCAG
EST: gi|33404892|gb|CF210519.1|CF210519
EST:     GATTCTAGGCAGGTATTTGGGCAAGGCCCTGATGTGGGTAACCAATATAG                         GTCTATTATCTTTACTAATGGGACTGAAGAGTTGAGACTGGCTGCTGTCAG
genomic: GATTCTAGGCAGGTATTTGGGCAAGGCCCTGATGTGGGTAACCAATATAGgtaactctca ... atgtctatagGTCTATTATCTTTACTAATGGGACTGAAGAGTTGAGACTGGCTGCTGTCAG
EST: gi|33404977|gb|CF210604.1|CF210604
EST:     GATTCTAGGCAGGTATTTGGGCAAGGCCCTGATGTGGGTAACCAATATAG                         GTCTATTATCTTTACTAATGGGACTGAAGAGTTGAGACTGGCTGCTGTCAG
genomic: GATTCTAGGCAGGTATTTGGGCAAGGCCCTGATGTGGGTAACCAATATAGgtaactctca ... atgtctatagGTCTATTATCTTTACTAATGGGACTGAAGAGTTGAGACTGGCTGCTGTCAG
EST: gi|71875950|gb|DT025005.1|DT025005
EST:     GATTCTAGGCAGGTATTTGGGCAAGGCCCTGATGTGGGTAACCAATATAG                         GTCTATTATCTTTACTAATGGGACTGAAGAGTTGAGACTGGCTGCTGTCAG
genomic: GATTCTAGGCAGGTATTTGGGCAAGGCCCTGATGTGGGTAACCAATATAGgtaactctca ... atgtctatagGTCTATTATCTTTACTAATGGGACTGAAGAGTTGAGACTGGCTGCTGTCAG
EST: gi|71875949|gb|DT025004.1|DT025004
EST:     GATTCTAGGCAGGTATTTGGGCAAGGCCCTGATGTGGGTAACCAATATAG                         GTCTATTATCTTTACTAATGGGACTGAAGAGTTGAGACTGGCTGCTGTCAG
genomic: GATTCTAGGCAGGTATTTGGGCAAGGCCCTGATGTGGGTAACCAATATAGgtaactctca ... atgtctatagGTCTATTATCTTTACTAATGGGACTGAAGAGTTGAGACTGGCTGCTGTCAG
EST: gi|110719966|gb|EE095534.1|EE095534
EST:     GATTCTAGGCAGGTATTTGGGCAAGGCCCTGATGTGGGTAACCAATATAG                         GTCTATTATCTTTACTAATGGGACTGAAGAGTTGAGACTGGCTGCTGTCAG
genomic: GATTCTAGGCAGGTATTTGGGCAAGGCCCTGATGTGGGTAACCAATATAGgtaactctca ... atgtctatagGTCTATTATCTTTACTAATGGGACTGAAGAGTTGAGACTGGCTGCTGTCAG
EST: gi|34545817|gb|CF514049.1|CF514049
EST:     GGGCAAGGCCCTGATGTGGGTGA-TAATATAT                         GTCTATTATCTTTACTAATGGGACCGATCGA-TCGAGACTGGCTGCTGTCA
genomic: GGGCAAGGCCCTGATGTGGGTAACCAATATAGgtaactctca ... atgtctatagGTCTATTATCTTTACTAATGGGACTGA-AGAGTTGAGACTGGCTGCTGTCA
EST: gi|161719951|gb|FC069029.1|FC069029
EST:     GATTCTAGGCAGGTATTTGGGCAAGGCCCTGATGTGGGTAACCAATATAG                         GTCTATTATCTTTACTAATGGGACTGAAGAGTTGAGACTGGCTGCTGTCAG
genomic: GATTCTAGGCAGGTATTTGGGCAAGGCCCTGATGTGGGTAACCAATATAGgtaactctca ... atgtctatagGTCTATTATCTTTACTAATGGGACTGAAGAGTTGAGACTGGCTGCTGTCAG
EST: gi|110716777|gb|EE092054.1|EE092054
EST:     GATTCTAGGCAGGTATTTGGGCAAGGCCCTGATGTGGGTAACCAATATAG                         GTCTATTATCTTTACTAATGGGACTGAAGAGTTGAGACTGGCTGCTGTCAG
genomic: GATTCTAGGCAGGTATTTGGGCAAGGCCCTGATGTGGGTAACCAATATAGgtaactctca ... atgtctatagGTCTATTATCTTTACTAATGGGACTGAAGAGTTGAGACTGGCTGCTGTCAG
EST: gi|71870654|gb|DT019709.1|DT019709
EST:     GATTCTAGGCAGGTATTTGGGCAAGGCCCTGATGTGGGTAACCAATATAG                         GTCTATTATCTTTACTAATGGGACTGAAGAGTTGAGACTGGCTGCTGTCAG
genomic: GATTCTAGGCAGGTATTTGGGCAAGGCCCTGATGTGGGTAACCAATATAGgtaactctca ... atgtctatagGTCTATTATCTTTACTAATGGGACTGAAGAGTTGAGACTGGCTGCTGTCAG
EST: gi|294966392|gb|GW839499.1|GW839499
EST:     GATTCTAGGCAGGTATTTGGGCAAGGCCCTGATGTGGGTAACCAATATAG                         GTCTATTATCTTTACTAATGGGACTGA
genomic: GATTCTAGGCAGGTATTTGGGCAAGGCCCTGATGTGGGTAACCAATATAGgtaactctca ... atgtctatagGTCTATTATCTTTACTAATGGGACTGA
EST: gi|161716432|gb|FC068424.1|FC068424
EST:     GATTCTAGGCAGGTATTTGGGCAAGGCCCTGATGTGGGTAACCAATATAG                         GTCTATTATCTTTACTAATGGGACTGAAGAGTTGAGACTGGCTGCTGTCAG
genomic: GATTCTAGGCAGGTATTTGGGCAAGGCCCTGATGTGGGTAACCAATATAGgtaactctca ... atgtctatagGTCTATTATCTTTACTAATGGGACTGAAGAGTTGAGACTGGCTGCTGTCAG
EST: gi|71855181|gb|DT004236.1|DT004236
EST:     GATTCTAGGCAGGTATTTGGGCAAGGCCCTGATGTGGGTAACCAATATAG                         GTCTATTATCTTTACTAATGGGACTGAAGAGTTGAGACTG
genomic: GATTCTAGGCAGGTATTTGGGCAAGGCCCTGATGTGGGTAACCAATATAGgtaactctca ... atgtctatagGTCTATTATCTTTACTAATGGGACTGAAGAGTTGAGACTG
EST: gi|34545903|gb|CF514135.1|CF514135
EST:     GGGCAAGGCCCTGATGTGGGTAACCAATATAG                         GTCTATTATCTTTACTAATGGGACTGAAGAGTTGAGACTGGCTGCTGTCAG
genomic: GGGCAAGGCCCTGATGTGGGTAACCAATATAGgtaactctca ... atgtctatagGTCTATTATCTTTACTAATGGGACTGAAGAGTTGAGACTGGCTGCTGTCAG
EST: gi|33408384|gb|CF214011.1|CF214011
EST:     GATTCTAGGCAGGTATTTGGGCAAGGCCCTGATGTGGGTAACCAATATAG                         GTCTATTATCTTTACTAATGGGACTGAAGAGTTGAGACTGGCTGCTGTCAG
genomic: GATTCTAGGCAGGTATTTGGGCAAGGCCCTGATGTGGGTAACCAATATAGgtaactctca ... atgtctatagGTCTATTATCTTTACTAATGGGACTGAAGAGTTGAGACTGGCTGCTGTCAG
EST: gi|33408641|gb|CF214268.1|CF214268
EST:     GATTCTAGGCAGGTATTTGGGCAAGGCCCTGATGTGGGTAACCAATATAG                         GTCTATTATCTTTACTAATGGGACTGAAGAGTTGAGACTGGCTGCTGTCAG
genomic: GATTCTAGGCAGGTATTTGGGCAAGGCCCTGATGTGGGTAACCAATATAGgtaactctca ... atgtctatagGTCTATTATCTTTACTAATGGGACTGAAGAGTTGAGACTGGCTGCTGTCAG
EST: gi|110718218|gb|EE094803.1|EE094803
EST:     GATTCTAGGCAGGTATTTGGGCAAGGCCCTGATGTGGGTAACCAATATAG                         GTCTATTATCTTTACTAATGGGACTGAAGAGTTGAGACTGGCTGCTGTCAG
genomic: GATTCTAGGCAGGTATTTGGGCAAGGCCCTGATGTGGGTAACCAATATAGgtaactctca ... atgtctatagGTCTATTATCTTTACTAATGGGACTGAAGAGTTGAGACTGGCTGCTGTCAG
EST: gi|161716720|gb|FC067841.1|FC067841
EST:     GATTCTAGGCAGGTATTTGGGCAAGGCCCTGATGTGGGTAACCAATATAG                         GTCTATTATCTTTACTAATGGGACTGAAGAGTTGAGACTGGCTGCTGTCAG
genomic: GATTCTAGGCAGGTATTTGGGCAAGGCCCTGATGTGGGTAACCAATATAGgtaactctca ... atgtctatagGTCTATTATCTTTACTAATGGGACTGAAGAGTTGAGACTGGCTGCTGTCAG
EST: gi|71855211|gb|DT004266.1|DT004266
EST:     GATTCTAGGCAGGTATTTGGGCAAGGCCCTGATGTGGGTAACCAATATAG                         GTCTATTATCTTTACTAATGGGACTGAAGAGTTGAGACTGGCTGCTGTCAG
genomic: GATTCTAGGCAGGTATTTGGGCAAGGCCCTGATGTGGGTAACCAATATAGgtaactctca ... atgtctatagGTCTATTATCTTTACTAATGGGACTGAAGAGTTGAGACTGGCTGCTGTCAG
EST: gi|30133186|gb|CB918525.1|CB918525
EST:     GATTCTAGGCAGGTATTTGGGCAAGGCCCTGATGTGGGTAACCAATATAG                         GTCTATTATCTTTACTAATGGGACTGAAGAGTTGAGACTGGCTGCTGTCAG
genomic: GATTCTAGGCAGGTATTTGGGCAAGGCCCTGATGTGGGTAACCAATATAGgtaactctca ... atgtctatagGTCTATTATCTTTACTAATGGGACTGAAGAGTTGAGACTGGCTGCTGTCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttctagttcattttaaaagtcatacttacccaatgaaccgatctatgtctatagGTCTATTATCTTTACTAATGGGACTGAAGAGTTGAGACTGGCTGCTGTCAGCAAAGAAAGAGAACAAACTGTGTCAAAGAGCAGTATTGTGACTACTCAA
                       tacttac  putative branch site (score: 1)
          attttaaaagtcata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaactctcatgacctggagcaacatcttctagttcattttaaaagtcatacttacccaatgaaccgatctatgtctatagGTCTATTATCTTTACTAATGGGACTGAAGAGTTGAGACTGGCTGCTGTCAGCAAAGAAAGAGAACAAACTGTGTCAAAGAGCAGTATTGTGACTACTCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG