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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acccaaaattgtcaggaagaggtttttttgagtgcaagtactcttacatgttttttgtgaaaccccgtgcattactcaacaaagatttaatgttttccagGAAGAAAATTTGTCGGCTATGAATACAGATCCATGGTACTCAGCTTACCACTATTCACATCCTCCACTTGTTGAAAGATTGGCTGCACTTGATGAACCCG

Basic information

species Vitis vinifera
transcript Vv15s0046g02040.t01
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv15s0046g02040.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: LOC_Os02g45650.1 (Oryza sativa), 3'ss of exon 13
acccaaaattgtcaggaagaggtttttttgagtgcaagtactcttacatgttttttgtgaaaccccgtgcattactcaacaaagatttaatgttttccagGAAGAAAATTTGTCGGCTATGAATACAGATCCATGGTACTCAGCTTACCACTATTCACATCCTCCACTTGTTGAAAGATTGGCTGCACTTGATGAACCCG
 |  |   | |         | |  | |||         ||    |||   |  |||  ||    | |    || |    ||     |      || |||||||| || || || || ||||| |||||||| ||||| ||||| |||||||| || ||||| || |||||||||||  |  |||| ||||| ||  | |
tcgtactgtcggttctcgttgttcgtattgcccttggtcacctgcacaaactgcttgcaaatttgcatagcctaatttggaatttgctttcaaatttcagGAAGAGAACTTATCTGCAATGAACACAGATCCGTGGTATTCAGCCTACCACTACTCCCATCCACCCCTTGTTGAAAGGCTCTCTGCTCTTGAAGACGCAG

upper sequence: Vv15s0046g02040.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GLYMA09G39150.1 (Glycine max), 3'ss of exon 13
acccaaaattgtcaggaagaggttttt---------ttgagtgcaagtactcttacatgttttttgtgaaaccccgtgcattactcaacaaagatttaatgttttccagGAAGAAAATTTGTCGGCTATGAATACAGATCCATGGTACTCAGCTTACCACTATTCACATCCTCCACTTGTTGAAAGATTGGCTGCACTTGATGAACCCG
|     |||| |||        | ||          ||  |||||||||   ||   ||||| | ||||      ||  | | ||| | |     |     ||||| |||| || ||| |||| ||||||||||||||||| |||||||| ||||| |||||||| |||||||| |||||||||||||||||||  || || ||||| |
attttcaattttcactttttattcttcctcgtgtcattttgtgcaagtagattt---tgtttctggtgatgggaagtaaaatgctctata-----tctgcattttc-agGAGGAGAATCTGTCAGCTATGAATACAGATCCTTGGTACTCTGCTTATCACTATTCTCATCCTCCCCTTGTTGAAAGATTGGCTGTGCTGGACGAACCGG

upper sequence: Vv15s0046g02040.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GLYMA18G47190.1 (Glycine max), 3'ss of exon 12
acccaaaattgtcaggaagaggtttttttgagtgcaagtactcttacatgttttttgtgaaaccccgtgcattactcaacaaagattta---atgt-tttccagGAAGAAAATTTGTCGGCTATGAATACAGATCCATGGTACTCAGCTTACCACTATTCACATCCTCCACTTGTTGAAAGATTGGCTGCACTTGATGAACCCG-
      |||| |||        | ||  | | ||| | ||     |      ||||||    ||  |||         | |  ||||||    ||  ||| ||||| || ||| | || ||||||||||||||||| |||||||| ||||| |||||||| |||||||| ||||||||||||||||| || || || ||||| | 
-ttttcaattttcactttttattcttcctca-tgctattatgtgcaaggagattttgtt---cctggtgatgggaagtaaagtgatttatacctgcattttcaggAGGAGAATCTTTCAGCTATGAATACAGATCCTTGGTACTCTGCTTATCACTATTCTCATCCTCCCCTTGTTGAAAGATTGGCCGCGCTGGACGAACCGGA

upper sequence: Vv15s0046g02040.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: AT4G01320.1 (Arabidopsis thaliana), 3'ss of exon 13
acccaaaattgtcaggaagaggtttttttgagtgcaagtactcttacatgttttttgtgaaaccccgtgcattactcaacaaagatttaatgttttccagGAAGAAAATTTGTCGGCTATGAATACAGATCCATGGTACTCAGCTTACCACTATTCACATCCTCCACTTGTTGAAAGATTGGCTGCACTTGATGAACCCG
          |||||  |           ||   |||  ||| |||| |    ||||||    | |   | | | |  |       ||    |||| |||||||| || || || || ||||| || ||||||| |||||||||||| ||||| ||||||||||| |||||||||||  |    ||  |||||| |   |
----------gtcagagaagataacaacagaacacaa--actgttacct-caatttgtg---tcacacacttaaatggattttttgttgggattttgcagGAAGAGAACTTATCAGCAATGAACACTGATCCATTGTACTCAGCTTATCACTACTCACATCCTCCTCTTGTTGAAAGGCTTCGAGCCATTGATGGAGAAG

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|110730873|gb|EE108453.1|EE108453
EST:     AAAAGCTTGGTTATGCTGCAGCACTTCGAGCTGGACTTGTGAAACTGCAG                         GAAGAAAATTTGTCGGCTATGAATACAGATCCATGGTACTCAGCTTACCAC
genomic: AAAAGCTTGGTTATGCTGCAGCACTTCGAGCTGGACTTGTGAAACTGCAGgtaatttatc ... tgttttccagGAAGAAAATTTGTCGGCTATGAATACAGATCCATGGTACTCAGCTTACCAC
EST: gi|351052220|gb|FQ452374.1|FQ452374
EST:     AAAAGCTTGGTTATGCTGCAGCACTTCGAGCTGGACTTGTGAAACTGCAG                         GAAGAAAATTTGTCGGCTATGAATACAGATCCATG
genomic: AAAAGCTTGGTTATGCTGCAGCACTTCGAGCTGGACTTGTGAAACTGCAGgtaatttatc ... tgttttccagGAAGAAAATTTGTCGGCTATGAATACAGATCCATG
EST: gi|110373389|gb|EC937620.1|EC937620
EST:     AAAAGCTTGGTTATGCTGCAGCACTTCGAGCTGGACTTGTGAAACTGCAG                         GAAGAAAATTTGTCGGCTATGAATACAGATCCATGGTACTCAGCTTACCAC
genomic: AAAAGCTTGGTTATGCTGCAGCACTTCGAGCTGGACTTGTGAAACTGCAGgtaatttatc ... tgttttccagGAAGAAAATTTGTCGGCTATGAATACAGATCCATGGTACTCAGCTTACCAC
EST: gi|110391978|gb|EC957064.1|EC957064
EST:     AAAAGCTTGGTTATGCTGCAGCACTTCGAGCTGGACTTGTGAAACTGCAG                         GAAGAAAATTTGTCGGCTATGAATACAGATCCATGGTACTCAGCTTACCAC
genomic: AAAAGCTTGGTTATGCTGCAGCACTTCGAGCTGGACTTGTGAAACTGCAGgtaatttatc ... tgttttccagGAAGAAAATTTGTCGGCTATGAATACAGATCCATGGTACTCAGCTTACCAC
EST: gi|110425833|gb|EC992226.1|EC992226
EST:     AAAAGCTTGGTTATGCTGCAGCACTTCGAGCTGGACTTGTGAAACTGCAG                         GAAGAAAATTTGTCGGCTATGAATACAGATCCATGGTACTCAGCTTACCAC
genomic: AAAAGCTTGGTTATGCTGCAGCACTTCGAGCTGGACTTGTGAAACTGCAGgtaatttatc ... tgttttccagGAAGAAAATTTGTCGGCTATGAATACAGATCCATGGTACTCAGCTTACCAC
EST: gi|110387119|gb|EC951763.1|EC951763
EST:     AAAAGCTTGGTTATGCTGCAGCACTTCGAGCTGGACTTGTGAAACTGCAG                         GAAGAAAATTTGTCGGCTATGAATACAGATCCATGGTACTCAGCTTACCAC
genomic: AAAAGCTTGGTTATGCTGCAGCACTTCGAGCTGGACTTGTGAAACTGCAGgtaatttatc ... tgttttccagGAAGAAAATTTGTCGGCTATGAATACAGATCCATGGTACTCAGCTTACCAC
EST: gi|351033796|gb|FQ447834.1|FQ447834
EST:     AAAAGCTTGGTTATGCTGCAGCACTTCGAGCTGGACTTGTGAAACTGCAG                         GAAGAAAAATTGTCGGCTAAGAATACAGATCC
genomic: AAAAGCTTGGTTATGCTGCAGCACTTCGAGCTGGACTTGTGAAACTGCAGgtaatttatc ... tgttttccagGAAGAAAATTTGTCGGCTATGAATACAGATCC
EST: gi|351044625|gb|FQ443156.1|FQ443156
EST:     AAAAGCTTGGTTATGCTGCAGCACTTCGAGCTGGACTTGTGAAACTGCCG                         GAAGAAAATTTGTCGGCTATGAAT
genomic: AAAAGCTTGGTTATGCTGCAGCACTTCGAGCTGGACTTGTGAAACTGCAGgtaatttatc ... tgttttccagGAAGAAAATTTGTCGGCTATGAAT
EST: gi|351029807|gb|FQ427647.1|FQ427647
EST:     AAAAGCTTGGTTATGCTGCAGCACTTCGAGCTGGACTTGTGAAACTGCAG                         GGAGAAAAATTGTCGG
genomic: AAAAGCTTGGTTATGCTGCAGCACTTCGAGCTGGACTTGTGAAACTGCAGgtaatttatc ... tgttttccagGAAGAAAATTTGTCGG
EST: gi|351052441|gb|FQ452474.1|FQ452474
EST:     AAAAGCTTGGTTATGCTGCAGCACTTCGAGCTGGACTTGTGAAACTGCAG                         GAAGAAAATTTGTCGGCTATGAATACAGATCCATGGTACTCAGCTTACCAC
genomic: AAAAGCTTGGTTATGCTGCAGCACTTCGAGCTGGACTTGTGAAACTGCAGgtaatttatc ... tgttttccagGAAGAAAATTTGTCGGCTATGAATACAGATCCATGGTACTCAGCTTACCAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acatgttttttgtgaaaccccgtgcattactcaacaaagatttaatgttttccagGAAGAAAATTTGTCGGCTATGAATACAGATCCATGGTACTCAGCTTACCACTATTCACATCCTCCACTTGTTGAAAGATTGGCTGCACTTGATGAACCCG
                                             tgttttcc  CT-rich tract
                                   aaagatttaatgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acccaaaattgtcaggaagaggtttttttgagtgcaagtactcttacatgttttttgtgaaaccccgtgcattactcaacaaagatttaatgttttccagGAAGAAAATTTGTCGGCTATGAATACAGATCCATGGTACTCAGCTTACCACTATTCACATCCTCCACTTGTTGAAAGATTGGCTGCACTTGATGAACCCG

-cccaaaa
- - - - - - -aggaaga
- - - - - - - - - - - - - - - - -gcaagta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaacccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtgcatt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - acaaaga