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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAAGGTGCAGATCCTGTTGTAGTTGCAGAGGATGGAAAAGTGAAGTCATTCCCTGTGATCTTGTTACCCAAGGAGAAGCTGGTTGATACCAATGGAGCAGgtatgaactctcttatttcattattcatgcctagagtgctgaaaatgaccaaccttcataaaggtttgcatcgtattgagattcagtgctcctgtcttct...

Basic information

species Vitis vinifera
transcript Vv13s0019g04470.t01
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv13s0019g04470.t01 (Vitis vinifera), 5'ss of exon 11
lower sequence: GRMZM2G135132_T01 (Zea mays), 5'ss of exon 12
--------------------------------------------------CAA-GGTGCAGATCCTGTTGTAGTTGCAGAGGATGGAAAAGTGAAGTCATTCCCTGTGATCTTGTTA--CCCAAGGAGAAGCTGGTTGAT--ACCAATGGAGCAGgtatgaactctcttatttcattatt-catgcctagagtgctgaaaatgaccaaccttcataaaggtttgcatcgtattgag-attcagtgctcctgtcttct-----
                                                  ||| || |||| | |   | |  ||   ||  | |    |||  |   ||| ||  |  | || | |  | |||     || |||||  |   | ||     |    ||  | | |    |   |||||| |||  |  ||  ||||||  |  | |    | ||   | | | | |  ||      |  || |  ||||  || ||     
GTGAAAACGTTCCCTGTGATCCTATTGCCCAAGGAGAAGCTTGTTGACACCAACGGCGCAGgtacatgtttctttagtgataa-gagttagtttatctatttccgatatttttttcattctcaaacgctagttggtttgttcgctaagatgtcttccatataatgttaactactattattgcattacatgaaagctgaacgtctctacgtcttattttgctgttcctgataacacccaaccaatcttccttgctcctcctag

upper sequence: Vv13s0019g04470.t01 (Vitis vinifera), 5'ss of exon 11
lower sequence: GRMZM2G089767_T01 (Zea mays), 5'ss of exon 10
CAAGGTGCAGATCCTGTTGTAGTTGCAGAGGATGGAAAAGTGAAGTCATTCCCTGTGATCTTGTTACCCAAGGAGAAGCTGGTTGATACCAATGGAGCAGgtat---gaactctcttatttcattattcatgcctagagtgctgaaaatgaccaaccttcataaaggtttgcatcgtattgagattcagtgctcctgtcttct
                                       |||||  | |||||||||||| | || || ||||||||||| ||||| |||||||| |||||||    ||||||  |  ||||   | |  |   || |  ||  |  | |    | |||  |      |||   | |  ||   |  |        | ||  |
---------------------------------------GTGAAAACTTTCCCTGTGATCCTCTTGCCTAAGGAGAAGCTTGTTGACACCAATGGTGCAGgtacttggaactcgatagtttc--cagtagtaa-tatatcgcatagcacgttgcagctttctttctccttgagccatcatgtagtctaccagcatggactcat

upper sequence: Vv13s0019g04470.t01 (Vitis vinifera), 5'ss of exon 11
lower sequence: GRMZM2G540538_T01 (Zea mays), 5'ss of exon 12
CAAGGTGCAGATCCTGTTGTAGTTGCAGAGGATGGAAAAGTGAAGTCATTCCCTGTGATCTTGTTACCCAAGGAGAAGCTGGTTGATACCAATGGAGCAGgtatgaactctcttatt--tcattattcatgcctagagtgctgaaaatgaccaaccttcataaaggtttgcatcgtattgagat-tcagtgctcctgtcttct
                                       |||||  | |||||||||||| | || |||||||||||||| ||||| ||||| || |||||||   |||   ||| |  |||  ||| ||   |   || ||       |   |  |||   |    |  | || |  | | ||   |||     |||  |||
---------------------------------------GTGAAAACGTTCCCTGTGATCCTATTGCCCAAGGAGAAGCTTGTTGACACCAACGGCGCAGgtacacacttctttagtgttcagaattaatttat---gttcttggttcaaaagagtttctctatttctgacgtctttctcaaatactagttggtttgttctct

upper sequence: Vv13s0019g04470.t01 (Vitis vinifera), 5'ss of exon 11
lower sequence: GLYMA13G20780.1 (Glycine max), 5'ss of exon 11
CAAGGTGCAGATCCTGTTGTAGTTGCAGAGGATGGAAAAGTGAAGTCATTCCCTGTGATCTTGTTACCCAAGGAGAAGCTGGTTGATACCAATGGAGCAGgtatg-aactctctta-tttcattattca-----tgcctagagtgctgaaaatgaccaaccttcataaaggtttgcatcgtattgagattcagtgctcctgtcttct
||||||||||||||||||   ||||| |||||||||||||||||    | ||| |||||   |||||| || |||||  | ||||| || |||||||||||||   | |  | ||  ||| | |||  |     |    | |||  |           |  ||    |   || |  |  |  | | ||||   |    |       
CAAGGTGCAGATCCTGTTTGCGTTGCCGAGGATGGAAAAGTGAAAATTTACCCCGTGATACCGTTACCTAAAGAGAAATTAGTTGACACAAATGGAGCAGgtacacagccatattgcttttagtatgtaaatgttagacaaagttatatgtgcagttgagtttatggacaattagtctgctcataaaattcgtggaagtt-------

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|46919754|gb|CN549083.1|CN549083
EST:     CCCTGTGATCTTGTTACCCAAGGAGAAGCTGGTTGATACCAATGGAGCAG                         GCGATGCATTCGTTGGAGGATTTTTGTCTCAGTTGGTTCAAGAGAAGCCGA
genomic: CCCTGTGATCTTGTTACCCAAGGAGAAGCTGGTTGATACCAATGGAGCAGgtatgaactc ... tgtgtggtagGCGATGCATTCGTTGGAGGATTTTTGTCTCAGTTGGTTCAAGAGAAGCCGA
EST: gi|110723004|gb|EE099818.1|EE099818
EST:     CCCTGTGATCTTGTTACCCAAGGAGAAGCTGGTTGATACCAATGGAGCAG                         GCGATGCATTCGTTGGAGGTTTTTTGTCTCAGTTGGTTCAAGAGAAGCCAA
genomic: CCCTGTGATCTTGTTACCCAAGGAGAAGCTGGTTGATACCAATGGAGCAGgtatgaactc ... tgtgtggtagGCGATGCATTCGTTGGAGGATTTTTGTCTCAGTTGGTTCAAGAGAAGCCGA
EST: gi|45771535|gb|CN007387.1|CN007387
EST:     CCCTGTGATCTTGTTACCCAAGGAGAAGCTGGTTGATACCAATGGAGCAG                         GCGATGCATTCGTTGGAGGTTTTTTGTCTCAGTTGGTTCAAGAGAAGCCAA
genomic: CCCTGTGATCTTGTTACCCAAGGAGAAGCTGGTTGATACCAATGGAGCAGgtatgaactc ... tgtgtggtagGCGATGCATTCGTTGGAGGATTTTTGTCTCAGTTGGTTCAAGAGAAGCCGA
EST: gi|83274601|gb|DV938698.1|DV938698
EST:     CCCTGTGATCTTGTTACCCAAGGAGAAGCTGGTTGATACCAATGGAGCAG                         GCGATGCATTCGTTGGAGGTTTTTTGTTTCAGTTGGTTC
genomic: CCCTGTGATCTTGTTACCCAAGGAGAAGCTGGTTGATACCAATGGAGCAGgtatgaactc ... tgtgtggtagGCGATGCATTCGTTGGAGGATTTTTGTCTCAGTTGGTTC
EST: gi|22008497|gb|BQ793531.1|BQ793531
EST:     CCCTGTGATCTTGTTACCCAAGGAGAAGCTGGTTGATACCAATGGAGCAG                         GCGATGCATTCGTTGGAGGTTTTTTGTCTCAGTTGGTTCAAGAGAAGCCAA
genomic: CCCTGTGATCTTGTTACCCAAGGAGAAGCTGGTTGATACCAATGGAGCAGgtatgaactc ... tgtgtggtagGCGATGCATTCGTTGGAGGATTTTTGTCTCAGTTGGTTCAAGAGAAGCCGA
EST: gi|110406918|gb|EC972505.1|EC972505
EST:     CCCTGTGATCTTGTTACCCAAGGAGAAGCTGGTTGATACCAATGGAGCAG                         GCGATGCATTCGTTGGAGGATTTTTGTCTCAGTTGGTTCAAGAGAAGCCGA
genomic: CCCTGTGATCTTGTTACCCAAGGAGAAGCTGGTTGATACCAATGGAGCAGgtatgaactc ... tgtgtggtagGCGATGCATTCGTTGGAGGATTTTTGTCTCAGTTGGTTCAAGAGAAGCCGA
EST: gi|32245916|gb|CD711735.1|CD711735
EST:     CCCTGTGATCTTGTTACCCAAGGAGAAGCTGGTTGATACCAATGGAGCAG                         GCGATGCATTCGTTGGAGGTTTTTTGTCTCAGTTGGTTCAAGAGAAGCCAA
genomic: CCCTGTGATCTTGTTACCCAAGGAGAAGCTGGTTGATACCAATGGAGCAGgtatgaactc ... tgtgtggtagGCGATGCATTCGTTGGAGGATTTTTGTCTCAGTTGGTTCAAGAGAAGCCGA
EST: gi|71874878|gb|DT023933.1|DT023933
EST:     CCCTGTGATCTTGTTACCCAAGGAGAAGCTGGTTGATACCAATGGAGCAG                         GCGATGCATTCGTTGGAGGTTTTTTGTCTCAGTTGGTTCAAGAGAAGCCAA
genomic: CCCTGTGATCTTGTTACCCAAGGAGAAGCTGGTTGATACCAATGGAGCAGgtatgaactc ... tgtgtggtagGCGATGCATTCGTTGGAGGATTTTTGTCTCAGTTGGTTCAAGAGAAGCCGA
EST: gi|77580852|gb|DV219346.1|DV219346
EST:     CCCTGTGATCTTGTTACCCAAGGAGAAGCTGGTTGATACCAATGGAGCAG                         GCGATGCATTCGTTGGAGGTTTTTTGTCTCAGTTGGTTCAAGAGAAGCCAA
genomic: CCCTGTGATCTTGTTACCCAAGGAGAAGCTGGTTGATACCAATGGAGCAGgtatgaactc ... tgtgtggtagGCGATGCATTCGTTGGAGGATTTTTGTCTCAGTTGGTTCAAGAGAAGCCGA
EST: gi|30329392|gb|CD012654.1|CD012654
EST:     CCCTGTGATCTTGTTACCCAAGGAGAAGCTGGTTGATACCAATGGAGCAG                         GCGATGCATTCGTTGGAGGATTTTTGTCTCAGTTGGTTCAAGAGAAGCCGA
genomic: CCCTGTGATCTTGTTACCCAAGGAGAAGCTGGTTGATACCAATGGAGCAGgtatgaactc ... tgtgtggtagGCGATGCATTCGTTGGAGGATTTTTGTCTCAGTTGGTTCAAGAGAAGCCGA
EST: gi|34415328|gb|CF414082.1|CF414082
EST:     CCTGTGGATCTTGTTACCCAAGGAGAGGCTGGTTGATACCAATGGAGCAG                         GCGATGCATTCGTTGGAGGATTTTTGTCTCAGTTGGTTCAAGAGAAGCCGA
genomic: CCTGT-GATCTTGTTACCCAAGGAGAAGCTGGTTGATACCAATGGAGCAGgtatgaactc ... tgtgtggtagGCGATGCATTCGTTGGAGGATTTTTGTCTCAGTTGGTTCAAGAGAAGCCGA
EST: gi|110723487|gb|EE100853.1|EE100853
EST:     CCCTGTGATCTTGTTACCCAAGGAGAAGCTGGTTGATACCAATGGAGCAG                         GCGATGCATTCGTTGGAGGTTTTTTGTCTCAGTTGGTTCAAGAGAAGCCAA
genomic: CCCTGTGATCTTGTTACCCAAGGAGAAGCTGGTTGATACCAATGGAGCAGgtatgaactc ... tgtgtggtagGCGATGCATTCGTTGGAGGATTTTTGTCTCAGTTGGTTCAAGAGAAGCCGA
EST: gi|110428447|gb|EC994919.1|EC994919
EST:     CCCTGTGATCTTGTTACCCAAGGAGAAGCTGGTTGATACCAATGGAGCAG                         GCGATGCATTCGTTGGAGGATTTTTGTCTCAGTTGGTTCAAGAGAAGCCGA
genomic: CCCTGTGATCTTGTTACCCAAGGAGAAGCTGGTTGATACCAATGGAGCAGgtatgaactc ... tgtgtggtagGCGATGCATTCGTTGGAGGATTTTTGTCTCAGTTGGTTCAAGAGAAGCCGA
EST: gi|32245456|gb|CD711275.1|CD711275
EST:     CCCTGTGATCTTGTTACCCAAGGAGAAGCTGGTTGATACCAATGGAGCAG                         GCGATGCATTCGTTGGAGGTTTTTTGTCTCAGTTGGTTCAAGAGAAGCCAA
genomic: CCCTGTGATCTTGTTACCCAAGGAGAAGCTGGTTGATACCAATGGAGCAGgtatgaactc ... tgtgtggtagGCGATGCATTCGTTGGAGGATTTTTGTCTCAGTTGGTTCAAGAGAAGCCGA
EST: gi|46910988|gb|CN546363.1|CN546363
EST:     CCCTGTGATCTTGTTACCCAAGGAGAAGCTGGTTGATACCAATGGAGCAG                         GCGATGCATTCGTTGGAGGATTTTTGTCTCAGTTGGTTCAAGAGAAGCCGA
genomic: CCCTGTGATCTTGTTACCCAAGGAGAAGCTGGTTGATACCAATGGAGCAGgtatgaactc ... tgtgtggtagGCGATGCATTCGTTGGAGGATTTTTGTCTCAGTTGGTTCAAGAGAAGCCGA
EST: gi|110715111|gb|EE092784.1|EE092784
EST:     CCCTGTGATCTTGTTACCCAAGGAGAAGCTGGTTGATACCAATGGAGCAG                         GCGATGCATTCGTTGGAGGTTTTTTGTCTCAGTTGGTTCAAGAGAAGCCAA
genomic: CCCTGTGATCTTGTTACCCAAGGAGAAGCTGGTTGATACCAATGGAGCAGgtatgaactc ... tgtgtggtagGCGATGCATTCGTTGGAGGATTTTTGTCTCAGTTGGTTCAAGAGAAGCCGA
EST: gi|22015287|gb|BQ800321.1|BQ800321
EST:     CCCTGTGATCTTGTTACCCAAGGAGAAGCTGGTTGATACCAATGGAGCAG                         GCGATGCATTCGTTGGAGGATTTTTGTCTCAGTTGGTTCAAGAGAAGCCGA
genomic: CCCTGTGATCTTGTTACCCAAGGAGAAGCTGGTTGATACCAATGGAGCAGgtatgaactc ... tgtgtggtagGCGATGCATTCGTTGGAGGATTTTTGTCTCAGTTGGTTCAAGAGAAGCCGA
EST: gi|27585920|gb|CB008615.1|CB008615
EST:     CCCTGTGATCTTGTTACCCAAGGAGAAGCTGGTTGATACCAATGGAGCAG                         GCGATGCATTCGTTGGAGGTTTTTTGTCTCAGTTGGTTCAAGAGAAGCCAA
genomic: CCCTGTGATCTTGTTACCCAAGGAGAAGCTGGTTGATACCAATGGAGCAGgtatgaactc ... tgtgtggtagGCGATGCATTCGTTGGAGGATTTTTGTCTCAGTTGGTTCAAGAGAAGCCGA
EST: gi|110425226|gb|EC991608.1|EC991608
EST:     CCCTGTGATCTTGTTACCCAAGGAGAAGCTGGTTGATACCAATGGAGCAG                         GGGATGCATTCGTTGGAGGTTTTTTGTCTCAGTTGGTTCAAGAGAAGCCTA
genomic: CCCTGTGATCTTGTTACCCAAGGAGAAGCTGGTTGATACCAATGGAGCAGgtatgaactc ... tgtgtggtagGCGATGCATTCGTTGGAGGATTTTTGTCTCAGTTGGTTCAAGAGAAGCCGA
EST: gi|110381672|gb|EC935088.1|EC935088
EST:     CCCTGTGATCTTGTTACCCAAGGAGAAGCTGGTTGATACCAATGGAGCAG                         GCGATGCATTCGTTGGAGGTTTTTTGTCTCAGTTGGTTCAAGAGAAGCCAA
genomic: CCCTGTGATCTTGTTACCCAAGGAGAAGCTGGTTGATACCAATGGAGCAGgtatgaactc ... tgtgtggtagGCGATGCATTCGTTGGAGGATTTTTGTCTCAGTTGGTTCAAGAGAAGCCGA
EST: gi|71882532|gb|DT031587.1|DT031587
EST:     CCCTGTGATCTTGTTACCCAAGGAGAAGCTGGTTGATACCAATGGAGCAG                         GCGATGCATTCGTTGGAGGATTTTTGTCTCAGTTGGTTCAAGAGAAGCCGA
genomic: CCCTGTGATCTTGTTACCCAAGGAGAAGCTGGTTGATACCAATGGAGCAGgtatgaactc ... tgtgtggtagGCGATGCATTCGTTGGAGGATTTTTGTCTCAGTTGGTTCAAGAGAAGCCGA
EST: gi|110425150|gb|EC991528.1|EC991528
EST:     CCCTGTGATCTTGTTACCCAAGGAGAAGCTGGTTGATACCAATGGAGCAG                         GGGATGCATTCGTTGGAGGTTTTTTGTCTCAGTTGGTTCAAGAGAAGCCTA
genomic: CCCTGTGATCTTGTTACCCAAGGAGAAGCTGGTTGATACCAATGGAGCAGgtatgaactc ... tgtgtggtagGCGATGCATTCGTTGGAGGATTTTTGTCTCAGTTGGTTCAAGAGAAGCCGA
EST: gi|30129613|gb|CB914952.1|CB914952
EST:     CCCTGTGATCTTGTTACCCAAGGAGAAGCTGGTTGATACCAATGGAGCAG                         GCGATGCATTCGTTGGAGGATTTTTGTCTCAGTTGGTTCAAGAGAAGCCGA
genomic: CCCTGTGATCTTGTTACCCAAGGAGAAGCTGGTTGATACCAATGGAGCAGgtatgaactc ... tgtgtggtagGCGATGCATTCGTTGGAGGATTTTTGTCTCAGTTGGTTCAAGAGAAGCCGA
EST: gi|110382513|gb|EC946810.1|EC946810
EST:     CCCTGTGATCTTGTTACCCAAGGAGAAGCTGGTTGATACCAATGGAGCAG                         GCGATGCATTCGTTGGAGGTTTTTTGTCTCAGTTGGTTCAAGAGAAGCCAA
genomic: CCCTGTGATCTTGTTACCCAAGGAGAAGCTGGTTGATACCAATGGAGCAGgtatgaactc ... tgtgtggtagGCGATGCATTCGTTGGAGGATTTTTGTCTCAGTTGGTTCAAGAGAAGCCGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAAGGTGCAGATCCTGTTGTAGTTGCAGAGGATGGAAAAGTGAAGTCATTCCCTGTGATCTTGTTACCCAAGGAGAAGCTGGTTGATACCAATGGAGCAGgtatgaactctcttatttcattattcatgcctagagtgctgaaaatgaccaaccttcataaaggtttgcatcgtattgagattcagtgctcctgtcttct

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaaaatg