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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...caaataattctgacgaggtttgctggttctggatgaagtttgtggtggtggtctatatatttgagtgatagaacttattctcatcctctgttgcaatcagGTTTTTGACATCACATCTCTACAAATATTCTCTCCGGATGAATTGGATTATTTGCTATGTGGCAGAAGAGAGTTGTGGGAG

Basic information

species Vitis vinifera
transcript Vv03s0038g02340.t01
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv03s0038g02340.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA11G11490.1 (Glycine max), 3'ss of exon 12
caaataattctgacgaggtttg-ctggttctg-gatgaagtttgtggtggtggtctatatatttgagtgatagaacttattctcatcctctgttgcaatcagGTTTTTGACATCACATCTCTACAAATATTCTCTCCGGATGAATTGGATTATTTGCTATGTGGCAGAAGAGAGTTGTGGGAG
  |||| ||   ||  ||     || |||    |||    |   | |     ||| | | | |  |    |   ||||   | | |  ||| ||  | |||||||||||||||| ||||| ||||||| || |||||  | ||| ||||||| ||||| |||||| | ||||| |||||| ||
--aatagttggaacttggaaaaactagtttgatgatttgttcatttgcttgagtccaaaaactaaacatttgtcacttgcccacttgttcttttcaattcagGTTTTTGACATCTCATCTTTACAAATTTTTTCTCCCCAAGAACTGGATTACTTGCTTTGTGGCCGGAGAGAATTGTGGAAG

upper sequence: Vv03s0038g02340.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA12G03640.1 (Glycine max), 3'ss of exon 12
caaataattctgacgaggtttg-ctggttctggatgaagtttgtggtggt---ggtctatatatttgagtgatagaacttattctcatcctctgttgcaatcagGTTTTTGACATCACATCTCTACAAATATTCTCTCCGGATGAATTGGATTATTTGCTATGTGGCAGAAGAGAGTTGTGGGAG
  |||| ||   ||  ||     || |||  |||| |  | |    | |     ||| | | | |  |    |   ||||   | | |  |||  |  | |||||||||||||||| ||||| ||||||| || |||||  | ||| ||||||| ||||| || ||| | ||||| |||||| ||
--aatagtttgaacttggaacaactagtt--ggataatttgttcatttgcttgagtccaaaaactaaacatttgtcactttcccacttgttcttgtcaattcagGTTTTTGACATCTCATCTTTACAAATTTTTTCTCCCCAAGAACTGGATTACTTGCTTTGCGGCCGGAGAGAATTGTGGAAG

upper sequence: Vv03s0038g02340.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: AT4G38600.1 (Arabidopsis thaliana), 3'ss of exon 12
-----------------------------------------------------------------caaataattctgacga-----ggtttgctggttct-------ggatgaagtttgtggtggtggtctatatatttgagtgatagaacttattctcatcctc-tgttgcaatcagGTTTTTGACATCACATCTCTACAAATATTCTCTCCGGATGAATTGGATTATTTGCTATGTGGCAGAAGAGAGTTGTGGGAG
                                                                  | | |||||||  ||     |  ||||   || |       ||  | |  ||    |  |    |   |  || | | | | ||| | |     ||  |   |    ||||||| |||||||| |||||||||||||||||| | ||   |||  |||| |||||||| |||||  | |||||||||||||||
gttaacagtctcgcagactttctgtctctttctttgtctattgcctttggcttctaaacataatatagaaaattctgtagattagagacttgcattttttctttttagggcggaccttaaacttttaccttcatttgttaacttacaaaacctttctgtttctgcacataattatcagGTGTTTGACATAACATCTCTACAAATATTCACCCCTTCTGAGCTGGACTATTTGCTGTGTGGTCGTAGAGAGTTGTGGGAG

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|37185673|gb|CF605026.1|CF605026
EST:     AAACTGGAATTATGCGGCAAATGGAAGCATTTAGATCAGGTTTCAATCAG                         GTTTTTGACATCACATCTCTACAAATATTCTCTCCGGATGAATTGGATTAT
genomic: AAACTGGAATTATGCGGCAAATGGAAGCATTTAGATCAGGTTTCAATCAGgttagcagct ... ttgcaatcagGTTTTTGACATCACATCTCTACAAATATTCTCTCCGGATGAATTGGATTAT
EST: gi|71879155|gb|DT028210.1|DT028210
EST:     AAACTGGAATTATGCGGCAAATGGAAGCATTTAGATCAGGTTTCAATCAG                         GTTTTTGACATCACATCTCTACAAATATTCTCTCCGGATGAATTGGATTAT
genomic: AAACTGGAATTATGCGGCAAATGGAAGCATTTAGATCAGGTTTCAATCAGgttagcagct ... ttgcaatcagGTTTTTGACATCACATCTCTACAAATATTCTCTCCGGATGAATTGGATTAT
EST: gi|37185190|gb|CF604543.1|CF604543
EST:     AAACTGGAATTATGCGGCAAATGGAAGCATTTAGATCAGGTTTCAATCAG                         GTTTTTGACATCACATCTCTACAAATATTCTCTCCGGATGAATTGGATTAT
genomic: AAACTGGAATTATGCGGCAAATGGAAGCATTTAGATCAGGTTTCAATCAGgttagcagct ... ttgcaatcagGTTTTTGACATCACATCTCTACAAATATTCTCTCCGGATGAATTGGATTAT
EST: gi|110376562|gb|EC941621.1|EC941621
EST:     AACTGGAATTATGCGGCAAATGGAAGCATTTAGATCAAGTTTTCA-TCAA                         GTTTTTGACATCACATCTCTACAAATATTCTCTCCGGATGAATTGGATTA
genomic: AACTGGAATTATGCGGCAAATGGAAGCATTTAGATCAGGTTT-CAATCAGgttagcagct ... ttgcaatcagGTTTTTGACATCACATCTCTACAAATATTCTCTCCGGATGAATTGGATTA
EST: gi|161714276|gb|FC064167.1|FC064167
EST:     AAACTGGAATTATGCGGCAAATGGAAGCATTTAGATCAGGTTTCAATCAG                         GTTTTTGACATCACATCTCTACAAATATTCTCTCCGGATGAATTGGATTAT
genomic: AAACTGGAATTATGCGGCAAATGGAAGCATTTAGATCAGGTTTCAATCAGgttagcagct ... ttgcaatcagGTTTTTGACATCACATCTCTACAAATATTCTCTCCGGATGAATTGGATTAT
EST: gi|30126932|gb|CB912271.1|CB912271
EST:     AAACTGGAATTATGCGGCAAATGGAAGCATTTAGATCAGGTTTCAATCAG                         GTTTTTGACATCACATCTCTACAAATATTCTCTCCGGATGAATTGGATTAT
genomic: AAACTGGAATTATGCGGCAAATGGAAGCATTTAGATCAGGTTTCAATCAGgttagcagct ... ttgcaatcagGTTTTTGACATCACATCTCTACAAATATTCTCTCCGGATGAATTGGATTAT
EST: gi|110684682|gb|EE062237.1|EE062237
EST:     AAACTGGAATTATGCGGCAAATGGAAGCATTTAGATCAGGTTTCAATCAG                         GTTTTTGACATTACATCTCTACAAATATTCTCTCCGGATGAATTGGATTAT
genomic: AAACTGGAATTATGCGGCAAATGGAAGCATTTAGATCAGGTTTCAATCAGgttagcagct ... ttgcaatcagGTTTTTGACATCACATCTCTACAAATATTCTCTCCGGATGAATTGGATTAT
EST: gi|110413831|gb|EC979644.1|EC979644
EST:     AAACTGGAATTATGCGGCAAATGGAAGCATTTAGATCAGGTTTCAATCAG                         GTTTTTGACATCACATCTCTACAAATATTCTCTCCGGATGAATTGGATTAT
genomic: AAACTGGAATTATGCGGCAAATGGAAGCATTTAGATCAGGTTTCAATCAGgttagcagct ... ttgcaatcagGTTTTTGACATCACATCTCTACAAATATTCTCTCCGGATGAATTGGATTAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggtggtctatatatttgagtgatagaacttattctcatcctctgttgcaatcagGTTTTTGACATCACATCTCTACAAATATTCTCTCCGGATGAATTGGATTATTTGCTATGTGGCAGAAGAGAGTTGTGGGAG
                                ttctcatcctctgtt  CT-rich tract
      tctatatattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
caaataattctgacgaggtttgctggttctggatgaagtttgtggtggtggtctatatatttgagtgatagaacttattctcatcctctgttgcaatcagGTTTTTGACATCACATCTCTACAAATATTCTCTCCGGATGAATTGGATTATTTGCTATGTGGCAGAAGAGAGTTGTGGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
caaataa
- - - -ttctgac
- - - - - - - - - -ttgctgg
- - - - - - - - - - - - - - ctggatg
- - - - - - - - - - - - - - - - - - - - - -ggtggtg