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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aagttcttgtttataggaagcaaaatttatgtagtatctaaataaatattgttctattttgcctttattcacctttgacataaatcgtgaaattgtgtagGCATACATGGTGGAGTTGTATCAAGATACACTTGTAGATCTTCTATTACCAAAGAATGCAAAGCGTTTGAAGCTGGACATTAAGAAAGATTCAAAG

Basic information

species Vitis vinifera
transcript Vv04s0044g02020.t01
intron # 19
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0044g02020.t01 (Vitis vinifera), 3'ss of exon 19
lower sequence: GLYMA11G09480.1 (Glycine max), 3'ss of exon 20
aagttcttgtttataggaagcaaaatttatgtagtatctaaataaatattgttctattttgcctttattcacctttgacataaatc-gtg-aaattgtgtagGCATACATGGTGGAGTTGTATCAAGATACACTTGTAGATCTTCTATTACCAAAGAATGCAAAGCGTTTGAAGCTGGACATTAAGAAAGATTCAAAG
  | | |  | |  ||  |   ||    |   | |  | | ||    | |    | | ||    || |      | ||| |   |  ||    ||  || ||||||| ||| |||| || |||||||||||||||||||||||||| ||||| ||||||||||||||||| ||  |||| |||||||| ||||| |||
tgggtataatgttgagcgacttaaccagaacaaatcacgagatttgcagtagcatgtgtt--tgttgtctgatctagacttctttttgtatgtatgatgcagGCATATATGTTGGAATTATATCAAGATACACTTGTAGATCTTCTGTTACCGAAGAATGCAAAGCGTTTAAAATTGGATATTAAGAAGGATTCCAAG

upper sequence: Vv04s0044g02020.t01 (Vitis vinifera), 3'ss of exon 19
lower sequence: GLYMA01G35950.1 (Glycine max), 3'ss of exon 20
-----aagtt-cttgtttatag-gaagcaaaatttatgtagtatctaaataaatattgttctattttgcctttattcacctttgacataaatcgtgaaattgtgtagGCATACATGGTGGAGTTGTATCAAGATACACTTGTAGATCTTCTATTACCAAAGAATGCAAAGCGTTTGAAGCTGGACATTAAGAAAGATTCAAAG
      |||  |||    |||   || ||  |  | || |||| | |  |   | ||||   || | | |||| ||    |||     |  |      ||  || ||||||| ||| |||| || |||||||||||||||||||||||||| ||||| ||||||||||||||||| ||  |||| |||||||| ||||| |||
atgttgagtgacttaaccataacaaatcatgaggtttgcagtagc-atgtgtttgttgtctgatctagactttttttttttttttttcatct------atgatgcagGCATATATGTTGGAATTATATCAAGATACACTTGTAGATCTTCTGTTACCGAAGAATGCAAAGCGTTTAAAATTGGATATTAAGAAGGATTCCAAG

upper sequence: Vv04s0044g02020.t01 (Vitis vinifera), 3'ss of exon 19
lower sequence: GLYMA16G21340.1 (Glycine max), 3'ss of exon 23
aagttcttgttt-ataggaagcaaaatttatgtagtatctaaataaatattgttctattttgcct--ttattcacctttgacataaatcgtga-aattgtgtagGCATACATGGTGGAGTTGTATCAAGATACACTTGTAGATCTTCTATTACCAAAGAATGCAAAGCGTTTGAAGCTGGACATTAAGAAAGATTCAAAG
  |||||| ||  ||           | |  |   | |  ||||    |  ||| |      | |  ||||     |||||  |   |||||  |||  || ||||||||||||||||||||||||| ||||| ||| |||||||  | ||||||||||||| ||||| ||| ||  |||| || ||||| ||||||| |
--gttctttttccattttcttttttgtcttagagttctgcaaatgttaaaagttttgcaaaacttggttatctttttttgatttc--tcgtgtcaatgatgcagGCATACATGGTGGAGTTGTATCAGGATACCCTTATAGATCTGTTGTTACCAAAGAATGGAAAGCCTTTAAAATTGGATATCAAGAAGGATTCAACG

upper sequence: Vv04s0044g02020.t01 (Vitis vinifera), 3'ss of exon 19
lower sequence: GLYMA09G32740.1 (Glycine max), 3'ss of exon 20
----aagttcttgtttataggaagcaaaatttatgtagtatctaaataaatattgttctattttgcctttattcacctttgacataaatcgtga-aattgtgtagGCATACATGGTGGAGTTGTATCAAGATACACTTGTAGATCTTCTATTACCAAAGAATGCAAAGCGTTTGAAGCTGGACATTAAGAAAGATTCAAAG
    |||||  | ||         |||   |  | |  | | |  | || | |||    |||||    ||||       |||  |   |||||  |||  || ||||||||||||||||||||||||| ||||| ||| |||||||    ||||||||||||| ||||| ||| ||  |||| || ||||| ||||||| |
tgaaaagtttatattgtccttttccaattgtctttttttttgtctaaaagttttgcaaaatttt---cttatcttttgctgatttc--tcgtgtcaatgatgcagGCATACATGGTGGAGTTGTATCAGGATACCCTTATAGATCT---GTTACCAAAGAATGGAAAGCATTTAAAATTGGATATCAAGAAGGATTCAACG

upper sequence: Vv04s0044g02020.t01 (Vitis vinifera), 3'ss of exon 19
lower sequence: AT5G65930.3 (Arabidopsis thaliana), 3'ss of exon 17
aagttcttgtttataggaagcaaaatttatgtagtatctaaataaatattgttctattttgcctttattcacctttgacataaatcgtgaaattgtgtagGCATACATGGTGGAGTTGTATCAAGATACACTTGTAGATCTTCTATTACCAAAGAATGCAAAGCGTTTGAAGCTGGACATTAAGAAAGATTCAAAG
                          | || |  ||||  |||| ||  |||  ||        | |       |    | |||     || || || ||||||| ||||||||  | |||||||| ||||||||||| ||| | |||||||| | |||||  || ||||| || || ||||| ||||||||||||
-------------------------gtaatttgttatcctaatagatgatgtgataaaagattatgacatcaactgactacaaa-----aagttatgcagGCATATATGGTGGAACTTTATCAAGACACACTTGTAGACCTTTTGTTACCAAAAAGTGCAAGACGCTTGAAACTAGAGATTAAAAAAGATTCAAAG

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|71877730|gb|DT026785.1|DT026785
EST:     TTTTTAAGATTATAAGGCGAGATGCCAACAAATTCTCATTCTCGTTAAAG                         GCATACGTGGTGGAGTTGTATCAAGATACACTTGTAGATCTTCTATTACCA
genomic: TTTTTAAGATTATAAAGCGAGATGCCAACAAATTCTCATTCTCGTTAAAGgtaacgtgac ... aattgtgtagGCATACATGGTGGAGTTGTATCAAGATACACTTGTAGATCTTCTATTACCA
EST: gi|71880280|gb|DT029335.1|DT029335
EST:     TTTTTAAGATTATAAAGCGAGATGCCAACAAATTCTCATTCTCGTTAAAG                         GCATACATGGTGGAGTTGTATCAAGATACACTTGTAGATCTTCTATTACCA
genomic: TTTTTAAGATTATAAAGCGAGATGCCAACAAATTCTCATTCTCGTTAAAGgtaacgtgac ... aattgtgtagGCATACATGGTGGAGTTGTATCAAGATACACTTGTAGATCTTCTATTACCA
EST: gi|351015272|gb|FQ445556.1|FQ445556
EST:     TTTTTAAGATTATAAAGCGAGATGCCAACAAATTCTCATTCTCGTTAAAG                         GCATACATGGTGGAGTTGTATCAAGATACACTTGTAGATCTTCTATTACAA
genomic: TTTTTAAGATTATAAAGCGAGATGCCAACAAATTCTCATTCTCGTTAAAGgtaacgtgac ... aattgtgtagGCATACATGGTGGAGTTGTATCAAGATACACTTGTAGATCTTCTATTACCA
EST: gi|351043062|gb|FQ443904.1|FQ443904
EST:     TTTTTAAGATTATAAAGCGAGATGCCAACAAATTCTCATTCTCGTTAAAG                         GCATACATGGTGGAGTTGTATCAAGATACACTTGTAGATCTTCTATTACCA
genomic: TTTTTAAGATTATAAAGCGAGATGCCAACAAATTCTCATTCTCGTTAAAGgtaacgtgac ... aattgtgtagGCATACATGGTGGAGTTGTATCAAGATACACTTGTAGATCTTCTATTACCA
EST: gi|351026499|gb|FQ428511.1|FQ428511
EST:     TTTTTAAGATTATAAAGCGAGATGCCAACAAATTCTCATTCTCGTTAAAG                         GCATACATGGTGGAGTTGTATCAAGATACACTTGTAGATCTTCTATTACCA
genomic: TTTTTAAGATTATAAAGCGAGATGCCAACAAATTCTCATTCTCGTTAAAGgtaacgtgac ... aattgtgtagGCATACATGGTGGAGTTGTATCAAGATACACTTGTAGATCTTCTATTACCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atattgttctattttgcctttattcacctttgacataaatcgtgaaattgtgtagGCATACATGGTGGAGTTGTATCAAGATACACTTGTAGATCTTCTATTACCAAAGAATGCAAAGCGTTTGAAGCTGGACATTAAGAAAGATTCAAAG
                           ctttgac  putative branch site (score: 4)
      ttctatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aagttcttgtttataggaagcaaaatttatgtagtatctaaataaatattgttctattttgcctttattcacctttgacataaatcgtgaaattgtgtagGCATACATGGTGGAGTTGTATCAAGATACACTTGTAGATCTTCTATTACCAAAGAATGCAAAGCGTTTGAAGCTGGACATTAAGAAAGATTCAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - -aagcaaa
- - - - - - - - - - - - - - - - - - - -aaataaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -acataaa