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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttagtttagattgaaatttagaaaaacttgtggttgcaaccactcttgatctggattaattttatatctagttgtcatttctgtacttgatcccctcaagGTACATGATGAGAGAGAAATGGATCGTGTTCTTGGAATAGAAGGGATTGAACTTATTGGCATCAATAACCGTAACCTTG

Basic information

species Vitis vinifera
transcript Vv12s0057g01240.t01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv12s0057g01240.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA02G42680.1 (Glycine max), 3'ss of exon 6
ttagtttagattgaaatttagaaaaacttgtggt-tgcaaccactcttgat-ctggattaattttatatctagttgtcatttctgtacttgatcccctcaagGTACATGATGAGAGAGAAATGGATCGTGTTCTTGGAATAGAAGGGATTGAACTTATTGGCATCAATAACCGTAACCTTG
|||  |  | ||  |   ||   | |  | |    ||||    || ||  | |  ||| ||    |    |  ||| ||||| | |  ||| |       |||| ||||||||||| ||| | ||||||||||||| ||| || |||||||||||||||||||| || |||||||| ||||
ttatctgtgcttacaccataattataggtctaccatgcagaatcttttatttcctgatgaacacgaggattttttgacattt-tatg-ttgcttgttcacagGTTCATGATGAGAGGGAATTTGATCGTGTTCTTGCAATTGAGGGGATTGAACTTATTGGCATTAACAACCGTAATCTTG

upper sequence: Vv12s0057g01240.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA14G05810.3 (Glycine max), 3'ss of exon 7
--ttagtttagattgaaatttagaaaaacttgtggt-tgcaaccactcttgatctggattaattttatatctagttgtcatttctgtacttgatcccctcaagGTACATGATGAGAGAGAAATGGATCGTGTTCTTGGAATAGAAGGGATTGAACTTATTGGCATCAATAACCGTAACCTTG----
  ||| ||  ||||  |   ||     |  | |    ||||  |  |  |   ||| || ||  | | |  |  ||  ||||| | |  |   | | | || ||| ||||||||||| ||| | ||||||||||||| |||||| |||||||| ||||||||||| || ||||| || ||||    
ccttatttgtgattacaccataattctaggtctaccatgcagtcttttatttcctg-atgaacatgagaatttttttacattt-tatgttccttactcaca-gGTTCATGATGAGAGGGAATTTGATCGTGTTCTTGCAATAGAGGGGATTGAGCTTATTGGCATTAACAACCGCAATCTTGGTAT

upper sequence: Vv12s0057g01240.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA14G05810.2 (Glycine max), 3'ss of exon 6
--ttagtttagattgaaatttagaaaaacttgtggt-tgcaaccactcttgatctggattaattttatatctagttgtcatttctgtacttgatcccctcaagGTACATGATGAGAGAGAAATGGATCGTGTTCTTGGAATAGAAGGGATTGAACTTATTGGCATCAATAACCGTAACCTTG
  ||| ||  ||||  |   ||     |  | |    ||||  |  |  |   ||| || ||  | | |  |  ||  ||||| | |  |   | | | || ||| ||||||||||| ||| | ||||||||||||| |||||| |||||||| ||||||||||| || ||||| || ||||
ccttatttgtgattacaccataattctaggtctaccatgcagtcttttatttcctg-atgaacatgagaatttttttacattt-tatgttccttactcaca-gGTTCATGATGAGAGGGAATTTGATCGTGTTCTTGCAATAGAGGGGATTGAGCTTATTGGCATTAACAACCGCAATCTTG

upper sequence: Vv12s0057g01240.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: AT2G04400.1 (Arabidopsis thaliana), 3'ss of exon 6
ttagtttagattgaaatttagaaaaacttgtggttgcaaccactcttgatctggattaattttatatctagttgtcatttctgtacttga-tcccctcaagGTACATGATGAGAGAGAAATGGATCGTGTTCTTGGAATAGAAGGGATTGAACTTATTGGCATCAATAACCGTAACCTTG
   || |   || || |  |  | || || ||       | | |    || | |  || |||| | | |   | | | |    || |||| |  |    ||||||||||||||||||| |||| |||||| |||||||||||||| || || ||| |||||||||||||||| |  ||||
---gtctct-ttcaattagatgacaaattatg-------caagttgaaatttag--tatttttttgtttcactcttaat---atatttgactttcaattagGTACATGATGAGAGAGAGATGGGTCGTGTACTTGGAATAGAAGGAATCGAGCTTGTTGGCATCAATAACCGAAGTCTTG

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|110421432|gb|EC987728.1|EC987728
EST:     GATACATGACTAAGATTTGCAAGATGCTTGGGTTGACAGCACTTGTTGAG                         GTACATGATGAGAGAGAAATGGATCGTGTTCTTGGAATAGAAGGGATTGAA
genomic: GATACATGACTAAGATTTGCAAGATGCTTGGGTTGGCAGCACTTGTTGAGgtatgaatgc ... tcccctcaagGTACATGATGAGAGAGAAATGGATCGTGTTCTTGGAATAGAAGGGATTGAA
EST: gi|110697753|gb|EE075019.1|EE075019
EST:     GATACATGACTAAGATTTGCAAGATGCTTGGGTTGACAGCACTTGTTGAG                         GTACATGATGAGAGAGAAATGGATCGTGTTCTTGGAATAGAAAGGAATGAA
genomic: GATACATGACTAAGATTTGCAAGATGCTTGGGTTGGCAGCACTTGTTGAGgtatgaatgc ... tcccctcaagGTACATGATGAGAGAGAAATGGATCGTGTTCTTGGAATAGAAGGGATTGAA
EST: gi|110691072|gb|EE068758.1|EE068758
EST:     GATACATGACTAAGATTTGCAAGATGCTTGGGTTGGCAGCACTTGTTGAG                         GTACATGATGAGAGAGAAATGGATCGTGTTCTTGGAATAGAAGGGATTGAA
genomic: GATACATGACTAAGATTTGCAAGATGCTTGGGTTGGCAGCACTTGTTGAGgtatgaatgc ... tcccctcaagGTACATGATGAGAGAGAAATGGATCGTGTTCTTGGAATAGAAGGGATTGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgatctggattaattttatatctagttgtcatttctgtacttgatcccctcaagGTACATGATGAGAGAGAAATGGATCGTGTTCTTGGAATAGAAGGGATTGAACTTATTGGCATCAATAACCGTAACCTTG
                                             tcccctc  CT-rich tract
         attaattttatatcta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttagtttagattgaaatttagaaaaacttgtggttgcaaccactcttgatctggattaattttatatctagttgtcatttctgtacttgatcccctcaagGTACATGATGAGAGAGAAATGGATCGTGTTCTTGGAATAGAAGGGATTGAACTTATTGGCATCAATAACCGTAACCTTG

- - - - gattgaaa
- - - - - - - - - -agaaaaa
- - - - - - - - - - - - - - -gtggttg
- - - - - - - - - - - - - - - - - - caaccac