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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attttcaaaattgataaatggattttgaaagatgtatactgggtgttttctttaatgtaaagagattatcaattacagagtgcaattggataccttgcagGCCCTTGTGGACGCACCTGATATGGTGAGATGCCAAATGAACTTTAAGAGGCTTTCACTCACAGATATCAAAATTGACATCAAAAGGGTGCCTAAGAAAA

Basic information

species Vitis vinifera
transcript Vv05s0049g01310.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0049g01310.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os02g40880.1 (Oryza sativa), 3'ss of exon 2
-------attttcaaaattgataaatggattttgaaagatgtatactg-ggtgttttctttaatgtaaagagattatcaattacagagtgcaattggataccttgcagGCCCTTGTGGACGCACCTGATATGGTGAGATGCCAAATGAACTTTAAGAGGCTTTCACTCACAGATATCAAAATTGACATCAAAAGGGTGCCTAAGAAAA
        || ||     | ||   |  | |  ||   |  |||| ||  ||| |||  ||| ||    || || |   |   | |  | |  |     |||    |||| |||||||| || ||||| ||||| || ||||| || ||||| ||||||||||| || || || ||||| |||||||||||| | || || ||||| |
ctattatgttatcgctgctcatttttctaatcggagttaattatattgtagtgctttgattattg----gatatcacataactctgttttctgtgaatcacc----agGCACTTGTGGATGCTCCTGACATGGTCAGGTGCCAGATCAACTTCAAGAGGCTTTCCCTGACTGACATCAAGATTGACATCAAACGTGTCCCGAAGAAGA

upper sequence: Vv05s0049g01310.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G168330_T02 (Zea mays), 3'ss of exon 2
attttcaaaattgataa-atggattttgaaagatgtatactgggtgttttctttaatgtaaagagattatcaattacagagtgcaattggataccttg---cagGCCCTTGTGGACGCACCTGATATGGTGAGATGCCAAATGAACTTTAAGAGGCTTTCACTCACAGATATCAAAATTGACATCAAAAGGGTGCCTAAGAAAA
  ||  | | || | || ||  ||||    ||  |    ||  ||  ||  |||  | ||   |    | || | |  |  |  |  || || |  ||   ||||| ||||||||||| ||||||||||| || ||||| || ||||| ||  |||| ||||| || || ||||| |||||||||||| | || || |||||  
-gttcgatatttaacaatatatatttgtggagccggtgcctcagtaattgatttggt-taggcattcaagcactcatggccttga--tgcattctatggaccagGCACTTGTGGACGCCCCTGATATGGTCAGGTGCCAGATTAACTTCAAACGGCTCTCACTTACTGACATCAAGATTGACATCAAACGCGTTCCCAAGAAGT

upper sequence: Vv05s0049g01310.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G140116_T01 (Zea mays), 3'ss of exon 2
attttcaaaattgataaatggattttgaaagatgtatactgggtgttttctttaatgtaaagagattatcaa--ttacagagtgcaattggataccttg---cagGCCCTTGTGGACGCACCTGATATGGTGAGATGCCAAATGAACTTTAAGAGGCTTTCACTCACAGATATCAAAATTGACATCAAAAGGGTGCCTAAGAAAA
  | |   ||   ||   ||  ||        | | |      || | |  || || |||  |     ||||     ||  |     ||| || |  ||   ||||| |||||||| || ||||||||||| || |||||  ||||||| ||| |||| ||||| || || ||||| |||||||||||| | || || ||||| |
--tctagcaacctatctctgcgttgccttgattatttgtct--tgctgtaattgat-taatcaagcattcaagccctcatcgccttgttgcattctgtgaaccagGCACTTGTGGATGCCCCTGATATGGTCAGGTGCCAGGTGAACTTCAAGCGGCTCTCACTTACTGACATCAAGATTGACATCAAACGTGTCCCCAAGAAGA

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|27581928|gb|CB004623.1|CB004623
EST:     AAGACTACGGCAGGCTCGTCGTCATAGTCGATGTCATTGATCAGAATCGG                         GCCCTTGTGGACGCACCTGATATGGTGAGATGCCAAATGAACTTTAAGAGG
genomic: AAGACTACGGCAGGCTCGTCGTCATAGTCGACGTCATTGATCAGAATCGGgtatgtgttt ... taccttgcagGCCCTTGTGGACGCACCTGATATGGTGAGATGCCAAATGAACTTTAAGAGG
EST: gi|110690588|gb|EE067820.1|EE067820
EST:     AAGACTACGGCAGGCTCGTCGTCATAGTCGATGTCATTGATCAGAATCGG                         GCCCTTGTGGACGCACCTGATATGGTGAGATGCCAAATGAACTTTAAGAGG
genomic: AAGACTACGGCAGGCTCGTCGTCATAGTCGACGTCATTGATCAGAATCGGgtatgtgttt ... taccttgcagGCCCTTGTGGACGCACCTGATATGGTGAGATGCCAAATGAACTTTAAGAGG
EST: gi|110691773|gb|EE070259.1|EE070259
EST:     AAGACTACGGCAGGCTCGTCGTCATAGTCGATGTCATTGATCAGAATCGG                         GCCCTTGTGGACGCACCTGATATGGTGAGATGCCAAATGAACTTTAAGAGG
genomic: AAGACTACGGCAGGCTCGTCGTCATAGTCGACGTCATTGATCAGAATCGGgtatgtgttt ... taccttgcagGCCCTTGTGGACGCACCTGATATGGTGAGATGCCAAATGAACTTTAAGAGG
EST: gi|110693797|gb|EE070342.1|EE070342
EST:     AGTCGATGTCATTGATCAGAATCGG                         GCCCTTGTGGACGCACCTGATATGGTGAGATGCCAAATGAACTTTAAGAGG
genomic: AGTCGACGTCATTGATCAGAATCGGgtatgtgttt ... taccttgcagGCCCTTGTGGACGCACCTGATATGGTGAGATGCCAAATGAACTTTAAGAGG
EST: gi|110397687|gb|EC963510.1|EC963510
EST:     AAGACTACGGCAGGCTCGTCGTCATAGTCGATGTCATTGATCAGAATCGG                         GCCCTTGTGGACGCACCTGATATGGTGAGATGCCAAATGAACTTTAAGAGG
genomic: AAGACTACGGCAGGCTCGTCGTCATAGTCGACGTCATTGATCAGAATCGGgtatgtgttt ... taccttgcagGCCCTTGTGGACGCACCTGATATGGTGAGATGCCAAATGAACTTTAAGAGG
EST: gi|110724784|gb|EE100916.1|EE100916
EST:     AAGACTACGGCAGGCTCGTCGTCATAGTCGATGTCATTGATCAGAATCGG                         GCCCTTGTGGACGCACCTGATATGGTGAGATGCCAAATGAACTTTAAGAGG
genomic: AAGACTACGGCAGGCTCGTCGTCATAGTCGACGTCATTGATCAGAATCGGgtatgtgttt ... taccttgcagGCCCTTGTGGACGCACCTGATATGGTGAGATGCCAAATGAACTTTAAGAGG
EST: gi|71879325|gb|DT028380.1|DT028380
EST:     AAGACTACGGCAGGCTCGTCGTCATAGTCGATGTCATTGATCAGAATCGG                         GCCCTTGTGGACGCACCTGATATGGTGAGATGCCAAATGAACTTTAAGAGG
genomic: AAGACTACGGCAGGCTCGTCGTCATAGTCGACGTCATTGATCAGAATCGGgtatgtgttt ... taccttgcagGCCCTTGTGGACGCACCTGATATGGTGAGATGCCAAATGAACTTTAAGAGG
EST: gi|77588138|gb|DV223280.1|DV223280
EST:     AAGACTACGGCAGGCTCGTCGTCATAGTCGATGTCATTGATCAGAATCGG                         GCCCTTGTGGACGCACCTGATATGGTGAGATGCCAAATGAACTTTAAGAGG
genomic: AAGACTACGGCAGGCTCGTCGTCATAGTCGACGTCATTGATCAGAATCGGgtatgtgttt ... taccttgcagGCCCTTGTGGACGCACCTGATATGGTGAGATGCCAAATGAACTTTAAGAGG
EST: gi|71883824|gb|DT032879.1|DT032879
EST:     AAGACTACGGCAGGCTCGTCGTCATAGTCGATGTCATTGATCAGAATCGG                         GCCCTTGTGGACGCACCTGATATGGTGAGATGCCAAATGAACTTTAAGAGG
genomic: AAGACTACGGCAGGCTCGTCGTCATAGTCGACGTCATTGATCAGAATCGGgtatgtgttt ... taccttgcagGCCCTTGTGGACGCACCTGATATGGTGAGATGCCAAATGAACTTTAAGAGG
EST: gi|110375750|gb|EC940763.1|EC940763
EST:     AAGACTACGGCAGGCTCGTCGTCATAGTCGATGTCATTGATCAGAATCGG                         GCCCTTGTGGACGCACCTGATATGGTGAGATGCCAAATGAACTTTAAGAGG
genomic: AAGACTACGGCAGGCTCGTCGTCATAGTCGACGTCATTGATCAGAATCGGgtatgtgttt ... taccttgcagGCCCTTGTGGACGCACCTGATATGGTGAGATGCCAAATGAACTTTAAGAGG
EST: gi|110689055|gb|EE064943.1|EE064943
EST:     AAGACTACGGCAGGCTCGTCGTCATAGTCGATGTCATTGATCAGAATCGG                         GCCCTTGTGGACGCACCTGATATGGTGAGATGCCAAATGAACTTTAAGAGG
genomic: AAGACTACGGCAGGCTCGTCGTCATAGTCGACGTCATTGATCAGAATCGGgtatgtgttt ... taccttgcagGCCCTTGTGGACGCACCTGATATGGTGAGATGCCAAATGAACTTTAAGAGG
EST: gi|34320490|gb|CF373244.1|CF373244
EST:     AAGACTACGGCAGGCTCGTCGTCATAGTCGATGTCATTGATCAGAATCGG                         GCCCTTGTGGACGCACCTGATATGGTGAGATGCCAAATGAACTTTAAGAGG
genomic: AAGACTACGGCAGGCTCGTCGTCATAGTCGACGTCATTGATCAGAATCGGgtatgtgttt ... taccttgcagGCCCTTGTGGACGCACCTGATATGGTGAGATGCCAAATGAACTTTAAGAGG
EST: gi|110695806|gb|EE074247.1|EE074247
EST:     AAGACTACGGCAGGCTCGTCGTCATAGTCGATGTCATTGATCAGAATCGG                         GCCCTTGTGGACGCACCTGATATGGTGAGATGCCAAATGAACTTTAAGAGG
genomic: AAGACTACGGCAGGCTCGTCGTCATAGTCGACGTCATTGATCAGAATCGGgtatgtgttt ... taccttgcagGCCCTTGTGGACGCACCTGATATGGTGAGATGCCAAATGAACTTTAAGAGG
EST: gi|110708991|gb|EE084059.1|EE084059
EST:     AAGACTACGGCAGGCTCGTCGTCATAGTCGATGTCATTGATCAGAATCGG                         GCCCTTGTGGACGCACCTGATATGGTGAGATGCCAAATGAACTTTAAGAGG
genomic: AAGACTACGGCAGGCTCGTCGTCATAGTCGACGTCATTGATCAGAATCGGgtatgtgttt ... taccttgcagGCCCTTGTGGACGCACCTGATATGGTGAGATGCCAAATGAACTTTAAGAGG
EST: gi|27584222|gb|CB006917.1|CB006917
EST:     AAGACTACGGCAGGCTCGTCGTCATAGTCGATGTCATTGATCAGAATCGG                         GCCCTTGTGGACGCACCTGATATGGTGAGATGCCAAATGAACTTTAAGAGG
genomic: AAGACTACGGCAGGCTCGTCGTCATAGTCGACGTCATTGATCAGAATCGGgtatgtgttt ... taccttgcagGCCCTTGTGGACGCACCTGATATGGTGAGATGCCAAATGAACTTTAAGAGG
EST: gi|110731703|gb|EE106347.1|EE106347
EST:     AAGACTACGGCAGGCTCGTCGTCATAGTCGATGTCATTGATCAGAATCGG                         GCCCTTGTGGACGCACCTGATATGGTGAGATGCCAAATGAACTTTAAGAGG
genomic: AAGACTACGGCAGGCTCGTCGTCATAGTCGACGTCATTGATCAGAATCGGgtatgtgttt ... taccttgcagGCCCTTGTGGACGCACCTGATATGGTGAGATGCCAAATGAACTTTAAGAGG
EST: gi|110705265|gb|EE081950.1|EE081950
EST:     AAGACTACGGCAGGCTCGTCGTCATAGTCGATGTCATTGATCAGAATCGG                         GCCCTTGTGGACGCACCTGATATGGTGAGATGCCAAATGAACTTTAAGAGG
genomic: AAGACTACGGCAGGCTCGTCGTCATAGTCGACGTCATTGATCAGAATCGGgtatgtgttt ... taccttgcagGCCCTTGTGGACGCACCTGATATGGTGAGATGCCAAATGAACTTTAAGAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttctttaatgtaaagagattatcaattacagagtgcaattggataccttgcagGCCCTTGTGGACGCACCTGATATGGTGAGATGCCAAATGAACTTTAAGAGGCTTTCACTCACAGATATCAAAATTGACATCAAAAGGGTGCCTAAGAAAA
    ctttaat  putative branch site (score: 4)
     tttaatgtaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attttcaaaattgataaatggattttgaaagatgtatactgggtgttttctttaatgtaaagagattatcaattacagagtgcaattggataccttgcagGCCCTTGTGGACGCACCTGATATGGTGAGATGCCAAATGAACTTTAAGAGGCTTTCACTCACAGATATCAAAATTGACATCAAAAGGGTGCCTAAGAAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - tcaaaat
- - - - - - - -aaatgga
- - - - - - - - - - - - -tgaaaga
- - - - - - - - - - - - - - - - - -atactgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaagaga