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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgctgttggatgtttgtttgaattatttttcgttcaaagataatgttgttatttgtctttttgtttctcggaaatctgttgaagctgatgtatgcgttgatttgcgttttgatgtggctttttagGTGAAATACTGTTCAGAAAACAACAAGCGTCTCATTCACTTCTCGACTTGTGAAGTCTATGGGAAAACGATTGGGAGCTTTCTTCCCAAAGATTCACCTC

Basic information

species Vitis vinifera
transcript Vv03s0017g00680.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv03s0017g00680.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA12G30490.2 (Glycine max), 3'ss of exon 2
gtatgctgttggatgtttgtttgaattatttttcgttcaaagataatgttgttatttgtctttttgtttctcggaaatctgttgaagctgatgtatgcgttgatttgcgttttgatgtggctttttagGTGAAATACTGTTCAGAAAACAACAAGCGTCTCATTCACTTCTCGACTTGTGAAGTCTATGGGAAAACGATTGGGAGCTTTCTTCCCAAAGATTCACCTC
                               | |||   |   | |  ||  | | | ||  ||| |||||  |   |||||       ||  |     ||||   |  ||   || ||| ||   ||||||| ||||||||||| |||||||||||||||||||| ||||| || |||||||||||||||||||||||||| ||||| || |||||||||   ||||
------------------------------gtgcgtcttacttttactttactttctctcccttt-tttctttgttttctgtgtgtttggaaattcaaattga---ggattggaatttgggttc--agGTGAAGTACTGTTCAGAGAACAACAAGCGTCTCATTCATTTCTCTACGTGTGAAGTCTATGGGAAAACGATTGGAAGCTTCCTCCCCAAAGATAGTCCTC

upper sequence: Vv03s0017g00680.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA11G19550.1 (Glycine max), 3'ss of exon 2
gtatgctgttggatgtttgtttgaattatttttcgttcaaagataatgttgttatttgtctttttgtttctcggaaatctgttgaagctgatgtatgcgttgatttgcgttttgatgtggctttttagGTGAAATACTGTTCAGAAAACAACAAGCGTCTCATTCACTTCTCGACTTGTGAAGTCTATGGGAAAACGATTGGGAGCTTTCTTCCCAAAGATTCACCTC
                 |   | | | |      |||||||  | |   ||| |   |      ||  ||| |    |   ||||     |||    ||| | |||| | ||||           ||||||||||||||||| || ||||||||||| || || || ||||| ||||| ||||| || ||||||||||||||   |||||| || ||||||   ||||
----------------gtaactaactaaccacctgttcaaat-tgaaaatgtgaaacgc-----tgaatcttgagggt---ttgagttctatgcg-acgtcgttttgtgctttg-----------tagGTGAAATACTGTTCCGAGAACAACAAGCGCCTTATCCATTTCTCCACTTGCGAAGTGTACGGGAAAACGATTGGAGCCTTTCTCCCTAAAGATAGTCCTC

upper sequence: Vv03s0017g00680.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA12G08930.1 (Glycine max), 3'ss of exon 2
gtatgctgttggatgtttgtttgaattatttttcgttcaaagataatgttgttatttgtctttttgtttctcggaaatctgttgaagctgatgtatgcgttgatttgcgttttgatgtggctttttagGTGAAATACTGTTCAGAAAACAACAAGCGTCTCATTCACTTCTCGACTTGTGAAGTCTATGGGAAAACGATTGGGAGCTTTCTTCCCAAAGATTCACCTC
       ||    |   |  || | | | |   ||||| ||  |     ||| | ||||     ||  ||| |  |||   ||||    |||     ||| | || |   |||        ||| ||||||||||||||||| || ||||||||||| || || || ||||| ||||| ||||| || || || ||||||||   |||||| || ||||||   ||||
-------gtaacttaactacttcactaactacccgttctaat-tgcaaatgtgaattgt-----tgaatcttg--aatgatttgagttcgattcg-acgtcgtttcgttcttt--------tttgtagGTGAAATACTGTTCCGAGAACAACAAGCGCCTTATCCATTTCTCTACTTGCGAAGTGTACGGAAAGACGATTGGAGCCTTTCTCCCTAAAGATAGTCCTC

upper sequence: Vv03s0017g00680.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT2G27860.1 (Arabidopsis thaliana), 3'ss of exon 2
gtatgctgttggatgtttgtttgaattatttttcgttcaaagataatgttgttatttgtctttttgtttctcggaaatctgttgaagctgatgtatgcgttgat--ttgcgttttgatgtggcttt-ttagGTGAAATACTGTTCAGAAAACAACAAGCGTCTCATTCACTTCTCGACTTGTGAAGTCTATGGGAAAACGATTGGGAGCTTTCTTCCCAAAGATTCACCTC
                      | ||   ||||| |       ||   | |||  |||| ||  | |  |||       | |||||| ||||| |  |  ||||  ||| ||  ||   ||| ||| |||||||||||||||||| || ||||||||||||||||||||||| || || |||||||| ||||| ||||| ||||| ||||||||||| || |||   ||||
----------------------gtatgtgttttcttct-----tagcttcgttcattgttttgctttagctcttg---tttttgaagttgatggagacagtgatgattgtgtaatgcgttggttttgttagGTGAAATACTGTTCTGAGAACAACAAGCGTCTCATTCACTTTTCTACCTGTGAAGTTTATGGAAAAACCATTGGAAGCTTTCTTCCTAAGGATCATCCTC

upper sequence: Vv03s0017g00680.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT1G08200.1 (Arabidopsis thaliana), 3'ss of exon 2
gtatgctgttggatgtttgtttgaattatttttcgttcaaagataatgttgttatttgtctttttgtttctcggaaatctgttgaagctgatgtatgcgttgatttgcgttttgatgtggctttttagGTGAAATACTGTTCAGAAAACAACAAGCGTCTCATTCACTTCTCGACTTGTGAAGTCTATGGGAAAACGATTGGGAGCTTTCTTCCCAAAGATTCACCTC
||||| | ||  ||| || |     || |||    |        ||| |||| | ||       | ||| |  |  ||  |  ||   |  |     | |||| | |   || | | ||| | | ||||| |||||||| ||||| |||||||||||||| |||||||| || ||||||||||| ||||| ||||| || || ||||||||||| || |||   ||||
gtatg-tattttatgcttttgcagtttgtttggtttagtggagcaattttgtaagtttgaggaatatttttatgtgatacg--gattttagttgtgacattgagtggtcattggttttgg-tatgtagGTTAAATACTGCTCAGAGAACAACAAGCGTCTGATTCACTTTTCCACTTGTGAAGTGTATGGAAAAACTATAGGAAGCTTTCTTCCAAAGGATCATCCTC

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|110732834|gb|EE108465.1|EE108465
EST:     CTCGTCCTCTCGATACGATTTACAGCAATTTCATTGATGCCCTTCCAGTG                         GTGAAATACTGTTCGGAAAACAACAAGCGTCTCATTCACTTCTCGACTTGT
genomic: CTCGTCCTCTCGATACGATTTACAGCAATTTCATTGATGCACTTCCAGTGgtatgctgtt ... ggctttttagGTGAAATACTGTTCAGAAAACAACAAGCGTCTCATTCACTTCTCGACTTGT
EST: gi|71857780|gb|DT006835.1|DT006835
EST:     CTCGTCCTCTCGATACGATTTACAGCAATTTCATTGATGCCCTTCCAGTG                         GTGAAATACTGTTCGGAAAACAACAAGCGTCTCATTCACTTCTCGACTTGT
genomic: CTCGTCCTCTCGATACGATTTACAGCAATTTCATTGATGCACTTCCAGTGgtatgctgtt ... ggctttttagGTGAAATACTGTTCAGAAAACAACAAGCGTCTCATTCACTTCTCGACTTGT
EST: gi|71857207|gb|DT006262.1|DT006262
EST:     CTCGTCCTCTCGATACGATTTACAGCAATTTCATTGATGCCCTTCCAGTG                         GTGAAATACTGTTCGGAAAACAACAAGCGTCTCATTCACTTCTCGACTTGT
genomic: CTCGTCCTCTCGATACGATTTACAGCAATTTCATTGATGCACTTCCAGTGgtatgctgtt ... ggctttttagGTGAAATACTGTTCAGAAAACAACAAGCGTCTCATTCACTTCTCGACTTGT
EST: gi|110387369|gb|EC952029.1|EC952029
EST:     CTCGTCCTCTCGATACGATTTACAGCAATTTCATTGATGCACTTCCAGTG                         GTGAAATACTGTTCAGAAAACAACAAGCGTCTCATTCACTTCTCGACTTGT
genomic: CTCGTCCTCTCGATACGATTTACAGCAATTTCATTGATGCACTTCCAGTGgtatgctgtt ... ggctttttagGTGAAATACTGTTCAGAAAACAACAAGCGTCTCATTCACTTCTCGACTTGT
EST: gi|71864027|gb|DT013082.1|DT013082
EST:     CTCGTCCTCTCGATACGATTTACAGCAATTTCATTGATGCACTTCCAGTG                         GTGAAATACTGTTCAGAAAACAACAAGCGTCTCATTCACTTCTCGACTTGT
genomic: CTCGTCCTCTCGATACGATTTACAGCAATTTCATTGATGCACTTCCAGTGgtatgctgtt ... ggctttttagGTGAAATACTGTTCAGAAAACAACAAGCGTCTCATTCACTTCTCGACTTGT
EST: gi|71865169|gb|DT014224.1|DT014224
EST:     CTCGTCCTCTCGATACGATTTACAGCAATTTCATTGATGCCCTTCCAGTG                         GTGAAATACTGTTCGGAAAACAACAAGCGTCTCATTCACTTCTCGACTTGT
genomic: CTCGTCCTCTCGATACGATTTACAGCAATTTCATTGATGCACTTCCAGTGgtatgctgtt ... ggctttttagGTGAAATACTGTTCAGAAAACAACAAGCGTCTCATTCACTTCTCGACTTGT
EST: gi|71855267|gb|DT004322.1|DT004322
EST:     CTCGTCCTCTCGATACGATTTACAGCAATTTCATTGATGCCCTTCCAGTG                         GTGAAATACTGTTCGGAAAACAACAAGCGTCTCATTCACTTCTCGACTTGT
genomic: CTCGTCCTCTCGATACGATTTACAGCAATTTCATTGATGCACTTCCAGTGgtatgctgtt ... ggctttttagGTGAAATACTGTTCAGAAAACAACAAGCGTCTCATTCACTTCTCGACTTGT
EST: gi|71859790|gb|DT008845.1|DT008845
EST:     CTCGTCCTCTCGATACGATTTACAGCAATTTCATTGATGCCCTTCCAGTG                         GTGAAATACTGTTCGGAAAACAACAAGCGTCTCATTCACTTCTCGACTTGT
genomic: CTCGTCCTCTCGATACGATTTACAGCAATTTCATTGATGCACTTCCAGTGgtatgctgtt ... ggctttttagGTGAAATACTGTTCAGAAAACAACAAGCGTCTCATTCACTTCTCGACTTGT
EST: gi|110686702|gb|EE064638.1|EE064638
EST:     CTCGTCCTCTCGATACGATTTACAGCAATTTCATTGATGCCCTTCCAGTG                         GTGAAATACTGTTCGGAAAACAACAAGCGTCTCATTCACTTCTCGACTTGT
genomic: CTCGTCCTCTCGATACGATTTACAGCAATTTCATTGATGCACTTCCAGTGgtatgctgtt ... ggctttttagGTGAAATACTGTTCAGAAAACAACAAGCGTCTCATTCACTTCTCGACTTGT
EST: gi|110359156|gb|EC920189.1|EC920189
EST:     CTCGTCCTCTCGATACGATTTACAGCAATTTCATTGATGCCCTTCCAGTG                         GTGAAATACTGTTCGGAAAACAACAAGCGTCTCATTCACTTCTCGACTTGT
genomic: CTCGTCCTCTCGATACGATTTACAGCAATTTCATTGATGCACTTCCAGTGgtatgctgtt ... ggctttttagGTGAAATACTGTTCAGAAAACAACAAGCGTCTCATTCACTTCTCGACTTGT
EST: gi|161710980|gb|FC060335.1|FC060335
EST:     CTCGTCCTCTCGATACGATTTACAGCAATTTCATTGATGCCCTTCCAGTG                         GTGAAATACTGTTCGGAAAACAACAAGCGTCTCATTCACTTCTCGACTTGT
genomic: CTCGTCCTCTCGATACGATTTACAGCAATTTCATTGATGCACTTCCAGTGgtatgctgtt ... ggctttttagGTGAAATACTGTTCAGAAAACAACAAGCGTCTCATTCACTTCTCGACTTGT
EST: gi|30253074|gb|CB970625.1|CB970625
EST:     CTCGTCCTCTCGATACGATTTACAGCAATTTCATTGATGCACTTCCAGTG                         GTGAAATACTGTTCAGAAAACAACAAGCGTCTCATTCACTTCTCGACTTGT
genomic: CTCGTCCTCTCGATACGATTTACAGCAATTTCATTGATGCACTTCCAGTGgtatgctgtt ... ggctttttagGTGAAATACTGTTCAGAAAACAACAAGCGTCTCATTCACTTCTCGACTTGT
EST: gi|30320980|gb|CD004242.1|CD004242
EST:     CTCGTCCTCTCGATACGATTTACAGCAATTTCATTGATGCCCTTCCAGTG                         GTGAAATACTGTTCGGAAAACAACAAGCGTCTCATTCACTTCTCGACTTGT
genomic: CTCGTCCTCTCGATACGATTTACAGCAATTTCATTGATGCACTTCCAGTGgtatgctgtt ... ggctttttagGTGAAATACTGTTCAGAAAACAACAAGCGTCTCATTCACTTCTCGACTTGT
EST: gi|110685502|gb|EE062276.1|EE062276
EST:     CTCGTCCTCTCGATACGATTTACAGCAATTTCATTGATGCACTTCCAGTG                         GTGAAATACTGTTCAGAAAACAACAAGCGTCTCATTCACTTCTCGACTTGT
genomic: CTCGTCCTCTCGATACGATTTACAGCAATTTCATTGATGCACTTCCAGTGgtatgctgtt ... ggctttttagGTGAAATACTGTTCAGAAAACAACAAGCGTCTCATTCACTTCTCGACTTGT
EST: gi|71862682|gb|DT011737.1|DT011737
EST:     CTCGTCCTCTCGATACGATTTACAGCAATTTCATTGATGCACTTCCAGTG                         GTGAAATACTGTTCAGAAAACAACAAGCGTCTCATTCACTTCTCGACTTGT
genomic: CTCGTCCTCTCGATACGATTTACAGCAATTTCATTGATGCACTTCCAGTGgtatgctgtt ... ggctttttagGTGAAATACTGTTCAGAAAACAACAAGCGTCTCATTCACTTCTCGACTTGT
EST: gi|77585098|gb|DV221638.1|DV221638
EST:     CTCGTCCTCTCGATACGATTTACAGCAATTTCATTGATGCACTTCCAGTG                         GTGAAATACTGTTCAGAAAACAACAAGCGTCTCATTCACTTCTCGACTTGT
genomic: CTCGTCCTCTCGATACGATTTACAGCAATTTCATTGATGCACTTCCAGTGgtatgctgtt ... ggctttttagGTGAAATACTGTTCAGAAAACAACAAGCGTCTCATTCACTTCTCGACTTGT
EST: gi|71855470|gb|DT004525.1|DT004525
EST:     CTCGTCCTCTCGATACGATTTACAGCAATTTCATTGATGCACTTCCAGTG                         GTGAAATACTGTTCAGAAAACAACAAGCGTCTCATTCACTTCTCGACTTGT
genomic: CTCGTCCTCTCGATACGATTTACAGCAATTTCATTGATGCACTTCCAGTGgtatgctgtt ... ggctttttagGTGAAATACTGTTCAGAAAACAACAAGCGTCTCATTCACTTCTCGACTTGT
EST: gi|71858973|gb|DT008028.1|DT008028
EST:     CTCGTCCTCTCGATACGATTTACAGCAATTTCATTGATGCCCTTCCAGTG                         GTGAAATACTGTTCGGAAAACAACAAGCGTCTCATTCACTTCTCGACTT
genomic: CTCGTCCTCTCGATACGATTTACAGCAATTTCATTGATGCACTTCCAGTGgtatgctgtt ... ggctttttagGTGAAATACTGTTCAGAAAACAACAAGCGTCTCATTCACTTCTCGACTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaaatctgttgaagctgatgtatgcgttgatttgcgttttgatgtggctttttagGTGAAATACTGTTCAGAAAACAACAAGCGTCTCATTCACTTCTCGACTTGTGAAGTCTATGGGAAAACGATTGGGAGCTTTCTTCCCAAAGATTCACCTC
                                    ttttgat  putative branch site (score: 4)
                                               cttttt  putative PPT
                                                ttttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgctgttggatgtttgtttgaattatttttcgttcaaagataatgttgttatttgtctttttgtttctcggaaatctgttgaagctgatgtatgcgttgatttgcgttttgatgtggctttttagGTGAAATACTGTTCAGAAAACAACAAGCGTCTCATTCACTTCTCGACTTGTGAAGTCTATGGGAAAACGATTGGGAGCTTTCTTCCCAAAGATTCACCTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT