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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aatactgttactcttctttctcttttaaaattgaagacatgtcttgagaaattatgagaatttagcaccctcactgaagatagtctcacttgacttacagGTGTGCGGAGCTGCTATGATGAGGGGAAGCGTGTGGCTGAGACTTTGATGTTTGATTATCATAGGCAACATGGGATAG

Basic information

species Vitis vinifera
transcript Vv06s0004g04390.t01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0004g04390.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GRMZM2G300412_T01 (Zea mays), 3'ss of exon 13
aatactgttactcttctttctcttttaaa--attgaagacatgtcttgagaaattatgagaatttagcaccctcactgaagatagtctcacttgactta---cagGTGTGCGGAGCTGCTATGATGAGGGGAAGCGTGTGGCTGAGACTTTGATGTTTGATTATCATAGGCAACATGGGATAG
  ||   ||  || |||     ||  ||   |||         | || | |||||||     |||      |||    |   |  | | ||||   ||    |||||||  |||| || ||||||||||| |||||||| |||||||| ||||||||||| ||||| | ||| ||||| || |
-gtaaatttgttcatctgaaatttgaaatttatttgctttggtttttcataaattatc----tttcaagttctcttacagttttatttaactttttttctatcagGTGTTAGGAGTTGTTATGATGAGGGTAAGCGTGTAGCTGAGACGTTGATGTTTGACTATCACAAGCAGCATGGCATTG

upper sequence: Vv06s0004g04390.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GRMZM2G382038_T01 (Zea mays), 3'ss of exon 8
aatactgttactcttctttctcttttaaaattgaag---acatgtcttgagaaattatgaga-atttagcaccctcactgaagatagtctcacttgactta--------cagGTGTGCGGAGCTGCTATGATGAGGGGAAGCGTGTGGCTGAGACTTTGATGTTTGATTATCATAGGCAACATGGGATAG
        ||   |||||  |||   |||||||||    |  ||  |||     | || |   || |  ||   || || |   |  | | | || ||||         |||||||  |||| || ||||||||||| |||||||| || ||||  ||||||||||| ||||| ||||| ||||| || |
-------gtaaatttcttcatctg--aaaattgaaatttatttgctttggtttttcataaattatctttcaagttctcttacagt--ttttatttaactttttttctatcagGTGTTAGGAGTTGTTATGATGAGGGTAAGCGTGTAGCAGAGATGTTGATGTTTGACTATCACAGGCAGCATGGCATTG

upper sequence: Vv06s0004g04390.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GRMZM2G177373_T02 (Zea mays), 3'ss of exon 7
aatactgttactcttctttctcttttaaaattgaag---acatgtcttgagaaattatgaga-atttagcaccctcactgaagatagtctcacttgactta--------cagGTGTGCGGAGCTGCTATGATGAGGGGAAGCGTGTGGCTGAGACTTTGATGTTTGATTATCATAGGCAACATGGGATAG
              | | |   | | |||||||||    |  ||  |||     | || |   || |  ||   || || |   |  | | | || ||||         |||||||  |||| || ||||||||||| |||||||| || ||||  ||||||||||| ||||| ||||| ||||| || |
---------gtaaatttgttcatctgaaaattgaaatttatttgctttggtttttcataaattatctttcaagttctcttacagt--ttttatttaactttttttctatcagGTGTTAGGAGTTGTTATGATGAGGGTAAGCGTGTAGCAGAGATGTTGATGTTTGACTATCACAGGCAGCATGGCATTG

upper sequence: Vv06s0004g04390.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GRMZM2G044027_T02 (Zea mays), 3'ss of exon 7
aatactgttactcttctttctcttttaaaattgaagacatg-tcttgagaaattatgagaatttagcaccctcactgaagatagtctcacttgactta-cagGTGTGCGGAGCTGCTATGATGAGGGGAAGCGTGTGGCTGAGACTTTGATGTTTGATTATCATAGGCAACATGGGATAG
  ||   ||  || |||  |  ||  || ||    |   || | || | ||||||| |   |  ||    || || |    |  | | | ||    || |||| ||  ||||||| ||||||||||| |||||||| || |||||  ||||||| || ||||| ||||| ||||| || |
-gtaaatttgttcatctgacaattgcaatatatttgctttgattttcataaattatcat--tcaagttatcttac-ggttttgatttgattttttctatcagGAGTCAGGAGCTGTTATGATGAGGGTAAGCGTGTAGCAGAGACGCTGATGTTCGACTATCACAGGCAGCATGGCATTG

upper sequence: Vv06s0004g04390.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA11G15020.1 (Glycine max), 3'ss of exon 7
aatactgttactcttctttctcttttaaaattgaagacatgtc---ttgagaaattatgagaatttagcaccctcactgaagatagtctcacttgacttacagGTGTGCGGAGCTGCTATGATGAGGGGAAGCGTGTGGCTGAGACTTTGATGTTTGATTATCATAGGCAACATGGGATAG
     |  | |     |  || |||| ||    |  |  | |    |  |  | |||||   || ||  |   ||   | |  |  |   |  |   | ||||| || || || ||||||||||||||||| ||||||||||| |||||||||||||||||||||||||| ||||| ||||
---cttaatgcaaggttaacttttttgaagcaaagaattttttcaatacaatatttatgtagatgtattatggtctaagcacttgattatatatctttaacagGAGTTCGTAGTTGCTATGATGAGGGGAAACGTGTGGCTGAAACTTTGATGTTTGATTATCATAGGCAGCATGGAATAG

upper sequence: Vv06s0004g04390.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA12G06990.1 (Glycine max), 3'ss of exon 7
----aatactgttactcttcttt--ctcttttaaaattgaagacatgtcttgaga-aat-tatgagaatttagcaccctcactgaagatagtctcacttgacttacagGTGTGCGGAGCTGCTATGATGAGGGGAAGCGTGTGGCTGAGACTTTGATGTTTGATTATCATAGGCAACATGGGATAG
    |   |  | |  |    ||  || ||||  ||   ||||  | | || | | ||| ||| |   | ||    | | | |  | |||   | |        ||||| || || || ||||||||||||||||| ||||||||||| |||||||||||||||||||||||||| ||||| ||||
tattagctccttaatgcaaggttgacttttttttaagcaaagaatttttttaatacaatgtattatggtctaaacacttgattatatatatcttta--------acagGAGTTCGTAGTTGCTATGATGAGGGGAAACGTGTGGCTGAAACTTTGATGTTTGATTATCATAGGCAGCATGGAATAG

upper sequence: Vv06s0004g04390.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA15G04500.1 (Glycine max), 3'ss of exon 8
--------------aatactgttactcttctttctcttttaaaattgaagacatgtcttgagaaattatgagaat-----ttagcaccctcactgaaga--tagtctcacttgacttacagGTGTGCGGAGCTGCTATGATGAGGGGAAGCGTGTGGCTGAGACTTTGATGTTTGATTATCATAGGCAACATGGGATAG
                 | | | |   | ||    |  ||| |||     ||   |  ||     || |    ||     | |  |     ||||| ||  ||     |    | |  |||| || || || ||||||||||||||||| || ||||||||||| |||||||||||||| |||||||| ||||| || |
gtagattccttcatttcattctcaacttgctaaagcgcttataataaggaactatttctgtatctttttatacatattaataaagatgtagactgaggacttaaatatatgataatatcagGAGTTCGTAGTTGCTATGATGAGGGGAAACGGGTGGCTGAGACATTGATGTTTGATTACCATAGGCAGCATGGAATTG

upper sequence: Vv06s0004g04390.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA11G15010.1 (Glycine max), 3'ss of exon 7
-aatactgttactcttctttctcttttaaaattgaagacatgtcttgagaaatt---atgagaatttagcaccctcactgaagatagtctcacttgacttacagGTGTGCGGAGCTGCTATGATGAGGGGAAGCGTGTGGCTGAGACTTTGATGTTTGATTATCATAGGCAACATGGGATAG
 |  | | |       |  ||   ||||| ||  |   ||| || | |    ||   |||    |||| ||    | || || |||     |  | |   ||||| || ||||| || ||||||||||| |||||||| || || |||||||||||||||||||||||||| ||||| || |
taggaatttggaatgaccatcgactttaatat--ataccatatcattatctcttggaatgttgctttatcaatagc-ctaaacataaaaatatgt-atgaacagGAGTTCGGAGTTGTTATGATGAGGGCAAGCGTGTTGCAGAAACTTTGATGTTTGATTATCATAGGCAGCATGGAATCG

upper sequence: Vv06s0004g04390.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA13G40960.1 (Glycine max), 3'ss of exon 8
--------------------------------------------------------------aatactgttactcttctttctcttttaaaattgaagacatgtcttgagaaattatgagaatttagcaccctcactgaagatagtctcacttgacttacagGTGTGCGGAGCTGCTATGATGAGGGGAAGCGTGTGGCTGAGACTTTGATGTTTGATTATCATAGGCAACATGGGATAG
                                                              ||||    |||      |  | |     |  |  |   ||   |||| | ||  | | ||    | |  || |  |||  ||     |    | |  |||| || || || ||||||||||||||||| || ||||| ||||| |||||||||||||| |||||||| |||||||| |
gtaggttccttcatttcattctcaacttgctaaagagcttcttaaatggaactatttctgtcaatatgactacaaactctaatttaacggagatatatgtatcctttgatacatattcataaagatgtagactga--gaacttaaatatatgataatatcagGAGTTCGTAGTTGCTATGATGAGGGGAAACGGGTGGCCGAGACATTGATGTTTGATTACCATAGGCAGCATGGGATTG

upper sequence: Vv06s0004g04390.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA12G06980.2 (Glycine max), 3'ss of exon 6
aatactgttactcttctttctcttttaaaattgaagacatgtcttgagaaat---tatgagaatttagcaccctcactgaagatagtctcacttgacttacagGTGTGCGGAGCTGCTATGATGAGGGGAAGCGTGTGGCTGAGACTTTGATGTTTGATTATCATAGGCAACATGGGATAG
|||  |  |   |||   | | |     |  ||      | || |||    |   ||||    |||          || || |||        ||    ||||| || ||||| || ||||||||||| |||||||| || || |||||||||||||||||||||||||| || || || |
aatgatcatcgactttaatatataccttatctgtccttttatcatgatctcttgatatgttgcttttatcaatagcctaaacataaaaatgtgtg---cacagGAGTTCGGAGTTGTTATGATGAGGGCAAGCGTGTTGCAGAAACTTTGATGTTTGATTATCATAGGCAGCACGGAATCG

upper sequence: Vv06s0004g04390.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: AT3G46440.1 (Arabidopsis thaliana), 3'ss of exon 6
aatactgttactcttctttctcttttaaaattgaagacatgtcttgagaaattatgagaatttagcaccctcactgaagatagtctcacttgacttacagGTGTGCGGAGCTGCTATGATGAGGGGAAGCGTGTGGCTGAGACTTTGATGTTTGATTATCATAGGCAACATGGGATAG
  ||    ||  |   | ||   ||| || |   | || | |||          ||  |||| | ||  || |   ||  | || ||  ||   | | ||||||  ||||||| |||||||| || |||||||| |||||||| ||||||||||| || || ||||||||||| || |
-gtaggagtaaacacttatcagcttttaattctca-acttatctg-------cgtgtcaattca-cattcttat--aacttggtttctatta--tgatagGTGTTAGGAGCTGTTATGATGAAGGCAAGCGTGTTGCTGAGACCTTGATGTTTGACTACCACAGGCAACATGGAATTG

upper sequence: Vv06s0004g04390.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: AT2G28760.1 (Arabidopsis thaliana), 3'ss of exon 5
-aatactgttactcttctttctcttttaaaattgaagacatgtcttgagaaattatgagaatttagcaccctcactgaagatagtctcacttgacttacagGTGTGCGGAGCTGCTATGATGAGGGGAAGCGTGTGGCTGAGACTTTGATGTTTGATTATCATAGGCAACATGGGATAG
  |     |||     || |   || ||| | |       | ||     || ||||||     || |||    | ||||  |  |        | |   ||||||  | ||||| |||||||| || || ||||| || |||||| | ||||||||||| ||||||||||||||||| |
gtaagtcattatatgactattatttgtaataatctcagtttatc-----aatttatgaa---ctaacacaa--aatgaatttgctggtggcacattataagGTGTTAGAAGCTGTTATGATGAAGGAAAACGTGTTGCCGAGACTCTTATGTTTGATTACCATAGGCAACATGGGATTG

upper sequence: Vv06s0004g04390.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: PP1S189_118V6.1 (Physcomitrella patens), 3'ss of exon 7
--------------------aatactgttactcttctttctcttttaaaattgaagacatgtcttgagaaattatgagaatttagcaccctcactgaagatagtctcacttgacttacagGTGTGCGGAGCTGCTATGATGAGGGGAAGCGTGTGGCTGAGACTTTGATGTTTGATTATCATAGGCAACATGGGATAG
                    |    || | | |          | |  | ||   ||  | |  |    ||| ||   |    |  |   |  || ||  | |  ||   |    |  ||| ||  | ||||||||||| ||||| |||||||| ||||||||| | |||||||| || |||||||| |||||  | |
gtaaatccaactcacgttacacgcttggtgcaccatcacgctctgtgcagtttctgaactctgatacacaatcattcta-cacaaaatattaccttaacgttgcttcttgtcttgtgtagGAGTAAGAAGCTGCTATGACGAGGGAAAGCGTGTTGCTGAGACTCTTATGTTTGACTACCATAGGCAGCATGGCGTTG

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|33409748|gb|CF215375.1|CF215375
EST:     TCTTGAGCATCCCCAAACTGAGAGCTATTGGGGAAATGTTAACCCAATAG                         GTGTGCGGAGCTGCTATGATGAGGGGAAGCGTGTGGCTGAGACTTTGATGT
genomic: TCTTGAGCATCCCCAAACTGAGAGCTATTGGGGAAATGTTAACCCAATAGgtatttgcat ... tgacttacagGTGTGCGGAGCTGCTATGATGAGGGGAAGCGTGTGGCTGAGACTTTGATGT
EST: gi|33408202|gb|CF213829.1|CF213829
EST:     TCTTGAGCATCCCCAAACTGAGAGCTATTGGGGAAATGTTAACCCAATAG                         GTGCGCGGAGCTGCTATGATGAGGGGAAGCGTGTGGCTGAGACTTTGATGT
genomic: TCTTGAGCATCCCCAAACTGAGAGCTATTGGGGAAATGTTAACCCAATAGgtatttgcat ... tgacttacagGTGTGCGGAGCTGCTATGATGAGGGGAAGCGTGTGGCTGAGACTTTGATGT
EST: gi|33407209|gb|CF212836.1|CF212836
EST:     TCTTGAGCATCCCCAAACTGAGAGCTATTGGGGAAATGTTAACCCAATAG                         GTGTGCGGAGCTGCTATGATGAGGGGAAGCGTGTGGCTGAGACTTTGATGT
genomic: TCTTGAGCATCCCCAAACTGAGAGCTATTGGGGAAATGTTAACCCAATAGgtatttgcat ... tgacttacagGTGTGCGGAGCTGCTATGATGAGGGGAAGCGTGTGGCTGAGACTTTGATGT
EST: gi|30297461|gb|CB974255.1|CB974255
EST:     TCTTGAGCATCCCCAAACTGAGAGCTATTGGGGAAATGTTAACCCAATAG                         GTGTGCGGAGCTGCTATGATGAGGGGAAGCGTGTGGCTGAGACTTTGATGT
genomic: TCTTGAGCATCCCCAAACTGAGAGCTATTGGGGAAATGTTAACCCAATAGgtatttgcat ... tgacttacagGTGTGCGGAGCTGCTATGATGAGGGGAAGCGTGTGGCTGAGACTTTGATGT
EST: gi|33407983|gb|CF213610.1|CF213610
EST:     TCTTGAGCATCCCCAAACTGAGAGCTATTGGGGAAATGTTAACCCAATAG                         GTGTGCGGAGCTGCTATGATGAGGGGAAGCGTGTGGCTGAGACTCTGATGT
genomic: TCTTGAGCATCCCCAAACTGAGAGCTATTGGGGAAATGTTAACCCAATAGgtatttgcat ... tgacttacagGTGTGCGGAGCTGCTATGATGAGGGGAAGCGTGTGGCTGAGACTTTGATGT
EST: gi|56408375|gb|CX016627.1|CX016627
EST:     TCTTGAGCATCCCCAAACTGAGAGCTATTGGGGAAATGTTAACCCAATAG                         GTGTGCGGAGCTGCTATGATGAGGGGAAGCGTGTGGCTGAGACTTTGATGT
genomic: TCTTGAGCATCCCCAAACTGAGAGCTATTGGGGAAATGTTAACCCAATAGgtatttgcat ... tgacttacagGTGTGCGGAGCTGCTATGATGAGGGGAAGCGTGTGGCTGAGACTTTGATGT
EST: gi|33406260|gb|CF211887.1|CF211887
EST:     TCTTGAGCATCCCCAAACTGAGAGCTATTGGGGAAATGTTAACCCAATAG                         GTGTGCGGAGCTGCTATGATGAGGGGAAGCGTGTGGCTGAGACTTTGATGT
genomic: TCTTGAGCATCCCCAAACTGAGAGCTATTGGGGAAATGTTAACCCAATAGgtatttgcat ... tgacttacagGTGTGCGGAGCTGCTATGATGAGGGGAAGCGTGTGGCTGAGACTTTGATGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gagaaattatgagaatttagcaccctcactgaagatagtctcacttgacttacagGTGTGCGGAGCTGCTATGATGAGGGGAAGCGTGTGGCTGAGACTTTGATGTTTGATTATCATAGGCAACATGGGATAG
                                      tctcactt  CT-rich tract
     attatgagaattta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aatactgttactcttctttctcttttaaaattgaagacatgtcttgagaaattatgagaatttagcaccctcactgaagatagtctcacttgacttacagGTGTGCGGAGCTGCTATGATGAGGGGAAGCGTGTGGCTGAGACTTTGATGTTTGATTATCATAGGCAACATGGGATAG

- - ctgttac
- - - - - - - - - - - - - -aaattga
- - - - - - - - - - - - - - - - - - acatgtc
- - - - - - - - - - - - - - - - - - - - - - - agaaatt