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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaatttgacaatcatctaaatgaattttgtagctcctttctgtctgtaaatgcttttttaatctctacatctaatatttgaagtcctgctgttttagGGATCAGATCACAAAGGGTATTCCTCAATGCTTCATAAAGCTTTGGAGGGCGCCATAATAGTGGAGAGTTTCCCCAAGACAACGGTGGATGTTTTTGCAT

Basic information

species Vitis vinifera
transcript Vv06s0004g02660.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0004g02660.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA12G08170.1 (Glycine max), 3'ss of exon 3
--gtaaatttgacaat-catctaaatgaattttgtag----ctcctttctgtctgtaaatgcttttttaatctctacatctaatatttgaagtcctgctgttttagGGATCAGATCACAAAGGGTATTCCTCAATGCTTCATAAAGCTTTGGAGGGCGCCATAATAGTGGAGAGTTTCCCCAAGACAACGGTGGATGTTTTTGCAT
   ||     | | || | | ||  |   || ||| |    || | |  |   | |  |||  | ||  |  |   | | |||||| | |  ||   |    |||||| ||||| ||||||| |||    |||||||||||||||||||||||||| || |||||| |||| |  |||||||||||||| |||||||| |||||||
gtatatgaaaggctatacttgtagcttttttctgttgtgttctgcatcttccatcttcatggctattggaagtagtcttttaatatattatatctcacgaagttagGGTTCAGACCACAAAGAGTACAGTTCAATGCTTCATAAAGCTTTGGAGGGAGCAATAATACTGGAAACATTCCCCAAGACAACTGTGGATGTCTTTGCAT

upper sequence: Vv06s0004g02660.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA11G20420.1 (Glycine max), 3'ss of exon 3
-------gtaaatttgacaatcatctaaatgaattttgtagctcctttctgtctgtaa-----atgcttttttaatctctacatctaatatttgaagtcctgctgttttagGGATCAGATCACAAAGGGTATTCCTCAATGCTTCATAAAGCTTTGGAGGGCGCCATAATAGTGGAGAGTTTCCCCAAGACAACGGTGGATGTTTTTGCAT
         |   |  ||    | || | |  || |||| | || | |   |||   |      || || ||| |  |   | |  ||||| | |  ||   |    | |||| ||||| ||||||| ||| |   | ||||||||||||||||||||||| || |||||| |||| |  |||||||||||||| ||||| ||||||||||
gtatatgaaaggctatacttgtaccttattttatgttgt-gttcttctgcatcttccatcttcgtggttatttgaagtagcctttcaatatattatatctcacaaagt-agGGTTCAGACCACAAAGAGTACTGTGCGATGCTTCATAAAGCTTTGGAGGGTGCAATAATACTGGAAACATTCCCCAAGACAACTGTGGACGTTTTTGCAT

upper sequence: Vv06s0004g02660.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT4G27490.1 (Arabidopsis thaliana), 3'ss of exon 4
gtaaatttgacaatcatctaaatgaattttgtagctcctttctgtctgtaaatgcttttttaatctctacatctaatatttgaagtcctgctgttttagGGATCAGATCACAAAGGGTATTCCTCAATGCTTCATAAAGCTTTGGAGGGCGCCATAATAGTGGAGAGTTTCCCCAAGACAACGGTGGATGTTTTTGCAT
                      | |  |    |  ||    |  |  ||     ||| ||| |||   | || || || |  |  |  || | ||||||||| | ||||||||||  ||||| ||||||||||| ||||| ||||| || |  |||||  ||||||  || || || ||||| || |||||||||||||
---------------------gtaatctccaaatttcgcaacatttggtgttaacttgtttcatc---aaatttagtaat--acattgtggtattttagGGAACTGATCACAAAGAATATTCATCAATGCTTCACAAAGCATTGGAAGGTGTAATAATGATGGAGACGTTTCCAAAAACAACCGTTGATGTTTTTGCAT

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|29783231|gb|CB349270.2|CB349270
EST:     TGAATTGTAATGTCAGCTATACTACTTTTGCCATGCCAATTCGTGGACAG                         GGATCAGATCACAAAGGGTATTCCTCAATGCTTCATAAAGCTTTGGAGGGC
genomic: TGAATTGTAATGTCAGCTATACTACTTTTGCCATGCCAATTCGTGGACAGgtaaatttga ... gctgttttagGGATCAGATCACAAAGGGTATTCCTCAATGCTTCATAAAGCTTTGGAGGGC
EST: gi|110726802|gb|EE102900.1|EE102900
EST:     TGAATTGTAATGTCAGCTATACTACTTTTGCCATGCCAATTCGTGGACAG                         GGATCAGATCACAAAGGGTATTCCTCAATGCTTCATAAAGCTTTGGAGGGC
genomic: TGAATTGTAATGTCAGCTATACTACTTTTGCCATGCCAATTCGTGGACAGgtaaatttga ... gctgttttagGGATCAGATCACAAAGGGTATTCCTCAATGCTTCATAAAGCTTTGGAGGGC
EST: gi|28970321|gb|CB349354.1|CB349354
EST:     TGAATTGTAATGTCAGCTATACTACTTTTGCCATGCCAATTCGTGGACAG                         GGATCAGATCACAAAGGGTATTCCTCAATGCTTCATAAAGCTTTGGAGGGC
genomic: TGAATTGTAATGTCAGCTATACTACTTTTGCCATGCCAATTCGTGGACAGgtaaatttga ... gctgttttagGGATCAGATCACAAAGGGTATTCCTCAATGCTTCATAAAGCTTTGGAGGGC
EST: gi|71856538|gb|DT005593.1|DT005593
EST:     TGAATTGTAATGTCAGCTATACTACTTTTGCCATGCCAATTCGTGGACAG                         GGATCAGATCACAAAGGGTATTCCTCAATGCTTCATAAAGCTTTGGAGGGC
genomic: TGAATTGTAATGTCAGCTATACTACTTTTGCCATGCCAATTCGTGGACAGgtaaatttga ... gctgttttagGGATCAGATCACAAAGGGTATTCCTCAATGCTTCATAAAGCTTTGGAGGGC
EST: gi|110428655|gb|EC995132.1|EC995132
EST:     TGAATTGTAATGTCAGCTATACTACTTTTGCCATGCCAATTCGTGGACAG                         GGATCAGATCACAAAGGGTATTCCTCAATGCTTCATAAAGCTTTGGAGGGC
genomic: TGAATTGTAATGTCAGCTATACTACTTTTGCCATGCCAATTCGTGGACAGgtaaatttga ... gctgttttagGGATCAGATCACAAAGGGTATTCCTCAATGCTTCATAAAGCTTTGGAGGGC
EST: gi|351026098|gb|FQ428110.1|FQ428110
EST:     TGAATTGTAATGTCAGCTATACTACTTTTGCCATGCCAATTCGTGGACAG                         GGATCAGATCACAAAGGGTATTCCTCAATGCTTCATAAAGCTTTGGAGGGC
genomic: TGAATTGTAATGTCAGCTATACTACTTTTGCCATGCCAATTCGTGGACAGgtaaatttga ... gctgttttagGGATCAGATCACAAAGGGTATTCCTCAATGCTTCATAAAGCTTTGGAGGGC
EST: gi|71859351|gb|DT008406.1|DT008406
EST:     TGAATTGTAATGTCAGCTATACTACTTTTGCCATGCCAATTCGTGGACAG                         GGATCAGATCACAAAGGGTATTCCTCAATGCTTCATAAAGCTTTGGAGGGC
genomic: TGAATTGTAATGTCAGCTATACTACTTTTGCCATGCCAATTCGTGGACAGgtaaatttga ... gctgttttagGGATCAGATCACAAAGGGTATTCCTCAATGCTTCATAAAGCTTTGGAGGGC
EST: gi|294965096|gb|GW836927.1|GW836927
EST:     TGAATTGTAATGTCAGCTATACTACTTTTGCCATGCCAATTCGTGGACAG                         GGATCAGATCACAAAGGGTATTCCTCAATGCTTCATAAAGCTTTGGAGGGC
genomic: TGAATTGTAATGTCAGCTATACTACTTTTGCCATGCCAATTCGTGGACAGgtaaatttga ... gctgttttagGGATCAGATCACAAAGGGTATTCCTCAATGCTTCATAAAGCTTTGGAGGGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctgtaaatgcttttttaatctctacatctaatatttgaagtcctgctgttttagGGATCAGATCACAAAGGGTATTCCTCAATGCTTCATAAAGCTTTGGAGGGCGCCATAATAGTGGAGAGTTTCCCCAAGACAACGGTGGATGTTTTTGCAT
                          atctaat  putative branch site (score: 3)
                                         tcctgct  putative PPT
     aaatgcttttttaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaatttgacaatcatctaaatgaattttgtagctcctttctgtctgtaaatgcttttttaatctctacatctaatatttgaagtcctgctgttttagGGATCAGATCACAAAGGGTATTCCTCAATGCTTCATAAAGCTTTGGAGGGCGCCATAATAGTGGAGAGTTTCCCCAAGACAACGGTGGATGTTTTTGCAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA