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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TACTTTGCTTAAACTGATTATGGGCCTAGAGAAGCCTATAGGAGGTGAAGTGCTGCTTGGCGAGCATAATGTCTTACCAAACTATTTTGAGCAGAATCAGgtgtgtcatagttattactggtgtgcttgttggattggatcttatatcatggcaattctagtaattcatgctttggtgcaagtaccacttttgttcatatgtattgccatttctgaatgaaattgacctacttaattttcag

Basic information

species Vitis vinifera
transcript Vv07s0031g01640.t01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv07s0031g01640.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GRMZM2G105570_T01 (Zea mays), 5'ss of exon 4
TACTTTGCTTAAACTGATTATGGGCCTAGAGAAGCCTATAGGAGGTGAAGTGCTGCTTGGCGAGCATAATGTCTTACCAAACTATTTTGAGCAGAATCAGgtgtgtcatagttatta---ctggtgtgct-tgttg-gattggatcttatatcatggcaattctagtaattcatgctttggtgcaagtaccacttttgttcatat-gta---ttgccatttctgaatgaaattgacctact-taattttcag----
 ||  |||||||||| ||  ||||  | ||||||||   ||| ||||| ||||| ||||| ||||||||||| || || |||||||||||||||||||||||    |  || || |     || | |  | | ||| | ||   ||  |||  ||| ||      |        | | |    || || ||   |      |||  |||   ||  |  ||    || | ||| |    || | || ||       
CACACTGCTTAAACTTATGTTGGGGATGGAGAAGCCACAAGGTGGTGAGGTGCTTCTTGGGGAGCATAATGTGTTGCCGAACTATTTTGAGCAGAATCAGgtaaaccg-agctactctgtttgttatcttctattgtggttatttcagataaaatgtcaccatggggggacttggttattagtcatgttcctactcaacaaatacagtaaagttatccctttcctattagattaatgggctatgatgttttaccag

upper sequence: Vv07s0031g01640.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA04G39670.1 (Glycine max), 5'ss of exon 4
TACTTTGCTTAAACTGATTATGGGCCTAGAGAAGCCTATAGGAGGTGAAGTGCTGCTTGGCGAGCATAATGTCTTACCAAACTATTTTGAGCAGAATCAGgtgtgtcatagttattactggtgtgcttgttggattggatcttatatcatggcaattctagtaattcatgct-ttggtgcaagtaccacttttgttcatatgtattgccatttctgaatgaaattgacct-acttaattttcag
|||||| || ||| ||||||||||  | || ||||| |  || ||||||||  ||||||| ||||||||||| ||||| ||||||||||||||||||||||||||  |   | |     |   || |      |||| |  | |  | |||    | |||  | ||| || | ||  ||  |  |         ||  | ||  |    |||| | | ||    |||| | | ||| ||  |||
TACTTTACTGAAATTGATTATGGGTTTGGAAAAGCCAACCGGGGGTGAAGTTTTGCTTGGGGAGCATAATGTATTACCTAACTATTTTGAGCAGAATCAGgtgtgctactttaacctaggaaatgtt-----aattgtaattcaattgatgaatttgctaccagttcctgttctttatgtcaacaa-------atttgtgtggttaataattttttagtg---ctgacttcatttatttaacag

upper sequence: Vv07s0031g01640.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA06G15200.1 (Glycine max), 5'ss of exon 4
TACTTTGCTTAAACTGATTATGGGCCTAGAGAAGCCTATAGGAGGTGAAGTGCTGCTTGGCGAGCATAATGTCTTACCAAACTATTTTGAGCAGAATCAGgtgtgtcatagttattactggtgtgcttgttggattggatcttatatcatggcaattctagtaattcatgctttggtgcaagtaccacttttgttcatatgtattgccatttctgaatgaaattgacctacttaattttcag
|||||| || ||| ||||||||||  | || ||||| |  || ||||||||  |||| || ||||||||||| ||||| ||||||||||||||||||||||||||  |   | |  |  |   ||||  ||| | |  |  | |||   | |  ||      | |||  | | || |      |  | ||||||   |   || |    |||  |     | || |  || ||||       
TACTTTACTGAAATTGATTATGGGTTTGGAAAAGCCAACTGGGGGTGAAGTTTTGCTCGGGGAGCATAATGTGTTACCTAACTATTTTGAGCAGAATCAGgtgtgctactttaaccaaggaaatgctaattgtaattaaattgataaatttgttatc-----agttccagttctg-tatgt-caaaaattttgt--gtggttaataattttttagtgctgacttcatttatttaacag----

upper sequence: Vv07s0031g01640.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: AT5G09930.1 (Arabidopsis thaliana), 5'ss of exon 4
TACTTTGCTTAAACTGATTATGGGCCTAGAGAAGCCTATAGGAGGTGAAGTGCTGCTTGGCGAGCATAATGTCTTACCAAACTATTTTGAGCAGAATCAGgtgtgtcatagttattactggtgtgcttgttggattggatcttatatcatggcaattctagtaattcatgctttggtgcaagtaccacttttgttcatatgtattgccatttctgaatgaaattgacctacttaattttcag
||| ||||| ||||| ||||||||  | |||||||||||  ||||||| ||| | ||||| ||||| ||||| || |||||||| || |||||||||||||| |||  || | || |       |||| || ||  | |||  | |  |   || || || | |||  || || | || |                                                              
TACATTGCTGAAACTTATTATGGGTTTGGAGAAGCCTATGAGAGGTGAGGTGATACTTGGGGAGCACAATGTATTGCCAAACTACTTCGAGCAGAATCAGgtttgttcta-tcatgaagaaatggctttttagag-gaatcagaaaata---cagttttactcatt--tgtttggctgtag-------------------------------------------------------------

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|30323437|gb|CD006699.1|CD006699
EST:     TGCTGCTTGGCGAGCATAATGTCTTACCAAACTATTTTGAGCAGAATCAG                         GCTGAGGCACTTGATTTGGATAAAACAGTGTTGCAAACTGTAGAAGACGTT
genomic: TGCTGCTTGGCGAGCATAATGTCTTACCAAACTATTTTGAGCAGAATCAGgtgtgtcata ... taattttcagGCTGAGGCACTTGATTTGGATAAAACAGTGTTGCAAACTGTAGAAGACGTT
EST: gi|37189985|gb|CF609334.1|CF609334
EST:     TGCTGCTTGGCGAGCATAATGTCTTACCAAACTATTTTGAGCAGAATCAG                         GCTGAGGCACTTGATTTGGATAAAACAGTGTTGCAAACTGTAGAAGACATT
genomic: TGCTGCTTGGCGAGCATAATGTCTTACCAAACTATTTTGAGCAGAATCAGgtgtgtcata ... taattttcagGCTGAGGCACTTGATTTGGATAAAACAGTGTTGCAAACTGTAGAAGACGTT
EST: gi|30301899|gb|CB978693.1|CB978693
EST:     TGCTGCTTGGCGAGCATAATGTCTTACCAAACTATTTTGAGCAGAATCAG                         GCTGAGGCACTTGATTTGGATAAAACAGTGTTGCAAACTGTAGAAGACGTT
genomic: TGCTGCTTGGCGAGCATAATGTCTTACCAAACTATTTTGAGCAGAATCAGgtgtgtcata ... taattttcagGCTGAGGCACTTGATTTGGATAAAACAGTGTTGCAAACTGTAGAAGACGTT
EST: gi|32268733|gb|CD717892.1|CD717892
EST:     TGCTGCTTGGCGAGCATAATGTCTTACCAAACTATTTTGAGCAGAATCAG                         GCTGAGGCACTTGATTTGGATAAAACAGTGTTGCAAACTGTAGAAGACGTT
genomic: TGCTGCTTGGCGAGCATAATGTCTTACCAAACTATTTTGAGCAGAATCAGgtgtgtcata ... taattttcagGCTGAGGCACTTGATTTGGATAAAACAGTGTTGCAAACTGTAGAAGACGTT
EST: gi|30322545|gb|CD005807.1|CD005807
EST:     TGCTGCTTGGCGAGCATAATGTCTTACCAAACTATTTTGAGCAGAATCAG                         GCTGAGGCACTTGATTTGGATAAAACAGTGTTGCAAACTGTAGAAGACGTT
genomic: TGCTGCTTGGCGAGCATAATGTCTTACCAAACTATTTTGAGCAGAATCAGgtgtgtcata ... taattttcagGCTGAGGCACTTGATTTGGATAAAACAGTGTTGCAAACTGTAGAAGACGTT
EST: gi|32269321|gb|CD718480.1|CD718480
EST:     TGCTGCTTGGCGAGCATAATGTCTTACCAAACTATTTTGAGCAGAATCAG                         GCTGAGGCACTTGATTTGGATAAAACAGTGTTGCAAACTGTAGAAGACGTT
genomic: TGCTGCTTGGCGAGCATAATGTCTTACCAAACTATTTTGAGCAGAATCAGgtgtgtcata ... taattttcagGCTGAGGCACTTGATTTGGATAAAACAGTGTTGCAAACTGTAGAAGACGTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TACTTTGCTTAAACTGATTATGGGCCTAGAGAAGCCTATAGGAGGTGAAGTGCTGCTTGGCGAGCATAATGTCTTACCAAACTATTTTGAGCAGAATCAGgtgtgtcatagttattactggtgtgcttgttggattggatcttatatcatggcaattctagtaattcatgctttggtgcaagtaccacttttgttcatatgtattgccatttctgaatgaaattgacctacttaattttcag

- - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG