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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctatcttgcacttaaaaaggaaaaaaaataaaagtagaataaacctagaaggatggggcacgtggaaatcaaatattgagatcgggttttggtttcacagGATACGAGGTGATCAGCAGCATTTTGTTCGCAGAGATGAGTTGAAG

Basic information

species Vitis vinifera
transcript Vv14s0171g00490.t01
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0171g00490.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: GRMZM2G130230_T02 (Zea mays), 3'ss of exon 14
-------------------------------------------------------------------------------------ctatcttgcacttaaaaaggaaaaaaaataaaagtagaataaacctagaaggatggggcacgtggaaat-caaatattgagatcgggttttggtttcacagGATACGAGGTGATCAGCAGCATTTTGTTCGCAGAGATGAGTTGAAG
                                                                                      |||| ||   |       || |  |    || |     |  |   | ||   ||     | |       |  | | |||  |       || ||   ||| ||| |||||||||||||||| |||||||||||||||||| |  ||
gtaagtgtcacccttttcgaccattctaacatatcgttcattacaaagaaactctctcaccctgaaatcgtggataactctacatatatcatgtcttgtgtgttgatagcattgcaaggcttcctctatgcaaaattttgcctttctttactgcacctacactgatctatacccatgtttctgcagAATAAGAGGTGATCAGCAGCACTTTGTTCGCAGAGATGAGCTACAG

upper sequence: Vv14s0171g00490.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: GLYMA19G24250.1 (Glycine max), 3'ss of exon 14
ctatcttgcacttaaaaaggaaaaaaaataaaag----tagaataaacctagaaggatggggcacgtggaaatcaaatattgagatcgggttttggtttcacagGATACGAGGTGATCAGCAGCATTTTGTTCGCAGAGATGAGTTGAAG
     ||| | ||| |      |   |  |  |      ||        |   |  |   |    |    ||  ||  || || || ||  ||  ||||  ||| ||   ||||||||||||||||||||||||||||||||||||||||
--gaattggaattacatgcattacttagcattatccatcagttctgttgtcagacaaattgatttgcatgaaataacaatggatattggaatt--gttttgcagAATTAAAGGTGATCAGCAGCATTTTGTTCGCAGAGATGAGTTGAAG

upper sequence: Vv14s0171g00490.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: GLYMA16G06850.2 (Glycine max), 3'ss of exon 14
---ctatcttgcacttaaaaaggaaaaaaaataaaagtagaataaacctagaaggatggggcacgtggaaatcaaatattgagatcgggttttggtttcacagGATACGAGGTGATCAGCAGCATTTTGTTCGCAGAGATGAGTTGAAG------------------------------------------------------
     |  | | |||  |      |   |   |  |||   ||    | |||   || |     | |  ||  ||  || || || ||  | || |||  ||| ||  ||||||||||||| |||||||||||||||||||||||||||                                                      
acaagaattggaactgcatgctttacttagcaatcagttctattg-tcaagacaaatagatt-tgcgttaaataacaatggatattggaatatg-ttttgcagAATTAGAGGTGATCAGCAACATTTTGTTCGCAGAGATGAGTTGAAGGTAAGATCATTACATGCTTGGTAGAGTATTGCAAGAGGGTCTTGCTTCACAAAC

upper sequence: Vv14s0171g00490.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: GLYMA16G06850.3 (Glycine max), 3'ss of exon 14
---ctatcttgcacttaaaaaggaaaaaaaataaaagtagaataaacctagaaggatggggcacgtggaaatcaaatattgagatcgggttttggtttcacagGATACGAGGTGATCAGCAGCATTTTGTTCGCAGAGATGAGTTGAAG
     |  | | |||  |      |   |   |  |||   ||    | |||   || |     | |  ||  ||  || || || ||  | || |||  ||| ||  ||||||||||||| |||||||||||||||||||||||||||
acaagaattggaactgcatgctttacttagcaatcagttctattg-tcaagacaaatagatt-tgcgttaaataacaatggatattggaatatg-ttttgcagAATTAGAGGTGATCAGCAACATTTTGTTCGCAGAGATGAGTTGAAG

upper sequence: Vv14s0171g00490.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: GLYMA19G22690.1 (Glycine max), 3'ss of exon 14
---------------------------------------------------------ctatctt---gcacttaaaaagga-aaaaaaataaaagtagaataaa---cctagaa-------------ggatggggcacgtggaaatcaaa--tattgagatcgggttttggtttcacagGATACGAGGTGATCAGCAGCATTTTGTTCGCAGAGATGAGTTGAAG
                                                           |||||   |   | ||| || | | || |||     |   || ||   | ||| |             | | |    |  |   ||  ||   ||||||||   ||  || ||||||||| ||  |||||||||| || |||||||||||||||||||||||||||
gtatgctcctctaatgacttcatctttgattgtttatggcttttttgtagaaaacagacatcttaaggtgttgaaagagtatacaagaatttggattacatgaattacttagcaaacagttttgtttgaaggaaatagttttgaacgaatattattgagaaatggaatttgtttcacagAATTAGAGGTGATCAACAACATTTTGTTCGCAGAGATGAGTTGAAG

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|352763752|gb|FQ473455.1|FQ473455
EST:     TATCAAGGGTTTACAATTCCAGAGGCTTATGAACGTCTAATTCTTGATAC                         GACACGAGGTGATCAGCAGCATTTTGTTCGCAGAGATGAGTTGAAG
genomic: TATCAAGGGTTTACAATTCCAGAGGCTTATGAACGTCTAATTCTTGATACgtatgacctc ... ggtttcacagGATACGAGGTGATCAGCAGCATTTTGTTCGCAGAGATGAGTTGAAG
EST: gi|110716825|gb|EE092144.1|EE092144
EST:     TATCAAGGGTTTACAATTCCAGAGGCTTATGAACGTCTAATTCTTGATAC                         GATACGAGGTGATCAGCAGCATTTTGTTCGCAGAGATGAGTTGAAG
genomic: TATCAAGGGTTTACAATTCCAGAGGCTTATGAACGTCTAATTCTTGATACgtatgacctc ... ggtttcacagGATACGAGGTGATCAGCAGCATTTTGTTCGCAGAGATGAGTTGAAG
EST: gi|351015046|gb|FQ444335.1|FQ444335
EST:     TATCAAGGGGTTACAATTCCAGAGGCTTATGAACGTCTAATTCTTGATAC                         GATACGAGGTGATCAGCAGCATTTTGTTCGCAGAGATGAGTTGAAG
genomic: TATCAAGGGTTTACAATTCCAGAGGCTTATGAACGTCTAATTCTTGATACgtatgacctc ... ggtttcacagGATACGAGGTGATCAGCAGCATTTTGTTCGCAGAGATGAGTTGAAG
EST: gi|352773448|gb|FQ472230.1|FQ472230
EST:     TATCAAGGGTTTACAATTCCAGAGGCTTATGAACGTCTAATTCTTGATAC                         GATACGAGGTGATCAGCAGCATTTTGTTCGCAGAGATGAGTTGAAG
genomic: TATCAAGGGTTTACAATTCCAGAGGCTTATGAACGTCTAATTCTTGATACgtatgacctc ... ggtttcacagGATACGAGGTGATCAGCAGCATTTTGTTCGCAGAGATGAGTTGAAG
EST: gi|110365367|gb|EC928242.1|EC928242
EST:     TATCAAGGGGTTACAATTCCAGAGGCTTATGAACGTCTAATTCTTGATAC                         GATACGAGGTGATCAGCAGCATTTTGTTCGCAGAGATGAGTTGAAG
genomic: TATCAAGGGTTTACAATTCCAGAGGCTTATGAACGTCTAATTCTTGATACgtatgacctc ... ggtttcacagGATACGAGGTGATCAGCAGCATTTTGTTCGCAGAGATGAGTTGAAG
EST: gi|110715492|gb|EE093605.1|EE093605
EST:     TATCAAGGGTTTACAATTCCAGAGGCTTATGAACGTCTAATTCTTGATAC                         GATACGAGGTGATCAGCAGCATTTTGTTCGCAGAGATGAGTTGAAG
genomic: TATCAAGGGTTTACAATTCCAGAGGCTTATGAACGTCTAATTCTTGATACgtatgacctc ... ggtttcacagGATACGAGGTGATCAGCAGCATTTTGTTCGCAGAGATGAGTTGAAG
EST: gi|33405782|gb|CF211409.1|CF211409
EST:     TATCAAGGGTTTACAATTCCAGAGGCTTATGAACGTCTAATTCTTGATAC                         GATACGAGGTGATCAGCAGCATTTTGTTCGCAGAGATGAGTTGAAG
genomic: TATCAAGGGTTTACAATTCCAGAGGCTTATGAACGTCTAATTCTTGATACgtatgacctc ... ggtttcacagGATACGAGGTGATCAGCAGCATTTTGTTCGCAGAGATGAGTTGAAG
EST: gi|110361886|gb|EC925389.1|EC925389
EST:     TATCAAGGGGTTACAATTCCAGAGGCTTATGAACGTCTAATTCTTGATAC                         GATACGAGGTGATCAGCAGCATTTTGTTCGCAGAGATGAGTTGAAG
genomic: TATCAAGGGTTTACAATTCCAGAGGCTTATGAACGTCTAATTCTTGATACgtatgacctc ... ggtttcacagGATACGAGGTGATCAGCAGCATTTTGTTCGCAGAGATGAGTTGAAG
EST: gi|352777103|gb|FQ474410.1|FQ474410
EST:     GGGTTTACAATTCCAGAGGCTTATGAACGTTTAATTCTTGATAC                         GATACGAGGTGATCAGCAGCATTTTGTTCGCAGAGATGAGTTGAAG
genomic: GGGTTTACAATTCCAGAGGCTTATGAACGTCTAATTCTTGATACgtatgacctc ... ggtttcacagGATACGAGGTGATCAGCAGCATTTTGTTCGCAGAGATGAGTTGAAG
EST: gi|30329436|gb|CD012698.1|CD012698
EST:     TATCAAGGGTTTACAATTCCAGAGGCTTATGAACGTCTAATTCTTGATAC                         GATACGAGGTGATCAGCAGCATTTTGTTCGCAGAGATGAGTTGAAG
genomic: TATCAAGGGTTTACAATTCCAGAGGCTTATGAACGTCTAATTCTTGATACgtatgacctc ... ggtttcacagGATACGAGGTGATCAGCAGCATTTTGTTCGCAGAGATGAGTTGAAG
EST: gi|110364587|gb|EC927954.1|EC927954
EST:     TATCAAGGGGTTACAATTCCAGAGGCTTATGAACGTCTAATTCTTGATAC                         GATACGAGGTGATCAGCAGCATTTTGTTCGCAGAGATGAGTTGAAG
genomic: TATCAAGGGTTTACAATTCCAGAGGCTTATGAACGTCTAATTCTTGATACgtatgacctc ... ggtttcacagGATACGAGGTGATCAGCAGCATTTTGTTCGCAGAGATGAGTTGAAG
EST: gi|110384476|gb|EC948916.1|EC948916
EST:     TATCAAGGGTTTACAATTCCAGAGGCTTATGAACGTCTAATTCTTGATAC                         GATACGAGGTGATCAGCAGCATTTTGTTCGCAGAGATGAGTTGAAG
genomic: TATCAAGGGTTTACAATTCCAGAGGCTTATGAACGTCTAATTCTTGATACgtatgacctc ... ggtttcacagGATACGAGGTGATCAGCAGCATTTTGTTCGCAGAGATGAGTTGAAG
EST: gi|110696408|gb|EE072500.1|EE072500
EST:     TATCAAGGGGTTACAATTCCAGAGGCTTATGAACGTCTAATTCTTGATAC                         GATACGAGGTGATCAGCAGCATTTTGTTCGCAGAGATGAGTTGAAG
genomic: TATCAAGGGTTTACAATTCCAGAGGCTTATGAACGTCTAATTCTTGATACgtatgacctc ... ggtttcacagGATACGAGGTGATCAGCAGCATTTTGTTCGCAGAGATGAGTTGAAG
EST: gi|352763934|gb|FQ465384.1|FQ465384
EST:     TATCAAGGGTTTACAATTCCAGAGGCTTATGAACGTCTAATTCTTGATAC                         GATACGAGGTGATCAGCAGCATTTTGTTCGCAGAGATGAGTTGAAG
genomic: TATCAAGGGTTTACAATTCCAGAGGCTTATGAACGTCTAATTCTTGATACgtatgacctc ... ggtttcacagGATACGAGGTGATCAGCAGCATTTTGTTCGCAGAGATGAGTTGAAG
EST: gi|352777620|gb|FQ466673.1|FQ466673
EST:     TATCAAGGGTTTACAATTCCAGAGGCTTATGAACGTTTAATTCTTGATAC                         GATACGAGGTGATCAGCAGCATTTTGTTCGCAGAGATGAGTTGAAG
genomic: TATCAAGGGTTTACAATTCCAGAGGCTTATGAACGTCTAATTCTTGATACgtatgacctc ... ggtttcacagGATACGAGGTGATCAGCAGCATTTTGTTCGCAGAGATGAGTTGAAG
EST: gi|352781379|gb|FQ468223.1|FQ468223
EST:     TATCAAGGGTTTACAATTCCAGAGGCTTATGAACGTCTAATTCTTGATAC                         GATACGAGGTGATCAGCAGCATTTTGTTCGCAGAGATGAGTTGAAG
genomic: TATCAAGGGTTTACAATTCCAGAGGCTTATGAACGTCTAATTCTTGATACgtatgacctc ... ggtttcacagGATACGAGGTGATCAGCAGCATTTTGTTCGCAGAGATGAGTTGAAG
EST: gi|71890077|gb|DT039132.1|DT039132
EST:     GGCTTATGAACGTCTAATTCTTGATAC                         GATACGAGGTGATCAGCAGCATTTTGTTCGCAGAGATGAGTTGAAG
genomic: GGCTTATGAACGTCTAATTCTTGATACgtatgacctc ... ggtttcacagGATACGAGGTGATCAGCAGCATTTTGTTCGCAGAGATGAGTTGAAG
EST: gi|352781474|gb|FQ468318.1|FQ468318
EST:     TATCAAGGGTTTACAATTCCAGAGGCTTATGAACGTCTAATTCTTGATAC                         GATACGAGGTGATCAGCAGCATTTTGTTCGCAGAGATGAGTTGAAG
genomic: TATCAAGGGTTTACAATTCCAGAGGCTTATGAACGTCTAATTCTTGATACgtatgacctc ... ggtttcacagGATACGAGGTGATCAGCAGCATTTTGTTCGCAGAGATGAGTTGAAG
EST: gi|110416304|gb|EC982275.1|EC982275
EST:     TATCAAGGGTTTACAATTCCAGAGGCTTATGAACGTCTAATTCTTGATAC                         GATACGAGGTGATCAGCAGCATTTTGTTCGCAGAGATGAGTTGAAG
genomic: TATCAAGGGTTTACAATTCCAGAGGCTTATGAACGTCTAATTCTTGATACgtatgacctc ... ggtttcacagGATACGAGGTGATCAGCAGCATTTTGTTCGCAGAGATGAGTTGAAG
EST: gi|110367670|gb|EC931616.1|EC931616
EST:     TATCAAGGGTTTACAATTCCAGAGGCTTATGAACGTCTAATTCTTGATAC                         GATACGAGGTGATCAGCAGCATTTTGTTCGCAGAGATGAGTTGAAG
genomic: TATCAAGGGTTTACAATTCCAGAGGCTTATGAACGTCTAATTCTTGATACgtatgacctc ... ggtttcacagGATACGAGGTGATCAGCAGCATTTTGTTCGCAGAGATGAGTTGAAG
EST: gi|110373098|gb|EC937308.1|EC937308
EST:     TATCAAGGGTTTACAATTCCAGAGGCTTATGAACGTCTAATTCTTGATAC                         GATACGAGGTGATCAGCAGCATTTTGTTCGCAGAGATGAGTTGAAG
genomic: TATCAAGGGTTTACAATTCCAGAGGCTTATGAACGTCTAATTCTTGATACgtatgacctc ... ggtttcacagGATACGAGGTGATCAGCAGCATTTTGTTCGCAGAGATGAGTTGAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagaaggatggggcacgtggaaatcaaatattgagatcgggttttggtttcacagGATACGAGGTGATCAGCAGCATTTTGTTCGCAGAGATGAGTTGAAG
                    aaatcaaatattga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctatcttgcacttaaaaaggaaaaaaaataaaagtagaataaacctagaaggatggggcacgtggaaatcaaatattgagatcgggttttggtttcacagGATACGAGGTGATCAGCAGCATTTTGTTCGCAGAGATGAGTTGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - cttgcac
- - - - - - - aaaagga
- - - - - - - - - - aaaaaaa
- - - - - - - - - - - - - - -aaaagta
- - - - - - - - - - - - - - - - - - - - aaaccta
- - - - - - - - - - - - - - - - - - - - - - - - - ggatggg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - cacgtgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaatcaa