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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttatcttcaaaggcactcatagctaaggagcttccaagaagtgtttttcgtttattgttggtatgtttctgttgtgaaatgtcttattattgttgggcagGGGAAGCAAAGCATCTCACTGGAACCCGGTGGTCAGTTTGAGCTTAGCGGTGCCCCTCTTGAAACTTTGCATCAAACCTGTGCTGAGGTTAATTCACACC

Basic information

species Vitis vinifera
transcript Vv02s0025g03530.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv02s0025g03530.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os07g27790.1 (Oryza sativa), 3'ss of exon 3
--------------------------------------------------------------------------------------------ttatcttcaaaggcactcatagctaaggagcttccaaga----agtgtttttcgtttattgttggtatgtttct-gttgtgaaatgtcttattattgttgggcagGGGAAGCAAAGCATCTCACTGGAACCCGGTGGTCAGTTTGAGCTTAGCGGTGCCCCTCTTGAAACTTTGCATCAAACCTGTGCTGAGGTTAATTCACACC
                                                                                             |  | | |    | || || |  ||  |      || |    ||| | ||  |   ||| || || |||| ||   |  ||  |   |   ||| ||||  ||||| ||||||||||| ||||| ||||| |||||||||||||| ||||| ||||| ||||||||||| || |||||||| ||||||||||| |||||||| |
gtagtattctgctcttatttcccctataataccaccttacatgacttagaccaacaattaacgtggagaaaatttccatgtgcttcactggagtgccgtaattaactctaatggaaaaacaaacaaaaacattacagtttgttctgacaatt-ttagtttgttccttaattcgaggtacttgtatatggttg--cagGGAAAGCAAAGCATTTCACTAGAACCTGGTGGTCAGTTTGAACTTAGTGGTGCTCCTCTTGAAACATTACATCAAACTTGTGCTGAGGTCAATTCACATC

upper sequence: Vv02s0025g03530.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os05g03820.2 (Oryza sativa), 3'ss of exon 3
----------------------------------------------------------------ttatcttcaaaggcactcatagctaaggagcttccaagaag-tg-----tttttcgtttattgttggtatgtttctgttgtgaaatgtcttattattgttgggcagGGGAAGCAAAGCATCTCACTGGAACCCGGTGGTCAGTTTGAGCTTAGCGGTGCCCCTCTTGAAACTTTGCATCAAACCTGTGCTGAGGTTAATTCACACC
                                                                  |    |  |   | |  ||    || | |   ||| ||  ||     || |||    | | || || | |  ||    | |     ||||| || ||||  ||||| || |||||||| ||||| ||||| || ||||||||||| ||||| ||||| ||||||||||| || |||||||| ||||||||||| |||||||| |
gtagtattcttctgttatttccgctatgagaccaccttacatgacttagaccaacaattaatgtggactgccgtaattaattctaatggagaaacaaacaaaaaaatgacagtttgttctgacaattttagtttatcccttaactcaggctacttat-atggttg--cagGGAAAACAAAGCATTTCACTAGAACCTGGCGGTCAGTTTGAACTTAGTGGTGCTCCTCTTGAAACATTACATCAAACTTGTGCTGAGGTCAATTCACATC

upper sequence: Vv02s0025g03530.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G111579_T01 (Zea mays), 3'ss of exon 2
ttatcttcaaaggcactcatagctaaggagcttccaagaagtgtttttcgtttattgttggtatgtttctgtt-------gtgaaatgtcttattattgttgg-gcagGGGAAGCAAAGCATCTCACTGGAACCCGGTGGTCAGTTTGAGCTTAGCGGTGCCCCTCTTGAAACTTTGCATCAAACCTGTGCTGAGGTTAATTCACACC
          ||   || | ||| ||  |      | | ||| |||||  | |  || |||   | ||| |||       |  |  |  ||| ||  |   |  | |||| ||||||||||||||||| ||||| || || || ||||| ||||| || || ||||| ||||| || |||||||| ||||||||||| ||||| || |
-------ttgagatgct-acagccaaacacaagttatgcagttttttttttcttctgatggctggcttcagtttatctttgcaaccttacttgtttctacggatgtagGGAAAGCAAAGCATCTCACTAGAACCTGGAGGCCAATTTGAACTTAGTGGCGCTCCTCTCGAAACATTACATCAAACTTGTGCTGAGGTCAATTCGCATC

upper sequence: Vv02s0025g03530.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G020096_T01 (Zea mays), 3'ss of exon 2
---ttatcttcaaaggcactcata--gctaaggagcttccaagaagtgtttttcgtttattgttggtatgtttctgttgtgaaatgtcttattattgttgggcagGGGAAGCAAAGCATCTCACTGGAACCCGGTGGTCAGTTTGAGCTTAGCGGTGCCCCTCTTGAAACTTTGCATCAAACCTGTGCTGAGGTTAATTCACACC
   | |    || |  ||   | |  | || | || ||   |    ||  | | |||| |   |  ||| ||| |    |||| ||| |   ||| | ||   |||| ||||||||||||||||| ||||| || || || ||||| ||||| || || ||||| ||||| || |||||||| ||||||||||| || ||||| |
ctttaaatgccacatccaaatagaaggttatgcagttttttaatgatggctctagtttctcagtt-tatctttgtaacctgaattgtttg--tatggatg--tagGGAAAGCAAAGCATCTCACTAGAACCTGGAGGCCAATTTGAACTTAGTGGCGCTCCTCTCGAAACGTTACATCAAACTTGTGCTGAGGTCAACTCACATC

upper sequence: Vv02s0025g03530.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA05G37850.3 (Glycine max), 3'ss of exon 3
ttatcttcaaaggcactcatagctaaggagcttccaagaagtgtttttcgtttattgttggtatgtttctgttgtgaaa--tgtcttattattgttgggcagGGGAAGCAAAGCATCTCACTGGAACCCGGTGGTCAGTTTGAGCTTAGCGGTGCCCCTCTTGAAACTTTGCATCAAACCTGTGCTGAGGTTAATTCACACC
            | |  | |  |  |   || || |  |  ||| |    |||  |    || |  |||  |||| |||  ||     |||| ||    ||||||||||| ||||| ||| |||| || |||||||||||||| ||||| || || ||||||||||| |||||||| || |||||||| |||||||| ||||
------------gtaagcctgac--atttgcatcaacaacatgtctaatattttcttccagtttaattcatttgttaaaattgcaacgttat-gtgaaccagGGGAAGCAGAGCATATCATTGGAGCCTGGTGGTCAGTTTGAACTTAGTGGAGCTCCTCTTGAAACCTTGCATCAGACTTGTGCTGAAGTTAATTCCCACC

upper sequence: Vv02s0025g03530.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA08G01750.1 (Glycine max), 3'ss of exon 3
ttatcttcaaaggcactcatagctaaggagcttccaagaagtgtttttcgtttattgttggtatgtttctgttgtgaaatgtcttattatt--gttgggcagGGGAAGCAAAGCATCTCACTGGAACCCGGTGGTCAGTTTGAGCTTAGCGGTGCCCCTCTTGAAACTTTGCATCAAACCTGTGCTGAGGTTAATTCACACC
     |       || |   | | |       || || |     ||||| |  |   ||  | ||||    |||     | | || | |||  ||    ||||||||||| ||||| ||| |||| || |||||||||||||| ||||| || || ||||||||||| |||||||| || |||||||| |||||||  ||||
----gtaggctaacatttgcatcaacaagatgtctaata-----ttttcttccag-attcatttgttaaaattgcatgttttgttgtcattatgtgaaccagGGGAAGCAGAGCATATCATTGGAGCCTGGTGGTCAGTTTGAACTTAGTGGAGCTCCTCTTGAAACCTTGCATCAGACTTGTGCTGAAGTTAATTTGCACC

upper sequence: Vv02s0025g03530.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT4G23100.3 (Arabidopsis thaliana), 3'ss of exon 3
-----------------------------------------------------------------------ttatcttcaaaggcactcatagctaaggagcttccaagaagtgtttttcgtttattgttggtatgtttctgttgtgaaatgtcttattattgttgggcagGGGAAGCAAAGCATCTCACTGGAACCCGGTGGTCAGTTTGAGCTTAGCGGTGCCCCTCTTGAAACTTTGCATCAAACCTGTGCTGAGGTTAATTCACACC
                                                                       ||| ||||| |  ||  || |   |  |   |   |  | || |   || ||| || ||  | || |   | |      |    |  | ||||||  ||||| ||||||||||| ||||| ||||| || |||||||| |||||||| ||||| |||||||| |||||||||||||| |||||||| || |||||||| |
gttaacattctcctgtgtttcatcttttgagccgtttattatttatatacattttcagcctgtagaacatgttagcttcatatacaa-cacaatgatcggtatattataaggtttcagtcttttttttttttt-tgctgtagataactcgttctgtccttttgttgaccagGGAAAGCAAAGCATTTCACTTGAACCTGGGGGTCAGTTCGAGCTTAGTGGTGCACCTCTTGAGACTTTGCATCAAACTTGTGCTGAAGTCAATTCACATC

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|351057110|gb|FQ450817.1|FQ450817
EST:     TCGGGTGGGATAAAATAATGGAAGGTGACAACATTATTGGACTCAAACAG                         GGGAAGCAAAGCATATCACTGGAACCCGGTGGTCAGTTAGAGCTTAGCGGT
genomic: TCGGGTGGGATAAAATAATGGAAGGTGACAACATTATTGGACTCAAACAGgtaaactgct ... tgttgggcagGGGAAGCAAAGCATCTCACTGGAACCCGGTGGTCAGTTTGAGCTTAGCGGT
EST: gi|30300777|gb|CB977571.1|CB977571
EST:     TCGGGTGGGATAAAATAATGGAAGGTGACAACATTATTGGACTCAAACAG                         GGGAAGCAAAGCATATCACTGGAACCCGGTGGTCAGTTTGAGCTTAGTGGT
genomic: TCGGGTGGGATAAAATAATGGAAGGTGACAACATTATTGGACTCAAACAGgtaaactgct ... tgttgggcagGGGAAGCAAAGCATCTCACTGGAACCCGGTGGTCAGTTTGAGCTTAGCGGT
EST: gi|351021548|gb|FQ429652.1|FQ429652
EST:     TCGGGTGGGATAAAATAATGGAAGGTGACAACATTATTGGACTCAAACAG                         GGGAAGCAAAGCATATCACTGGAACCCGGTGGTCAGTTTGAGCTTAGCGGT
genomic: TCGGGTGGGATAAAATAATGGAAGGTGACAACATTATTGGACTCAAACAGgtaaactgct ... tgttgggcagGGGAAGCAAAGCATCTCACTGGAACCCGGTGGTCAGTTTGAGCTTAGCGGT
EST: gi|349828851|gb|FQ419184.1|FQ419184
EST:     TCGGGTGGGATAAAATAATGGAAGGTGACAACATTATTGGACTCAAACAG                         GGGAAGCAAAGCATATCACTGGAACCCGGTGGTCAGTTTGAGCTTAGCGGT
genomic: TCGGGTGGGATAAAATAATGGAAGGTGACAACATTATTGGACTCAAACAGgtaaactgct ... tgttgggcagGGGAAGCAAAGCATCTCACTGGAACCCGGTGGTCAGTTTGAGCTTAGCGGT
EST: gi|349809354|gb|FQ401122.1|FQ401122
EST:     TCGGGTGGGATAAAATAATGGAAGGTGACAACATTATTGGACTCAAACAG                         GGGAAGCAAAGCATATCACTGGAACCCGGTGGTCAGTTTGAGCTTAGCGGT
genomic: TCGGGTGGGATAAAATAATGGAAGGTGACAACATTATTGGACTCAAACAGgtaaactgct ... tgttgggcagGGGAAGCAAAGCATCTCACTGGAACCCGGTGGTCAGTTTGAGCTTAGCGGT
EST: gi|349816669|gb|FQ404916.1|FQ404916
EST:     TCGGGTGGGATAAAATAATGGAAGGTGACAACATTATTGGACTCAAGCAG                         GGGAAGCAAAGCATATCACTGGAACCCGGTGGTCAGTTTGAGCTTAGCGGT
genomic: TCGGGTGGGATAAAATAATGGAAGGTGACAACATTATTGGACTCAAACAGgtaaactgct ... tgttgggcagGGGAAGCAAAGCATCTCACTGGAACCCGGTGGTCAGTTTGAGCTTAGCGGT
EST: gi|349815261|gb|FQ400416.1|FQ400416
EST:     TCGGGTGGGATAAAATAATGGAAGGTGACAACATTATTGGACTCAAACAG                         GGGAAGCAAAGCATATCACTGGAACCCGGTGGTCAGTTTGAGCTTAGCGGT
genomic: TCGGGTGGGATAAAATAATGGAAGGTGACAACATTATTGGACTCAAACAGgtaaactgct ... tgttgggcagGGGAAGCAAAGCATCTCACTGGAACCCGGTGGTCAGTTTGAGCTTAGCGGT
EST: gi|71886560|gb|DT035615.1|DT035615
EST:     TCGGGTGGGATAAAATAATGGAAGGTGACAACATTATTGGACTCAAACAG                         GGGAAGCAAAGCATATCACTGGAACCCGGTGGTCAGTTTGAGCTTAGTGGT
genomic: TCGGGTGGGATAAAATAATGGAAGGTGACAACATTATTGGACTCAAACAGgtaaactgct ... tgttgggcagGGGAAGCAAAGCATCTCACTGGAACCCGGTGGTCAGTTTGAGCTTAGCGGT
EST: gi|351042065|gb|FQ456275.1|FQ456275
EST:     TCGGGTGGGATAAAATAATGGAAGGTGACAACATTATTGGACTCAAACAG                         GGGAAGCAAAGCATATCACTGGAACCCGGTGGTCAGTTTGAGCTTAGCGGT
genomic: TCGGGTGGGATAAAATAATGGAAGGTGACAACATTATTGGACTCAAACAGgtaaactgct ... tgttgggcagGGGAAGCAAAGCATCTCACTGGAACCCGGTGGTCAGTTTGAGCTTAGCGGT
EST: gi|30132095|gb|CB917434.1|CB917434
EST:     ATTGGACTCAAACAG                         GGGAAGCAAAGCATATCACTGGAACCCGGTGGCCAGTTTGAGCTTAGCGGT
genomic: ATTGGACTCAAACAGgtaaactgct ... tgttgggcagGGGAAGCAAAGCATCTCACTGGAACCCGGTGGTCAGTTTGAGCTTAGCGGT
EST: gi|349832994|gb|FQ416372.1|FQ416372
EST:     TCGGGTGGGATAAAATAATGGAAGGTGACAACATTATTGGACTCAAACAG                         GGGAAGCAAAGCATATCACTGGAACCCGGTGGTCAGTTTGAGCTTAGCGGT
genomic: TCGGGTGGGATAAAATAATGGAAGGTGACAACATTATTGGACTCAAACAGgtaaactgct ... tgttgggcagGGGAAGCAAAGCATCTCACTGGAACCCGGTGGTCAGTTTGAGCTTAGCGGT
EST: gi|349808498|gb|FQ405642.1|FQ405642
EST:     TCGGGTGGGATAAAATAATGGAAGGTGACAACATTATTGGACTCAAACAG                         GGGAAGCAAAGCATATCACTGGAACCCGGTGGTCAGTTTGAGCTTAGCGGT
genomic: TCGGGTGGGATAAAATAATGGAAGGTGACAACATTATTGGACTCAAACAGgtaaactgct ... tgttgggcagGGGAAGCAAAGCATCTCACTGGAACCCGGTGGTCAGTTTGAGCTTAGCGGT
EST: gi|351012028|gb|FQ429834.1|FQ429834
EST:     TCGGGTGGGATAAAATAATGGAAGGTGACAACATTATTGGACTCAAACAG                         GGGAAGCAAAGCATATCACTGGAACCCGGTGGTCAGTTTGAGCTTAGCGGT
genomic: TCGGGTGGGATAAAATAATGGAAGGTGACAACATTATTGGACTCAAACAGgtaaactgct ... tgttgggcagGGGAAGCAAAGCATCTCACTGGAACCCGGTGGTCAGTTTGAGCTTAGCGGT
EST: gi|349820754|gb|FQ404128.1|FQ404128
EST:     TCGGGTGGGATAAAATAATGGAAGGTGACAACATTATTGGACTCAAACAG                         GGGAAGCAAAGCATATCACTGGAACCCGGTGGTCAGTTTGAGCTTAGCGGT
genomic: TCGGGTGGGATAAAATAATGGAAGGTGACAACATTATTGGACTCAAACAGgtaaactgct ... tgttgggcagGGGAAGCAAAGCATCTCACTGGAACCCGGTGGTCAGTTTGAGCTTAGCGGT
EST: gi|71885452|gb|DT034507.1|DT034507
EST:     TCGGGTGGGATAAAATAATGGAAGGTGACAACATTATTGGACTCAAACAG                         GGGAAGCAAAGCATATCACTGGAACCCGGTGGTCAGTTTGAGCTTAGTGGT
genomic: TCGGGTGGGATAAAATAATGGAAGGTGACAACATTATTGGACTCAAACAGgtaaactgct ... tgttgggcagGGGAAGCAAAGCATCTCACTGGAACCCGGTGGTCAGTTTGAGCTTAGCGGT
EST: gi|351016353|gb|FQ446213.1|FQ446213
EST:     TCGGGTGGGATAAAATAATGGAAGGTGACAACATTATTGGACTCAAACAG                         GGGAAGCAAAGCATATCACTGGAACCCGGTGGTCAGTTTGAGCTTAGCGGT
genomic: TCGGGTGGGATAAAATAATGGAAGGTGACAACATTATTGGACTCAAACAGgtaaactgct ... tgttgggcagGGGAAGCAAAGCATCTCACTGGAACCCGGTGGTCAGTTTGAGCTTAGCGGT
EST: gi|349810574|gb|FQ402817.1|FQ402817
EST:     TCGGGTGGGATAAAATAATGGAAGGTGACAACATTATTGGACTCAAACAG                         GGGAAGCAAAGCATATCACTGGAACCCGGTGGTCAGTTTGAGCTTAGCGGT
genomic: TCGGGTGGGATAAAATAATGGAAGGTGACAACATTATTGGACTCAAACAGgtaaactgct ... tgttgggcagGGGAAGCAAAGCATCTCACTGGAACCCGGTGGTCAGTTTGAGCTTAGCGGT
EST: gi|349822020|gb|FQ408349.1|FQ408349
EST:     TCGGGTGGGATAAAATAATGGAAGGTGACAACATTATTGGACTCAAACAG                         GGGAAGCAAAGCATATCACTGGAACCCGGTGGTCAGTTTGAGCTTAGCGGT
genomic: TCGGGTGGGATAAAATAATGGAAGGTGACAACATTATTGGACTCAAACAGgtaaactgct ... tgttgggcagGGGAAGCAAAGCATCTCACTGGAACCCGGTGGTCAGTTTGAGCTTAGCGGT
EST: gi|349810984|gb|FQ405972.1|FQ405972
EST:     TCGGGTGGGATAAAATAATGGAAGGTGACAACATTATTGGACTCAAACCG                         GGGAAAGCAAAGCAT
genomic: TCGGGTGGGATAAAATAATGGAAGGTGACAACATTATTGGACTCAAACAGgtaaactgct ... tgttgggcagGGGAA-GCAAAGCAT
EST: gi|161721321|gb|FC070054.1|FC070054
EST:     TCGGGTGGGATAAAATAATGGAAGGTGACAACATTATTGGACTCAAACAG                         GGGAAGCAAAGCATATCACTGGAACCCGGTGGTCAGTTTGAGCTTAGTGGT
genomic: TCGGGTGGGATAAAATAATGGAAGGTGACAACATTATTGGACTCAAACAGgtaaactgct ... tgttgggcagGGGAAGCAAAGCATCTCACTGGAACCCGGTGGTCAGTTTGAGCTTAGCGGT
EST: gi|349809614|gb|FQ414504.1|FQ414504
EST:     TCGGGTGGGATAAAATAATGGAAGGTGACAACATTATTGGACTCAAACAG                         GGGAAGCAAAGCATATCACTGGAACCCGGTGGTCAGTTTGAGCTTAGCGGT
genomic: TCGGGTGGGATAAAATAATGGAAGGTGACAACATTATTGGACTCAAACAGgtaaactgct ... tgttgggcagGGGAAGCAAAGCATCTCACTGGAACCCGGTGGTCAGTTTGAGCTTAGCGGT
EST: gi|349813304|gb|FQ411544.1|FQ411544
EST:     TCGGGTGGGATAAAATAATGGAAGGTGACAACATTATTGGACTCATACAG                         GGGAAGCAAAGCAT
genomic: TCGGGTGGGATAAAATAATGGAAGGTGACAACATTATTGGACTCAAACAGgtaaactgct ... tgttgggcagGGGAAGCAAAGCAT
EST: gi|161712407|gb|FC061712.1|FC061712
EST:     TCGGGTGGGATAAAATAATGGAAGGTGACAACATTATTGGACTCAAACAG                         GGGAAACAAAGCATATCACTGGAACCCGGTGGTCAGTTTGAGCTTAGTGGT
genomic: TCGGGTGGGATAAAATAATGGAAGGTGACAACATTATTGGACTCAAACAGgtaaactgct ... tgttgggcagGGGAAGCAAAGCATCTCACTGGAACCCGGTGGTCAGTTTGAGCTTAGCGGT
EST: gi|33403484|gb|CF209111.1|CF209111
EST:     TCGGGTGGGATAAAATAATGGAAGGTGACAACATTATTGGACTCAAACAG                         GGGGATCAAAG-ATTATCACTGGAACCCGGTGGTCAGTTTGAGCTTAGTGG
genomic: TCGGGTGGGATAAAATAATGGAAGGTGACAACATTATTGGACTCAAACAGgtaaactgct ... tgttgggcagGGGAAGCAAAGCATC-TCACTGGAACCCGGTGGTCAGTTTGAGCTTAGCGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttcgtttattgttggtatgtttctgttgtgaaatgtcttattattgttgggcagGGGAAGCAAAGCATCTCACTGGAACCCGGTGGTCAGTTTGAGCTTAGCGGTGCCCCTCTTGAAACTTTGCATCAAACCTGTGCTGAGGTTAATTCACACC
                               aaatgtcttattatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttatcttcaaaggcactcatagctaaggagcttccaagaagtgtttttcgtttattgttggtatgtttctgttgtgaaatgtcttattattgttgggcagGGGAAGCAAAGCATCTCACTGGAACCCGGTGGTCAGTTTGAGCTTAGCGGTGCCCCTCTTGAAACTTTGCATCAAACCTGTGCTGAGGTTAATTCACACC

- - - - - - -cactcat
- - - - - - - - - - - - - - -gcttcca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggtatgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctgttgt