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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaacaaattcaaatttatcattcctatgtagtagttgagcacatttagttttcatgaactcgcctagtctgatatttatgtaattttttttttttcatagGAGTCATGCCCTTCTGTAAAAAACATTCTCCTCCTGGATTCTGAAGGAAAACGTGTAGCTGTCAAGTACTATTGTGACGACTGGCCAACAAATAATGCTA

Basic information

species Vitis vinifera
transcript Vv10s0003g02760.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv10s0003g02760.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os02g21250.1 (Oryza sativa), 3'ss of exon 2
aaacaaattcaaatttatcat--tcctatgtagtagttgagcacatttagttttcatgaactcgcctagtctgat-atttatg--taattttttttttttcatagGAGTCATGCCCTTCTGTAAAAAACATTCTCCTCCTGGATTCTGAAGGAAAACGTGTAGCTGTCAAGTACTATTGTGACGACTGGCCAACAAATAATGCTA
        |    || || |   |   ||| || | |     || |||  | | | |        ||  | | || ||| |||  |     ||||  || || |||| || ||||||||||| || |||||| | || |||||||||||||| |||||||| || || || ||||  |  || || ||| | |  |||    | |
-----tgcttttgttgatgaacatgaaatgcagcattaagtaactttttctgtcctttgcacaagctcatgtaatgattcatgattgtccattttcgttacacagGAATCTTGCCCTTCTGTGAAGAACATTTTGCTTCTGGATTCTGAAGGGAAACGTGTTGCCGTGAAATACTTCTCGGATGATTGGTCTAGTAATGCGTCAA

upper sequence: Vv10s0003g02760.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G314679_T06 (Zea mays), 3'ss of exon 2
-----aaacaaattcaaatttatcattcctatgtagtagt-tgagcaca--------tttagttttcatgaact-----cgcctagtctgatatttatgtaat--tttttttttttcatagGAGTCATGCCCTTCTGTAAAAAACATTCTCCTCCTGGATTCTGAAGGAAAACGTGTAGCTGTCAAGTACTATTGTGACGACTGGCCAACAAATAATGCTA
      | |   ||| | ||| |  |||| ||  |  | | |||  ||         |||||| || |   ||      || |   | | ||   |||  | |  | | | | ||||| |||| || ||||||||||| || |||||| | || ||||||||||||||||| ||||| ||||| ||||| |  |  || ||                    
gaagttaccgttttcgattttgt--ttccgataaaaaaatatgaaaacggtaatggttttagtgtttaccgaccgtttccgaccgttttaatccctattcagTGATATGTCTGTTTCACAGGAATCTTGCCCTTCTGTGAAGAACATTTTACTTCTGGATTCTGAAGGAAAGCGTGTTGCTGTAAAGTATTTCTCAGATGAT-------------------

upper sequence: Vv10s0003g02760.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G314679_T05 (Zea mays), 3'ss of exon 2
aaacaaattcaaatttatcattcctatgtagtagttg-agcacatttagttttcatgaact-----cgcctagtctgatatttatgtaat--tttttttttttcatagGAGTCATGCCCTTCTGTAAAAAACATTCTCCTCCTGGATTCTGAAGGAAAACGTGTAGCTGTCAAGTACTATTGTGACGACTGGCCAACAAATAATGCTA
        |    |     |     || |   |   | |     |||||| || |   ||      || |   | | ||   |||  | |  | | | | ||||| |||| || ||||||||||| || |||||| | || ||||||||||||||||| ||||| ||||| ||||| |  |  || || ||||| || |||    | |
--------ttgtttccgataaaaaaatatgaaaacggtaatggttttagtgtttaccgaccgtttccgaccgttttaatccctattcagtgatatgtctgtttcacagGAATCTTGCCCTTCTGTGAAGAACATTTTACTTCTGGATTCTGAAGGAAAGCGTGTTGCTGTAAAGTATTTCTCAGATGATTGGCCGACTAATGCATCAA

upper sequence: Vv10s0003g02760.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT1G60970.1 (Arabidopsis thaliana), 3'ss of exon 1
-------aaacaaattcaaatttatcattcctatgtagtagttgagcacatttagttttcatgaactcgcctagtctgatatttatgtaattttttttttttcatagGAGTCATGCCCTTCTGTAAAAAACATTCTCCTCCTGGATTCTGAAGGAAAACGTGTAGCTGTCAAGTACTATTGTGACGACTGGCCAACAAATAATGCTA
         ||  |||||  ||   |  |   || |  | ||||   |  || | | |   | ||      || |||  |   | |||  |  ||  ||     ||||| |    |||    || ||||||||  | ||  |||||||||||||||| |||||||| || ||||| || |  || |||||||||||||||   ||| 
ttactgttcactgattcatgtt---ctgttacatcttttggttggtgattttcaatatctcttaatct--ttattctatt--ctgtgttttcattacttacatttagGAATTGCCCCCAAAAGTGAAAAACATCTTGCTTTTGGATTCTGAAGGAAAGCGTGTAGCGGTTAAGTATTACTCAGATGACTGGCCAACAAATTCAGCTC

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|351019718|gb|FQ439535.1|FQ439535
EST:     GCGGACAAATTTTCCGGCAAAACCGTCAAACATG                         GAGTCATGCCCTTCTGTAAAAAACATTCTCCTCCTGGATTCTGAAGGAAAA
genomic: GCGGACAAATTTTCCGGCAAAACCGTCAAACATGgtcagttttt ... tttttcatagGAGTCATGCCCTTCTGTAAAAAACATTCTCCTCCTGGATTCTGAAGGAAAA
EST: gi|110373435|gb|EC937671.1|EC937671
EST:     TTCCGGC-AAACCGTCAAACATG                         GAGTCATGCCCTTCTGTAAAAAACATTCTCCTCCTGGATTCTGAAGGAAAA
genomic: TTCCGGCAAAACCGTCAAACATGgtcagttttt ... tttttcatagGAGTCATGCCCTTCTGTAAAAAACATTCTCCTCCTGGATTCTGAAGGAAAA
EST: gi|110379625|gb|EC944835.1|EC944835
EST:     TCCGGCGAAACCGTCAAACATG                         GAGTCATGCCCTTCTGTAAAAAACATTCTCCTCCTGGATTCTGAAGGAAAA
genomic: TCCGGCAAAACCGTCAAACATGgtcagttttt ... tttttcatagGAGTCATGCCCTTCTGTAAAAAACATTCTCCTCCTGGATTCTGAAGGAAAA
EST: gi|110699583|gb|EE076708.1|EE076708
EST:     TTTTCCGGCAAAACCGTCAAACATG                         GAGTCATGCCCTTCTGTAAAAAACATTCTCCTCCTGGATTCTGAAGGAAAA
genomic: TTTTCCGGCAAAACCGTCAAACATGgtcagttttt ... tttttcatagGAGTCATGCCCTTCTGTAAAAAACATTCTCCTCCTGGATTCTGAAGGAAAA
EST: gi|110722790|gb|EE099364.1|EE099364
EST:     ATCGCGGACAAATTTTCCGGCAAAACCGTCAAACATG                         GAGTCATGCCCTTCTGTAAAAAACATTCTCCTCCTGGATTCTGAAGGAAAA
genomic: ATCGCGGACAAATTTTCCGGCAAAACCGTCAAACATGgtcagttttt ... tttttcatagGAGTCATGCCCTTCTGTAAAAAACATTCTCCTCCTGGATTCTGAAGGAAAA
EST: gi|351018368|gb|FQ439180.1|FQ439180
EST:     GCGGACAAATTTTCCGGCAAAACCGTCAAACATG                         GAGTCATGCCCTTCTGTAAAAAACATTCTCCTCCTGGATTCTGAAGGAAAA
genomic: GCGGACAAATTTTCCGGCAAAACCGTCAAACATGgtcagttttt ... tttttcatagGAGTCATGCCCTTCTGTAAAAAACATTCTCCTCCTGGATTCTGAAGGAAAA
EST: gi|351040188|gb|FQ425274.1|FQ425274
EST:     ATCGCGGACAAATTTTCCGGCAAAACCGTCAAACATG                         GAGTCATGCCCTTCTGTAAAAAACATTCTCCTCCTGGATTCTGAAGGAAAA
genomic: ATCGCGGACAAATTTTCCGGCAAAACCGTCAAACATGgtcagttttt ... tttttcatagGAGTCATGCCCTTCTGTAAAAAACATTCTCCTCCTGGATTCTGAAGGAAAA
EST: gi|110701897|gb|EE079989.1|EE079989
EST:     ATCGCGGACAAATTTTCCGGCAAAACCGTCAAACATG                         GAGTCATGCCCTTCTGTAAAAAACATTCTCCTCCTGGATTCTGAAGGAAAA
genomic: ATCGCGGACAAATTTTCCGGCAAAACCGTCAAACATGgtcagttttt ... tttttcatagGAGTCATGCCCTTCTGTAAAAAACATTCTCCTCCTGGATTCTGAAGGAAAA
EST: gi|32250089|gb|CD715908.1|CD715908
EST:     ATCGCGGACAAATTTTCCGGCAAAACCGTCAAACATG                         GAGTCATGCCCTTCTGTAAAAAACATTCTCCTCCTGGATTCTGAAGGAAAA
genomic: ATCGCGGACAAATTTTCCGGCAAAACCGTCAAACATGgtcagttttt ... tttttcatagGAGTCATGCCCTTCTGTAAAAAACATTCTCCTCCTGGATTCTGAAGGAAAA
EST: gi|110686798|gb|EE064846.1|EE064846
EST:     ATCGCGGACAAATTTTCCGGCGAAACCGTCAAACATG                         GAGTCATGCCCTTCTGTAAAAAACATTCTCCTCCTGGATTCTGAAGGAAAA
genomic: ATCGCGGACAAATTTTCCGGCAAAACCGTCAAACATGgtcagttttt ... tttttcatagGAGTCATGCCCTTCTGTAAAAAACATTCTCCTCCTGGATTCTGAAGGAAAA
EST: gi|349832724|gb|FQ422082.1|FQ422082
EST:     GCGGACAAATTTTCCGGCAAAACCGTCAAACATG                         GAGTCATGCCCTTCTGTAAAAAACATTCTCCTCCTGGATTCTGAAGGAAAA
genomic: GCGGACAAATTTTCCGGCAAAACCGTCAAACATGgtcagttttt ... tttttcatagGAGTCATGCCCTTCTGTAAAAAACATTCTCCTCCTGGATTCTGAAGGAAAA
EST: gi|32250057|gb|CD715876.1|CD715876
EST:     ATCGCGGACAAATTTTCCGGCAAAACCGTCAAACATG                         GAGTCATGCCCTTCTGTAAAAAACATTCTCCTCCTGGATTCTGAAGGAAAA
genomic: ATCGCGGACAAATTTTCCGGCAAAACCGTCAAACATGgtcagttttt ... tttttcatagGAGTCATGCCCTTCTGTAAAAAACATTCTCCTCCTGGATTCTGAAGGAAAA
EST: gi|351043288|gb|FQ444009.1|FQ444009
EST:     ATCGCGGACAAATTTTCCGGCAAAACCGTCAAACATG                         GAGTCATGCCCTTCTGTAAAAAACATTCTCCTCCTGGATTCTGAAGGAAAA
genomic: ATCGCGGACAAATTTTCCGGCAAAACCGTCAAACATGgtcagttttt ... tttttcatagGAGTCATGCCCTTCTGTAAAAAACATTCTCCTCCTGGATTCTGAAGGAAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagttttcatgaactcgcctagtctgatatttatgtaattttttttttttcatagGAGTCATGCCCTTCTGTAAAAAACATTCTCCTCCTGGATTCTGAAGGAAAACGTGTAGCTGTCAAGTACTATTGTGACGACTGGCCAACAAATAATGCTA
                     gtctgat  putative branch site (score: 4)
                                      ttttttttttttcat  putative PPT
                   tagtctgatatttatg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaacaaattcaaatttatcattcctatgtagtagttgagcacatttagttttcatgaactcgcctagtctgatatttatgtaattttttttttttcatagGAGTCATGCCCTTCTGTAAAAAACATTCTCCTCCTGGATTCTGAAGGAAAACGTGTAGCTGTCAAGTACTATTGTGACGACTGGCCAACAAATAATGCTA

aaacaaa
- - - - - - - - -tcattcc
- - - - - - - - - - - - - - - - - - - - - - - - - - catgaac