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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttagttttttttcacccaaatgatcctggtaaagcctcatgatatagtgtttccataatattttgcaattttattttattcatctactcttgtagAATGTGAGCACATTGACAATCCTTGTAATGGGGAAAGGTGGTGTTGGAAAATCTTCAACTGTAAACTCAATCATAGGGGAAAGAGCAGTTGCTGTCAGTG

Basic information

species Vitis vinifera
transcript Vv02s0109g00360.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv02s0109g00360.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os03g13730.2 (Oryza sativa), 3'ss of exon 2
-----------------------------------------------------------------gtttagttttt-tttcacccaaatgatc-ctggtaa-agcctcatgatatagtgtttccataatattttgcaattttattttattcatctactcttgt---agAATGTGAGCACATTGACAATCCTTGTAATGGGGAAAGGTGGTGTTGGAAAATCTTCAACTGTAAACTCAATCATAGGGGAAAGAGCAGTTGCTGTCAGTG
                                                                  |   | | || ||| ||     |  |  |||||   |      || | |  |  | |     |  | ||    | | ||||| |  | |  |  ||    |||||||||||||||||||||| || || |||||||| || || || || || || || || || ||||| ||| | || || || |  | | ||||||| |
gtattacacgcctatgcaaacgcttcttttatggactggttaatggattggcgatgattatatatatcccgctcttgttttacgttgttagtaactggtggtaattgtgtgttttgttactccgtctgtgatgtgattgtatgttttactgctttgtttgtgatgaagAATGTGAGCACATTGACAATTCTGGTGATGGGGAAGGGCGGGGTGGGGAAGTCATCCACCGTCAACTCCATCGTTGGCGAGAGGGTCGCTACTGTCAGCG

upper sequence: Vv02s0109g00360.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G157157_T02 (Zea mays), 3'ss of exon 2
gtttagttttttttcacccaaatgatcctggtaaagcctcatgatatagtgtttccataatattttgcaat---tttattttattcatctactcttgt-----agAATGTGAGCACATTGACAATCCTTGTAATGGGGAAAGGTGGTGTTGGAAAATCTTCAACTGTAAACTCAATCATAGGGGAAAGAGCAGTTGCTGTCAGTG
     ||  | | | |  |||  |||  | ||         |    || || |||  ||| | || |  ||   |  || || | | | |  |  ||      || ||||||||||||| ||||| || || |||||||||||||| || ||||| || || ||||| ||||| ||| | ||||| || |  |   ||||||| |
---aggtagtatattagtcaag-gattgtcgtgtttttgggttggtta-tgcttctttaagaattggtgatcaatgcatgttctgcttgtgtttgtgatgtgaagGATGTGAGCACATTAACAATTCTGGTGATGGGGAAAGGTGGAGTGGGAAAGTCATCCACTGTTAACTCCATCGTTGGGGAGAGGGTTGCCTCTGTCAGCG

upper sequence: Vv02s0109g00360.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G159777_T01 (Zea mays), 3'ss of exon 2
gtttagttttttttcacccaaatgatcctggtaaagcctcatgat-atagtgtttccataatattttgcaat-tttattttattcatctact---cttgtagAATGTGAGCACATTGACAATCCTTGTAATGGGGAAAGGTGGTGTTGGAAAATCTTCAACTGTAAACTCAATCATAGGGGAAAGAGCAGTTGCTGTCAGTG
     ||  | | | |  |||| |||  | ||     ||  || | ||  | |||  | | |  |   ||||   | || | ||  | |        || || ||||||||||||||||||| || || ||||||||||| || || || || || || ||||| ||||| ||| | ||||| ||    |   ||||||| |
--gaggtagtatattagtcaaaggatagtcgtgttttctgctggttatgttctttaaaaattggtgatcaatgcatgttctgtttgtgtttgtggtatgaagGATGTGAGCACATTGACAATTCTGGTGATGGGGAAAGGCGGAGTGGGGAAGTCATCTACTGTTAACTCCATCGTCGGGGAGAGGATCGCCACTGTCAGCG

upper sequence: Vv02s0109g00360.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA19G30210.1 (Glycine max), 3'ss of exon 2
--------------gtttagttttttttcac--------ccaaatgatcctggtaaagcctcatgatatagtgtttccataatatttt------gcaatttta-ttttattcatctactcttgtagAATGTGAGCACATTGACAATCCTTGTAATGGGGAAAGGTGGTGTTGGAAAATCTTCAACTGTAAACTCAATCATAGGGGAAAGAGCAGTTGCTGTCAGTG
               |||  || |   |  |        || ||| || ||  | |    | ||| | || ||||   | ||| ||||      || ||   | ||| ||   | |  |  |||||||||||| | | ||||| || ||||| ||||| ||||| ||||||||||||||||||||||| ||||| ||||| ||||||||||  ||| |  | ||| 
gttttatttttattattttattctcccttgcaaattatacctaattatgcttattattgtttatgttttactgttgatacaatttttttgttctgctatgcgaatttcatggttgttatggtgtagAATGTGAACTCCTTGACTATACTTGTGATGGGAAAAGGAGGTGTTGGAAAATCTTCAACTGTGAACTCCATCATTGGGGAAAGAGTGGTTTCGATTAGTC

upper sequence: Vv02s0109g00360.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA03G00600.1 (Glycine max), 3'ss of exon 2
-------gtttagttttttttcacccaaatgat-cctggtaaagcct---------catgatatagtgtt--tccataatattttgcaattttattttatt---------------catctactct--tgtagAATGTGAGCACATTGACAATCCTTGTAATGGGGAAAGGTGGTGTTGGAAAATCTTCAACTGTAAACTCAATCATAGGGGAAAGAGCAGTTGCTGTCAGTG
        |||| || ||  || | ||||| || |||  |   || |          ||| | || ||||  | |||  | |||| |  |||| ||||  |                 | |  | |  |||||||||||| | | || || || ||||| ||||| ||||||||||||||||||||||||||||| ||||| ||||| ||||| ||||  ||| |  | | | 
gttttatttttatttattactctctcaaattatacctaattgtgcttatttatgtttatgctttactgttgatgcatgttttttttcttttttttttttctgctgtgcgaatttcatgtttgttatggtgtagAATGTGAACTCCTTAACTATACTTGTGATGGGAAAAGGTGGTGTTGGAAAATCTTCAACTGTGAACTCCATCATTGGGGATAGAGTGGTTTCGATTAATC

upper sequence: Vv02s0109g00360.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT5G05000.3 (Arabidopsis thaliana), 3'ss of exon 1
gtttagttttttttcacccaaatgatcctggtaaagcctcatgatatagtgtttccataatattttgcaattttattttattcatctactcttgtagAATGTGAGCACATTGACAATCCTTGTAATGGGGAAAGGTGGTGTTGGAAAATCTTCAACTGTAAACTCAATCATAGGGGAAAGAGCAGTTGCTGTCAGTG
  ||  ||| || |  |     | |||        || |  || |   || | | | |    |   |  |||| |        |   |||  ||||| |||||||| |  | ||  ||||||||||||||||||||||||||||||| || |||||||| || ||| | ||||| || | ||| | ||| || ||| 
-gttcctttcttgtttctagcttcatct-------gctttctgttt--gtttcttcttgtcttagagagatttaagaaagaaaaaaaactggtgtagGATGTGAGCTCGCTAACGGTCCTTGTAATGGGGAAAGGTGGTGTTGGAAAGTCATCAACTGTGAATTCAGTTATAGGCGAGAAAGCTGCTGCAGTTAGTA

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|351032042|gb|FQ460299.1|FQ460299
EST:     CTGTTACACAGACCAAATTGATTGAACTGCTGGGAAAACTAAAGCAGGAG                         AATGTGAGCACATTGACAATCCTTGTAATGGGGAAAGGTGGTGTTGGAAAA
genomic: CTGTTACACAGACCAAATTGATTGAACTGCTGGGAAAACTAAAGCAGGAGgtttagtttt ... actcttgtagAATGTGAGCACATTGACAATCCTTGTAATGGGGAAAGGTGGTGTTGGAAAA
EST: gi|351025046|gb|FQ433463.1|FQ433463
EST:     CTGTTACACAGACCAAATTGATTGAACTGCTGGGAAAACTAAAGCAGGAG                         AATGTGAGCACATTGACAATCCTTGTAATGGGGAAAGGTGGTGTTGGAAAA
genomic: CTGTTACACAGACCAAATTGATTGAACTGCTGGGAAAACTAAAGCAGGAGgtttagtttt ... actcttgtagAATGTGAGCACATTGACAATCCTTGTAATGGGGAAAGGTGGTGTTGGAAAA
EST: gi|71876475|gb|DT025530.1|DT025530
EST:     CTATTACACAGACCAAATTGATTGAACTGCTGGGAAAACTAAAGCAGGAG                         AATGTGAGCACATTGACAATCCTTGTAATGGGGAAAGGTGGTGTTGGAAAA
genomic: CTGTTACACAGACCAAATTGATTGAACTGCTGGGAAAACTAAAGCAGGAGgtttagtttt ... actcttgtagAATGTGAGCACATTGACAATCCTTGTAATGGGGAAAGGTGGTGTTGGAAAA
EST: gi|351049167|gb|FQ449889.1|FQ449889
EST:     CTGTTACACAGACCAAATTGATTGAACTGCTGGGAAAACTAAAGCAGGAG                         AATGTGAGCACATTGACAATCCTTGTAATGGGGAAAGGTGGTGTTGGAAAA
genomic: CTGTTACACAGACCAAATTGATTGAACTGCTGGGAAAACTAAAGCAGGAGgtttagtttt ... actcttgtagAATGTGAGCACATTGACAATCCTTGTAATGGGGAAAGGTGGTGTTGGAAAA
EST: gi|33401498|gb|CF207125.1|CF207125
EST:     ATTGATTGAACTGCTGGGAAAACTAAAGCAGGAG                         AATGTGAGCACATTGACAATCCTTGTAATGGGGAAAGGTGGTGTTGGAAAA
genomic: ATTGATTGAACTGCTGGGAAAACTAAAGCAGGAGgtttagtttt ... actcttgtagAATGTGAGCACATTGACAATCCTTGTAATGGGGAAAGGTGGTGTTGGAAAA
EST: gi|352789810|gb|FQ478625.1|FQ478625
EST:     CTGTTACACAGACCAAATTGATCGAACTGCTGGGAAAACTAAAGCAGGAG                         AATGTGAGCACATTGACAATCCTTGTAATGGGGAAAGGTGGTGTTGGAAAA
genomic: CTGTTACACAGACCAAATTGATTGAACTGCTGGGAAAACTAAAGCAGGAGgtttagtttt ... actcttgtagAATGTGAGCACATTGACAATCCTTGTAATGGGGAAAGGTGGTGTTGGAAAA
EST: gi|71875744|gb|DT024799.1|DT024799
EST:     CTATTACACAGACCAAATTGATTGAACTGCTGGGAAAACTAAAGCAGGAG                         AATGTGAGCACATTGACAATCCTTGTAATGGGGAAAGGTGGTGTTGGAAAA
genomic: CTGTTACACAGACCAAATTGATTGAACTGCTGGGAAAACTAAAGCAGGAGgtttagtttt ... actcttgtagAATGTGAGCACATTGACAATCCTTGTAATGGGGAAAGGTGGTGTTGGAAAA
EST: gi|349822372|gb|FQ412636.1|FQ412636
EST:     CTGTTACACAGACCAAATTGATTGAACTGCTGGGAAAACTAAAGCAGGAG                         AATGTGAGCACATTGACAATCCTTGTAATGGGGAAAGGTGGTGTTGGAAAA
genomic: CTGTTACACAGACCAAATTGATTGAACTGCTGGGAAAACTAAAGCAGGAGgtttagtttt ... actcttgtagAATGTGAGCACATTGACAATCCTTGTAATGGGGAAAGGTGGTGTTGGAAAA
EST: gi|352798838|gb|FQ478473.1|FQ478473
EST:     CTGCTACACAGACCAAATTGATTGAACTGCTGGGAAAACTAACGCAGGAG                         AATGTGAGCACATTGACAATCCTTGTAATGGGGAAAGGTGGTGTTGGAAAA
genomic: CTGTTACACAGACCAAATTGATTGAACTGCTGGGAAAACTAAAGCAGGAGgtttagtttt ... actcttgtagAATGTGAGCACATTGACAATCCTTGTAATGGGGAAAGGTGGTGTTGGAAAA
EST: gi|351045998|gb|FQ441381.1|FQ441381
EST:     CTGTTACACAGACCAAATTGATTGAACTGCTGGGAAAACTAAAGCAGGAG                         AATGTGAGCACATTGGCAATCCTTGTAATGGGGAAAGGTGGTGTTGGAAAA
genomic: CTGTTACACAGACCAAATTGATTGAACTGCTGGGAAAACTAAAGCAGGAGgtttagtttt ... actcttgtagAATGTGAGCACATTGACAATCCTTGTAATGGGGAAAGGTGGTGTTGGAAAA
EST: gi|351027316|gb|FQ444565.1|FQ444565
EST:     CTATTACACAGACCAAATTGATTGAACTGCTGGGAAAACTAAAGCAGGAG                         AATGTGAGCACATTGACAATCCTTGTAATGGGGAAAGGTGGTGTTGGAAAA
genomic: CTGTTACACAGACCAAATTGATTGAACTGCTGGGAAAACTAAAGCAGGAGgtttagtttt ... actcttgtagAATGTGAGCACATTGACAATCCTTGTAATGGGGAAAGGTGGTGTTGGAAAA
EST: gi|351032119|gb|FQ460376.1|FQ460376
EST:     CTGTTACACAGACCAAATTGATTGAACTGCTGGGAAAACTAAAGCAGGAG                         AATGTGAGCACATTGGCAATCCTTGTAATGGGGAAAGGTGGTGTTGGAAAA
genomic: CTGTTACACAGACCAAATTGATTGAACTGCTGGGAAAACTAAAGCAGGAGgtttagtttt ... actcttgtagAATGTGAGCACATTGACAATCCTTGTAATGGGGAAAGGTGGTGTTGGAAAA
EST: gi|352786750|gb|FQ481125.1|FQ481125
EST:     CTGTTACACAGACCAAATTGATTGAACTGCTGGGAAAACTAAAGCAGGAG                         AATGTGAGCACATTGACAATCCTTGTAATGGGGAAAGGTGGTGTTGGAAAA
genomic: CTGTTACACAGACCAAATTGATTGAACTGCTGGGAAAACTAAAGCAGGAGgtttagtttt ... actcttgtagAATGTGAGCACATTGACAATCCTTGTAATGGGGAAAGGTGGTGTTGGAAAA
EST: gi|351012367|gb|FQ430052.1|FQ430052
EST:     CTGTTACACAGACCAAATTGATTGAACTGCTGGGAAAACTAAAGCAGGAG                         AATGTGAGCACATTGACAATCCTTGTAATGGGGAAAGGTGGTGTTGGAAAA
genomic: CTGTTACACAGACCAAATTGATTGAACTGCTGGGAAAACTAAAGCAGGAGgtttagtttt ... actcttgtagAATGTGAGCACATTGACAATCCTTGTAATGGGGAAAGGTGGTGTTGGAAAA
EST: gi|161710146|gb|FC061044.1|FC061044
EST:     CTGTTACACAGACCAAATTGATTGAACTGCTGGGAAAACTAAAGCAGGAG                         AATGTGAGCACATTGACAATCCTTGTAATGGGGAAAGGTGGTGTTGGAAAA
genomic: CTGTTACACAGACCAAATTGATTGAACTGCTGGGAAAACTAAAGCAGGAGgtttagtttt ... actcttgtagAATGTGAGCACATTGACAATCCTTGTAATGGGGAAAGGTGGTGTTGGAAAA
EST: gi|351052014|gb|FQ455307.1|FQ455307
EST:     CTGTTACACAGACCAAATTGATCGAACTGCTGGGAAAACTAAAGCAGGAG                         AATGTGAGCACATTGACAATCCTTGTAATGGGGAAAGGTGGTGTTGGAAAA
genomic: CTGTTACACAGACCAAATTGATTGAACTGCTGGGAAAACTAAAGCAGGAGgtttagtttt ... actcttgtagAATGTGAGCACATTGACAATCCTTGTAATGGGGAAAGGTGGTGTTGGAAAA
EST: gi|110694471|gb|EE071604.1|EE071604
EST:     CTGTTACACAGACCAAATTGATTGAACTGCTGGGAAAACTAAAGCAGGAG                         AATGTGAGCACATTGACAATCCTTGTAATGGGGAAAGGTGGTGTTGGAAAA
genomic: CTGTTACACAGACCAAATTGATTGAACTGCTGGGAAAACTAAAGCAGGAGgtttagtttt ... actcttgtagAATGTGAGCACATTGACAATCCTTGTAATGGGGAAAGGTGGTGTTGGAAAA
EST: gi|351035432|gb|FQ459699.1|FQ459699
EST:     CTGTTACACAGACCAAATTGATCGAACTGCTGGGAAAACTAAAGCAGGAG                         AATGTGAGCACATTGACAATCCTTGTAATGGGGAAAGGTGGTGTTGGAAAA
genomic: CTGTTACACAGACCAAATTGATTGAACTGCTGGGAAAACTAAAGCAGGAGgtttagtttt ... actcttgtagAATGTGAGCACATTGACAATCCTTGTAATGGGGAAAGGTGGTGTTGGAAAA
EST: gi|351038581|gb|FQ464447.1|FQ464447
EST:     CTATTACACAGACCAAATTGATTGAACTGCTGGGAAAACTAAAGCAGGAG                         AATGTGAGCACATTGACAATCCTTGTAATGGGGAAAGGTGGTGTTGGAAAA
genomic: CTGTTACACAGACCAAATTGATTGAACTGCTGGGAAAACTAAAGCAGGAGgtttagtttt ... actcttgtagAATGTGAGCACATTGACAATCCTTGTAATGGGGAAAGGTGGTGTTGGAAAA
EST: gi|351015670|gb|FQ427155.1|FQ427155
EST:     NTGTTACACAGACCAAATTGATTGAACTGCTGGGAAAACTAAAGCAGGAG                         AATGTGAGCACATTGACAATCCTTGTAATGGGGAAAGGTGGTGTTGGAAAA
genomic: CTGTTACACAGACCAAATTGATTGAACTGCTGGGAAAACTAAAGCAGGAGgtttagtttt ... actcttgtagAATGTGAGCACATTGACAATCCTTGTAATGGGGAAAGGTGGTGTTGGAAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatatagtgtttccataatattttgcaattttattttattcatctactcttgtagAATGTGAGCACATTGACAATCCTTGTAATGGGGAAAGGTGGTGTTGGAAAATCTTCAACTGTAAACTCAATCATAGGGGAAAGAGCAGTTGCTGTCAGTG
                                          tctactctt  CT-rich tract
         tttccataatattttg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttagttttttttcacccaaatgatcctggtaaagcctcatgatatagtgtttccataatattttgcaattttattttattcatctactcttgtagAATGTGAGCACATTGACAATCCTTGTAATGGGGAAAGGTGGTGTTGGAAAATCTTCAACTGTAAACTCAATCATAGGGGAAAGAGCAGTTGCTGTCAGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG