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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAAGGAGTTTGTTGTCTTAACAGAGTTGCTCATGAGGCAGTTATTGAAATTGGATGGCATTGAGGCTGAAGGAGAAGCAAAAGTGCAGAGAAGGGCTGAGgttagtagccaatgccagagcgtaactttttttagttaagatattttatccttgtttttcaagcttgttgtagatgtacaattttatattgtttccagga...

Basic information

species Vitis vinifera
transcript Vv08s0058g00130.t01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0058g00130.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GRMZM2G014720_T01 (Zea mays), 5'ss of exon 3
CAAGGAGTTTGTTGTCTTAACAGAGTTGCTCATGAGGCAGTTATTGAAATTGGATGGCATTGAGGCTGAAGGAGAAGCAAAAGTGCAGAGAAGGGCTGAGgttagtagccaatgccagagcgtaactttttttagttaagatattttatccttgtttttcaagcttgttgtagatgtacaattttatattgtt-tccagga--
 || || ||||||||||| || ||| |||| |||| |||| |  ||||| | ||||||||||| ||||||||||||||||  |  ||||| | |||||||||    | | ||      | ||   ||  | ||    ||  |  |  ||| |   |    | || |      ||   | |  |||||  |||  | ||  |  
TAAAGAATTTGTTGTCTTGACGGAGCTGCTTATGATGCAGCTGCTGAAACTCGATGGCATTGAAGCTGAAGGAGAAGCAAGGGCACAGAGGAAGGCTGAGgtacacaactaaac---aatcgctgctgatattttcaaacgtgctacatcttcaatgagaatgcattacagcgactgaaatgtttatgatgtaatgcatcagg

upper sequence: Vv08s0058g00130.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA03G06660.1 (Glycine max), 5'ss of exon 3
CAAGGAGTTTGTTGTCTTAACAGAGTTGCTCATGAGGCAGTTATTGAAATTGGATGGCATTGAGGCTGAAGGAGAAGCAAAAGTGCAGAGAAGGGCTGAGgttagtagcca--atgccagagcgtaactttttttagttaagatattttatccttgtttttcaagcttgttgtagatgtacaattttatattgtttccagga-
 || |||||| ||||  | ||||||||||| ||||| || ||  ||||| ||||||| |||||||| ||||| ||||||||  |||||||||  |||||||| ||||   |  ||     ||    |   ||   | || |  ||| |     || || || ||  |||      |||||    |  ||  ||   |||  | 
GAAAGAGTTTCTTGTGCTGACAGAGTTGCTTATGAGTCAATTGCTGAAACTGGATGGTATTGAGGCAGAAGGTGAAGCAAAGTTGCAGAGAAAAGCTGAGgt-agtatttatgatattgcagttgcaaagttgaaatttgaattatatgtctgttattgttgaaatttgaatcttatgtattggtcaatcatgc--ccaacaa

upper sequence: Vv08s0058g00130.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA01G30910.1 (Glycine max), 5'ss of exon 3
CAAGGAGTTTGTTGTCTTAACAGAGTTGCTCATGAGGCAGTTATTGAAATTGGATGGCATTGAGGCTGAAGGAGAAGCAAAAGTGCAGAGAAGGGCTGAGgttagtagcca--atgccagagc------gtaactttttttagttaagatattttatccttgtttttcaagcttgttgtagatgtacaattttatattgtttccagga
 || |||||| ||||  | |||||| |||| ||||| || ||  ||||| ||||||| |||||||||||||| ||||||||  |||||||||  |||||||| ||||   |  ||   | ||       ||    ||||  | |  |  | | ||||  |||| |||      | |  |  ||| |   || | ||||| |       
GAAAGAGTTTCTTGTGCTGACAGAGCTGCTTATGAGTCAATTGCTGAAACTGGATGGTATTGAGGCTGAAGGTGAAGCAAAGTTGCAGAGAAAAGCTGAGgt-agtatttatgatattacagttgcaaagttgaattttgaaatatatgtctgttattgttgtcttttcccactctatttcatgcaatcttatgtattggt-------

upper sequence: Vv08s0058g00130.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA07G18660.1 (Glycine max), 5'ss of exon 4
CAAGGAGTTTGTTGTCTTAACAGAGTTGCTCATGAGGCAGTTATTGAAATTGGATGGCATTGAGGCTGAAGGAGAAGCAAAAGTGCAGAGAAGGGCTGAGgtta-gtagccaatgccagagcgtaactttttttagttaagatattttatccttgtttttcaagcttgttgtag-atgtacaattttatat-tgtttccagga
||| |||||| |  | |  ||||||||||| |||||||| ||  ||||| ||||| | |||||||||||||| |||| |||  |||||||||  ||||||||   ||      ||  |||   ||    ||      |||   ||| | |  | ||| ||   | || || | | || |||||  |   |  | ||   |   
CAAAGAGTTTTTGATGTCCACAGAGTTGCTTATGAGGCAATTGCTGAAACTGGATAGTATTGAGGCTGAAGGTGAAGTAAAGCTGCAGAGAAAAGCTGAGgtagtgtttatggtgttagaatttataacttaaattctaactaattgtgtattagttatt-gtgtttattttggtatttacaaaatcccacctattagtaa--

upper sequence: Vv08s0058g00130.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA18G43530.1 (Glycine max), 5'ss of exon 6
CAAGGAGTTTGTTGTCTTAACAGAGTTGCTCATGAGGCAGTTATTGAAATTGGATGGCATTGAGGCTGAAGGAG---AAGCAAAAGTGCAGAGAAGGGCTGAGgtta-gtagccaatgccagagcgtaactttttttagttaagatattttatccttgtttttcaagcttgtt---gtagatgtacaattttatattgtttccagga
    |||||| |  | |  ||||||||||| |||||||| ||  ||||| ||||||| |||||||||||||| |   ||| |||  |||||||||  ||||||||   ||      ||  ||||| |  ||   || | || |  |||||     ||  || |   | || ||   |||     | |||   ||||  ||   |   
---AGAGTTTTTGATGTCCACAGAGTTGCTTATGAGGCAATTGCTGAAACTGGATGGTATTGAGGCTGAAGGTGGTGAAGTAAAGCTGCAGAGAAAAGCTGAGgtagtgtttatggtgttagagctt--ctaacttaattttaactatttgtgtattagttattgtgtttattttggtattctcaaaatcccatatatttaatat--

upper sequence: Vv08s0058g00130.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: AT3G51780.1 (Arabidopsis thaliana), 5'ss of exon 3
CAAGGAGTTTGTTGTCTTAACAGAGTTGCTCATGAGGCAGTTATTGAAATTGGATGGCATTGAGGCTGAAGGAGAAGCAAAAGTGCAGAGAAGGGCTGAGgttagtagccaatgccagagcgtaactttttttagttaagatattttatccttgtttttcaagcttgttgtagatgtacaattttatattgtttccagga-
   ||||||||   |     ||||| | || ||||||||| |  | |||||||||||||||||||||||||| || || ||||| ||| | | |||||||||||||   |            |  |||| || ||      ||     |    || ||   ||  | | | |||| ||  | ||    ||  |    | | 
GCGGGAGTTTGACATGGCTGCAGAGCTTCTTATGAGGCAGCTGCTCAAATTGGATGGCATTGAGGCTGAAGGGGACGCTAAAGTACAGCGTAAGGCTGAGgttagttttc------------ttgctttgttaagcatgtttacacggtaagagtgttaatagagt-tggaagatatatgagttgtggtttgtgttggcag

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|46917519|gb|CN546848.1|CN546848
EST:     TGGATGGCATCGAGGCTGAAGGAGAAGCAAAAGTGCAGAGAAGGGCTGAG                         GTTCGACGTGTCCAGAGCCTTGTGGAGATGCTAGACACCCTGAAAGCAAGA
genomic: TGGATGGCATTGAGGCTGAAGGAGAAGCAAAAGTGCAGAGAAGGGCTGAGgttagtagcc ... ccccgaacagGTTCGACGTGTCCAGAGCCTTGTGGAGATGCTAGACACCCTGAAAGCAAGA
EST: gi|29782541|gb|CB347936.2|CB347936
EST:     TGGATGGCATCGAGGCTGAAGGAGAAGCAAGAGTGCAGAGAAGGGCTGAG                         GTTCGACGTGTCCAGAGCCTTGTGGAGATGCTAGACACCCTGAAAGCAAGA
genomic: TGGATGGCATTGAGGCTGAAGGAGAAGCAAAAGTGCAGAGAAGGGCTGAGgttagtagcc ... ccccgaacagGTTCGACGTGTCCAGAGCCTTGTGGAGATGCTAGACACCCTGAAAGCAAGA
EST: gi|33404286|gb|CF209913.1|CF209913
EST:     TGGATGGCATCGAGGCTGAAGGAGAAGCAAAAGTGCAGAGAAGGGCTGAG                         GTTCGACGTGTCCAGAGCCTTGTGGAGATGCTAGACACCCTGAAAGCAAGA
genomic: TGGATGGCATTGAGGCTGAAGGAGAAGCAAAAGTGCAGAGAAGGGCTGAGgttagtagcc ... ccccgaacagGTTCGACGTGTCCAGAGCCTTGTGGAGATGCTAGACACCCTGAAAGCAAGA
EST: gi|30303224|gb|CB980018.1|CB980018
EST:     TGGATGGCATCGAGGCTGAAGGAGAAGCAAAAGTGCAGAGAAGGGCTGAG                         GTTCGACGTGTCCAGAGCCTTGTGGAGGTGCTAGACACCCTGAAAGCAAGA
genomic: TGGATGGCATTGAGGCTGAAGGAGAAGCAAAAGTGCAGAGAAGGGCTGAGgttagtagcc ... ccccgaacagGTTCGACGTGTCCAGAGCCTTGTGGAGATGCTAGACACCCTGAAAGCAAGA
EST: gi|110699931|gb|EE077391.1|EE077391
EST:     TGGATGGCATCGAGGCTGAAGGAGAAGCAAAAGTGCAGAGAAGGGCTGAG                         GTTCGACGTGTCCAGAGCCTTGTGGAGATGCTAGACACCCTGAAAGCAAGA
genomic: TGGATGGCATTGAGGCTGAAGGAGAAGCAAAAGTGCAGAGAAGGGCTGAGgttagtagcc ... ccccgaacagGTTCGACGTGTCCAGAGCCTTGTGGAGATGCTAGACACCCTGAAAGCAAGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAAGGAGTTTGTTGTCTTAACAGAGTTGCTCATGAGGCAGTTATTGAAATTGGATGGCATTGAGGCTGAAGGAGAAGCAAAAGTGCAGAGAAGGGCTGAGgttagtagccaatgccagagcgtaactttttttagttaagatattttatccttgtttttcaagcttgttgtagatgtacaattttatattgtttccagga

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA