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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaaaaaagccttcgtgtggttaacttcaagtagttgggatataatgttgtgttgttttgttatattatgttggttcttattgtgttccttgcttgtgcagAGGGGTTTTGAACAACAGTGGCTGTCACTTACATTCTCTAAGGCAATATTTCTTGGCAATGGTCTAATTGCCATTCTGTCTGGATTGTTTGGAAATGTAC

Basic information

species Vitis vinifera
transcript Vv02s0025g02420.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv02s0025g02420.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os03g02380.2 (Oryza sativa), 3'ss of exon 3
aaaaaaagccttcgtgtg-gttaacttca--agtagttgggatataatgttgtgt-tgttttgttatattat----gttggttcttattgtgttccttgcttgtgcagAGGGGTTTTGAACAACAGTGGCTGTCACTTACATTCTCTAAGGCAATATTTCTTGGCAATGGTCTAATTGCCATTCTGTCTGGATTGTTTGGAAATGTAC
        ||||   ||  |  ||||||   | |   |   |   ||| |  | | ||  || | |  || |    ||    | | |   ||    || |||   ||||| ||||||||   ||| ||||||||  | |||||||| ||||| ||||||||||||||||| ||  | || ||| | || ||  | |||| |||  | |
--------ccttgtcgtttgcaaacttctccaatgtattacagtcaatttcttatctgcgttatcaatttttcactgtaaagtttaaccttggcatttcctttcacagAGAGGTTTTGATTCACAATGGCTGTCGATCACATTCTCCAAGGCTATATTTCTTGGCAATGGCCTGGTCGCAATTGTATCCGGGCTATTTGCAAACCTGC

upper sequence: Vv02s0025g02420.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G067638_T01 (Zea mays), 3'ss of exon 3
aaaaaaagccttcgtgtggttaacttcaagtagttgggatataatgttgtgttgttttgttatattat-gttggttctt----attgtgttccttgcttgtgcagAGGGGTTTTGAACAACAGTGGCTGTCACTTACATTCTCTAAGGCAATATTTCTTGGCAATGGTCTAATTGCCATTCTGTCTGGATTGTTTGGAAATGTAC
          ||  | |   |||    ||     | |       |||| | |  ||   || | || | | ||    |     ||| |   |     |||| ||||  || ||||| | ||| ||| ||||  | |||||||| ||||| ||||||||||||||||||||| | |||||| |  ||||  | |||| |||| | |
-----tcttttttatttttctaatgataaagccattgatggctttgttttctcattcccttttgttcttgctgacaatgggcaattttacactgatattgtacagAAAGGATTTGATCCACAATGGTTGTCGATAACATTCTCCAAGGCTATATTTCTTGGCAATGGTCTAGTGGCCATTGTTGCTGGCCTATTTGCAAATTTTC

upper sequence: Vv02s0025g02420.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA04G41090.1 (Glycine max), 3'ss of exon 3
------aaaaaaagccttcgtgtggttaacttcaagtagttgggatataatgttgtgttgttttgttatattatgttggttcttattgtgttccttgcttgtgcagAGGGGTTTTGAACAACAGTGGCTGTCACTTACATTCTCTAAGGCAATATTTCTTGGCAATGGTCTAATTGCCATTCTGTCTGGATTGTTTGGAAATGTAC
        | || |  ||  | |  ||   |     ||   ||| ||    ||||| |   ||| | ||  |  ||||  | || || | ||      |||| |||||||| ||||| ||||| ||||||||| | |||||||||||||| ||||||||||| ||||||||  |||| ||| |||||||  |||||||||||||||
ttcttattacaatgttttttttttttttggtcttgatatccgggttac---gttgtcta--tttatgattctgagttgtctgtttttttttttaaacattgt-cagAGGGGCTTTGATCAACAATGGCTGTCATTAACATTCTCTAAGGCTATATTTCTTGGAAATGGTCTTGTTGCTATTTTGTCTGGGCTGTTTGGAAATGTAC

upper sequence: Vv02s0025g02420.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA06G13760.2 (Glycine max), 3'ss of exon 3
aaaaaaagccttcgtgtggttaacttcaagtagt-tgggatataatgttgtgttgttttgt-tatattatgttggttcttattgtgttccttgcttgtgcagAGGGGTTTTGAACAACAGTGGCTGTCACTTACATTCTCTAAGGCAATATTTCTTGGCAATGGTCTAATTGCCATTCTGTCTGGATTGTTTGGAAATGTAC
      |  |||| |||    |  ||    | || | |  |    | ||||   ||| ||| | ||| ||  ||  |    |  | ||     | |   |||||||| ||||| ||||| ||||| ||| | |||||||| ||||| ||||||||||| ||||||||  |||| ||| |||||||  |||||||||||||||
--gtgtatacttcttgttacaatttttttttggtcttgttttccttcttgttacgttgtgtatttatgattctgaattgcctgtttttttaaacatcgtcagAGGGGCTTTGATCAACAATGGCTATCATTAACATTCTCAAAGGCTATATTTCTTGGAAATGGTCTTGTTGCTATTTTGTCTGGGCTGTTTGGAAATGTAC

upper sequence: Vv02s0025g02420.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT3G49310.1 (Arabidopsis thaliana), 3'ss of exon 3
aaaaaaagccttcgtgtggttaacttcaagtagttgggatataat-gttgtgttgttttgttata---ttatgttggttcttattgtgttccttgc--ttgtgcagAGGGGTTTTGAACAACAGTGGCTGTCACTTACATTCTCTAAGGCAATATTTCTTGGCAATGGTCTAATTGCCATTCTGTCTGGATTGTTTGGAAATGTAC
     |||  |   |   |  ||    ||  | ||   |  |  | ||  | | |||| | ||||   | ||||   || || | | ||||    |   | ||||||||   ||||| ||||||||||||||||||||||||||||||||  |||||||||| || |||||  | || || || || ||||||||||| ||| | |
-----aaggttggataatgaaaaaagtaaagacttataagcttttagtgatttcgtttagctatagcttgatgtgaatttttctcg-gttctgaacaactatgcagAGGAACTTTGAGCAACAGTGGCTGTCACTTACATTCTCTAAGGCTGTATTTCTTGGAAACGGTCTGGTGGCTATCCTTTCGGGATTGTTTGGCAATCTTC

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|351042244|gb|FQ442711.1|FQ442711
EST:     CTCTGCTTTTTTCAGCCTTTGAATCATGGCTAGTTGCAGAACACAACAAG                         AGGGGTTTTGAACAACAGTGGCTGTCACTTACATTCTCTAAGGCAATATTT
genomic: CTCTGCTTTTTTCAGCCTTTGAATCATGGCTAGTTGCAGAACACAACAAGgtgagaacta ... gcttgtgcagAGGGGTTTTGAACAACAGTGGCTGTCACTTACATTCTCTAAGGCAATATTT
EST: gi|351046994|gb|FQ454604.1|FQ454604
EST:     CTCTGCTTTTTTCAGCCTTTGAATCATGGCTAGTTGCAGAACACAACAAG                         AGGGGTTTTGAACAACAGTGGCTGTCACTTACATTCTCTAAGGCAATATTT
genomic: CTCTGCTTTTTTCAGCCTTTGAATCATGGCTAGTTGCAGAACACAACAAGgtgagaacta ... gcttgtgcagAGGGGTTTTGAACAACAGTGGCTGTCACTTACATTCTCTAAGGCAATATTT
EST: gi|349829349|gb|FQ419881.1|FQ419881
EST:     CTCTGCTTTTTTCAGCCTTTGAATCATGGCTAGTTGCAGAACACAACAAG                         AGGGGTTTTGAACAACAGTGGCTGTCACTTACATTCTCTAAGGCAATATTT
genomic: CTCTGCTTTTTTCAGCCTTTGAATCATGGCTAGTTGCAGAACACAACAAGgtgagaacta ... gcttgtgcagAGGGGTTTTGAACAACAGTGGCTGTCACTTACATTCTCTAAGGCAATATTT
EST: gi|351024947|gb|FQ433364.1|FQ433364
EST:     CTCTGCTTTTTTCAGCCTTTGAATCATGGCTAGTTGCAGAACACAACAAG                         AAGGGTTTTGAACAACAGTGGCTGTCACTTACATTCTCTAAAGCAATATTT
genomic: CTCTGCTTTTTTCAGCCTTTGAATCATGGCTAGTTGCAGAACACAACAAGgtgagaacta ... gcttgtgcagAGGGGTTTTGAACAACAGTGGCTGTCACTTACATTCTCTAAGGCAATATTT
EST: gi|351045803|gb|FQ440988.1|FQ440988
EST:     CTCTGCTTTTTTCAGCCTTTGAATCATGGCTAGTTGCAGAACACAACAAG                         AGGGGTTTTGAACAACAGTGGCTGTCACTTACATTCTCTAAGGCAATATTT
genomic: CTCTGCTTTTTTCAGCCTTTGAATCATGGCTAGTTGCAGAACACAACAAGgtgagaacta ... gcttgtgcagAGGGGTTTTGAACAACAGTGGCTGTCACTTACATTCTCTAAGGCAATATTT
EST: gi|351044296|gb|FQ452848.1|FQ452848
EST:     CTCTGCTTTTTTCAGCCTTTGAATCATGGCTAGTTGCAGAACACAACAAG                         AGGGGTTTTGAACAACAGTGGCTGTCACTTACATTCTCTAAGGCAATATTT
genomic: CTCTGCTTTTTTCAGCCTTTGAATCATGGCTAGTTGCAGAACACAACAAGgtgagaacta ... gcttgtgcagAGGGGTTTTGAACAACAGTGGCTGTCACTTACATTCTCTAAGGCAATATTT
EST: gi|351053919|gb|FQ441685.1|FQ441685
EST:     CTCTGCTTTTTTCAGCCTTTGAATCATGGCTAGTTGCAGAACACAACAAG                         AGGGGTTTTGAACAACAGTGGCTGTCACTTACATTCTCTAAGGCAATATTT
genomic: CTCTGCTTTTTTCAGCCTTTGAATCATGGCTAGTTGCAGAACACAACAAGgtgagaacta ... gcttgtgcagAGGGGTTTTGAACAACAGTGGCTGTCACTTACATTCTCTAAGGCAATATTT
EST: gi|351017775|gb|FQ436128.1|FQ436128
EST:     CTCTGCTTTTTTCAGCCTTTGAATCATGGCTAGTTGCAGAACACAACAAG                         AGGGGTTTTGAACAACAGTGGCTGTCACTTACATTCTCTAAGGCAATATTT
genomic: CTCTGCTTTTTTCAGCCTTTGAATCATGGCTAGTTGCAGAACACAACAAGgtgagaacta ... gcttgtgcagAGGGGTTTTGAACAACAGTGGCTGTCACTTACATTCTCTAAGGCAATATTT
EST: gi|110698059|gb|EE075637.1|EE075637
EST:     CTCTGCTTTTTTCAGCCTTTGAATCATGGCTAGTTGCAGAACACAACAAG                         AGGGGTTTTGAACAACAGTGGCTGTCACTTACATTCTCTAAGGCAATATTT
genomic: CTCTGCTTTTTTCAGCCTTTGAATCATGGCTAGTTGCAGAACACAACAAGgtgagaacta ... gcttgtgcagAGGGGTTTTGAACAACAGTGGCTGTCACTTACATTCTCTAAGGCAATATTT
EST: gi|110708440|gb|EE085985.1|EE085985
EST:     CTCTGCTTTTTTCAGCCTTTGAATCATGGCTAGTTGCAGAACACAACAAG                         AGGGGTTTTGAACAACAGTGGCTGTCACTTACATTCTCTAAGGCAATATTT
genomic: CTCTGCTTTTTTCAGCCTTTGAATCATGGCTAGTTGCAGAACACAACAAGgtgagaacta ... gcttgtgcagAGGGGTTTTGAACAACAGTGGCTGTCACTTACATTCTCTAAGGCAATATTT
EST: gi|351052785|gb|FQ456512.1|FQ456512
EST:     CTCTGCTTTTTTCAGCCTTTGAATCATGGCTAGTTGCAGAACACAACAAG                         AGGGGTTTTGAACAACAGTGGCTGTCACTTACATTCTCTAAGGCAATATTT
genomic: CTCTGCTTTTTTCAGCCTTTGAATCATGGCTAGTTGCAGAACACAACAAGgtgagaacta ... gcttgtgcagAGGGGTTTTGAACAACAGTGGCTGTCACTTACATTCTCTAAGGCAATATTT
EST: gi|349828828|gb|FQ419161.1|FQ419161
EST:     CTCTGCTTTTTTCAGCCTTTGAATCATGGCTAGTTGCAGAACACAACAAG                         AGGGGTTTTGAACAACAGTGGCTGTCACTTACATTCTCTAAGGCAATATTT
genomic: CTCTGCTTTTTTCAGCCTTTGAATCATGGCTAGTTGCAGAACACAACAAGgtgagaacta ... gcttgtgcagAGGGGTTTTGAACAACAGTGGCTGTCACTTACATTCTCTAAGGCAATATTT
EST: gi|349832411|gb|FQ420972.1|FQ420972
EST:     CTCTGCTTTTTTCAGCCTTTGAATCATGGCTAGTTGCAGAACACAACAAG                         AGGGGTTTTGAACAACAGTGGCTGTCACTTACATTCTCTAAGGCAATATTT
genomic: CTCTGCTTTTTTCAGCCTTTGAATCATGGCTAGTTGCAGAACACAACAAGgtgagaacta ... gcttgtgcagAGGGGTTTTGAACAACAGTGGCTGTCACTTACATTCTCTAAGGCAATATTT
EST: gi|351038992|gb|FQ457667.1|FQ457667
EST:     CTCTGCTTTTTTCAGCCTTTGAATCATGGCTAGTTGCAGAACACAACAAG                         AGGGGTTTTGAACAACAGTGGCTGTCACTTACATTCTCTAAGGCAATATTT
genomic: CTCTGCTTTTTTCAGCCTTTGAATCATGGCTAGTTGCAGAACACAACAAGgtgagaacta ... gcttgtgcagAGGGGTTTTGAACAACAGTGGCTGTCACTTACATTCTCTAAGGCAATATTT
EST: gi|351039728|gb|FQ464766.1|FQ464766
EST:     CTCTGCTTTTTTCAGCCTTTGAATCATGGCTAGTTGCAGAACACAACAAG                         AGGGGTTTTGAACAACAGTGGCTGTCACTTACATTCTCTAAGGCAATATTT
genomic: CTCTGCTTTTTTCAGCCTTTGAATCATGGCTAGTTGCAGAACACAACAAGgtgagaacta ... gcttgtgcagAGGGGTTTTGAACAACAGTGGCTGTCACTTACATTCTCTAAGGCAATATTT
EST: gi|161718597|gb|FC068198.1|FC068198
EST:     CTCTGCTTTTTTCAGCCTTTGAATCATGGCTAGTTGCAGAACACAACAAG                         AGGGGTTTTGAACAACAGTGGCTGTCACTTACATTCTCTAAGGCAATATTT
genomic: CTCTGCTTTTTTCAGCCTTTGAATCATGGCTAGTTGCAGAACACAACAAGgtgagaacta ... gcttgtgcagAGGGGTTTTGAACAACAGTGGCTGTCACTTACATTCTCTAAGGCAATATTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttgtgttgttttgttatattatgttggttcttattgtgttccttgcttgtgcagAGGGGTTTTGAACAACAGTGGCTGTCACTTACATTCTCTAAGGCAATATTTCTTGGCAATGGTCTAATTGCCATTCTGTCTGGATTGTTTGGAAATGTAC
                                       ttccttgctt  CT-rich tract
      ttgttttgttatatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaaaaaagccttcgtgtggttaacttcaagtagttgggatataatgttgtgttgttttgttatattatgttggttcttattgtgttccttgcttgtgcagAGGGGTTTTGAACAACAGTGGCTGTCACTTACATTCTCTAAGGCAATATTTCTTGGCAATGGTCTAATTGCCATTCTGTCTGGATTGTTTGGAAATGTAC

aaaaaaa
- - - - - - - - - - - - -tcaagta
- - - - - - - - - - - - - - - - - - - - - - tgttgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - atgttgg