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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattgtggattctcggggcttttttcccatttagagtatctctagatatgatttctgaatttttgatcgatcaaattgtatatggggatctagGTGACGAAGTGGATGTTAAGCAAAGGTCAAGGGAGAACAATGGGGAGCTATTTCACACTGCTGAATGCTTTGGCAGAGGATGGGAGGCTTGATGAAGCCG

Basic information

species Vitis vinifera
transcript Vv16s0050g01450.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv16s0050g01450.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G040970_T01 (Zea mays), 3'ss of exon 2
--gtattgtggattctcggggcttt-tttcccatttaga-gtatctcta-gata--tgatttctgaatttttgatcgatcaaattgtatatggggatctagGTGACGAAGTGGATGTTAAGCAAAGGTCAAGGGAGAACAATGGGGAGCTATTTCACACTGCTGAATGCTTTGGCAGAGGATGGGAGGCTTGATGAAGCCG
    ||| |   ||  |    ||     |   ||||||  ||  || ||  |||    | |  |   ||| ||| |    | | ||   |   | |||||||| |  || |||||||| | ||||||||||||||  |||||||| ||||||| |||  || |||||||||||   ||||||||  || |||| ||||| |
accaattttcctttaccaatactacacctgtgatttagttgttcctttataataacaaactcttttttttctgaactgaaacaatgaccacatg-atctagGTCATTAAATGGATGTTCAACAAAGGTCAAGGGAAGACAATGGGAAGCTATTACACCTTGTTGAATGCTTTGATCGAGGATGGACGGATTGAGGAAGCAG

upper sequence: Vv16s0050g01450.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G105827_T03 (Zea mays), 3'ss of exon 4
-----gtattgtggattctcggggcttt-tttcccatttaga-gtatctcta-gatatgatttctgaatttttgatcgatcaaattgt-atatggggatctagGTGACGAAGTGGATGTTAAGCAAAGGTCAAGGGAGAACAATGGGGAGCTATTTCACACTGCTGAATGCTTTGGCAGAGGATGGGAGGCTTGATGAAGCCG
      | || |  ||| |     ||   |||   ||||||  ||  || ||  |||  |   |   ||| |  |  ||   ||| |  | |||   |||||||| |  || |||||||| | ||||||||| ||||  |||||||||||||||| |||  || |||||||||||   ||||| ||  || |||| ||||| |
ctgttttttttttcattattcatactacatttatgatttagttgttcctttataataacaaaaccttattctgaactgaaacaatggccacatg---atctagGTCATTAAATGGATGTTCAACAAAGGTCAGGGGAAGACAATGGGGAGCTATTACACCTTGTTGAATGCTTTGATCGAGGACGGACGGATTGAGGAAGCAG

upper sequence: Vv16s0050g01450.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA16G29590.1 (Glycine max), 3'ss of exon 4
gtattgtggattctcggggctt---ttttcccatttagagtatctctagatatgatttctgaatt----tttgatcgatcaaattgtatatggggatctagGTGACGAAGTGGATGTTAAGCAAAGGTCAAGGGAGAACAATGGGGAGCTATTTCACACTGCTGAATGCTTTGGCAGAGGATGGGAGGCTTGATGAAGCCG
 |||| | | ||| |    ||    | ||   ||    | | |   | |  ||    | |||| |    |    |    ||||||  | ||||   | ||||| || ||||||||| ||||||||||||||||||  |||||||| |||||||||||| | || |||||||| | ||||||||   | ||||||||||| |
-tattattgtttccctattctcccctatttgtatccctactcttcatggggatagcctgtgaactaacatccatttatgcaaattacaaatggcactgtagGTAACAAAGTGGATGCTAAGCAAAGGTCAAGGGAAGACAATGGGAAGCTATTTCACATTACTTAATGCTTTAGTAGAGGATGACCGTCTTGATGAAGCTG

upper sequence: Vv16s0050g01450.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA09G24100.1 (Glycine max), 3'ss of exon 4
gtattgtggattctcggggcttttttcccatttag--agtatctctagatatgatttctgaatt----tttgatcgatcaaattgtatatggggatctagGTGACGAAGTGGATGTTAAGCAAAGGTCAAGGGAGAACAATGGGGAGCTATTTCACACTGCTGAATGCTTTGGCAGAGGATGGGAGGCTTGATGAAGCCG
 ||||    |||||       || | ||||| |    | | |   | |  ||    | |||| |    |  |      ||||||  | ||||   | ||| | || || |||||| |||||||||||||||| |  |||||||| |||||||||||| | || |||||||| | ||||||||   | ||||| ||||| |
ttatttatcattctttccctattctccccatatccctattcttcatggggatagcctgtgaactaacatccgcatatgcaaattacaaatggcactgtagATAACAAAATGGATGCTAAGCAAAGGTCAAGGAAAGACAATGGGAAGCTATTTCACATTACTTAATGCTTTAGTAGAGGATGACCGTCTTGACGAAGCTG

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|351046546|gb|FQ453162.1|FQ453162
EST:     AAGCTTTGAAGACCCTTGAGGATCAAAAAGAATGGAAGAGGATGATTCAG                         GCGACAAAGTGGATGTTAAGCAAAGGGCAAGGGAGAACAATGGGGAGCTAT
genomic: AAGCTTTGAAGACCCTTGAGGATCAAAAAGAATGGAAGAGGATAATTCAGgtattgtgga ... ggggatctagGTGACGAAGTGGATGTTAAGCAAAGGTCAAGGGAGAACAATGGGGAGCTAT
EST: gi|351054436|gb|FQ450519.1|FQ450519
EST:     AAGCTTTGAAGACCCTTGAGGATCAAAAAGAATGGAAGAGGATAATTCAG                         GTGACGAAGTGGATGTTAAGCAAAGGTCAAGGGAGAACAATGGGGAGCTAT
genomic: AAGCTTTGAAGACCCTTGAGGATCAAAAAGAATGGAAGAGGATAATTCAGgtattgtgga ... ggggatctagGTGACGAAGTGGATGTTAAGCAAAGGTCAAGGGAGAACAATGGGGAGCTAT
EST: gi|351033744|gb|FQ462274.1|FQ462274
EST:     AAGCTTTGAAGACCCTTGAGGATCAAAAAGAATGGAAGAGGATGATTCAG                         GTGACAAAGTGGATGTTAAGCAAAGGTCAAGGGAGAACAATGGGGAGCTAT
genomic: AAGCTTTGAAGACCCTTGAGGATCAAAAAGAATGGAAGAGGATAATTCAGgtattgtgga ... ggggatctagGTGACGAAGTGGATGTTAAGCAAAGGTCAAGGGAGAACAATGGGGAGCTAT
EST: gi|349822100|gb|FQ408429.1|FQ408429
EST:     AAGCTTTGAAGACCCTTGAGGATCAAAAAGAATGGAAGAGGATAATTCAG                         GTGACGAAGTGGATGTTAAGCAAAGGTCAAGGGAGAACAATGGGGAGCTAT
genomic: AAGCTTTGAAGACCCTTGAGGATCAAAAAGAATGGAAGAGGATAATTCAGgtattgtgga ... ggggatctagGTGACGAAGTGGATGTTAAGCAAAGGTCAAGGGAGAACAATGGGGAGCTAT
EST: gi|349814396|gb|FQ398836.1|FQ398836
EST:     AAGCTTTGAAGACCCTTGAGGATCAAAAAGAATGGAAGAGGATAATTCAG                         GTGACGAAGTGGATGTTAAGCAAAGGTCAAGGGAGAACAATGGGGAGCTAT
genomic: AAGCTTTGAAGACCCTTGAGGATCAAAAAGAATGGAAGAGGATAATTCAGgtattgtgga ... ggggatctagGTGACGAAGTGGATGTTAAGCAAAGGTCAAGGGAGAACAATGGGGAGCTAT
EST: gi|349815708|gb|FQ400864.1|FQ400864
EST:     AAGCTTTGAAGACCCTTGAGGATCAAAAAGAATGGAAGAGGATAATTCAG                         GTGACAAAGTGGATGTTAAGCAAAGGTCAAGGGAGAACAATGGGGAGCTAT
genomic: AAGCTTTGAAGACCCTTGAGGATCAAAAAGAATGGAAGAGGATAATTCAGgtattgtgga ... ggggatctagGTGACGAAGTGGATGTTAAGCAAAGGTCAAGGGAGAACAATGGGGAGCTAT
EST: gi|351055367|gb|FQ441965.1|FQ441965
EST:     AAGCTTTGAAGACCCTTGAGGATCAAAAAGAATGGAAGAGGATAATTCAG                         GTGACAAAGTGGATGTTAAGCAAAGGTCAAGGGAGAACAATGGGGAGCTAT
genomic: AAGCTTTGAAGACCCTTGAGGATCAAAAAGAATGGAAGAGGATAATTCAGgtattgtgga ... ggggatctagGTGACGAAGTGGATGTTAAGCAAAGGTCAAGGGAGAACAATGGGGAGCTAT
EST: gi|22014552|gb|BQ799586.1|BQ799586
EST:     AAGCTTTGAAGACCCTTGAGGATCAAAAAGAATGGAAGAGGATAATTCAG                         GTGACAAAGTGGATGTTAAGCAAAGGTCAAGGGAGAACAATGGGGAGCTAT
genomic: AAGCTTTGAAGACCCTTGAGGATCAAAAAGAATGGAAGAGGATAATTCAGgtattgtgga ... ggggatctagGTGACGAAGTGGATGTTAAGCAAAGGTCAAGGGAGAACAATGGGGAGCTAT
EST: gi|349827078|gb|FQ421351.1|FQ421351
EST:     AAGCTTTGAAGACCCTTGAGGATCAAAAAGAATGGAAGAGGATAATTCAG                         GTGACGAAGTGGATGTTAAGCAAAGGTCAAGGGAGAACAATGGGGAGCTAT
genomic: AAGCTTTGAAGACCCTTGAGGATCAAAAAGAATGGAAGAGGATAATTCAGgtattgtgga ... ggggatctagGTGACGAAGTGGATGTTAAGCAAAGGTCAAGGGAGAACAATGGGGAGCTAT
EST: gi|294965603|gb|GW837202.1|GW837202
EST:     AAGCTTTGAAGACCCTTGAGGATCAAAAAGAATGGACGAGGATAATTCAG                         GTGACAAAGTGGATGT
genomic: AAGCTTTGAAGACCCTTGAGGATCAAAAAGAATGGAAGAGGATAATTCAGgtattgtgga ... ggggatctagGTGACGAAGTGGATGT
EST: gi|22013491|gb|BQ798525.1|BQ798525
EST:     AAGCTTTGAAGACCCTTGAGGATCAAAAAGAATGGAAGAGGATAATTCAG                         GTGACAAAGTGGATGTTAAGCAAAGGTCAAGGGAGAACAATGGGGAGCTAT
genomic: AAGCTTTGAAGACCCTTGAGGATCAAAAAGAATGGAAGAGGATAATTCAGgtattgtgga ... ggggatctagGTGACGAAGTGGATGTTAAGCAAAGGTCAAGGGAGAACAATGGGGAGCTAT
EST: gi|351052433|gb|FQ452466.1|FQ452466
EST:     AAGCTTTGAAGACCCTTGAGGATCAAAAAGAATGGAAGAGGATAATTCAG                         GTGACAAAGTGGATGTTAAGCAAAGGTCAAGGGAGAACAATGGGGAGCTAT
genomic: AAGCTTTGAAGACCCTTGAGGATCAAAAAGAATGGAAGAGGATAATTCAGgtattgtgga ... ggggatctagGTGACGAAGTGGATGTTAAGCAAAGGTCAAGGGAGAACAATGGGGAGCTAT
EST: gi|352781628|gb|FQ468926.1|FQ468926
EST:     AAGCTTTGAAGACCCTTGAGGATCAAAAAGAATGGAAGAGGATAATTCAG                         GTGACGAAGTGGATGTTAAGCAAAGGTCAAGGGAGAACAATGGGGAGCTAT
genomic: AAGCTTTGAAGACCCTTGAGGATCAAAAAGAATGGAAGAGGATAATTCAGgtattgtgga ... ggggatctagGTGACGAAGTGGATGTTAAGCAAAGGTCAAGGGAGAACAATGGGGAGCTAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctctagatatgatttctgaatttttgatcgatcaaattgtatatggggatctagGTGACGAAGTGGATGTTAAGCAAAGGTCAAGGGAGAACAATGGGGAGCTATTTCACACTGCTGAATGCTTTGGCAGAGGATGGGAGGCTTGATGAAGCCG
                      ttttgat  putative branch site (score: 4)
            atttctgaattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattgtggattctcggggcttttttcccatttagagtatctctagatatgatttctgaatttttgatcgatcaaattgtatatggggatctagGTGACGAAGTGGATGTTAAGCAAAGGTCAAGGGAGAACAATGGGGAGCTATTTCACACTGCTGAATGCTTTGGCAGAGGATGGGAGGCTTGATGAAGCCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC