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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tattttttccttctttcctgatttatggagattattttgaagataagagtctgctaggtttccttatgattttgtatatccactttgaatgaaaacttagGTTGGGTACATCAGATAATCTTCTCCTCTCAATTCAAGAGAAGATAAAGTGGGCAGATACCATGAGTGAGTTGGACAAGAAACACCGAAAGGAAGTCGAA

Basic information

species Vitis vinifera
transcript Vv15s0021g01580.t01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv15s0021g01580.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA15G35760.1 (Glycine max), 3'ss of exon 6
tattttttccttctttcctgatttatggagattattttgaagataagagtctgctaggtttccttatgattttgtatatccactt-tgaatga-aaacttagGTTGGGTACATCAGATAATCTTCTCCTCTCAATTCAAGAGAAGATAAAGTGGGCAGATACCATGAGTGAGTTGGACAAGAAACACCGAAAGGAAGTCGAA
      ||  |  |    | |||| |  | |   |  | |   |  |  | || |     || | |  ||  |  |  |  | |  ||| ||  |||| |||||||  ||||||||| ||||| ||  | |||||||||||||||||||||||||| ||| | ||||||||  | |||||||| ||| | |||||||| |||
ctccaattggtattggtattatttttatacaaagtgctaacttttgggatgtgatta--ctcttcaaaatactaaaatttaattcatgactgggaaacatagGTTGACTACATCAGAAAATCTGCTTGTTTCAATTCAAGAGAAGATAAAGTGGGCTGATGCTATGAGTGAAATTGACAAGAAGCACAGGAAGGAAGTGGAA

upper sequence: Vv15s0021g01580.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA04G34910.1 (Glycine max), 3'ss of exon 6
tattttttccttctttcctgatttatggagattattttgaagataagagtctgctaggtttccttatgattttgtatatccactttgaa--tgaaaacttagGTTGGGTACATCAGATAATCTTCTCCTCTCAATTCAAGAGAAGATAAAGTGGGCAGATACCATGAGTGAGTTGGACAAGAAACACCGAAAGGAAGTCGAA
  |||     |  | |     | | |   | |  |||| | |||  ||    | |    | |   || |||||| |  |  | |    |  |  |||| |||||||  ||||||||| ||||| ||  | |||||||||||||| ||||| ||||| ||| | ||||||||  | || ||||| | | | ||||| || |||
--tttcaaaatggtatatatctatgttctgctattttttaggatttgatcgagtttctctccaaaataattttgaaatttaattcatgactttgaaacatagGTTGTCTACATCAGAAAATCTACTTGTTTCAATTCAAGAGAAAATAAAATGGGCTGATGCTATGAGTGAAATTGAGAAGAAGCGCAGGAAGGATGTGGAA

upper sequence: Vv15s0021g01580.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA18G48710.1 (Glycine max), 3'ss of exon 6
tattttttccttctttcctgatttatgga--gattattttgaagataagagtctgctaggtttccttatgattttgtatatccactttgaa--tgaaaacttagGTTGGGTACATCAGATAATCTTCTCCTCTCAATTCAAGAGAAGATAAAGTGGGCAGATACCATGAGTGAGTTGGACAAGAAACACCGAAAGGAAGTCGAA
   ||||        |    || ||||    | |  |||| | |||  ||    | |    | |   ||  | ||| |  |  | |    |  |  |||| |||||||  ||||||||| ||||| ||  | |||||||||||||| ||||| ||||| ||| | ||||||||  | || ||||| ||| | ||||| || || 
---ttttcaaaatggtatatatctatgttctgctattttttaggatttgatcgagtttctctccaaaatactgttgaaatttaattcatgactttgaaacataGGTTGTCTACATCAGAAAATCTGCTTGTTTCAATTCAAGAGAAAATAAAATGGGCTGATGCTATGAGTGAAATTGAGAAGAAGCACAGGAAGGATGTGGA-

upper sequence: Vv15s0021g01580.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA13G25690.1 (Glycine max), 3'ss of exon 6
tattttttccttctttcctgatttatggagattattttgaagataagagtctgctaggtttccttatgattttgtatatccactt-tgaatga-aaacttagGTTGGGTACATCAGATAATCTTCTCCTCTCAATTCAAGAGAAGATAAAGTGGGCAGATACCATGAGTGAGTTGGACAAGAAACACCGAAAGGAAGTCGAA
  | | |    |   |  || | | ||   |  |  |   |  |    || ||  |    || | |  ||  |  |  |  | |  ||| ||  |||| |||||||  ||||||||| ||| | ||  | |||||||||||||||||||| ||||| ||| | ||||||||  | |||||||| ||| | ||||| || |||
--tgtctcaaattggtaatggtatttgtttaccaagtgctaatttttggtatgtgactcctcttcaaaatactaaaatttaattcatgactgggaaacgtagGTTGTCTACATCAGAAAATATGCTTGTTTCAATTCAAGAGAAGATAAAATGGGCTGATGCAATGAGTGAAATTGACAAGAAGCACAGGAAGGATGTGGAA

upper sequence: Vv15s0021g01580.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: AT1G02090.1 (Arabidopsis thaliana), 3'ss of exon 6
---------------------------tatttttt-ccttct-ttcctgatttatggagattattttgaagataagagt---ctgctag-gtttccttatgattttgtatatccactttgaatgaaaacttagGTTGGGTACATCAGATAATCTTCTCCTCTCAATTCAAGAGAAGATAAAGTGGGCAGATACCATGAGTGAGTTGGACAAGAAACACCGAAAGGAAGTCGAA
                            ||||||| |||||| |  || |||    ||  || |     |  | ||| |     ||||  |    | ||   |||| | | |   |    |||  |    |||||||   || ||||| ||||| ||| | ||||||||||| ||||| || ||||| || |  ||||||||| ||||||| ||||| || |||||||  |||
gtagttttcttcttcccttagatccaggattttttgccttctatatctaattataagaacttgtacgtgatgttagaatacatggctaatgacgtcctactcttttatgtgttggccc-aaattgatgtctagGTTGAACACGTCAGAGAATCTGCTCATTTCAATTCAAGACAAGATCAAATGGGCGGACAATATGAGTGAGATGGACAAAAAACATCGTAAGGAAGCAGAA

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|351022721|gb|FQ428630.1|FQ428630
EST:     GATCTGAGACCCGGGCAACTCGGGTGTATGATTCAAACATTATCAAATTG                         GTTGGGTACATCAGATAATCTTCTCCTCTCAATTTCA-GAGAAGATAAAGT
genomic: GATCTGAGACCCGGGCAACTCGGGTGTATGATTCAAACATTATCAAATTGgtaatatata ... gaaaacttagGTTGGGTACATCAGATAATCTTCTCCTCTCAATT-CAAGAGAAGATAAAGT
EST: gi|351024207|gb|FQ423630.1|FQ423630
EST:     GATCTGAGACCCGGGCAACTCGGGTGTATGATTCAAACATTATCAAATTG                         GTTGGGTACATCAGATAATCTTCTCCTCTCAATTCAAGAGAAGAATAA-GT
genomic: GATCTGAGACCCGGGCAACTCGGGTGTATGATTCAAACATTATCAAATTGgtaatatata ... gaaaacttagGTTGGGTACATCAGATAATCTTCTCCTCTCAATTCAAGAGAAGA-TAAAGT
EST: gi|351030256|gb|FQ432194.1|FQ432194
EST:     GATCTGAGACCCGGGCAACTCGGGTGTATGATTCAAACATTATCAAATTG                         GTTGGGTACATCAGATAATCTTCTCCTCTCAATTCAAGAGAAGATAAAGTG
genomic: GATCTGAGACCCGGGCAACTCGGGTGTATGATTCAAACATTATCAAATTGgtaatatata ... gaaaacttagGTTGGGTACATCAGATAATCTTCTCCTCTCAATTCAAGAGAAGATAAAGTG
EST: gi|161721497|gb|FC069725.1|FC069725
EST:     GATCTGAGACCCGGGCAACTCGGGTGTATGATTCAAACATTATCAAATTG                         GTTGGGTACATCAGATAATCTTCTCCTCTCAATTCAAGAGAAGATAAAGTG
genomic: GATCTGAGACCCGGGCAACTCGGGTGTATGATTCAAACATTATCAAATTGgtaatatata ... gaaaacttagGTTGGGTACATCAGATAATCTTCTCCTCTCAATTCAAGAGAAGATAAAGTG
EST: gi|351028781|gb|FQ433211.1|FQ433211
EST:     GATCTGAGACCCGGGCAACTCGGGTGTATGATTCAAACATTATCAAATTG                         GTTGGGTACATCAGATAATCTTCTCCTCTCAATTCAAGAGAAGATAAAGTG
genomic: GATCTGAGACCCGGGCAACTCGGGTGTATGATTCAAACATTATCAAATTGgtaatatata ... gaaaacttagGTTGGGTACATCAGATAATCTTCTCCTCTCAATTCAAGAGAAGATAAAGTG
EST: gi|352798513|gb|FQ480538.1|FQ480538
EST:     GATCTGAGACCCGGGCAACTCGGGTGTATGATTCAAACATTATCAAATTG                         GTTGAGTACATCAGATAATCTTCTCCTCTCAATTCAAGAGAAGATAAAATG
genomic: GATCTGAGACCCGGGCAACTCGGGTGTATGATTCAAACATTATCAAATTGgtaatatata ... gaaaacttagGTTGGGTACATCAGATAATCTTCTCCTCTCAATTCAAGAGAAGATAAAGTG
EST: gi|351039449|gb|FQ461316.1|FQ461316
EST:     GATCTGAGACCCGGGCAACTCGGGTGTATGATTCATACATTATCAAATTG                         GTTGGGTACATCAGATAATCTTCTCCTCTCAATTCAAGAGAAAATAAAGTG
genomic: GATCTGAGACCCGGGCAACTCGGGTGTATGATTCAAACATTATCAAATTGgtaatatata ... gaaaacttagGTTGGGTACATCAGATAATCTTCTCCTCTCAATTCAAGAGAAGATAAAGTG
EST: gi|352791342|gb|FQ479729.1|FQ479729
EST:     GATCTGAGACCCGGGCAACTCGGGTGTATGATTCAAACATTATCAAATTG                         GTTGAGTACATCAGATAATCTTCTCCTCTCAATT
genomic: GATCTGAGACCCGGGCAACTCGGGTGTATGATTCAAACATTATCAAATTGgtaatatata ... gaaaacttagGTTGGGTACATCAGATAATCTTCTCCTCTCAATT
EST: gi|351025041|gb|FQ433458.1|FQ433458
EST:     GATCTGAGACCCGGGCAACTCGGGTGTATGATTCAAACATTATCAAATTG                         GTTGGGTACATCA
genomic: GATCTGAGACCCGGGCAACTCGGGTGTATGATTCAAACATTATCAAATTGgtaatatata ... gaaaacttagGTTGGGTACATCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agagtctgctaggtttccttatgattttgtatatccactttgaatgaaaacttagGTTGGGTACATCAGATAATCTTCTCCTCTCAATTCAAGAGAAGATAAAGTGGGCAGATACCATGAGTGAGTTGGACAAGAAACACCGAAAGGAAGTCGAA
                  ttatgattttgtatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tattttttccttctttcctgatttatggagattattttgaagataagagtctgctaggtttccttatgattttgtatatccactttgaatgaaaacttagGTTGGGTACATCAGATAATCTTCTCCTCTCAATTCAAGAGAAGATAAAGTGGGCAGATACCATGAGTGAGTTGGACAAGAAACACCGAAAGGAAGTCGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - -tccttct
- - - - - - - ttcctga
- - - - - - - - - - - - - - - - - - - -aagataa
- - - - - - - - - - - - - - - - - - - - - - - -agtctgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tatccac