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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgttttgagttcagaattttttgggatcaccatttgcagaggactgtggactttgatttgaagcttacattacgattttgaattgaattttttgatgtagGGATTGGAACTCATTCCTTCAGAAAATTTCACATCGGTATCTGTAATGCAAGCCGTTGGATCAGTCATGACTAATAAATATAGTGAAGGGTATCCTGGTG

Basic information

species Vitis vinifera
transcript Vv18s0001g07960.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0001g07960.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA14G36280.2 (Glycine max), 3'ss of exon 3
-------tgttttgagttcagaattttttgggatcaccatttgcagaggactgtggactttgatttgaagcttacattacgattttgaa--ttgaattttttga----tgtagGGATTGGAACTCATTCCTTCAGAAAATTTCACATCGGTATCTGTAATGCAAGCCGTTGGATCAGTCATGACTAATAAATATAGTGAAGGGTATCCTGGTG
        |  ||   |||   | |  || |  |  |  |      |  | |  |   |  ||||| | || |   |   | ||  | |  ||   || |  |     ||||||| || ||||| || ||||| ||||||||||| ||| | || || |||||||| |||||||| || ||||| |||||||| |||||||| ||||||||||
gtgaatccgagtttcattctacagtgctttgctttgctttgaattaataaataagctttccgattttatgcatgattgttgtttacggaagtttgtttgtacggaatttgtagGGGTTCGAACTTATACCTTCGGAAAATTTCACGTCGCTGTCGGTGATGCAAGCAGTTGGATCGGTGATGACGAATAAATACAGTGAAGGATATCCTGGTG

upper sequence: Vv18s0001g07960.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA02G38160.2 (Glycine max), 3'ss of exon 3
-----------tgttttgagttcagaattttttgggatcaccatttg-cagaggactgtggactttgatttgaagcttacattacgatt-ttgaattgaattttttg------atgtagGGATTGGAACTCATTCCTTCAGAAAATTTCACATCGGTATCTGTAATGCAAGCCGTTGGATCAGTCATGACTAATAAATATAGTGAAGGGTATCCTGGTG
           | |  |      ||| |  ||||   | |   || |   ||  | |   |  |  ||||| | || ||  |   | || | ||| |  ||||| |         |||||| || ||||| || ||||| || |||||||| ||| | || || ||||||||||||||||| || ||||| |||||||| || ||||| ||||| ||||
gtgaatccaagtttcattgtagtagagtgctttgctttgaagtttggattgataaatagcgtttccgattttatgcataattgttgtttatggaagtttattttgtacggaatgcgtagGGGTTCGAACTTATACCTTCGGAGAATTTCACGTCGCTGTCGGTGATGCAAGCCGTTGGATCGGTGATGACGAATAAATACAGCGAAGGATATCCCGGTG

upper sequence: Vv18s0001g07960.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT5G26780.3 (Arabidopsis thaliana), 3'ss of exon 3
tgttttgagttcagaattttttg-ggatcaccatttgcagaggactgtggactttgatttga-agcttacattacgattttgaattgaattttttgatgtagGGATTGGAACTCATTCCTTCAGAAAATTTCACATCGGTATCTGTAATGCAAGCCGTTGGATCAGTCATGACTAATAAATATAGTGAAGGGTATCCTGGTG
 || |  |   || |||||  || | || | ||  | || |    |     |||||||||      ||     | ||| ||     || ||||||     ||||||| ||||| || || ||||| |||||||| ||  ||||||| |||||||||||||| || || ||||||||||| ||||||||||| || ||||| |
-gtatcaa---caaaatttagtgagaatgatcaaattcacatatatagaagctttgatttattgatttgggggatgatgtta---cgagtttttt----cagGGATTTGAACTTATACCGTCAGAGAATTTCACTTCTCTATCTGTGATGCAAGCCGTTGGTTCTGTTATGACTAATAAGTATAGTGAAGGATACCCTGGAG

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|352776821|gb|FQ472708.1|FQ472708
EST:     ATCCGGAAATCGCTGACATCATTGAGCTCGAGAAAGCGAGGCAATGGAAG                         GGATTGGAACTCATTCCTTCAGAAAATTTCACATCGGTATCTGTAATGCAA
genomic: ATCCGGAAATCGCTGACATCATTGAGCTCGAGAAAGCGAGGCAATGGAAGgtgtatgacc ... tttgatgtagGGATTGGAACTCATTCCTTCAGAAAATTTCACATCGGTATCTGTAATGCAA
EST: gi|352795184|gb|FQ477294.1|FQ477294
EST:     ATCCGGAAATCGCTGACATCATTGAGCTCGAGAAAGCGAGGCAATGGAAG                         GGATTGGAACTCATTCCTTCAGAAAATTTCACATCGGTATCTGTAATGCAA
genomic: ATCCGGAAATCGCTGACATCATTGAGCTCGAGAAAGCGAGGCAATGGAAGgtgtatgacc ... tttgatgtagGGATTGGAACTCATTCCTTCAGAAAATTTCACATCGGTATCTGTAATGCAA
EST: gi|71862434|gb|DT011489.1|DT011489
EST:     ATCCGGAAATCGCTGACATCATTGAGCTCGAGAAAGCGAGGCAATGGAAG                         GGATTGGAACTCATTCCTTCAGAAAATTTCACATCGGTATCTGTAATGCAA
genomic: ATCCGGAAATCGCTGACATCATTGAGCTCGAGAAAGCGAGGCAATGGAAGgtgtatgacc ... tttgatgtagGGATTGGAACTCATTCCTTCAGAAAATTTCACATCGGTATCTGTAATGCAA
EST: gi|352764989|gb|FQ473637.1|FQ473637
EST:     ATCCGGAAATCGCTGACATCATTGAGCTCGAGAAAGCGAGGCAATGGAAG                         GGATTGGAACTCATTCCTTCAGAAAATTTCACATCGGTATCTGTAATGCAA
genomic: ATCCGGAAATCGCTGACATCATTGAGCTCGAGAAAGCGAGGCAATGGAAGgtgtatgacc ... tttgatgtagGGATTGGAACTCATTCCTTCAGAAAATTTCACATCGGTATCTGTAATGCAA
EST: gi|71855735|gb|DT004790.1|DT004790
EST:     ATCCGGAAATCGCTGACATCATTGAGCTCGAGAAAGCGAGGCAATGGAAG                         GGATTGGAACTCATTCCTTCAGAAAATTTCACATCGGTATCTGTAATGCAA
genomic: ATCCGGAAATCGCTGACATCATTGAGCTCGAGAAAGCGAGGCAATGGAAGgtgtatgacc ... tttgatgtagGGATTGGAACTCATTCCTTCAGAAAATTTCACATCGGTATCTGTAATGCAA
EST: gi|71854985|gb|DT004040.1|DT004040
EST:     ATCCGGAAATCGCTGACATCATTGAGCTCGAGAAAGCGAGGCAATGGAAG                         GGATTGGAACTCATTCCTTCAGAAAATTTCACATCGGTATCTGTAATGCAA
genomic: ATCCGGAAATCGCTGACATCATTGAGCTCGAGAAAGCGAGGCAATGGAAGgtgtatgacc ... tttgatgtagGGATTGGAACTCATTCCTTCAGAAAATTTCACATCGGTATCTGTAATGCAA
EST: gi|71858517|gb|DT007572.1|DT007572
EST:     ATCCGGAAATCGCTGACATCATTGAGCTCGAGAAAGCGAGGCAATGGAAG                         GGATTGGAACTCATTCCTTCAGAAAATTTCACATCGGTATCTGTAATGCAA
genomic: ATCCGGAAATCGCTGACATCATTGAGCTCGAGAAAGCGAGGCAATGGAAGgtgtatgacc ... tttgatgtagGGATTGGAACTCATTCCTTCAGAAAATTTCACATCGGTATCTGTAATGCAA
EST: gi|71857493|gb|DT006548.1|DT006548
EST:     ATCCGGAAATCGCTGACATCATTGAGCTCGAGAAAGCGAGGCAATGGAAG                         GGATTGGAACTCATTCCTTCAGAAAATTTCACATCGGTATCTGTAATGCAA
genomic: ATCCGGAAATCGCTGACATCATTGAGCTCGAGAAAGCGAGGCAATGGAAGgtgtatgacc ... tttgatgtagGGATTGGAACTCATTCCTTCAGAAAATTTCACATCGGTATCTGTAATGCAA
EST: gi|71858780|gb|DT007835.1|DT007835
EST:     ATCCGGAAATCGCTGACATCATTGAGCTCGAGAAAGCGAGGCAATGGAAG                         GGATTGGAACTCATTCCTTCAGAAAATTTCACATCGGTATCTGTAATGCAA
genomic: ATCCGGAAATCGCTGACATCATTGAGCTCGAGAAAGCGAGGCAATGGAAGgtgtatgacc ... tttgatgtagGGATTGGAACTCATTCCTTCAGAAAATTTCACATCGGTATCTGTAATGCAA
EST: gi|71854655|gb|DT003710.1|DT003710
EST:     ATCCGGAAATCGCTGACATCATTGAGCTCGAGAAAGCGAGGCAATGGAAG                         GGATTGGAACTCATTCCTTCAGAAAATTTCACATCGGTATCTGTAATGCAA
genomic: ATCCGGAAATCGCTGACATCATTGAGCTCGAGAAAGCGAGGCAATGGAAGgtgtatgacc ... tttgatgtagGGATTGGAACTCATTCCTTCAGAAAATTTCACATCGGTATCTGTAATGCAA
EST: gi|161708846|gb|FC059632.1|FC059632
EST:     ATCCGGAAATCGCTGACATCATTGAGCTCGAGAAAGCGAGGCAATGGAAG                         GGATTGGAACTCATTCCTTCAGAAAATTTCACATCGGTATCTGTAATGCAA
genomic: ATCCGGAAATCGCTGACATCATTGAGCTCGAGAAAGCGAGGCAATGGAAGgtgtatgacc ... tttgatgtagGGATTGGAACTCATTCCTTCAGAAAATTTCACATCGGTATCTGTAATGCAA
EST: gi|352781776|gb|FQ469074.1|FQ469074
EST:     ATCCGGAAATCGCTGACATCATTGAGCTCGAGAAAGCGAGGCAATGGAAG                         GGATTGGAACTCATTCCTTCAGAAAATTTCACATCGGTATCTGTAATGCAA
genomic: ATCCGGAAATCGCTGACATCATTGAGCTCGAGAAAGCGAGGCAATGGAAGgtgtatgacc ... tttgatgtagGGATTGGAACTCATTCCTTCAGAAAATTTCACATCGGTATCTGTAATGCAA
EST: gi|110359383|gb|EC920779.1|EC920779
EST:     ATCCGGAAATCGCTGACATCATTGAGCTCGAGAAAGCGAGGCAATGGAAG                         GGATTGGAACTCATTCCTTCAGAAAATTTCACATCGGTATCTGTAATGCAA
genomic: ATCCGGAAATCGCTGACATCATTGAGCTCGAGAAAGCGAGGCAATGGAAGgtgtatgacc ... tttgatgtagGGATTGGAACTCATTCCTTCAGAAAATTTCACATCGGTATCTGTAATGCAA
EST: gi|71858467|gb|DT007522.1|DT007522
EST:     ATCCGGAAATCGCTGACATCATTGAGCTCGAGAAAGCGAGGCAATGGAAG                         GGATTGGAACTCATTCCTTCAGAAAATTTCACATCGGTATCTGTAATGCAA
genomic: ATCCGGAAATCGCTGACATCATTGAGCTCGAGAAAGCGAGGCAATGGAAGgtgtatgacc ... tttgatgtagGGATTGGAACTCATTCCTTCAGAAAATTTCACATCGGTATCTGTAATGCAA
EST: gi|294966030|gb|GW837397.1|GW837397
EST:     ATCCGGAAATCGCTGACATCATTGAGCTCGAGAAAGCGAGGCAATGGAAG                         GGATTGGAACTCATTCCTTCAGAAAATTTCACATCGGTATCTGTAATGCAA
genomic: ATCCGGAAATCGCTGACATCATTGAGCTCGAGAAAGCGAGGCAATGGAAGgtgtatgacc ... tttgatgtagGGATTGGAACTCATTCCTTCAGAAAATTTCACATCGGTATCTGTAATGCAA
EST: gi|71855977|gb|DT005032.1|DT005032
EST:     ATCCGGAAATCGCTGACATCATTGAGCTCGAGAAAGCGAGGCAATGGAAG                         GGATTGGAACTCATTCCTTCAGAAAATTTCACATCGGTATCTGTAATGCAA
genomic: ATCCGGAAATCGCTGACATCATTGAGCTCGAGAAAGCGAGGCAATGGAAGgtgtatgacc ... tttgatgtagGGATTGGAACTCATTCCTTCAGAAAATTTCACATCGGTATCTGTAATGCAA
EST: gi|71857388|gb|DT006443.1|DT006443
EST:     ATCCGGAAATCGCTGACATCATTGAGCTCGAGAAAGCGAGGCAATGGAAG                         GGATTGGAACTCATTCCTTCAGAAAATTTCACATCGGTATCTGTAATGCAA
genomic: ATCCGGAAATCGCTGACATCATTGAGCTCGAGAAAGCGAGGCAATGGAAGgtgtatgacc ... tttgatgtagGGATTGGAACTCATTCCTTCAGAAAATTTCACATCGGTATCTGTAATGCAA
EST: gi|352764283|gb|FQ471263.1|FQ471263
EST:     ATCCGGAAATCGCTGACATCATTGAGCTCGAGAAAGCGAGGCAATGGAAG                         GGATTGGAACTCATTCCTTCAGAAAATTTCACATCGGTATCTGTAATGCAA
genomic: ATCCGGAAATCGCTGACATCATTGAGCTCGAGAAAGCGAGGCAATGGAAGgtgtatgacc ... tttgatgtagGGATTGGAACTCATTCCTTCAGAAAATTTCACATCGGTATCTGTAATGCAA
EST: gi|352768688|gb|FQ467900.1|FQ467900
EST:     ATCCGGAAATCGCTGACATCATTGAGCTCGAGAAAGCGAGGCAATGGAAG                         GGATTGGAACTCATTCCTTCAGAAAATTTCACATCGGTATCTGTAATGCAA
genomic: ATCCGGAAATCGCTGACATCATTGAGCTCGAGAAAGCGAGGCAATGGAAGgtgtatgacc ... tttgatgtagGGATTGGAACTCATTCCTTCAGAAAATTTCACATCGGTATCTGTAATGCAA
EST: gi|71858984|gb|DT008039.1|DT008039
EST:     ATCCGGAAATCGCTGACATCATTGAGCTCGAGAAAGCGAGGCAATGGAAG                         GGATTGGAACTCATTCCTTCAGAAAATTTCACATCGGTATCTGTAATGCAA
genomic: ATCCGGAAATCGCTGACATCATTGAGCTCGAGAAAGCGAGGCAATGGAAGgtgtatgacc ... tttgatgtagGGATTGGAACTCATTCCTTCAGAAAATTTCACATCGGTATCTGTAATGCAA
EST: gi|71859287|gb|DT008342.1|DT008342
EST:     ATCCGGAAATCGCTGACATCATTGAGCTCGAGAAAGCGAGGCAATGGAAG                         GGATTGGAACTCATTCCTTCAGAAAATTTCACATCGGTATCTGTAATGCAA
genomic: ATCCGGAAATCGCTGACATCATTGAGCTCGAGAAAGCGAGGCAATGGAAGgtgtatgacc ... tttgatgtagGGATTGGAACTCATTCCTTCAGAAAATTTCACATCGGTATCTGTAATGCAA
EST: gi|161713667|gb|FC062807.1|FC062807
EST:     ATCCGGAAATCGCTGACATCATTGAGCTCGAGAAAGCGAGGCAATGGAAG                         GGATTGGAACTCATTCCTTCAGAAAATTTCACATCGGTATCTGTAATGCAA
genomic: ATCCGGAAATCGCTGACATCATTGAGCTCGAGAAAGCGAGGCAATGGAAGgtgtatgacc ... tttgatgtagGGATTGGAACTCATTCCTTCAGAAAATTTCACATCGGTATCTGTAATGCAA
EST: gi|352765325|gb|FQ466022.1|FQ466022
EST:     ATCCGGAAATCGCTGACATCATTGAGCTCGAGAAAGCGAGGCAATGGAAG                         GGATTGGAACTCATTCCTTCAGAAAATTTCACATCGGTATCTGTAATGCAA
genomic: ATCCGGAAATCGCTGACATCATTGAGCTCGAGAAAGCGAGGCAATGGAAGgtgtatgacc ... tttgatgtagGGATTGGAACTCATTCCTTCAGAAAATTTCACATCGGTATCTGTAATGCAA
EST: gi|71856061|gb|DT005116.1|DT005116
EST:     ATCCGGAAATCGCTGACATCATTGAGCTCGAGAAAGCGAGGCAATGGAAG                         GGATTGGAACTCATTCCTTCAGAAAATTTCACATCGGTATCTGTAATGCAA
genomic: ATCCGGAAATCGCTGACATCATTGAGCTCGAGAAAGCGAGGCAATGGAAGgtgtatgacc ... tttgatgtagGGATTGGAACTCATTCCTTCAGAAAATTTCACATCGGTATCTGTAATGCAA
EST: gi|71857262|gb|DT006317.1|DT006317
EST:     ATCCGGAAATCGCTGACATCATTGAGCTCGAGAAAGCGAGGCAATGGAAG                         GGATTGGAACTCATTCCTTCAGAAAATTTCACATCGGTATCTGTAATGCAA
genomic: ATCCGGAAATCGCTGACATCATTGAGCTCGAGAAAGCGAGGCAATGGAAGgtgtatgacc ... tttgatgtagGGATTGGAACTCATTCCTTCAGAAAATTTCACATCGGTATCTGTAATGCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtggactttgatttgaagcttacattacgattttgaattgaattttttgatgtagGGATTGGAACTCATTCCTTCAGAAAATTTCACATCGGTATCTGTAATGCAAGCCGTTGGATCAGTCATGACTAATAAATATAGTGAAGGGTATCCTGGTG
                                          tttttt  CT-rich tract
                             attttgaattgaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgttttgagttcagaattttttgggatcaccatttgcagaggactgtggactttgatttgaagcttacattacgattttgaattgaattttttgatgtagGGATTGGAACTCATTCCTTCAGAAAATTTCACATCGGTATCTGTAATGCAAGCCGTTGGATCAGTCATGACTAATAAATATAGTGAAGGGTATCCTGGTG

- - - - - - - - - ttttggg
- - - - - - - - - - - - - - - catttgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgaagct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aattgaa