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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcattttgttcttgtgttttgcattaagctatctaaagatatcatatataaatgcttatttcttctttctgggttaattatcagTATACCATCGAGGAAAAGGTGATTGAGAGAGCTTATAAAAAATTGGCACTCGATGCTTTGGTGATTCAACAAGGACGGTTAGCAGAGCAGAAAA

Basic information

species Vitis vinifera
transcript Vv05s0020g01780.t01
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0020g01780.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: LOC_Os05g05780.1 (Oryza sativa), 3'ss of exon 12
-----gttcattttgttcttgtgtttt---gcattaagctatc--taaa-gatatcatatataaatgcttatttct--tctttctgggttaattat-cagTATACCATCGAGGAAAAGGTGATTGAGAGAGCTTATAAAAAATTGGCACTCGATGCTTTGGTGATTCAACAAGGACGGTTAGCAGAGCAGAAAA
      || | ||| || |    |||     || |    || |  |||   ||||| | |||  ||   |||  |      | ||   |    ||| |||||||| || ||||||||||||||||||||||||||||| ||  | || || ||||||||||| || ||||| || || || |||||||||||| 
gttttatttaatttattttaagatttaaaaacactggtttagcactaagcaatatcttctatttatttatataacagaatatgcttcatattctatgcagTATACAATTGAGGAAAAGGTGATTGAGAGAGCTTATAAGAAGCTTGCCCTGGATGCTTTGGTCATACAACAGGGTCGATTGGCAGAGCAGAAAG

upper sequence: Vv05s0020g01780.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: 13113.m00246 (Oryza sativa), 3'ss of exon 12
gttcattttgttcttgtgttttgcattaagctatctaaagatatcatatataaatgcttatttcttctttctggg---ttaattatcagTATACCATCGAGGAAAAGGTGATTGAGAGAGCTTATAAAAAATTGGCACTCGATGCTTTGGTGATTCAACAAGGACGGTTAGCAGAGCAGAAAA
      |||||   | | || |  |  |   ||  |||  || |  | |||  ||   ||        |   |     |||||| |||||||||||||||||| || ||||||||||| || || || ||  | ||| | ||||||||||| ||||||||||| ||  | ||||||||||| |
-----gtttgtcaatcttttctttagaatattacgtaacaatcttttgtattgatatctaagataggatgacgaaaacttaatt-tcagTATACCATCGAGGAGAAAGTGATTGAGAGGGCATACAAGAAGCTTGCATTGGATGCTTTGGTCATTCAACAAGGCCGACTGGCAGAGCAGAAGA

upper sequence: Vv05s0020g01780.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GRMZM2G010085_T01 (Zea mays), 3'ss of exon 9
gttcattttgttcttgtgttttgcattaagctatctaaagatatcatatataaatgcttatttcttctt-tctgggttaattatcagTATACCATCGAGGAAAAGGTGATTGAGAGAGCTTATAAAAAATTGGCACTCGATGCTTTGGTGATTCAACAAGGACGGTTAGCAGAGCAGAAAA
|||  ||  |||  |   ||    ||||   ||     | || | |||  |  |    |||      |  |       || |  ||||| || || ||||||||||||||||||||||| ||||| ||  | ||| | ||||||||||| ||||| |||||||| || |||||||||||||
gtttgtt--gtttctagattaataattactgtagtgccaaattttatacttctacctgtatggaagataatgcaaacaaaattacagTACACTATTGAGGAAAAGGTGATTGAGAGAGCATATAAGAAGCTAGCATTGGATGCTTTGGTTATTCAGCAAGGACGATTGGCAGAGCAGAAAA

upper sequence: Vv05s0020g01780.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: AC235535.1_FGT001 (Zea mays), 3'ss of exon 12
gttcattttgttcttgtgttttgcattaagctatctaaagatatcatatataaatgcttatttctt---ctttctgggttaattatcagTATACCATCGAGGAAAAGGTGATTGAGAGAGCTTATAAAAAATTGGCACTCGATGCTTTGGTGATTCAACAAGGACGGTTAGCAGAGCAGAAAA
|||  ||  |||  |  | ||  || ||| | ||      | ||  ||| |  ||    ||||         |       || |  ||||| || |||||||||||||||||||||||||| ||||| ||  | ||| | |||||||| || ||||| |||||||| |               
gtttgtt--gtttcta-gattaacagtaa-ccatagtgctaaattctatgttgatatcaatttggaagATAATGCAAACGAAATTACAGTACACTATCGAGGAAAAGGTGATTGAGAGAGCATATAAGAAGCTAGCATTGGATGCTTTAGTTATTCAGCAAGGACGAT---------------

upper sequence: Vv05s0020g01780.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: AT3G06400.1 (Arabidopsis thaliana), 3'ss of exon 12
gttcattttgttcttgtgttttgcattaagctatctaaagatatcatatataaatgcttatttcttctttctgggttaattatcagTATACCATCGAGGAAAAGGTGATTGAGAGAGCTTATAAAAAATTGGCACTCGATGCTTTGGTGATTCAACAAGGACGGTTAGCAGAGCAGAAAA
|||  | |  |    |||  ||   | ||| ||   | ||  || | |  |  |   ||| || |   ||    |||  ||  |||| | | || ||||| || |||||||| |||||||| || || || ||||| |||||| |||| |||||||||||  | || ||||| |||||||
gttggtctcctctccgtgaatt---tcaagttaaa-acagccatgagaggtttaaaattaattatgtgtt----gtttgtttacagTCTGCTATTGAGGAGAAAGTGATTGAAAGAGCTTACAAGAAGTTAGCACTTGATGCTCTGGTTATTCAACAAGGGAGATTGGCAGAACAGAAAA

upper sequence: Vv05s0020g01780.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: AT5G18620.1 (Arabidopsis thaliana), 3'ss of exon 12
gttcattttgttcttgtgttttgcattaagctatctaaagatatcatatataaatgcttatttcttctttctgggttaattat-cagTATACCATCGAGGAAAAGGTGATTGAGAGAGCTTATAAAAAATTGGCACTCGATGCTTTGGTGATTCAACAAGGACGGTTAGCAGAGCAGAAAA
|||  | |||| |   |||   | || |||     |||  ||  | |  | || |    | |  ||||   | |||   |||| ||| || | || ||||  || || |||||||||||||| || || |||||||| |||||| |||| ||||| |||||  | || ||||| |||||||
gttactcttgtacccatgt---gtatgaag-----taagaatgacctggagaact-tgaactaattctgcattggtc--ttatgcagAATGCTATTGAGGCTAAAGTCATTGAGAGAGCTTACAAGAAGTTGGCACTTGATGCTCTGGTTATTCAGCAAGGGAGATTGGCAGAACAGAAAA

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|29781883|gb|CB346697.2|CB346697
EST:     ATCGGATTGGTCAAAAGAAAGAAGTTCAAGTGTTTCGATTCTGCACAGAG                         TATACCATCGAGGAAAAGGTGATCGAGAGAGCTTATAAAAAATTGGCACTC
genomic: ATCGGATTGGTCAAAAGAAAGAAGTTCAAGTGTTTCGATTCTGCACAGAGgttcattttg ... taattatcagTATACCATCGAGGAAAAGGTGATTGAGAGAGCTTATAAAAAATTGGCACTC






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatctaaagatatcatatataaatgcttatttcttctttctgggttaattatcagTATACCATCGAGGAAAAGGTGATTGAGAGAGCTTATAAAAAATTGGCACTCGATGCTTTGGTGATTCAACAAGGACGGTTAGCAGAGCAGAAAA
     aaagatatcatatata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttcattttgttcttgtgttttgcattaagctatctaaagatatcatatataaatgcttatttcttctttctgggttaattatcagTATACCATCGAGGAAAAGGTGATTGAGAGAGCTTATAAAAAATTGGCACTCGATGCTTTGGTGATTCAACAAGGACGGTTAGCAGAGCAGAAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG