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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtacaataatgcccctagcccactccaatattctccatgcctcatctgaacagaattgtaatttcaaaattatcaccaaattgcagGGAAAGTATCATGGGACATTCGATTTTATTTTCGTGGACGCTGACAAGGACAACTACCTGAACTACCACAAAAGGCTGATTGATCTGGTCAAGGTTGGAG

Basic information

species Vitis vinifera
transcript Vv07s0031g00350.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv07s0031g00350.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G127948_T04 (Zea mays), 3'ss of exon 6
----------gtaagtacaataatgcccctagcccactccaatattctccatgcctcatctga-acagaattgtaatttcaaaattatcaccaaat-tgcagGGAAAGTATCATGGGACATTCGATTTTATTTTCGTGGACGCTGACAAGGACAACTACCTGAACTACCACAAAAGGCTGATTGATCTGGTCAAGGTTGGAG------------------------------------------------
          |  ||  |   |   |       |  | || ||||    |  |    |  ||| |    ||        |     | ||  ||  |  |||||  ||| | || ||| | ||||| ||  | ||||||||||| ||||||||||||||||| ||||||||| |  ||||| |  | ||||| ||| | || |                                                
gtacgaaatggccaggccgccagatctgtgcttcttcgcctatatcgatcgagtagaagttgacatgacatctcggacccgtgtctgtctgcatctgcgcaggagaagaaccacgggtcgttcgacttcgtcttcgtggacgccgacaagGACAACTACCTCAACTACCACGAGCGGCTGCTGAAGCTGGTGAAGCTGGGCGGCCTCATCGGCTACGACAACACGCTGTGGAACGGCTCCGTCGTGCTCC

upper sequence: Vv07s0031g00350.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G127948_T02 (Zea mays), 3'ss of exon 5
----------gtaagtacaataatgcccctagcccactccaatattctccatgcctcatctga-acagaattgtaatttcaaaattatcaccaaat-tgcagGGAAAGTATCATGGGACATTCGATTTTATTTTCGTGGACGCTGACAAGGACAACTACCTGAACTACCACAAAAGGCTGATTGATCTGGTCAAGGTTGGAG
          |  ||  |   |   |       |  | || ||||    |  |    |  ||| |    ||        |     | ||  ||  |  |||||  ||| | || ||| | ||||| ||  | ||||||||||| ||||||||||||||||| ||||||||| |  ||||| |  | ||||| ||| | || |
gtacgaaatggccaggccgccagatctgtgcttcttcgcctatatcgatcgagtagaagttgacatgacatctcggacccgtgtctgtctgcatctgcgcagGAGAAGAACCACGGGTCGTTCGACTTCGTCTTCGTGGACGCCGACAAGGACAACTACCTCAACTACCACGAGCGGCTGCTGAAGCTGGTGAAGCTGGGCG

upper sequence: Vv07s0031g00350.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA11G05800.2 (Glycine max), 3'ss of exon 4
-----------------gtaagtacaataatgcccctagcccactccaatattctccatgcctcatctgaacagaattgtaatttcaaaattat---caccaaat-tgcagGGAAAGTATCATGGGACATTCGATTTTATTTTCGTGGACGCTGACAAGGACAACTACCTGAACTACCACAAAAGGCTGATTGATCTGGTCAAGGTTGGAG
                      |   || ||   | |     | | | | ||| |  ||   |    |     ||| |  ||||  || ||| |   ||    ||  ||||| |||| || | ||  | |||||||| || |  ||||| ||||| |||||||||||| ||||||||||||| ||| ||||||| || || |||||||| |
gtgcgttcaattaatcatcccattttattattaactttttttagtacgaaattatgtatatttatgttagcttgaaataaaatt--aatattgtacgcattgcatgcgcagGAAAAGAATAAGGGAGCGTTCGATTTCATCTATGTGGATGCTGATAAGGACAACTACTTGAACTACCACAAGAGGGTGATTGAGCTTGTGAAGGTTGGGG

upper sequence: Vv07s0031g00350.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA17G18750.1 (Glycine max), 3'ss of exon 2
-------------gtaagtacaataatgcccctagcccactccaatattctccatgcctcatctgaacagaattgtaatttcaaaattatcaccaaattgcagGGAAAGTATCATGGGACATTCGATTTTATTTTCGTGGACGCTGACAAGGACAACTACCTGAACTACCACAAAAGGCTGATTGATCTGGTCAAGGTTGGAG
              |  | | |||||  | | |       |  || | ||    |  |  |  | ||  ||    |  |   ||||||||  | |  ||| |||   |  |  | ||  | ||| |||| |||||||||||||| || ||||| || ||| ||||||| ||||| ||| |||||||||| || ||| || | |
ttttacaaactcactttgcaaaataaaactcttt-tatgttttaa-actcgagtttacaaactttaatcgacacatg-tactaaaattatgtcaattttgtagGAGGACAACAAGGGAGCCTTCAATTTCATTTTCGTGGACGCCGATAAGGATAATTACTTGAACTATCACAAGAGGGTGATTGATCTTGTGAAGATTAGGG

upper sequence: Vv07s0031g00350.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA17G18800.1 (Glycine max), 3'ss of exon 4
------gtaagtacaataatgcccctag-----cccactccaatatt-ctccatgcctca--tctgaacagaattgtaatttcaaaattatcaccaaattgcagGGAAAGTATCATGGGACATTCGATTTTATTTTCGTGGACGCTGACAAGGACAACTACCTGAACTACCACAAAAGGCTGATTGATCTGGTCAAGGTTGGAG
       | |  | || ||      ||         | |  || ||| ||  |    | |  | | || | | |        | ||| |||  | |  ||||||| |||  |  | ||| | || |||||  |||||||||| ||||| |||||||| ||| ||||||||||||| ||| |  | || || || ||| ||||||
tgtttcttgaaaaaaaaaacttatataaaagtatttattttaaaattactttaaattttaaatttaaataaactcac----cctaaactatgtcaattttgcagGAAAATAAAAAGGGGTCGTTGGATTTCGTTTTCGTGGATGCTGATAAGGACAATTACTTGAACTACCACAAGAGGGTACTAGAGCTTGTGAAGATTGGAG

upper sequence: Vv07s0031g00350.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA01G39460.1 (Glycine max), 3'ss of exon 4
gtaagtacaataatgcccctagcccactccaatattctccatgcctcatctgaacagaattgtaatttcaaaattatcaccaaattgcagGGAAAGTATCATGGGACATTCGATTTTATTTTCGTGGACGCTGACAAGGACAACTACCTGAACTACCACAAAAGGCTGATTGATCTGGTCAAGGTTGGAG
||  || || | || ||   | |  |      ||||     |   |    ||||   ||| |   |     | | ||        |||||| |||| || | ||  | |||||||| || |  ||||| ||||| |||||||| ||| ||||||||||||| ||| ||||||| || || ||| |||| |
gtgcgttcagtgattcc---atcttatatgtgtatttaatgttattagcttgaaattaatggctttgattgattcattg------tgcagGAAAAGAATAAGGGAGCTTTCGATTTCATCTATGTGGATGCTGATAAGGACAATTACTTGAACTACCACAAGAGGGTGATTGAGCTTGTGAAGCTTGGGG

upper sequence: Vv07s0031g00350.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: PP1S16_28V6.1 (Physcomitrella patens), 3'ss of exon 4
---gtaagtacaataatgcccctagcccactccaatattctccatgcctcatctgaaca---gaattgtaatttcaaaattatcacc----aaattgcagGGAAAGTATCATGGGACATTCGATTTTATTTTCGTGGACGCTGACAAGGACAACTACCTGAACTACCACAAAAGGCTGATTGATCTGGTCAAGGTTGGAG
   | ||||  || ||       ||        || |    |  |   | | |||   |   ||     | |    | |||   | |    || | |||||  ||| |||| |   | ||||| || || ||||| ||||| ||||| |||||||| |||||||||||||| | ||| ||  |  |||| | ||| ||||
caaggaagtgtaagaagctgtacagggtgtggaaagaaaaacagttattgacctgtctatgtgaggccaactcatcagattgcaaacttggaattggcagGACAAGAATCACGATTCTTTCGACTTCATCTTCGTAGACGCGGACAAAGACAACTATCTGAACTACCACAAGAAGCTCATGAAGTTGGTGAGGGTGGGAG

upper sequence: Vv07s0031g00350.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: EFJ22516 (Selaginella moellendorffii), 3'ss of exon 4
gtaagtacaataatgcccctagcccactccaatattctccatgcctcatctgaacagaattgtaatttcaaaattatcaccaaattgcagGGAAAGTATCATGGGACATTCGATTTTATTTTCGTGGACGCTGACAAGGACAACTACCTGAACTACCACAAAAGGCTGATTGATCTGGTCAAGGTTGGAG
             |   | |    || | |||  || ||  |  || | ||  |   ||    |||    | | | ||      | |||||    | |||||||  ||||||| || || || ||||| |||||||||||||| ||| ||||||||||||| ||| ||||   | |||| || || ||||
------------gtaagctt---tcaatacaac-ttttctttatcttaccttgaaccaacgacaatgctgacactttc-----ctcgcagGAGGCGAATCATGGCGCATTCGACTTCATCTTTGTGGATGCTGACAAGGACAATTACTTGAACTACCACAAGAGGTTGATCTCTTTGGTTAAAGTCGGAG

upper sequence: Vv07s0031g00350.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: EFJ11728 (Selaginella moellendorffii), 3'ss of exon 4
gtaagtacaataatgcccctagcccactccaatattctccatgcctcatctgaacagaattgtaatttcaaaattatcaccaaattgcagGGAAAGTATCATGGGACATTCGATTTTATTTTCGTGGACGCTGACAAGGACAACTACCTGAACTACCACAAAAGGCTGATTGATCTGGTCAAGGTTGGAG
             |   | |    || | |||  || ||  |  || | ||  |   ||    |||    | | | ||      | |||||    | |||||||  | ||||| || || || ||||| |||||||||||||| ||| ||||||||||||| ||| ||||   | |||| || || ||||
------------gtaagctt---tcaatacaac-ttttctttatcttaccttgaaccaacgacaatgctgacactttc-----ctcgcagGAGGCGAATCATGGCGCGTTCGACTTCATCTTTGTGGATGCTGACAAGGACAATTACTTGAACTACCACAAGAGGTTGATCTCTTTGGTTAAAGTCGGAG

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|71859221|gb|DT008276.1|DT008276
EST:     ATTTCAGAGAAAGTCCAGCCCTCCCGGTTCTTGATCAGATGATAGAAGAT                         GGAAAGTATCATGGGACGTTCGATTTTATTTTCGTGGACGCTGACAAGGAC
genomic: ATTTCAGAGAAGGTCCAGCCCTCCCGGTTCTTGATCAGATGATAGAAGATgtaagtacaa ... caaattgcagGGAAAGTATCATGGGACATTCGATTTTATTTTCGTGGACGCTGACAAGGAC
EST: gi|37185179|gb|CF604532.1|CF604532
EST:     ATTTCAGAGAAGGTCCAGCCCTCACGGTTCTTGATCAGATGATAGAAGAT                         GGAAAGTATCATGGGACGTTCGATTTTA
genomic: ATTTCAGAGAAGGTCCAGCCCTCCCGGTTCTTGATCAGATGATAGAAGATgtaagtacaa ... caaattgcagGGAAAGTATCATGGGACATTCGATTTTA
EST: gi|71857191|gb|DT006246.1|DT006246
EST:     ATTTCAGAGAAGGTCCAGCCCTCCCGGTTCTTGATCAGATGATAGAAGAT                         GGAAAGTATCATGGGACGTTCGATTTTATTTTCGTGGACGCTGACAAGGAC
genomic: ATTTCAGAGAAGGTCCAGCCCTCCCGGTTCTTGATCAGATGATAGAAGATgtaagtacaa ... caaattgcagGGAAAGTATCATGGGACATTCGATTTTATTTTCGTGGACGCTGACAAGGAC
EST: gi|71858580|gb|DT007635.1|DT007635
EST:     ATTTCAGAGAAGGTCCAGCCCTCCCGGTTCTTGATCATATGATAGAAGAT                         GGAAAGTATCATGGGACGTTCGATTTTATTTTCGTGGACGCTGACAAGGAC
genomic: ATTTCAGAGAAGGTCCAGCCCTCCCGGTTCTTGATCAGATGATAGAAGATgtaagtacaa ... caaattgcagGGAAAGTATCATGGGACATTCGATTTTATTTTCGTGGACGCTGACAAGGAC
EST: gi|352785883|gb|FQ475886.1|FQ475886
EST:     ATTTCAGAGAAGGTCCAGCCCTCCCGGTTCTTGATCAGATGATAGAAGAT                         GGAAAGTATCATGGGACGTTCGATTTTATTTTCGTGGACGCTGACAAGGAC
genomic: ATTTCAGAGAAGGTCCAGCCCTCCCGGTTCTTGATCAGATGATAGAAGATgtaagtacaa ... caaattgcagGGAAAGTATCATGGGACATTCGATTTTATTTTCGTGGACGCTGACAAGGAC
EST: gi|30128852|gb|CB914191.1|CB914191
EST:     ATTTCAGAGAAGGTCCAGCCCTCCCGGTTCTTGATCAGATGATAGAAGAT                         GGAAAGTATCATGGGACATTCGATTTTATTTTCGTGGACGCTGACAAGGAC
genomic: ATTTCAGAGAAGGTCCAGCCCTCCCGGTTCTTGATCAGATGATAGAAGATgtaagtacaa ... caaattgcagGGAAAGTATCATGGGACATTCGATTTTATTTTCGTGGACGCTGACAAGGAC
EST: gi|110728674|gb|EE104447.1|EE104447
EST:     ATTTCAGAGAAGGTCCAGCCCTCCCGGTTCTTGATCAGATGATAGAAGAT                         GGAAAGTATCATGGGACGTTCGATTTTATTTTCGTGGACGCTGACAAGGAC
genomic: ATTTCAGAGAAGGTCCAGCCCTCCCGGTTCTTGATCAGATGATAGAAGATgtaagtacaa ... caaattgcagGGAAAGTATCATGGGACATTCGATTTTATTTTCGTGGACGCTGACAAGGAC
EST: gi|110701151|gb|EE078431.1|EE078431
EST:     ATTTCAGAGAAGGTCCAGCCCTCCCGGTTCTTGATCAGATGATAGAAGAT                         GGAAAGTATCATGGGACATTCGATTTTATTTTCGTGGACGCTGACAAGGAC
genomic: ATTTCAGAGAAGGTCCAGCCCTCCCGGTTCTTGATCAGATGATAGAAGATgtaagtacaa ... caaattgcagGGAAAGTATCATGGGACATTCGATTTTATTTTCGTGGACGCTGACAAGGAC
EST: gi|37189880|gb|CF609229.1|CF609229
EST:     ATTTCAGAGAAGGTCCAGCCCTCCCGGTTCTTGATCAGATGATAGAAGAT                         GGAAAGTATCATGGGACGTTCGATTT
genomic: ATTTCAGAGAAGGTCCAGCCCTCCCGGTTCTTGATCAGATGATAGAAGATgtaagtacaa ... caaattgcagGGAAAGTATCATGGGACATTCGATTT
EST: gi|71856551|gb|DT005606.1|DT005606
EST:     ATTTCAGAGAAGGTCTAGCCCTCCCGGTTCTTGATCAGATGATAGAAGAT                         GGAAAGTATCATGGGACGTTCGATTTTATTTTCGTGGACGCTGACAAGGAC
genomic: ATTTCAGAGAAGGTCCAGCCCTCCCGGTTCTTGATCAGATGATAGAAGATgtaagtacaa ... caaattgcagGGAAAGTATCATGGGACATTCGATTTTATTTTCGTGGACGCTGACAAGGAC
EST: gi|29782008|gb|CB346952.2|CB346952
EST:     ATTTCAGAGAAGGTCCAGCCCTCCCGGTTCTTGATCAGATGATAGAAGAT                         GGAAAGTATCATGGGACGTTCGATTTTATTTTCGTGGACGCTGACAAGGAC
genomic: ATTTCAGAGAAGGTCCAGCCCTCCCGGTTCTTGATCAGATGATAGAAGATgtaagtacaa ... caaattgcagGGAAAGTATCATGGGACATTCGATTTTATTTTCGTGGACGCTGACAAGGAC
EST: gi|30124789|gb|CB910128.1|CB910128
EST:     ATTTCAGAGAAGGTCCAGCCCTCCCGGTTCTTGATCAGATGATAGAAGAT                         GGAAAGTATCATGGGACGTTCGATTTTATTTTCGTGGACGCTGACAAGGAC
genomic: ATTTCAGAGAAGGTCCAGCCCTCCCGGTTCTTGATCAGATGATAGAAGATgtaagtacaa ... caaattgcagGGAAAGTATCATGGGACATTCGATTTTATTTTCGTGGACGCTGACAAGGAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctccatgcctcatctgaacagaattgtaatttcaaaattatcaccaaattgcagGGAAAGTATCATGGGACATTCGATTTTATTTTCGTGGACGCTGACAAGGACAACTACCTGAACTACCACAAAAGGCTGATTGATCTGGTCAAGGTTGGAG
                    agaattgtaatttcaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtacaataatgcccctagcccactccaatattctccatgcctcatctgaacagaattgtaatttcaaaattatcaccaaattgcagGGAAAGTATCATGGGACATTCGATTTTATTTTCGTGGACGCTGACAAGGACAACTACCTGAACTACCACAAAAGGCTGATTGATCTGGTCAAGGTTGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG