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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gctctttgttgagcatgatgtatatcttttgaatgtgatgtggttcctttcttccaagaaggatttttctaatttctaataatacaagaatgatttacagCATGGTAGCTGATGTCCACCGCACATTACTTTACGGTGGTATCTTTTTGTACCCTGCTGATAAGAAGAGCCCCAACGGAAAACTGCG

Basic information

species Vitis vinifera
transcript Vv18s0072g00770.t01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0072g00770.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: LOC_Os05g36270.1 (Oryza sativa), 3'ss of exon 8
---gctctttgttgagcatga-tgtatatcttt----tgaatg-tgatgtggttcctttcttccaagaaggatttttctaatttctaataatacaagaatgatttacagCATGGTAGCTGATGTCCACCGCACATTACTTTACGGTGGTATCTTTTTGTACCCTGCTGATAAGAAGAGCCCCAACGGAAAACTGCG
    |  ||  ||||   ||| ||    |  ||    |||||  |||  ||     ||| ||          ||  |||  ||    ||  | ||          |||| ||||| |||||||||||||| || || || || || || || |||||||||||||| ||| |||||||||| ||||||||||| ||
cttacagttatttgaatttgaatgctctttcttacactgaatactgaactgaacatttttttggttatgttgttgctctgcttctggatggtcca---------cacagTATGGTTGCTGATGTCCACCGTACTTTGCTATATGGAGGCATATTTTTGTACCCTGCGGATCAGAAGAGCCCAAACGGAAAACTTCG

upper sequence: Vv18s0072g00770.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: LOC_Os05g36270.3 (Oryza sativa), 3'ss of exon 8
---gctctttgttgagcatga-tgtatatcttt----tgaatg-tgatgtggttcctttcttccaagaaggatttttctaatttctaataatacaagaatgatttacagCATGGTAGCTGATGTCCACCGCACATTACTTTACGGTGGTATCTTTTTGTACCCTGCTGATAAGAAGAGCCCCAACGGAAAACTGCG-------------
    |  ||  ||||   ||| ||    |  ||    |||||  |||  ||     ||| ||          ||  |||  ||    ||  | ||          |||| ||||| |||||||||||||| || || || || || || || |||||||||||||| ||| |||||||||| ||||||||||| ||             
cttacagttatttgaatttgaatgctctttcttacactgaatactgaactgaacatttttttggttatgttgttgctctgcttctggatggtcca---------cacagTATGGTTGCTGATGTCCACCGTACTTTGCTATATGGAGGCATATTTTTGTACCCTGCGGATCAGAAGAGCCCAAACGGAAAACTTCGGTATGCTGATGCA

upper sequence: Vv18s0072g00770.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: LOC_Os01g64660.1 (Oryza sativa), 3'ss of exon 9
-----------------------------------------------------------------gctctttgttgagcatgatgtatatcttttgaatgtgatgtggttcctttcttccaagaaggatttttctaatttctaataatacaagaatgatttacagCATGGTAGCTGATGTCCACCGCACATTACTTTACGGTGGTATCTTTTTGTACCCTGCTGATAAGAAGAGCCCCAACGGAAAACTGCG-------------
                                                                  | || ||||| |  | ||  |  | | |  |||  |||||  |  |      ||||  |  ||| |  | |    || |  | |  || |||||| ||| ||||| |||||||||||||| || || || || || ||  | |||||||||||||| || ||||||||||| || |||||||| ||             
gtgatcattttttttgggtgacaatgtatataacctagctgtagttattaataggagcttttttgaccctctgttgtgattcataaaagtttct--aataggatgtaatcacca----ccaattaacattgtagtgacag-tattgcttcctga-tgatttgcagTATGGTTGCTGATGTCCACCGTACGTTGCTATATGGAGGAGTATTTTTGTACCCTGCAGACAAGAAGAGCCCAAATGGAAAACTCCGGTACACATTAAGC

upper sequence: Vv18s0072g00770.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: LOC_Os01g64660.4 (Oryza sativa), 3'ss of exon 7
-----------------------------------------------------------------gctctttgttgagcatgatgtatatcttttgaatgtgatgtggttcctttcttccaagaaggatttttctaatttctaataatacaagaatgatttacagCATGGTAGCTGATGTCCACCGCACATTACTTTACGGTGGTATCTTTTTGTACCCTGCTGATAAGAAGAGCCCCAACGGAAAACTGCG
                                                                  | || ||||| |  | ||  |  | | |  |||  |||||  |  |      ||||  |  ||| |  | |    || |  | |  || |||||| ||| ||||| |||||||||||||| || || || || || ||  | |||||||||||||| || ||||||||||| || |||||||| ||
gtgatcattttttttgggtgacaatgtatataacctagctgtagttattaataggagcttttttgaccctctgttgtgattcataaaagtttct--aataggatgtaatcacca----ccaattaacattgtagtgacag-tattgcttcctga-tgatttgcagTATGGTTGCTGATGTCCACCGTACGTTGCTATATGGAGGAGTATTTTTGTACCCTGCAGACAAGAAGAGCCCAAATGGAAAACTCCG

upper sequence: Vv18s0072g00770.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GRMZM2G322953_T03 (Zea mays), 3'ss of exon 7
gctctttgt-tgagcatgatgtatatcttttgaatgtgatgtggttcctttcttccaagaaggatttttcta-atttctaataatacaagaatgatttacagCATGGTAGCTGATGTCCACCGCACATTACTTTACGGTGGTATCTTTTTGTACCCTGCTGATAAGAAGAGCCCCAACGGAAAACTGCG
 || || || |   |  | | | |   | ||   | |  | |   |       |  ||      || || |  | || |  |  |    ||||| ||| ||| ||||| ||||||||||| ||||| ||||| ||||| || || ||||||||||| || ||  ||||||| || ||||| ||||| ||
-ctattggtatctactcgtttttttcttctttttttttgtttaactaaaacggttgaatctatgttgttgtggacttgtggtcct-tgtgaatggtttgcagTATGGTTGCTGATGTCCATCGCACCTTACTATACGGGGGCATATTTTTGTACCCAGCAGACCAGAAGAGTCCAAACGGGAAACTACG

upper sequence: Vv18s0072g00770.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GRMZM5G836250_T03 (Zea mays), 3'ss of exon 8
---------------------------------------------------------------------gctctttgttgagcatgatgtata-----tcttttgaatgtgatgtggttcctttcttccaagaaggatttttctaatttctaataata--caagaatgatttacagCATGGTAGCTGATGTCCACCGCACATTACTTTACGGTGGTATCTTTTTGTACCCTGCTGATAAGAAGAGCCCCAACGGAAAACTGCG
                                                                     ||  |||    |  | || | ||       || ||||  |   | |  | |      |  || |      |  || ||   |  | ||         | ||| |||| ||||| ||||| || ||||| || || || ||||| ||| | |||||||||||||||||  |||||| ||| |||||||| || ||
gtgagtcgatcgatcgatctttcactatagatctccaccagtacaaaaatgaatgaacgtatgcatgcggccgtttacatatgacgaaggatgatggtactgttgatagctttatactgcaacgactaaaacacactactcgctgatcgatgctgatggtttgcttttattaacagTATGGTTGCTGACGTGCACCGTACCTTGCTATACGGCGGTGTGTTTTTGTACCCTGCTGACGAGAAGAACCCAAACGGAAAGCTCCG

upper sequence: Vv18s0072g00770.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA16G28310.1 (Glycine max), 3'ss of exon 10
gctctttgttgagcatgatgtatatcttttgaatgtgatgtggttcctttcttccaagaaggatttttctaatttctaataatacaagaatgatttaca------gCATGGTAGCTGATGTCCACCGCACATTACTTTACGGTGGTATCTTTTTGTACCCTGCTGATAAGAAGAGCCCCAACGGAAAACTGCG
  |  |  |  |  |   | ||   |  |||||||||        |       ||||||   | |||| |  | |   | | ||  | |    | ||||      |||||||||||||||| || || || || ||||| || || |||||||||||||||||||| || || || || || |||||||| ||
--ttctcatgaactactgtctactgcacttgaatgtggc----cacagaatgaccaagattaactttttttttcttccaaattatgacatctgtatacatgaacagCATGGTAGCTGATGTTCATCGTACGTTGCTTTATGGAGGCATCTTTTTGTACCCTGCTGACAAAAAAAGTCCAAATGGAAAACTTCG

upper sequence: Vv18s0072g00770.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: PP1S385_43V6.1 (Physcomitrella patens), 3'ss of exon 8
---------------------------------------------------------gctctttgttgagcatgatgtatatcttttgaatgtgatgtggttcctttcttccaagaaggatttttctaatttctaataa----------tacaagaatgattta-cagCATGGTAGCTGATGTCCACCGCACATTACTTTACGGTGGTATCTTTTTGTACCCTGCTGATAAGAAGAGCCCCAACGGAAAACTGCG
                                                         || ||  | |    | |||  | |||    || |   | |   ||  | || |  | |    || |   |  || |   ||           | |  |  |  |||  ||| |||||||| || || ||| | ||  | || ||||| ||||||||| ||||||||| ||| |||||||||||||| ||||| ||  |
gtacaagcacgattgtgtacacaaaactctcatttcctacaattgcacagcaaaaatgcactcgggtacata-gatcaagatcggg-gactagaaagctctttatatcatatacgtgatatctaattgcttcccggtatgattctctgttgcgggtttattttttcagTATGGTAGCGGACGTTCACAGAACTCTTCTATACGGAGGTATCTTTATGTACCCTGGTGACAAGAAGAGCCCCAAGGGAAAGCTCAG

upper sequence: Vv18s0072g00770.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: EFJ36627 (Selaginella moellendorffii), 3'ss of exon 8
gctctttgttgagcatgatgtatatcttttgaatgtgatgtggttcctttcttccaagaaggatttttctaatttctaataatacaagaatgatttacagCATGGTAGCTGATGTCCACCGCACATTACTTTACGGTGGTATCTTTTTGTACCCTGCTGATAAGAAGAGCCCCAACGGAAAACTGCG
                                                                                  |  ||   ||||||  || ||||||||||||||||| |||||| |  | |||||||| || ||  ||||||| ||||| || |||||||||   |||||| | ||
---------------------------------------------------------------------------------gtcaaactttgatttttagTATGGTAGCTGATGTCCATCGCACACTTTTGTACGGTGGAATTTTCATGTACCCAGCTGACAAAAAGAGCCCCTTTGGAAAATTACG

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|32247391|gb|CD713210.1|CD713210
EST:     AAGTTCCCCAAAGATGGTTCATCACCAAAATCTCTACGATACATTGGAAG                         CATGGTAGCTGATGTCCACCGCACATTACTTTACGGTGGTATCTTTTTGTA
genomic: AAGTTCCCCAAAGATGGTTCATCACCAAAATCTCTACGATACATTGGAAGgtatcatgaa ... tgatttacagCATGGTAGCTGATGTCCACCGCACATTACTTTACGGTGGTATCTTTTTGTA
EST: gi|32271549|gb|CD720708.1|CD720708
EST:     AAGTTCCCCAAAGATGGTTCATCACCAAAATCTCTACGATACATTGGAAG                         CATGGTAGCTGATGTCCACCGCACATTACTTTACGGTGGTATCTTTTTGTA
genomic: AAGTTCCCCAAAGATGGTTCATCACCAAAATCTCTACGATACATTGGAAGgtatcatgaa ... tgatttacagCATGGTAGCTGATGTCCACCGCACATTACTTTACGGTGGTATCTTTTTGTA
EST: gi|32267853|gb|CD717012.1|CD717012
EST:     AAGTTCCCCAAAGATGGTTCATCACCAAAATCTCTACGATACATTGGAAG                         CATGGTAGCTGATGTCCACCGCACATTACTTTACGGTGGTATCTTTTTGTA
genomic: AAGTTCCCCAAAGATGGTTCATCACCAAAATCTCTACGATACATTGGAAGgtatcatgaa ... tgatttacagCATGGTAGCTGATGTCCACCGCACATTACTTTACGGTGGTATCTTTTTGTA
EST: gi|32270796|gb|CD719955.1|CD719955
EST:     AAGTTCCCCAAAGATGGTTCATCACCAAAATCTCTACGATACATTGGAAG                         CATGGTAGCTGATGTCCACCGCACATTACTTTACGGTGGTATCTTTTTGTA
genomic: AAGTTCCCCAAAGATGGTTCATCACCAAAATCTCTACGATACATTGGAAGgtatcatgaa ... tgatttacagCATGGTAGCTGATGTCCACCGCACATTACTTTACGGTGGTATCTTTTTGTA
EST: gi|110361485|gb|EC924959.1|EC924959
EST:     AAGTTCCCCAAAGATGGTTCATCACCAAAATCTCTACGATACATTGGAAG                         CATGGTAGCTGATGTCCACCGCACATTACTTTACGGTGGTATCTTTTTGTA
genomic: AAGTTCCCCAAAGATGGTTCATCACCAAAATCTCTACGATACATTGGAAGgtatcatgaa ... tgatttacagCATGGTAGCTGATGTCCACCGCACATTACTTTACGGTGGTATCTTTTTGTA
EST: gi|30324923|gb|CD008185.1|CD008185
EST:     AAGTTCCCCAAAGATGGTTCATCACCAAAATCTCTACGATACATTGGAAG                         CATGGTAGCTGATGTCCACCGCACATTACTTTACGGTGGTATCTTTTTGTA
genomic: AAGTTCCCCAAAGATGGTTCATCACCAAAATCTCTACGATACATTGGAAGgtatcatgaa ... tgatttacagCATGGTAGCTGATGTCCACCGCACATTACTTTACGGTGGTATCTTTTTGTA
EST: gi|32270921|gb|CD720080.1|CD720080
EST:     AAGTTCCCCAAAGATGGTTCATCACCAAAATCTCTACGATACATTGGAAG                         CATGGTAGCTGATGTCCACCGCACATTACTTTACGGTGGTATCTTTTTGTA
genomic: AAGTTCCCCAAAGATGGTTCATCACCAAAATCTCTACGATACATTGGAAGgtatcatgaa ... tgatttacagCATGGTAGCTGATGTCCACCGCACATTACTTTACGGTGGTATCTTTTTGTA
EST: gi|110371021|gb|EC934722.1|EC934722
EST:     AAGTTCCCCAAAGATGGTTCATCACCAAAATCTCTACGATACATTGGAAG                         CATGGTAGCTGATGTCCACCGCACATTACTTTACGGTGGTATCTTTTTGTA
genomic: AAGTTCCCCAAAGATGGTTCATCACCAAAATCTCTACGATACATTGGAAGgtatcatgaa ... tgatttacagCATGGTAGCTGATGTCCACCGCACATTACTTTACGGTGGTATCTTTTTGTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cctttcttccaagaaggatttttctaatttctaataatacaagaatgatttacagCATGGTAGCTGATGTCCACCGCACATTACTTTACGGTGGTATCTTTTTGTACCCTGCTGATAAGAAGAGCCCCAACGGAAAACTGCG
                            ttctaat  putative branch site (score: 2)
                 atttttctaatttcta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gctctttgttgagcatgatgtatatcttttgaatgtgatgtggttcctttcttccaagaaggatttttctaatttctaataatacaagaatgatttacagCATGGTAGCTGATGTCCACCGCACATTACTTTACGGTGGTATCTTTTTGTACCCTGCTGATAAGAAGAGCCCCAACGGAAAACTGCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - gcatgat
- - - - - - - - - - - - - - - gaatgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - agaagga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -acaagaa