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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctgcaacttgaagtattaagtttttaactgttctttcccccactaggtctaatgaacagggaatgttgtttgagcagCTTGCACAAGGTGGCACTGCTGTAGGGACTGGATTGAACACAAAGAAAGG

Basic information

species Vitis vinifera
transcript Vv07s0005g00880.t01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv07s0005g00880.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: LOC_Os03g21950.1 (Oryza sativa), 3'ss of exon 7
gtctgcaacttgaagtattaagtttttaactgttctttcccccactag-gtctaatga--acagggaatgttgtttg---agcagCTTGCACAAGGTGGCACTGCTGTAGGGACTGGATTGAACACAAAGAAAGG
   | | ||   || | || | | |||   | |    |      | |  ||  |||||   | |   || || ||||   |||||||||| |||||||| ||||| || || || || |||||||| ||||||||
--gtactacactaa-tgttcaatatttgtttttagaatgatatgcaaaagttgaatgatttctgatcatattttttgctgagcagCTTGCTCAAGGTGGAACTGCAGTTGGAACGGGCTTGAACACTAAGAAAGG

upper sequence: Vv07s0005g00880.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GRMZM2G010823_T01 (Zea mays), 3'ss of exon 7
gtctgcaacttgaagtattaagtttttaactgttctttcccccactaggtctaatgaacagggaatgttgt-ttgagcagCTTGCACAAGGTGGCACTGCTGTAGGGACTGGATTGAACACAAAGAAAGG
              ||| ||   |  |||   || ||| |   || |  |   |  |      | | || |  |||||||||||| |||||||| ||||| || || ||||| |||||||| ||||||||
--------------gtactatactgctaatgtttgttttctttacaaattaacactactgataattattttgctgagcagCTTGCTCAAGGTGGAACTGCAGTTGGAACTGGCTTGAACACCAAGAAAGG

upper sequence: Vv07s0005g00880.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA02G01920.1 (Glycine max), 3'ss of exon 7
---gtctgcaacttgaagtattaagtttttaact---gttctttcccccactaggtctaa-tgaacagggaatgttgtttgagcagCTTGCACAAGGTGGCACTGCTGTAGGGACTGGATTGAACACAAAGAAAGG
      | ||| |  ||    ||| |  ||         | ||| |      || ||| | | ||   |  || ||| |||| |||||||| || ||||| || |||||||||||||||||||| |||||||| ||
gttagattcaaatgcaaaagctaactgcttgttcttcactatttacttttagagttctgactaaagcagagattttgcttgaacagCTTGCCCAGGGTGGGACAGCTGTAGGGACTGGATTGAATACAAAGAAGGG

upper sequence: Vv07s0005g00880.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA10G02040.2 (Glycine max), 3'ss of exon 7
gtctgcaacttgaagtattaagttt--ttaactgttctttccc--ccact-----aggtctaa-tgaacagggaatgttgtttgagcagCTTGCACAAGGTGGCACTGCTGTAGGGACTGGATTGAACACAAAGAAAGG
   |  |  || ||||| |||   |   |   |||||||  |     |||     || ||| | | ||   |  || ||  |||| |||||||| || ||||| || |||||||||||||||||||| |||||||| ||
-gttagacattcaagtactaaagctaactgcttgttcttcactatttacttttggagttctgactaaagcagagattttacttgaacagCTTGCCCAGGGTGGTACAGCTGTAGGGACTGGATTGAATACAAAGAAGGG

upper sequence: Vv07s0005g00880.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA02G01930.2 (Glycine max), 3'ss of exon 7
gtctgcaacttgaagtattaa--gtttttaactgttct-------ttcccccactaggtctaatgaacagggaatgttgtttgagcagCTTGCACAAGGTGGCACTGCTGTAGGGACTGGATTGAACACAAAGAAAGG
||  |  |||| |||||  ||   |   |   ||||||       || |      || |||| | | ||| |  ||||  |||| |||||||| || ||||| || |||||||||||||||||||| || ||||| ||
gttagacactt-aagtacaaaccataactgcttgttctacactatttacttttggagttctactaagcagagg-tgttacttgaacagCTTGCCCAGGGTGGTACAGCTGTAGGGACTGGATTGAATACCAAGAAGGG

upper sequence: Vv07s0005g00880.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: AT5G50950.3 (Arabidopsis thaliana), 3'ss of exon 6
gtctgcaacttgaag-tattaagtttttaactgttctttcccccactaggtctaatgaacagggaat-------gttgtttgagcagCTTGCACAAGGTGGCACTGCTGTAGGGACTGGATTGAACACAAAGAAAGG
|| || || |   |  | || ||  | | | |     ||   |    || |  | ||| |   || |         ||||||   |||||||||||||||| |||||||| ||||| ||||| ||||| ||||||||
gtttggaaatgatatctcttgaggatctgatttcatattattctcaaagtttcattgagctctgacttgttagaaatgtttgtctagCTTGCACAAGGTGGAACTGCTGTTGGGACCGGATTAAACACTAAGAAAGG

upper sequence: Vv07s0005g00880.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: AT2G47510.2 (Arabidopsis thaliana), 3'ss of exon 8
----------gtctgcaacttgaagtattaagttttta-actgttctttcccccact-aggtctaatgaacagggaatgttgtttgagcagCTTGCACAAGGTGGCACTGCTGTAGGGACTGGATTGAACACAAAGAAAGG
             |     |||  |   | | ||  |  |||  ||        ||| ||||||||    | || ||||||   ||  ||||||||||||||||| ||||| || ||||| ||||| ||||| ||||||||
gtttgggaaatgatatcttttggggatctgatttcctgtacttctccagtttatactgaggtctaacttgctggaaatgtt---tggccagCTTGCACAAGGTGGAACTGCGGTTGGGACAGGATTAAACACTAAGAAAGG

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|352794271|gb|FQ479513.1|FQ479513
EST:     TGAAATATGGAATTGACCGTGTCACATGCACTCTACCCCGCATGTATCAG                         CTTGCACAAGGTGGCACTGCTGTAGGGACTGGATTGAACACAAAGAAAGG
genomic: TGAAATATGGAATTGACCGTGTCACATGCACTCTACCCCGCATGTATCAGgtctgcaact ... gtttgagcagCTTGCACAAGGTGGCACTGCTGTAGGGACTGGATTGAACACAAAGAAAGG
EST: gi|351045827|gb|FQ441012.1|FQ441012
EST:     TGAAATATGGAATTGACCGTGTCACATGCACTCTACCCCGCATGTATCAG                         CTTGCACAAGGTGGCACTGCTGTAGGGACTGGATTGAACACAAAGAAAGG
genomic: TGAAATATGGAATTGACCGTGTCACATGCACTCTACCCCGCATGTATCAGgtctgcaact ... gtttgagcagCTTGCACAAGGTGGCACTGCTGTAGGGACTGGATTGAACACAAAGAAAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttaactgttctttcccccactaggtctaatgaacagggaatgttgtttgagcagCTTGCACAAGGTGGCACTGCTGTAGGGACTGGATTGAACACAAAGAAAGG
                           taatgaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtctgcaacttgaagtattaagtttttaactgttctttcccccactaggtctaatgaacagggaatgttgtttgagcagCTTGCACAAGGTGGCACTGCTGTAGGGACTGGATTGAACACAAAGAAAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA