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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ccttcttcttctttataatttggttctttttactgtatgaattttttgttaaaacacttggaaccatatgtttgcctgctcactgccatttgtttcctagGAAATTGCTTGGTACATGGGTAAGGAGCTGGGAAAGATCAACATAAAGAGGTTTGCTGATGGTGAAATTTATGTTCAGTTGGAAGAGAGTGTTAGAGGGT

Basic information

species Vitis vinifera
transcript Vv02s0012g00530.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv02s0012g00530.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os02g03540.1 (Oryza sativa), 3'ss of exon 2
-ccttcttcttctttataatttggttctttttactgtatgaattttttgttaaaacacttggaaccatatgtttgcctgctcactgccatttgtttcctagGAAATTGCTTGGTACATGGGTAAGGAGCTGGGAAAGATCAACATAAAGAGGTTTGCTGATGGTGAAATTTATGTTCAGTTGGAAGAGAGTGTTAGAGGGT
   |   | |   || | |   |   |  ||   ||  |||||  ||  |   |        ||| | |  |     |  |   ||   | |  |    ||||||| ||  | ||| ||||    || || || ||||| |||||||| |||||||||||||| ||||| |||||||||||  |||| || || || || |
atttaagtgtgacttgttacaagtagcacttgtttgactgaatggttaatctcacagtgccaaacta-agatggaagtttttcttgttgtcttatctgcagGAAATAGCAAGTTACTTGGGCTTAGAACTTGGGAAGATTAACATAAAAAGGTTTGCTGATGGCGAAATATATGTTCAGTTACAAGAAAGCGTAAGGGGAT

upper sequence: Vv02s0012g00530.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G038791_T01 (Zea mays), 3'ss of exon 2
ccttcttcttctttataatt-tggttctttttactgtatgaattttttgt-taaaacacttggaaccatatgtttgcctgctcactgccatttgtttcctagGAAATTGCTTGGTACATGGGTAAGGAGCTGGGAAAGATCAACATAAAGAGGTTTGCTGATGGTGAAATTTATGTTCAGTTGGAAGAGAGTGTTAGAGGGT
 | ||      ||| ||||   |  |  || ||       ||| | || | |    ||     ||  || | |||      || |||   |||  |    |||| || ||  | ||| ||||    || || || ||||| | ||||||||||||||||||||||||||| |||||||||||| |||| |||||  | || |
-cctcaatagatttttaatgacgaataattataaacaggaaatatgttatctcgttcatgcctaataatttctttatggtatc-ctgtatttttatgaacagGAGATAGCAAGTTACTTGGGGCTAGAACTTGGGAAGATAACCATAAAGAGGTTTGCTGATGGTGAAATATATGTTCAGTTGCAAGAAAGTGTACGGGGCT

upper sequence: Vv02s0012g00530.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA17G16400.3 (Glycine max), 3'ss of exon 2
ccttcttcttctttataatttggttctt---tttactgtatgaattttttgttaaaacacttggaaccatatgtttgcctgctcactgccatttgtttcctagGAAATTGCTTGGTACATGGGTAAGGAGCTGGGAAAGATCAACATAAAGAGGTTTGCTGATGGTGAAATTTATGTTCAGTTGGAAGAGAGTGTTAGAGGGT
   | |    || || ||||  |||  |   | | |||| |   | ||  | |       |||      | |||| |  | || || |  ||   ||   |||||||||||| ||||||||||   ||| || ||||||||   ||| ||| | ||||||||||||||||| ||||| |||||  |||||||||||||||| |
---tttgtggctataaaattaagttagtatatatgctgtctttttattgggctggtttttttgttgagttttgttggttttctaacggtaatggtttgattagGAAATTGCTCGGTACATGGGCCTGGAACTCGGAAAGATTTCCATCAAGCGATTTGCTGATGGTGAAATATATGTCCAGTTACAAGAGAGTGTTAGAGGTT

upper sequence: Vv02s0012g00530.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA05G06110.1 (Glycine max), 3'ss of exon 2
ccttcttcttctttataatttggttc-tttttactgtatgaattttttgttaaaac-acttggaaccatatgtttgcctgctcactgccatttgtttcctagGAAATTGCTTGGTACATGGGTAAGGAGCTGGGAAAGATCAACATAAAGAGGTTTGCTGATGGTGAAATTTATGTTCAGTTGGAAGAGAGTGTTAGAGGGT
   |    |  | || |||   |||  | | |  ||| |   | ||  | |      | |||      | |||  |  | || || |   |   ||   |||||||||||| ||||||||||   ||| || ||||||||   ||| ||| | ||||||||||||||||| ||||| |||||  |||||||||||||||| |
--gttgcttgatataaaataaagttggtatatggtgtctttttattgggctggttttatttgttgagttttgtgggttttctaaccgtgttgctttgattagGAAATTGCTCGGTACATGGGCCTGGAACTTGGAAAGATTTCCATCAAGCGATTTGCTGATGGTGAAATCTATGTCCAGTTACAAGAGAGTGTTAGAGGTT

upper sequence: Vv02s0012g00530.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT1G32380.1 (Arabidopsis thaliana), 3'ss of exon 2
ccttcttcttctttataa-tttggttctttttactgtatgaattttttgttaaaacacttggaaccatatgtttgcctgctcactgccatttgtttcctagGAAATTGCTTGGTACATGGGTAAGGAGCTGGGAAAGATCAACATAAAGAGGTTTGCTGATGGTGAAATTTATGTTCAGTTGGAAGAGAGTGTTAGAGGGT
   |  | ||||  | |  ||||||| | |||  |     | |||| |  |          |||  ||||| |   ||  |    |  ||||  |    |||||||||||||||| ||||||  |||||| || ||| | | ||||||||| ||||||||||| || || ||||||||| |  |||| ||||||||||| |
--gtagttttctcgagacctttggttgtcttttttaatcaagttttcttctggt-------gaagtatatgctaaactctt----ggaattt--tgtgaagGAAATTGCTTGGTATATGGGTCTGGAGCTTGGGAAGGTTAGCATAAAGAGATTTGCTGATGGAGAGATCTATGTTCAGCTCAAAGAAAGTGTTAGAGGTT

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|71862733|gb|DT011788.1|DT011788
EST:     GTGACCGGTTGAAAATATTCTCTGGCACAGCAAATCCCACACTTTCTAAG                         GAAATTGCTTGGTACATGGGTAAGGAGCTGGGAAAGATCAACATAAAGAGG
genomic: GTGACCGGTTGAAAATATTCTCTGGCACAGCAAATCCCACACTTTCTAAGgtattcatta ... tgtttcctagGAAATTGCTTGGTACATGGGTAAGGAGCTGGGAAAGATCAACATAAAGAGG
EST: gi|71863567|gb|DT012622.1|DT012622
EST:     GTGACCGGTTGAAAATATTCTCTGGCACAGCAAATCCCACACTTTCTAAG                         GAAATTGCTTGGTACATGGGTAAGGAGCTGGGAAAGATCAACATAAAGAGG
genomic: GTGACCGGTTGAAAATATTCTCTGGCACAGCAAATCCCACACTTTCTAAGgtattcatta ... tgtttcctagGAAATTGCTTGGTACATGGGTAAGGAGCTGGGAAAGATCAACATAAAGAGG
EST: gi|351052954|gb|FQ453941.1|FQ453941
EST:     GTGACCGGTTGAAAATATTCTCTGGCACAGCAAATCCCACACTTTCTAAG                         GAAATTGCTTGGTACATGGGTAAGGAGCTGGGAAAGATCAACATAAAGAGG
genomic: GTGACCGGTTGAAAATATTCTCTGGCACAGCAAATCCCACACTTTCTAAGgtattcatta ... tgtttcctagGAAATTGCTTGGTACATGGGTAAGGAGCTGGGAAAGATCAACATAAAGAGG
EST: gi|351033460|gb|FQ462111.1|FQ462111
EST:     GTGACCGGTTGAAAATATTCTCTGGCACAGCAAATCCCACACTTTCTAAG                         GAAATTGCTTGGTACATGGGTAAGGAGCTGGGAAAGATCAACATAAAGAGG
genomic: GTGACCGGTTGAAAATATTCTCTGGCACAGCAAATCCCACACTTTCTAAGgtattcatta ... tgtttcctagGAAATTGCTTGGTACATGGGTAAGGAGCTGGGAAAGATCAACATAAAGAGG
EST: gi|161719281|gb|FC064821.1|FC064821
EST:     GTGACCGGTTGAAAATATTCTCTGGCACAGCAAATCCCACACTTTCTAAG                         GAAATTGCTTGGTACATGGGTAAGGAGCTGGGAAAGATCAACATAAAGAGG
genomic: GTGACCGGTTGAAAATATTCTCTGGCACAGCAAATCCCACACTTTCTAAGgtattcatta ... tgtttcctagGAAATTGCTTGGTACATGGGTAAGGAGCTGGGAAAGATCAACATAAAGAGG
EST: gi|71860602|gb|DT009657.1|DT009657
EST:     GTGACCGGTTGAAAATATTCTCTGGCACAGCAAATCCCACACTTTCTAAG                         GAAATTGCTTGGTACATGGGTAAGGAGCTGGGAAAGATCAACATAAAGAGG
genomic: GTGACCGGTTGAAAATATTCTCTGGCACAGCAAATCCCACACTTTCTAAGgtattcatta ... tgtttcctagGAAATTGCTTGGTACATGGGTAAGGAGCTGGGAAAGATCAACATAAAGAGG
EST: gi|71862323|gb|DT011378.1|DT011378
EST:     GTGACCGGTTGAAAATATTCTCTGGCACAGCAAATCCCACACTTTCTAAG                         GAAATTGCTTGGTACATGGGTAAGGAGCTGGGAAAGATCAACATAAAGAGG
genomic: GTGACCGGTTGAAAATATTCTCTGGCACAGCAAATCCCACACTTTCTAAGgtattcatta ... tgtttcctagGAAATTGCTTGGTACATGGGTAAGGAGCTGGGAAAGATCAACATAAAGAGG
EST: gi|71861933|gb|DT010988.1|DT010988
EST:     GTGACCGGTTGAAAATATTCTCTGGCACAGCAAATCCCACACTTTCTAAG                         GAAATTGCTTGGTACATGGGTAAGGAGCTGGGAAAGATCAACATAAAGAGG
genomic: GTGACCGGTTGAAAATATTCTCTGGCACAGCAAATCCCACACTTTCTAAGgtattcatta ... tgtttcctagGAAATTGCTTGGTACATGGGTAAGGAGCTGGGAAAGATCAACATAAAGAGG
EST: gi|110376340|gb|EC941395.1|EC941395
EST:     GTGACCGGTTGAAAATATTCTCTGGCACAGCAAATCCCACACTTTCTAAG                         GAAATTGCTTGGTACATGGGTAAGGAGCTGGGAAAGATCAACATAAAGAGG
genomic: GTGACCGGTTGAAAATATTCTCTGGCACAGCAAATCCCACACTTTCTAAGgtattcatta ... tgtttcctagGAAATTGCTTGGTACATGGGTAAGGAGCTGGGAAAGATCAACATAAAGAGG
EST: gi|294966332|gb|GW837583.1|GW837583
EST:     GTGACCGGTTGAAAATATTCTCTGGCACAGCAAATCCCACACTTTCTAAG                         GAAATTGCTTGGTACATGGGTAAGGAGCTGGGAAAGATCAACATAAAGAGG
genomic: GTGACCGGTTGAAAATATTCTCTGGCACAGCAAATCCCACACTTTCTAAGgtattcatta ... tgtttcctagGAAATTGCTTGGTACATGGGTAAGGAGCTGGGAAAGATCAACATAAAGAGG
EST: gi|30253361|gb|CB970912.1|CB970912
EST:     GTGACCGGTTGAAAATATTCTCTGGCACAGCAAATCCCACACTTTCTAAG                         GAAATTGCTTGGTACATGGGTAAGGAGCTGGGAAAGATCAACATAAAGAGG
genomic: GTGACCGGTTGAAAATATTCTCTGGCACAGCAAATCCCACACTTTCTAAGgtattcatta ... tgtttcctagGAAATTGCTTGGTACATGGGTAAGGAGCTGGGAAAGATCAACATAAAGAGG
EST: gi|71864254|gb|DT013309.1|DT013309
EST:     GTGACCGGTTGAAAATATTCTCTGGCACAGCAAATCCCACACTTTCTAAG                         GAAATTGCTTGGTACATGGGTAAGGAGCTGGGAAAGATCAACATAAAGAGG
genomic: GTGACCGGTTGAAAATATTCTCTGGCACAGCAAATCCCACACTTTCTAAGgtattcatta ... tgtttcctagGAAATTGCTTGGTACATGGGTAAGGAGCTGGGAAAGATCAACATAAAGAGG
EST: gi|71863548|gb|DT012603.1|DT012603
EST:     GTGACCGGTTGAAAATATTCTCTGGCACAGCAAATCCCACACTTTCTAAG                         GAAATTGCTTGGTACATGGGTAAGGAGCTGGGAAAGATCAACATAAAGAGG
genomic: GTGACCGGTTGAAAATATTCTCTGGCACAGCAAATCCCACACTTTCTAAGgtattcatta ... tgtttcctagGAAATTGCTTGGTACATGGGTAAGGAGCTGGGAAAGATCAACATAAAGAGG
EST: gi|110698297|gb|EE075660.1|EE075660
EST:     GTGACCGGTTGAAAATATTCTCTGGCACAGCAAATCCCACACTTTCTAAG                         GAAATTGCTTGGTACATGGGTAAGGAGCTGGGAAAGATCAACATAAAGAGG
genomic: GTGACCGGTTGAAAATATTCTCTGGCACAGCAAATCCCACACTTTCTAAGgtattcatta ... tgtttcctagGAAATTGCTTGGTACATGGGTAAGGAGCTGGGAAAGATCAACATAAAGAGG
EST: gi|352789974|gb|FQ479584.1|FQ479584
EST:     GTGACCGGTTGAAAATATTCTCTGGCACAGCAAATCCCACACTTTCTAAG                         GAAATTGCTTGGTACATGGGTAAGGAGCTGGGAAAGATCAACATAAAGAGG
genomic: GTGACCGGTTGAAAATATTCTCTGGCACAGCAAATCCCACACTTTCTAAGgtattcatta ... tgtttcctagGAAATTGCTTGGTACATGGGTAAGGAGCTGGGAAAGATCAACATAAAGAGG
EST: gi|71862331|gb|DT011386.1|DT011386
EST:     GTGACCGGTTGAAAATATTCTCTGGCACAGCAAATCCCACACTTTCTAAG                         GAAATTGCTTGGTACATGGCTAAGGAGCTGGGAAAGATCAACATAAAGAGG
genomic: GTGACCGGTTGAAAATATTCTCTGGCACAGCAAATCCCACACTTTCTAAGgtattcatta ... tgtttcctagGAAATTGCTTGGTACATGGGTAAGGAGCTGGGAAAGATCAACATAAAGAGG
EST: gi|71862062|gb|DT011117.1|DT011117
EST:     GTGACCGGTTGAAAATATTCTCTGGCACAGCAAATCCCACACTTTCTAAG                         GAAATTGCTTGGTACATGGGTAAGGAGCTGGGAAAGATCAACATAAAGAGG
genomic: GTGACCGGTTGAAAATATTCTCTGGCACAGCAAATCCCACACTTTCTAAGgtattcatta ... tgtttcctagGAAATTGCTTGGTACATGGGTAAGGAGCTGGGAAAGATCAACATAAAGAGG
EST: gi|71862839|gb|DT011894.1|DT011894
EST:     GTGACCGGTTGAAAATATTCTCTGGCACAGCAAATCCCACACTTTCTAAG                         GAAATTGCTTGGTACATGGGTAAGGAGCTGGGAAAGATCAACATAAAGAGG
genomic: GTGACCGGTTGAAAATATTCTCTGGCACAGCAAATCCCACACTTTCTAAGgtattcatta ... tgtttcctagGAAATTGCTTGGTACATGGGTAAGGAGCTGGGAAAGATCAACATAAAGAGG
EST: gi|351030850|gb|FQ438886.1|FQ438886
EST:     GTGACCGGTTGAAAATATTCTCTGGCACAGCAAATCCCACACTTTCTAAG                         GAAATTGCTTGGTACATGGGTAAGGAGCTGGGAAAGATCAACATAAAGAGG
genomic: GTGACCGGTTGAAAATATTCTCTGGCACAGCAAATCCCACACTTTCTAAGgtattcatta ... tgtttcctagGAAATTGCTTGGTACATGGGTAAGGAGCTGGGAAAGATCAACATAAAGAGG
EST: gi|71860796|gb|DT009851.1|DT009851
EST:     GTGACCGGTTGAAAATATTCTCTGGCACAGCAAATCCCACACTTTCTAAG                         GAAATTGCTTGGTACATGGGTAAGGAGCTGGGAAAGATCAACATAAAGAGG
genomic: GTGACCGGTTGAAAATATTCTCTGGCACAGCAAATCCCACACTTTCTAAGgtattcatta ... tgtttcctagGAAATTGCTTGGTACATGGGTAAGGAGCTGGGAAAGATCAACATAAAGAGG
EST: gi|110719024|gb|EE096529.1|EE096529
EST:     GTGACCGGTTGAAAATATTCTCTGGCACAGCAAATCCCACACTTTCTAAG                         GAAATTGCTTGGTACATGGGTAAGGAGCTGGGAAAGATCAACATAAAGAGG
genomic: GTGACCGGTTGAAAATATTCTCTGGCACAGCAAATCCCACACTTTCTAAGgtattcatta ... tgtttcctagGAAATTGCTTGGTACATGGGTAAGGAGCTGGGAAAGATCAACATAAAGAGG
EST: gi|71862732|gb|DT011787.1|DT011787
EST:     GTGACCGGTTGAAAATATTCTCTGGCACAGCAAATCCCACACTTTCTAAG                         GAAATTGCTTGGTACATGGGTAAGGAGCTGGGAAAGATCAACATAAAGAGG
genomic: GTGACCGGTTGAAAATATTCTCTGGCACAGCAAATCCCACACTTTCTAAGgtattcatta ... tgtttcctagGAAATTGCTTGGTACATGGGTAAGGAGCTGGGAAAGATCAACATAAAGAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgttaaaacacttggaaccatatgtttgcctgctcactgccatttgtttcctagGAAATTGCTTGGTACATGGGTAAGGAGCTGGGAAAGATCAACATAAAGAGGTTTGCTGATGGTGAAATTTATGTTCAGTTGGAAGAGAGTGTTAGAGGGT
                               tgctcac  putative branch site (score: 2)
                                           tttgtttcct  putative PPT
                    atatgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ccttcttcttctttataatttggttctttttactgtatgaattttttgttaaaacacttggaaccatatgtttgcctgctcactgccatttgtttcctagGAAATTGCTTGGTACATGGGTAAGGAGCTGGGAAAGATCAACATAAAGAGGTTTGCTGATGGTGAAATTTATGTTCAGTTGGAAGAGAGTGTTAGAGGGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
-cttcttc
- - - - - - - - - - - - - - - - ctgtatg
- - - - - - - - - - - - - - - - - - - - - - - - - aaaacac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaccata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgcctgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cactgcc