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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagtttcctggagcttacttatgatgattggtactactcatatttgtattttgtgaaagatttctgaaaataaacaattgtgctcctgtaccagGTTTATGAGCCAGTGGAAGAAGGCTCTTACATCAAAATGATTGATATGGTTGGTGGCCAAGATGGACAGATACAG

Basic information

species Vitis vinifera
transcript Vv06s0004g06920.t01
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0004g06920.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: LOC_Os05g07130.2 (Oryza sativa), 3'ss of exon 13
gtagtttcctggagcttacttatgatga-ttggtac-tactca-tatttgtattttgtgaaagatttctgaaaataa--acaattgtgctcctgtaccagGTTTATGAGCCAGTGGAAGAAGGCTCTTACATCAAAATGATTGATATGGTTGGTGGCCAAGATGGACAGATACAG
   ||||| |  || |   || |  |||   | |   |||  | || || |    |     ||   | |   | | |  | ||  ||  |||| |   |||| |||||||||||| | ||||| |||||||| |||||||||||||||||    || || |  || ||| |||||
---gtttcgtctagttatattgtattgagccgatgtataccaagtaattctgacctccatgagtcctttagtattgattaaaacggttttccttttgtagGTGTATGAGCCAGTGCAGGAAGGTTCTTACATTAAAATGATTGATATGGTAAAAGGGCAGGGAGGCCAGTTACAG

upper sequence: Vv06s0004g06920.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GRMZM5G824405_T02 (Zea mays), 3'ss of exon 11
gtagtttcctggagcttacttatgatgattggtactactcatatttgtattttgtgaaagattt-------ctgaaaataaacaattgtgctcctgtaccagGTTTATGAGCCAGTGGAAGAAGGCTCTTACATCAAAATGATTGATATGGTTGGTGGCCAAGATGGACAGATACAG
   || |      ||  | ||||  | | |  ||   | || ||   | |||||| ||  || |        |  |  |||||| ||     ||| |  ||||| ||||| || ||||||||||| |||||||| ||||||||||| |||||| ||||  | |  || ||  || ||
---gtctgtaattgccaaattatattaaatattatatcaca-atacattttttgtcaagaatatagtatagttatatgtaaacattttgaaaccttt-tcagGTCTATGAACCGGTGGAAGAAGGTTCTTACATAAAAATGATTGACATGGTTAGTGGGAAGGGGGGCCAACTAAAG

upper sequence: Vv06s0004g06920.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GLYMA11G27870.1 (Glycine max), 3'ss of exon 14
gtagtttcctggagcttacttatgatgattggtactactcatatttgtattttgtgaaagatttctgaaaataaacaattgtgctcctgtaccagGTTTATGAGCCAGTGGAAGAAGGCTCTTACATCAAAATGATTGATATGGTTGGTGGCCAAGATGGACAGATACAG
             ||     ||| | |    |||||  | ||  ||||      |||    ||||   ||||||    |||    | || |||||||||||||| ||||  | ||||| |||||||| |||||||||||||||||  |||| || | |||||| ||||| 
-------------gcaagtctataacgt---gtactttttatgattgttcaagctgagctttttccttaaataat--gttgattccatgcaccagGTTTATGAGACAGTTAATGAAGGATCTTACATAAAAATGATTGATATGGTCAGTGGGCATGGTGGACAAATACAA

upper sequence: Vv06s0004g06920.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GLYMA18G06770.1 (Glycine max), 3'ss of exon 15
gtagtttcctggagcttacttatgatgattggtactactcatatttgtattttgtgaaagatttctgaaaataaacaattgtgctcctgtaccagGTTTATGAGCCAGTGGAAGAAGGCTCTTACATCAAAATGATTGATATGGTTGGTGGCCAAGATGGACAGATACAG
                 |  ||| ||     |||||  | ||  ||||  |  |  |    ||||   ||||||    |||      || |||||||||||||| ||||  | ||||| |||||||| |||||||||||||||||  |||| || | |||||| ||||| 
---------------gcaagtat-ataccgtgtactttttatgattgtgcta-gctacctttttccttaaataat--gttgattctatgcaccagGTTTATGAGACAGTTAATGAAGGATCTTACATAAAAATGATTGATATGGTCAGTGGGCATGGTGGACAAATACAA

upper sequence: Vv06s0004g06920.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GLYMA14G37520.1 (Glycine max), 3'ss of exon 21
gtagtttcctggagcttacttatgatgattggtactactcatatttgtattttgtgaaagatttctgaaaataaacaattgtgctcctgtaccagGTTTATGAGCCAGTGGAAGAAGGCTCTTACATCAAAATGATTGATATGGTTGGTGGCCAAGATGGACAGATACAG-----
                         |  ||   | |  | ||   | |     ||||    || ||  ||||||    |||   || | ||||||||||||||| | || |||||||| |||||||| ||||||||||| ||||   |||| || |  || || |||||      
------------------------gtacttttaaattttaatggctattcaaggtgagcttttgctttaaataat--gttgatttcatataccagGTTTATGAGACCGTAGAAGAAGGATCTTACATAAAAATGATTGACATGGCCAGTGGACATGGAGGGCAAATACAAGTAAG

upper sequence: Vv06s0004g06920.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GLYMA14G37520.3 (Glycine max), 3'ss of exon 13
gtagtttcctggagcttacttatgatgattggtactactcatatttgtattttgtgaaagatttctgaaaataaacaattgtgctcctgtaccagGTTTATGAGCCAGTGGAAGAAGGCTCTTACATCAAAATGATTGATATGGTTGGTGGCCAAGATGGACAGATACAG
                         |  ||   | |  | ||   | |     ||||    || ||  ||||||    |||   || | ||||||||||||||| | || |||||||| |||||||| ||||||||||| ||||   |||| || |  || || ||||| 
------------------------gtacttttaaattttaatggctattcaaggtgagcttttgctttaaataat--gttgatttcatataccagGTTTATGAGACCGTAGAAGAAGGATCTTACATAAAAATGATTGACATGGCCAGTGGACATGGAGGGCAAATACAA

upper sequence: Vv06s0004g06920.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GLYMA11G27410.1 (Glycine max), 3'ss of exon 19
gtagtttcctggagcttacttatgatgattggtactactcatatttgtattttgtgaaagatttctgaaaataaacaattgtgctcctgtaccagGTTTATGAGCCAGTGGAAGAAGGCTCTTACATCAAAATGATTGATATGGTTGGTGGCCAAGATGGACAGATACAG
                               |||||  | ||  || |      |||    ||||   ||||||    |||    | || |||||||||||||| ||||  | ||||| |||||||| |||||||||||||||||  |||| || | |||||| ||||| 
-------------------------------gtactttttatgatttttcaagctgagctttttccttaaataat--gttgattccatgcaccagGTTTATGAGACAGTTAATGAAGGATCTTACATAAAAATGATTGATATGGTCAGTGGGCATGGTGGACAAATACAA

upper sequence: Vv06s0004g06920.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GLYMA02G39390.1 (Glycine max), 3'ss of exon 13
gtagtttcctggagcttacttatgatgattggtactactcatatttgtattttgtgaaagatttctgaaaataaacaattgtgctcctgtaccagGTTTATGAGCCAGTGGAAGAAGGCTCTTACATCAAAATGATTGATATGGTTGGTGGCCAAGATGGACAGATACAG
              ||| | |||| |  ||   | |  | ||   | |     ||||    || ||  ||||||    |||   || | | ||||||||||||| | || |||||||| |||||||| ||||||||||| ||||   |||| || |  || || ||||| 
--------gcaagtctttcatatg-tactttcaaattttaatggctattcaaggtgagcttttgctttaaataat--gttgatttcatatgccagGTTTATGAGACGGTAGAAGAAGGATCTTACATAAAAATGATTGACATGGCCAGTGGACATGGAGGGCAAATACAA

upper sequence: Vv06s0004g06920.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: AT1G07110.1 (Arabidopsis thaliana), 3'ss of exon 13
-------------------------------------gtagtttcctggagcttactta--tgatgattggtactac-tcatatttgtattttgtgaaagatttctgaaaataaacaattgtgctcctgtaccagGTTTATGAGCCAGTGGAAGAAGGCTCTTACATCAAAATGATTGATATGGTTGGTGGCCAAGATGGACAGATACAG
                                      |   ||  |  |||||| |||  |  |  ||| | |  | || | || ||| ||   || | || | |||   ||      | |  |  | | ||||||||||||||| || |||||||| || |||||||||||||||||||||||  ||||  | | |||||||||||| 
gtcggtacacaaacctgcactttctaaacgtgtcctaattactttttaaagcttagttaacttttctttgatgcaccatcgtcttggtacttaa-gacaaatgt-tgagctta-----ctctttttttttgccagGTTTATGAGCCTGTAGAAGAAGGTTCGTACATCAAAATGATTGATATGGTCAGTGGGAACGGTGGACAGATACAA

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|30322291|gb|CD005553.1|CD005553
EST:     TTGAAGCTGGATTACAGGACTTCAAAATTCGATTAGCAAATTATGAAAAA                         GTTTATGAGCCAGTGGAAGAAGGCTCTTACATCAAAATGATTGATATGGTT
genomic: TTGAAGCTGGATTACAGGACTTCAAAATTCGATTAGCAAATTATGAAAAAgtagtttcct ... cctgtaccagGTTTATGAGCCAGTGGAAGAAGGCTCTTACATCAAAATGATTGATATGGTT
EST: gi|30321972|gb|CD005234.1|CD005234
EST:     TTGAAGCTGGATTACAGGACTTCAAAATTCGATTAGCAAATTATGAAAAA                         GTTTATGAGCCAGTGGAAGAAGGCTCTTACATCAAAATGATTGATATGGTT
genomic: TTGAAGCTGGATTACAGGACTTCAAAATTCGATTAGCAAATTATGAAAAAgtagtttcct ... cctgtaccagGTTTATGAGCCAGTGGAAGAAGGCTCTTACATCAAAATGATTGATATGGTT
EST: gi|27580319|gb|CB003014.1|CB003014
EST:     TTGAAGCTGGATTACAGGACTTCAAAATTCGATTAGCAAATTATGAAAAA                         GTTTATGAGCCAGTGGAAGAAGGCTCTTACATCAAAATGATTGATATGGTT
genomic: TTGAAGCTGGATTACAGGACTTCAAAATTCGATTAGCAAATTATGAAAAAgtagtttcct ... cctgtaccagGTTTATGAGCCAGTGGAAGAAGGCTCTTACATCAAAATGATTGATATGGTT
EST: gi|27581545|gb|CB004240.1|CB004240
EST:     TTGAAGCTGGATTACAGGACTTCAAAATTCGATTAGCAAATTATGAAAAA                         GTTTATGAGCCAGTGGAAGAAGGCTCTTACATCAAAATGATTGATATGGTT
genomic: TTGAAGCTGGATTACAGGACTTCAAAATTCGATTAGCAAATTATGAAAAAgtagtttcct ... cctgtaccagGTTTATGAGCCAGTGGAAGAAGGCTCTTACATCAAAATGATTGATATGGTT
EST: gi|27580309|gb|CB003004.1|CB003004
EST:     TTGAAGCTGGATTACAGGACTTCAAAATTCGATTAGCAAATTATGAAAAA                         GTTTATGAGCCAGTGGAAGAAGGCTCTTACATCAAAATGATTGATATGGTT
genomic: TTGAAGCTGGATTACAGGACTTCAAAATTCGATTAGCAAATTATGAAAAAgtagtttcct ... cctgtaccagGTTTATGAGCCAGTGGAAGAAGGCTCTTACATCAAAATGATTGATATGGTT
EST: gi|32250239|gb|CD716058.1|CD716058
EST:     TTGAAGCTGGATTACAGGACTTCAAAATTCGATTAGCAAATTATGAAAAA                         GTTTATGAGCCAGTGGAAGAAGGCTCTTACATCAAAATGATTGATATGGTT
genomic: TTGAAGCTGGATTACAGGACTTCAAAATTCGATTAGCAAATTATGAAAAAgtagtttcct ... cctgtaccagGTTTATGAGCCAGTGGAAGAAGGCTCTTACATCAAAATGATTGATATGGTT
EST: gi|30321898|gb|CD005160.1|CD005160
EST:     TTGAAGCTGGATTACAGGACTTCAAAATTCGATTAGCAAATTATGAAAAA                         GTTTATGAGCCAGTGGAAGAAGGCTCTTACATCAAAATGATTGATATGGTT
genomic: TTGAAGCTGGATTACAGGACTTCAAAATTCGATTAGCAAATTATGAAAAAgtagtttcct ... cctgtaccagGTTTATGAGCCAGTGGAAGAAGGCTCTTACATCAAAATGATTGATATGGTT
EST: gi|30321402|gb|CD004664.1|CD004664
EST:     TTGAAGCTGGATTACAGGACTTCAAAATTCGATTAGCAAATTATGAAAAA                         GTTTATGAGCCAGTGGAAGAAGGCTCTTACATCAAAATGATTGATATGGTT
genomic: TTGAAGCTGGATTACAGGACTTCAAAATTCGATTAGCAAATTATGAAAAAgtagtttcct ... cctgtaccagGTTTATGAGCCAGTGGAAGAAGGCTCTTACATCAAAATGATTGATATGGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atatttgtattttgtgaaagatttctgaaaataaacaattgtgctcctgtaccagGTTTATGAGCCAGTGGAAGAAGGCTCTTACATCAAAATGATTGATATGGTTGGTGGCCAAGATGGACAGATACAG
                                         tgctcct  CT-rich tract
                    atttctgaaaataaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagtttcctggagcttacttatgatgattggtactactcatatttgtattttgtgaaagatttctgaaaataaacaattgtgctcctgtaccagGTTTATGAGCCAGTGGAAGAAGGCTCTTACATCAAAATGATTGATATGGTTGGTGGCCAAGATGGACAGATACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA