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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagatttgttcactttttattgatgtggtaatttatttcattcctattcatttggcatgttggatgttattattatttattgtcatgatgaagtactttttcgttgaaaaacaaagtacttttccaattcttttgcaatcttgtcgatctgatttgcctgggatgtggttatgtacttattattctttaatatagGATGCTGGTGTATGAATATGTGAACAATGGCAACTTAGAACAGTGGCTTCATGGAGCTATGCGCCAATATGGCAACCTTACTTGGGAGGCCCGCATGAAG

Basic information

species Vitis vinifera
transcript Vv12s0028g00310.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv12s0028g00310.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os01g44110.1 (Oryza sativa), 3'ss of exon 4
gtaagatttgttcactttttattgatgtggtaatttatttcattcctattcatttggcatgttggatgttattattatttattgtcatgatgaagtactttttcgttgaaaaacaaagtacttttccaattcttttgcaatcttgtcgatctgatttgcctgggatgtggttatgtacttattattctttaatatagGATGCTGGTGTATGAATATGTGAACAATGGCAACTTAGAACAGTGGCTTCATGGAGCTATGCGCCAATATGGCAACCTTACTTGGGAGGCCCGCATGAAG
                                                                                            ||  |  ||| | |         |   | || |       | ||    ||| |   || |  | |  |   ||  |    || |    ||  || |||||||  ||||| |||||||||||| |||||| || || ||||| || ||||||||||||||||||||||||||  ||||     |||  |||||    || ||||||
--------------------------------------------------------------------------------------------aaacaaatttgcatcacctgtttagaaatttgtggttgcatcttaggctctaggatatattgtatatcacagaaata---atatgacaatggttttttaata--gGATGTTGGTGTATGAATTTGTGAATAACGGTAACTTGGAGCAGTGGCTTCATGGAGCTATGCGCCAGCATGGTGTTTTTAGCTGGGAAAATCGTATGAAG

upper sequence: Vv12s0028g00310.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os10g35450.1 (Oryza sativa), 3'ss of exon 3
gtaagatttgttcactttttattgatgtggtaatttatttcattcctattcatttggcatgttggatgttattattatttattgtcatgatgaagtactttttcgttgaaaaacaaagtacttttccaattcttttgcaatcttgtcgatctgatttgcctgggatgtggttatgtacttattattctttaatatagGATGCTGGTGTATGAATATGTGAACAATGGCAACTTAGAACAGTGGCTTCATGGAGCTATGCGCCAATATGGCAACCTTACTTGGGAGGCCCGCATGAAG
                                                                       ||| |  ||| ||   ||   || |  || || ||      |||   ||||      ||  ||||| | |||  |  |  |   |  |||   || ||       |||| ||||  |  |     ||||||| || || ||||||||||| || || ||||||||||||||||||||||| || ||||||||| ||||    ||||| ||||| ||||| ||||| 
-----------------------------------------------------------------------ttagtggttagtg--gtgtccaaatctttctttgt----gtacatcatact------atgtttttgtagtctattaaacttccat--cctatcatctg-------acttgttatattcca-----gGATGCTTGTATACGAATATGTGAATAACGGGAACTTAGAACAGTGGCTTCATGGTGCCATGCGCCAACATGGTGTTCTTACCTGGGAAGCCCGAATGAAA

upper sequence: Vv12s0028g00310.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os01g47470.1 (Oryza sativa), 3'ss of exon 3
gtaagatttgttcactttttattgatgtggtaatttatttcattcctattcatttggcatgttggatgttattattatttattgtcatgatgaagtactttttcgttgaaaaacaaagtacttttccaattcttttgcaatcttgtcgatctgatttgcctgggatgtggttatgtacttattattctttaatatagGATGCTGGTGTATGAATATGTGAACAATGGCAACTTAGAACAGTGGCTTCATGGAGCTATGCGCCAATATGGCAACCTTACTTGGGAGGCCCGCATGAAG---
                                                                                         ||| |     | ||| ||      |   || | |   ||||   | |     |||||     || ||  |   | |  | |   | | || | |||||     |  |||||||| || ||||||||||| |||||||| ||| ||||||| ||||||||||| || ||| |       |||| ||||||||||||   ||| ||||||   
-----------------------------------------------------------------------------------------atggaaattctgttccttc-----ccttgtgcataatcaatatgtgtttt-ccttgttcccttgtttctcactgtacattgaccttttctgaatattcacc--tgcagGATGCTTGTCTATGAATATGTCAACAATGGAAACCTAGAACAATGGCTTCATGGGGCCATGAGTGGG---GGCATCCTTACTTGGGAAAACCGTATGAAGATT

upper sequence: Vv12s0028g00310.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G010953_T01 (Zea mays), 3'ss of exon 1
gtaagatttgttcactttttattgatgtggtaatttatttcattcctattcatttggcatgttggatgttattattatttattgtcatgatgaagtactttttcgttgaaaaacaaagtacttttccaattcttttgcaatcttgtcgatctgatttgcctgggatgtggttatgtacttattattctttaatatagGATGCTGGTGTATGAATATGTGAACAATGGCAACTTAGAACAGTGGCTTCATGGAGCTATGCGCCAATATGGCAACCTTACTTGGGAGGCCCGCATGAAG
                                                                                          | ||||  | | | |     |  |||| ||  | | |  ||| | ||| || ||||  || | || |   |  |  ||  |  |   | ||| ||   ||| |  |||||||| ||||| || |||||||| ||||| ||||||||||||||||||||||| || ||||| ||  | ||    ||||||||||||||||| ||||| 
------------------------------------------------------------------------------------------taaagtggtgtatggacaccattcaaa-tatatatgc--ttcatatgccatattgtt-atttaatctattttag-cgttctcctaatcatatcatg--ttattccagGATGCTTGTGTACGAGTATGTGAATAATGGGAACTTAGAACAGTGGCTTCATGGTGCAATGCGTCAGCACGGTGTTCTTACTTGGGAGGCCCGGATGAAA

upper sequence: Vv12s0028g00310.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G026301_T01 (Zea mays), 3'ss of exon 3
gtaagatttgttcactttttattgatgtggtaatttatttcattcctattcatttggcatgttggatgttattattatttattgtcatgatgaagtactttttcgttgaaaaacaaagtacttttccaattcttttgcaatcttgtcgatctgatttgcctgggatgtggttatgtacttattattctttaatatagGATGCTGGTGTATGAATATGTGAACAATGGCAACTTAGAACAGTGGCTTCATGGAGCTATGCGCCAATATGGCAACCTTACTTGGGAGGCCCGCATGAAG
                                                                                       || | || ||  ||  | | ||||   |   ||  ||||  |     |    || ||||   | | || |   || |   || |    |  | ||      ||| |  |||||||| |||||||| || ||||||||||| || |||||||||||||||||||| || ||||| ||  ||||    ||||||||||| ||||| ||||| 
-------------------------------------------------------------------------------------agtggttaa-tatattaccatggaaatcta---tatgtttcatacatcat----atattgttt-tttaatctatttgag---tgttctcattatcatatcctcttactccagGATGCTTGTGTATGAGTACGTGAACAATGGAAATTTAGAACAGTGGCTTCATGGTGCCATGCGTCAGCATGGTGTTCTTACTTGGGAAGCCCGGATGAAA

upper sequence: Vv12s0028g00310.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G017386_T02 (Zea mays), 3'ss of exon 4
gtaagatttgttcactttttattgatgtggtaatttatttcattcctattcatttggcatgttggatgttattattatttattgtcatgatgaagtactttttcgttgaaaaacaaagta-cttttccaattcttttgcaatcttgtcgatctgatttgcctgggatgtggttatgtacttattattctttaatatagGATGCTGGTGTATGAATATGTGAACAATGGCAACTTAGAACAGTGGCTTCATGGAGCTATGCGCCAATATGGCAACCTTACTTGGGAGGCCCGCATGAAG
                                                                                               | |  ||| |   |||       || ||  |  |     |||   || ||  |   || || || |  | |  ||  ||       |||  | |||||||  ||||||| || ||||| |  ||||||||||| || ||||| ||||||||||||||||||||||  ||   |||     |||  |||||    |||||||||
----------------------------------------------------------------------------------------------ttgcccttttggcaaaagcttgcataactcctgtagaaagtttctgattttaccc-ccttatatgtcatgtaaatg-ctacaactgcattcctttttaata--gGATGCTAGTATATGAGTTCGTGAACAATGGTAATTTAGAGCAGTGGCTTCATGGAGCTATGCATCAGCGTGGTGTTTTTAGCTGGGAAAATCGCATGAAG

upper sequence: Vv12s0028g00310.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA02G45540.1 (Glycine max), 3'ss of exon 4
gtaagatttgttcactttttattgatgtggtaatttatttcattcctattcatttggcatgttggatgttattattatttattgtcatgatgaagtactttttcgttgaaaaacaaa-gtacttttccaattcttttgcaatcttgtcgatctgatttgcctgggatgtggttatgtacttattattctttaatatagGATGCTGGTGTATGAATATGTGAACAATGGCAACTTAGAACAGTGGCTTCATGGAGCTATGCGCCAATATGGCAACCTTACTTGGGAGGCCCGCATGAAG
                                                                                            |  | ||  || ||  ||||   ||  ||   ||     | | ||       | |  || |  | || |    |||     |||| |||     |   || |  ||| |||| ||||||||||||||||||||||| ||||||||||| ||| | ||||||   |||| ||||||||| |  ||||| ||||||||||||||||| 
--------------------------------------------------------------------------------------------atattctactttgtccaaaattgaacataagcttttctctatgttatgtctctatatatgtattctgtc-ataatga----atgtgcttcccgattgatatt-cagGCTGCTTGTGTATGAATATGTGAACAATGGTAACTTAGAACAATGGTTACATGGAAACATGCACCAATATGGGACGCTTACCTGGGAGGCCCGCATGAAA

upper sequence: Vv12s0028g00310.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA14G03290.1 (Glycine max), 3'ss of exon 2
gtaagatttgttcactttttattgatgtggtaatttattt-cattcctattcatttggcatgttggatgttattattatt-----tattgtcatgatga-agtactttttcgttgaaaaacaaagtacttttccaattcttttgcaatcttgtcgatctgatttgcctgggatgtggttatgtacttattattctttaatatagGATGCTGGTGTATGAATATGTGAACAATGGCAACTTAGAACAGTGGCTTCATGGAGCTATGCGCCAATATGGCAACCTTACTTGGGAGGCCCGCATGAAG
|||| |  | |||  | |||    |  |    ||  | |  || |     | || | |||  ||   | | | || || |       |||   | |||| |||  | ||    | |     ||| |     |  ||   |||  |  | || |   |||   ||  |||  ||   |  |||| |||  |  |   || |  ||| |||| ||||||||||||||||||||||| ||||||||||| ||| | |||||||  ||||  |||||||| |  ||||| ||||||||||||||||| 
gtaaaaaatattctttgttttcctacattagtatccactaacactttgtattatattgcacattcattctcaataatagtgccagctttgggtttatgatagtcatattctacttagtccgaaattggacat--aagcttttctctgtgttatgtctct---ttatctgtcataatga-atgtgcttcctgattgatatt-cagGCTGCTTGTGTATGAATATGTGAACAATGGTAACTTAGAACAATGGTTACATGGAGACATGCATCAATATGGAACACTTACCTGGGAGGCCCGCATGAAA

upper sequence: Vv12s0028g00310.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA18G12830.1 (Glycine max), 3'ss of exon 2
gtaagatttgttcactttttattgatgtggtaatttatttcattcctattcatttggcatgttggatgttattattatttattgtcatgatgaagtactttttcgttgaaaaacaaagtacttttccaattcttttgcaatcttgtcgatctgatttgcctgggatgtggttatgtacttattattctttaatatagGATGCTGGTGTATGAATATGTGAACAATGGCAACTTAGAACAGTGGCTTCATGGAGCTATGCGCCAATATGGCAACCTTACTTGGGAGGCCCGCATGAAG-
 |||| |||||  |  | | |   |||    |  || |  | |   |||||  |   ||  ||  |   | |  ||  |  | ||| |  |       ||||| ||  ||||    |  |      |  ||| ||   |      ||  | |  ||        ||| ||||     || |||         |  ||| ||||||||||||||||||| |||||||| ||||||||||| ||||| ||||| |||||| ||||| | || |  ||||| ||||| || || |||||  
-taagctttgtaaaaatatcacaaatgc---atattttcccttctatattcgat---cacattacaaactttattttgtggtggtcttagtcttac-tttttttgtcaaaaatttgaacagaacatcttttccttgttatatagttctttttctttcataataaatgcggttgccgtctgatt---------tgcaggTTGCTGGTGTATGAATATGTAAACAATGGTAACTTAGAACAATGGCTACATGGGGCTATGAGCCAACAAGGGACACTTACCTGGGAAGCTCGAATGAAAG

upper sequence: Vv12s0028g00310.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA08G42170.2 (Glycine max), 3'ss of exon 2
gtaagatttgttcactttttattgatgtggtaatttatttcattcctattcatttggcatgttggatgttatt----attatttattgtcat-gatgaagtactttttcgttgaaaaacaaagtacttttccaattcttttgcaatcttgtcgatctgatttgcctgggatgtggttatgtacttattattctttaatatagGATGCTGGTGTATGAATATGTGAACAATGGCAACTTAGAACAGTGGCTTCATGGAGCTATGCGCCAATATGGCAACCTTACTTGGGAGGCCCGCATGAAG
||||  || ||    || ||| ||   |   ||| |     || | ||||    |   ||  |  ||   |||    | | | | |||| || ||||   |||||||  ||  ||||    |  |      |  ||| ||   |      ||  | |  |||      ||| |||||     || |||         |  ||| ||||||| |||||||||||||||||||| ||||||||||| ||||| ||||| |||||| ||||| | || |  ||||| ||||| ||||| ||||| 
gtaaacttggtg---ttcttaatg-catcaaaatatcaccaatgcatatttcccttctatactcaatcacattgcaaactttattttgtgatagatgtgttacttttctgtcaaaaatttgaacagaacatcttttccttgttatatagttctttttcctttattatagatttggttgccgtctgatt---------tgcagGTTGCTGGTATATGAATATGTGAACAATGGTAACTTAGAACAATGGCTACATGGGGCTATGAGCCAACAAGGGACACTTACCTGGGAAGCCCGGATGAAA

upper sequence: Vv12s0028g00310.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT2G42960.1 (Arabidopsis thaliana), 3'ss of exon 2
gtaagatttgttcactttttattgatgtggtaatttatttcattcctattcatttggcatgttggatgttattattatttattgtcatgatgaagtactttttcgttgaaaaacaaagtacttttccaattcttttgcaatcttgtcgatctgatttgcctgggatgtggttatgtacttattattctttaatatagGATGCTGGTGTATGAATATGTGAACAATGGCAACTTAGAACAGTGGCTTCATGGAGCTATGCGCCAATATGGCAACCTTACTTGGGAGGCCCGCATGAAG
                                                                                                                     ||   | ||  | |  | |  ||||   | || |  ||| |  ||   ||    ||  ||     || |  | |||  |||||||| || ||||| ||||| || | ||| ||||||||||| ||||| |||||||| ||||| ||| |||| || || |||||||| || || ||||| 
---------------------------------------------------------------------------------------------------------------------gtgagtctc--acttgtctttaatccatttgagc-aattggattgtactgaatctaaata-----taatgatgaatgcagGATGCTTGTTTATGAGTATGTTAATAGTGGTAACTTAGAACAATGGCTACATGGAGCAATGCGGCAACATGGAAATCTCACTTGGGAAGCACGGATGAAA

upper sequence: Vv12s0028g00310.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT3G59110.1 (Arabidopsis thaliana), 3'ss of exon 3
gtaagatttgttcactttttattgatgtggtaatttatttcattcctattcatttggcatgttggatgttattattatttattgtcatgatgaa-gtactttttcgttgaaaaacaaagtacttttccaattcttttgcaatcttgtcgatctgatttgcctgggatgtggttatgtacttattattctttaatatagGATGCTGGTGTATGAATATGTGAACAATGGCAACTTAGAACAGTGGCTTCATGGAGCTATGCGCCAATATGGCAACCTTACTTGGGAGGCCCGCATGAAG
                                                              ||  | | | |  | | | || |||   |||| |||||  |   ||         |||| | | | |    || | | | |   | ||    | ||| |    ||||    || |   | || |  | ||||  |||||||| || ||||| |||||||| | ||| ||||||||||| ||||| |||||||| ||| |  || |  |||  || ||||||||||| |||||||| 
-------------------------------------------------------------gtgagtctgact--tgtctcttatcagtctgaatgtactactaatttagtctcatgagtaatctccta----ttgtactaccgaataga---aacttgtccc--atgtatcaattt--ctgttttgatgtaatgcagGATGCTTGTTTATGAGTATGTGAATAGTGGTAACTTAGAACAATGGCTACATGGAGCCATGGGAAAACAAAGCACTCTCACTTGGGAGGCTCGCATGAAA

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|71875365|gb|DT024420.1|DT024420
EST:     CATAAAAATCTTGTGCGACTTTTGGGCTATTGCATAGAAGGAGTTCACAG                         GATGCTGGTGTATGAATATGTGAACAATGGCAACTTAGAACAGTGGCTTCA
genomic: CATAAAAATCTTGTGCGACTTTTGGGCTATTGCATAGAAGGAGTTCACAGgtaagatttg ... tttaatatagGATGCTGGTGTATGAATATGTGAACAATGGCAACTTAGAACAGTGGCTTCA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtcgatctgatttgcctgggatgtggttatgtacttattattctttaatatagGATGCTGGTGTATGAATATGTGAACAATGGCAACTTAGAACAGTGGCTTCATGGAGCTATGCGCCAATATGGCAACCTTACTTGGGAGGCCCGCATGAAG
                                            ctttaat  putative branch site (score: 4)
                                       ttattcttt  CT-rich tract
                            ttatgtacttattatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagatttgttcactttttattgatgtggtaatttatttcattcctattcatttggcatgttggatgttattattatttattgtcatgatgaagtactttttcgttgaaaaacaaagtacttttccaattcttttgcaatcttgtcgatctgatttgcctgggatgtggttatgtacttattattctttaatatagGATGCTGGTGTATGAATATGTGAACAATGGCAACTTAGAACAGTGGCTTCATGGAGCTATGCGCCAATATGGCAACCTTACTTGGGAGGCCCGCATGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT