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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttaatcttctattttcctttataactgttagaaaggcatggaacattcttttagttcgattccattcaaatctataaagatatccttttgagttctttagGTACGTTTAAATTGACACTTCAGTTTTCGGAGGAGTATCCAAACAAACCACCAACAGTGCGATTTGTTTCCCGTATGTTCCATCCAAATA

Basic information

species Vitis vinifera
transcript Vv17s0000g05820.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv17s0000g05820.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os05g08960.1 (Oryza sativa), 3'ss of exon 3
ttaatcttctattttcctttataactgttagaaaggcatggaacattcttttagttcgattccat-tcaaatctataaagatatcct---tttgagttctttagGTACGTTTAAATTGACACTTCAGTTTTCGGAGGAGTATCCAAACAAACCACCAACAGTGCGATTTGTTTCCCGTATGTTCCATCCAAATA
    || | | | |   | |     | ||      | | |   ||    ||    ||  || ||| | ||  || | ||  |||  |   || |   ||   ||||||||| ||  |||||||||||||| | || || ||||| ||||| ||||| ||||||||||||||||| || ||||| ||||| || |
----tcctttttgtatttattggcattttgttcttgtacgtgtcaccaattgtactcttttacatgttaacactgtcaaattatgtttacttcgccatcgccagGTACGTTCAAGCTGACACTTCAGTTTACTGAAGATTATCCTAACAAGCCACCTACAGTGCGATTTGTTTCTCGGATGTTTCATCCTAACA

upper sequence: Vv17s0000g05820.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G110983_T04 (Zea mays), 3'ss of exon 3
ttaatcttctattttcctttataactgttagaaaggcatggaacattcttttagttcgattccattca--aatctataaagatatccttttgagttctttagGTACGTTTAAATTGACACTTCAGTTTTCGGAGGAGTATCCAAACAAACCACCAACAGTGCGATTTGTTTCCCGTATGTTCCATCCAAATA
   | ||  ||  ||| | | | |||            ||           | ||| | |||  | |    |   |||     |  | | |    |  | ||||||||||||  |||| || ||||||   || || |||||||||||||||||||| ||||||||||||||  | ||||||||||| || |
-acagctcttagattc-tgtgtcactagcttgtctttctgagcttactacatggtttgcttctgtcctttgactgatatgctaactcctgttttattctcagGTACGTTTAAGCTGACTCTCCAGTTTAATGAAGAATATCCAAACAAACCACCAACTGTGCGATTTGTTTCTAGGATGTTCCATCCTAACA

upper sequence: Vv17s0000g05820.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA04G34170.2 (Glycine max), 3'ss of exon 3
-------------ttaatcttctattttcctttataactgtta-gaaaggcatggaacattc----ttttagttcgattccat---tcaaatctataaagatatccttttgagttctttagGTACGTTTAAATTGACACTTCAGTTTTCGGAGGAGTATCCAAACAAACCACCAACAGTGCGATTTGTTTCCCGTATGTTCCATCCAAATA
             || | |    || || ||  | |||  ||  |||| |  ||  |  |      || |  ||| ||    |   | | ||   |     |    ||||||||| || ||| ||||| || ||||| || |||||| | ||||| |||||||| ||||||||||| ||||||||||| || || ||||| ||||||||||
gtgagtggatttctttaccgaagatcttactagaaaacaattttgaaatgtttgtcaagtgtcaggttctttttccatcttgtgtgttacataactgtgtgtcatattttgagttattcagGCACGTTCAAGTTGACTCTCCAGTTTACTGAGGATTATCCAAATAAACCACCAACTGTGCGATTTGTGTCTCGCATGTTTCATCCAAATA

upper sequence: Vv17s0000g05820.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA05G01270.1 (Glycine max), 3'ss of exon 3
------ttaatcttctattttcctttataactgttagaaaggcatggaacattcttttagttcgattccattcaaatctataaagatatccttttgagttctttagGTACGTTTAAATTGACACTTCAGTTTTCGGAGGAGTATCCAAACAAACCACCAACAGTGCGATTTGTTTCCCGTATGTTCCATCCAAATA
       | ||  ||   |   ||||||   ||| |    ||  |   |  || | |  |  |  |  ||    ||| | || | ||     |||||||| |  ||| |||||||| ||||| || || ||| | ||||| ||||||||||| |||||||| || |||||||| || || ||||| |||||||| |
tggatgctcatagtcagataatctttatgtatgt-acttgggagtcatattttttctctgaacattatcaccataatgtctacatat-----tttgagttatccagGCACGTTTAAGTTGACTCTCCAATTTACTGAGGATTATCCAAACAAGCCACCAACTGTACGATTTGTCTCTCGAATGTTTCATCCAAACA

upper sequence: Vv17s0000g05820.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA17G10640.1 (Glycine max), 3'ss of exon 3
---------ttaatcttctattttcctttataactgttagaaaggcatggaacattcttttagttcgattccattcaaatctataaagatatccttttgagttctttagGTACGTTTAAATTGACACTTCAGTTTTCGGAGGAGTATCCAAACAAACCACCAACAGTGCGATTTGTTTCCCGTATGTTCCATCCAAATA
          || ||   || | |  | | ||  || | || || |||      |||| |||     ||  || | |  |||| | |       ||||||||| |  ||| |||||||| ||||  ||||| ||| | ||||| ||||||||||| |||||||| || |||||||| || || ||||| || ||||| |
tggatgatcatagtcagataatctt-tatgtatatgcttgagagtcatatttt-ttctcttaacattatcacaataatgtctacata-------ttttgagttatccagGCACGTTTAAGTTGATTCTTCAATTTACTGAGGATTATCCAAACAAGCCACCAACTGTACGATTTGTCTCTCGAATGTTTCACCCAAACA

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|351044280|gb|FQ447634.1|FQ447634
EST:     TCCAGATGACACTCCATGGGATGGAG                         GTACGTTTAAATTGACACTTCAGTTTTCGGAGGAGTATCCAAACAAACCAC
genomic: TCCAGATGACACTCCATGGGATGGAGgtgagtctat ... agttctttagGTACGTTTAAATTGACACTTCAGTTTTCGGAGGAGTATCCAAACAAACCAC
EST: gi|349823648|gb|FQ415058.1|FQ415058
EST:     TCCAGATGACACTCCATGGGATGGAG                         GTACATTTAAATTGACACTTCAGTTTTCGGAGGAGTATCCAAACAAACCAC
genomic: TCCAGATGACACTCCATGGGATGGAGgtgagtctat ... agttctttagGTACGTTTAAATTGACACTTCAGTTTTCGGAGGAGTATCCAAACAAACCAC
EST: gi|351029672|gb|FQ427512.1|FQ427512
EST:     TCCAGATGACACTCCATGGGATGGAG                         GTACATTTAAATTGACACTTCAGTTTTCGGAGGAGTATCCAAACAAACCAC
genomic: TCCAGATGACACTCCATGGGATGGAGgtgagtctat ... agttctttagGTACGTTTAAATTGACACTTCAGTTTTCGGAGGAGTATCCAAACAAACCAC
EST: gi|110726002|gb|EE103053.1|EE103053
EST:     TCCAGATGACACTCCATGGGATGGAG                         GTACGTTTAAATTGACACTTCAGTTTTCGGAGGAGTATCCAAACAAACCAC
genomic: TCCAGATGACACTCCATGGGATGGAGgtgagtctat ... agttctttagGTACGTTTAAATTGACACTTCAGTTTTCGGAGGAGTATCCAAACAAACCAC
EST: gi|110426330|gb|EC992735.1|EC992735
EST:     TCCAGATGACACTCCATGGGATGGAG                         GTACGTTTAAATTGACACTTCAGTTTTCGGAGGAGTATCCAAACAAACCAC
genomic: TCCAGATGACACTCCATGGGATGGAGgtgagtctat ... agttctttagGTACGTTTAAATTGACACTTCAGTTTTCGGAGGAGTATCCAAACAAACCAC
EST: gi|349812793|gb|FQ410435.1|FQ410435
EST:     TCCAGATGACACTCCATGGGATGGAG                         GTACGTTTAAATTGACACTTCAGTTTTCGGAGGAGTATCCAAACAAACCAC
genomic: TCCAGATGACACTCCATGGGATGGAGgtgagtctat ... agttctttagGTACGTTTAAATTGACACTTCAGTTTTCGGAGGAGTATCCAAACAAACCAC
EST: gi|351040450|gb|FQ434583.1|FQ434583
EST:     TCCAGATGACACTCCATGGGATGGAG                         GTACGTTTAAATTGACACTTCAGTTTTCGGAGGAGTATCCAAACAAACCAC
genomic: TCCAGATGACACTCCATGGGATGGAGgtgagtctat ... agttctttagGTACGTTTAAATTGACACTTCAGTTTTCGGAGGAGTATCCAAACAAACCAC
EST: gi|351033819|gb|FQ447857.1|FQ447857
EST:     TCCAGATGACACTCCATGGGATGGAG                         GTACGTTTAAATTGACACTTCAGTTTTCGGAGGAGTATCCAAACAAACCAC
genomic: TCCAGATGACACTCCATGGGATGGAGgtgagtctat ... agttctttagGTACGTTTAAATTGACACTTCAGTTTTCGGAGGAGTATCCAAACAAACCAC
EST: gi|351024032|gb|FQ423455.1|FQ423455
EST:     TCCAGATGACACTCCATGGGATGGAG                         GTACATTTAAATTGACACTTCAGTTTTCGGAGGAGTATCCAAACAAACCAC
genomic: TCCAGATGACACTCCATGGGATGGAGgtgagtctat ... agttctttagGTACGTTTAAATTGACACTTCAGTTTTCGGAGGAGTATCCAAACAAACCAC
EST: gi|349830568|gb|FQ416866.1|FQ416866
EST:     TCCAGATGACACTCCATGGGATGGAG                         GTACATTTAAATTGACACTTCAGTTTTCGGAGGAGTATCCAAACAAACCAC
genomic: TCCAGATGACACTCCATGGGATGGAGgtgagtctat ... agttctttagGTACGTTTAAATTGACACTTCAGTTTTCGGAGGAGTATCCAAACAAACCAC
EST: gi|351031294|gb|FQ445319.1|FQ445319
EST:     TCCAGATGACACTCCATGGGATGGAG                         GTACATTTAAATTGACACTTCAGTTTTCGGAGGAGTATCCAAACAAACCAC
genomic: TCCAGATGACACTCCATGGGATGGAGgtgagtctat ... agttctttagGTACGTTTAAATTGACACTTCAGTTTTCGGAGGAGTATCCAAACAAACCAC
EST: gi|351014290|gb|FQ437292.1|FQ437292
EST:     TCCAGATGACACTCCATGGGATGGAG                         GTACATTTAAATTGACACTTCAGTTTTCGGAGGAGTATCCAAACAAACCAC
genomic: TCCAGATGACACTCCATGGGATGGAGgtgagtctat ... agttctttagGTACGTTTAAATTGACACTTCAGTTTTCGGAGGAGTATCCAAACAAACCAC
EST: gi|110731799|gb|EE106527.1|EE106527
EST:     TCCAGATGACACTCCATGGGATGGAG                         GTACGTTTAAATTGACACTTCAGTTTTCGGAGGAGTATCCAAACAAACCAC
genomic: TCCAGATGACACTCCATGGGATGGAGgtgagtctat ... agttctttagGTACGTTTAAATTGACACTTCAGTTTTCGGAGGAGTATCCAAACAAACCAC
EST: gi|349826891|gb|FQ418982.1|FQ418982
EST:     TCCAGATGACACTCCATGGGATGGAG                         GTACGTTTAAATTGACACTTCAGTTTTCGGAGGAGTATCCAAACAAACCAC
genomic: TCCAGATGACACTCCATGGGATGGAGgtgagtctat ... agttctttagGTACGTTTAAATTGACACTTCAGTTTTCGGAGGAGTATCCAAACAAACCAC
EST: gi|351035318|gb|FQ459585.1|FQ459585
EST:     TCCAGATGACACTCCATGGGATGGAG                         GTACATTTAAATTGACACTTCAGTTTTCGGAGGAGTATCCAAACAAACCAC
genomic: TCCAGATGACACTCCATGGGATGGAGgtgagtctat ... agttctttagGTACGTTTAAATTGACACTTCAGTTTTCGGAGGAGTATCCAAACAAACCAC
EST: gi|110700261|gb|EE078097.1|EE078097
EST:     TCCAGATGACACTCCATGGGATGGAG                         GTACGTTTAAATTGACACTTCAGTTTTCGGAGGAGTATCCAAACAAACCAC
genomic: TCCAGATGACACTCCATGGGATGGAGgtgagtctat ... agttctttagGTACGTTTAAATTGACACTTCAGTTTTCGGAGGAGTATCCAAACAAACCAC
EST: gi|110421523|gb|EC987821.1|EC987821
EST:     TCCAGATGACACTCCATGGGATGGAG                         GTACGTTTAAATTGACACTTCAGTTTTCGGAGGAGTATCCAAACAAACCAC
genomic: TCCAGATGACACTCCATGGGATGGAGgtgagtctat ... agttctttagGTACGTTTAAATTGACACTTCAGTTTTCGGAGGAGTATCCAAACAAACCAC
EST: gi|349824373|gb|FQ417760.1|FQ417760
EST:     TCCAGATGACACTCCATGGGATGGAG                         GTACATTTAAATTGACACTTCAGTTTTCGGAGGAGTATCCAAACAAACCAC
genomic: TCCAGATGACACTCCATGGGATGGAGgtgagtctat ... agttctttagGTACGTTTAAATTGACACTTCAGTTTTCGGAGGAGTATCCAAACAAACCAC
EST: gi|351014644|gb|FQ437646.1|FQ437646
EST:     TCCAGATGACACTCCATGGGATGGAG                         GTACGTTTAAATTGACACTTCAGTTTTCGGAGGAGTATCCAAACAAACCAC
genomic: TCCAGATGACACTCCATGGGATGGAGgtgagtctat ... agttctttagGTACGTTTAAATTGACACTTCAGTTTTCGGAGGAGTATCCAAACAAACCAC
EST: gi|351044244|gb|FQ447598.1|FQ447598
EST:     TCCAGATGACACTCCATGGGATGGAG                         GTACGTTTAAATTGACACTTCAGTTTTCGGAGGAGTATCCAAACAAACCAC
genomic: TCCAGATGACACTCCATGGGATGGAGgtgagtctat ... agttctttagGTACGTTTAAATTGACACTTCAGTTTTCGGAGGAGTATCCAAACAAACCAC
EST: gi|110361377|gb|EC924844.1|EC924844
EST:     TCCAGATGACACTCCATGGGATGGAG                         GCACGTTTAAATTGACACTTCAGTTTTCGGAGGAGTATCCAAACAAACCAC
genomic: TCCAGATGACACTCCATGGGATGGAGgtgagtctat ... agttctttagGTACGTTTAAATTGACACTTCAGTTTTCGGAGGAGTATCCAAACAAACCAC
EST: gi|351013685|gb|FQ433837.1|FQ433837
EST:     TCCAGATGACACTCCATGGGATGGAG                         GTACGTTTAAATTGACACTTCAGTTTTCGGAGGAGTATCCAAACAAACCAC
genomic: TCCAGATGACACTCCATGGGATGGAGgtgagtctat ... agttctttagGTACGTTTAAATTGACACTTCAGTTTTCGGAGGAGTATCCAAACAAACCAC
EST: gi|349823308|gb|FQ402507.1|FQ402507
EST:     TCCAGATGACACTCCATGGGATGGAG                         GTACGTTTAAATTGACACTTCAGTTTTCGGAGGAGTATCCAAACAAACCAC
genomic: TCCAGATGACACTCCATGGGATGGAGgtgagtctat ... agttctttagGTACGTTTAAATTGACACTTCAGTTTTCGGAGGAGTATCCAAACAAACCAC
EST: gi|110389048|gb|EC953859.1|EC953859
EST:     TCCAGATGACACTCCATGGGATGGAG                         GTACGTTTAAATTGACACTTCAGTTTTCGGAGGAGTATCCAAACAAACCAC
genomic: TCCAGATGACACTCCATGGGATGGAGgtgagtctat ... agttctttagGTACGTTTAAATTGACACTTCAGTTTTCGGAGGAGTATCCAAACAAACCAC
EST: gi|351016912|gb|FQ424339.1|FQ424339
EST:     TCCAGATGACACTCCATGGGATGGAG                         GTACATTTAAATTGACACTTCAGTTTTCGGAGGAGTATCCAAACAAACCAC
genomic: TCCAGATGACACTCCATGGGATGGAGgtgagtctat ... agttctttagGTACGTTTAAATTGACACTTCAGTTTTCGGAGGAGTATCCAAACAAACCAC
EST: gi|349829768|gb|FQ421286.1|FQ421286
EST:     TCCAGATGACACTCCATGGGGTGGAG                         GTACATTTAAATTGACACTTCAGTTTTCGGAGGAGTATCCAAACAAACCAC
genomic: TCCAGATGACACTCCATGGGATGGAGgtgagtctat ... agttctttagGTACGTTTAAATTGACACTTCAGTTTTCGGAGGAGTATCCAAACAAACCAC
EST: gi|351029101|gb|FQ435301.1|FQ435301
EST:     TCCAGATGACACTCCATGGGATGGAG                         GTACATTTAAATTGACACTTCAGTTTTCGGAGGAGTATCCAAACAAACCAC
genomic: TCCAGATGACACTCCATGGGATGGAGgtgagtctat ... agttctttagGTACGTTTAAATTGACACTTCAGTTTTCGGAGGAGTATCCAAACAAACCAC
EST: gi|30302161|gb|CB978955.1|CB978955
EST:     TCCAGATGACACTCCATGGGATGGAG                         GTACGTTTAAATTGACACTTCAGTTTTCGGAGGAGTATCCAAACAAACCAC
genomic: TCCAGATGACACTCCATGGGATGGAGgtgagtctat ... agttctttagGTACGTTTAAATTGACACTTCAGTTTTCGGAGGAGTATCCAAACAAACCAC
EST: gi|351024814|gb|FQ430639.1|FQ430639
EST:     TCCAGATGACACTCCATGGGATGGAG                         GTACATTTAAATTGACACTTCAGTTTTCGGAGGAGTATCCAAACAAACCAC
genomic: TCCAGATGACACTCCATGGGATGGAGgtgagtctat ... agttctttagGTACGTTTAAATTGACACTTCAGTTTTCGGAGGAGTATCCAAACAAACCAC
EST: gi|351053304|gb|FQ459172.1|FQ459172
EST:     TCCAGATGACACTCCATGGGATGGAG                         GTACGTTTAAATTGACACTTCAGTTTTCGGAGGAGTATCCAAACAAACCAC
genomic: TCCAGATGACACTCCATGGGATGGAGgtgagtctat ... agttctttagGTACGTTTAAATTGACACTTCAGTTTTCGGAGGAGTATCCAAACAAACCAC
EST: gi|110714545|gb|EE091578.1|EE091578
EST:     TCCAGATGACACTCCATGGGATGGAG                         GTACGTTTAAATTGACACTTCAGTTTTCGGAGGAGTATCCAAACAAACCAC
genomic: TCCAGATGACACTCCATGGGATGGAGgtgagtctat ... agttctttagGTACGTTTAAATTGACACTTCAGTTTTCGGAGGAGTATCCAAACAAACCAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcttttagttcgattccattcaaatctataaagatatccttttgagttctttagGTACGTTTAAATTGACACTTCAGTTTTCGGAGGAGTATCCAAACAAACCACCAACAGTGCGATTTGTTTCCCGTATGTTCCATCCAAATA
                                               ttcttt  CT-rich tract
                      aaatctataaagatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttaatcttctattttcctttataactgttagaaaggcatggaacattcttttagttcgattccattcaaatctataaagatatccttttgagttctttagGTACGTTTAAATTGACACTTCAGTTTTCGGAGGAGTATCCAAACAAACCACCAACAGTGCGATTTGTTTCCCGTATGTTCCATCCAAATA

- - - - - - - - - - - - ctgttag
- - - - - - - - - - - - - - - - - -gcatgga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccattca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ataaaga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccttttg