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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aatagaagatgatcttttaaaattggatcactgtgtgagaggagttgtctttattttggtttctctgactgaagtggagtggcttcaaattgttttgtagGTGTTTTTGAGAAAGTAGGAATTGAACCACAAGTGCAAAGGATTGGTAAATACAAAAGTGCAGGGGATCAACTTACACGCAAAACGATGTCTGAAGAAAA

Basic information

species Vitis vinifera
transcript Vv17s0000g04680.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv17s0000g04680.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G122843_T02 (Zea mays), 3'ss of exon 3
aatagaagatgatcttttaaaattggatcactgtgtgagaggagttgtctttattttggtttctctgactgaagtggagtggcttcaaattgttttgt--agGTGTTTTTGAGAAAGTAGGAATTGAACCACAAGTGCAAAGGATTGGTAAATACAAAAGTGCAGGGGATCAACTTACACGCAAAACGATGTCTGAAGAAAA
 | ||  | | ||  |||| | ||   |  |      | |  | ||   |  | |   ||| ||||||  | | |  | |   ||||||||   | |   ||||||  |||||||||| |||||||||||  || | ||||| |||||||||||||||||||| || ||||||||| ||||||| |  |||||  | |||  
tacagttggtcatactttacattttattatcccacacacataacttaaatgcagta-agttcctctgagggta-tctaataatttcaaattccatcggtaagGTGTCCTTGAGAAAGTTGGAATTGAACCGGAAATTCAAAGAATTGGTAAATACAAAAGTGCCGGAGATCAACTTGCACGCAAGAGCATGTCAAATGAAGT

upper sequence: Vv17s0000g04680.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA17G09020.1 (Glycine max), 3'ss of exon 3
aatagaagatgatcttttaaaattggatcactgtgtgagaggagttgtct--ttattttggtt--tctctgactgaagtggagtggcttcaaattgttttgt-agGTGTTTTTGAGAAAGTAGGAATTGAACCACAAGTGCAAAGGATTGGTAAATACAAAAGTGCAGGGGATCAACTTACACGCAAAACGATGTCTGAAGAAAA
    ||    | ||| |  |  | ||| ||      ||     ||| | |  | | | | |||   ||   ||| |  |    || | |  | |  || | | ||||||||| |||||  | |||||||||||| ||||| |||||||||| ||||||||||||| ||| ||||||||||| || ||||| |||||||||||  |
----gacaccggtctct-gacttaggaccaaaaatagacccttgttctttgatgactatagttagcctaaaactaattttttatgtcatttattaattctcttagGTGTTTTAGAGAATCTTGGAATTGAACCAGAAGTGGAAAGGATTGGCAAATACAAAAGTGTAGGAGATCAACTTACCCGTAAAACCATGTCTGAAGATCA

upper sequence: Vv17s0000g04680.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA04G31180.1 (Glycine max), 3'ss of exon 3
-------aatagaagatgatcttttaaaattggatcactgtgtgagaggagttgtctttattttggtttctctgactgaagtggagtggcttcaaattgttttgtagGTGTTTTTGAGAAAGTAGGAATTGAACCACAAGTGCAAAGGATTGGTAAATACAAAAGTGCAGGGGATCAACTTACACGCAAAACGATGTCTGAAGAAAA
       ||||  |    ||| ||| ||||      | | | |||  |    | |   ||          | ||  |||  |    |   | |   |||||||  ||| ||||| || ||  |||||||||||||||||||| |||||||||| ||||||||||||||||| ||||||||  | || | ||| ||||||||||||||
attattgaatattaataaatcattttaaatatttaaattctatgatgg---ctataaataagcctaaacttgtgtttgacatcattttattac---ttgtttt-cagGCGTTTTAGATAACATAGGAATTGAACCACAAGTGGAAAGGATTGGAAAATACAAAAGTGCAGGAGATCAACTAGCTCGAAGAACCATGTCTGAAGAAAA

upper sequence: Vv17s0000g04680.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA06G22870.1 (Glycine max), 3'ss of exon 3
-----aatagaagatgatcttttaaaattggatcactgtg-tgagaggagttgtctttattttggtttctctgactgaagtggagtggcttcaaattgttttgtagGTGTTTTTGAGAAAGTAGGAATTGAACCACAAGTGCAAAGGATTGGTAAATACAAAAGTGCAGGGGATCAACTTACACGCAAAACGATGTCTGAAGAAAA
        | | | ||   ||| || |||  |   || || ||     |  |     ||      ||| | ||  |||  |    |   |   |||||||||  |||| |||| || ||  |||||||||||||||||||| |||||||||| ||||||||||||||||| ||||| ||  | || | ||| ||||||||||||||
gttctggaacatgctgcagtttaaatatttaaattctatgatggctataaataagcctaaaac--tttttgtgtttgacatcattttatt---aattgtttt-cagGTATTTTAGAAAACATAGGAATTGAACCACAAGTGGAAAGGATTGGAAAATACAAAAGTGCAGGAGATCAGCTAGCTCGAAGAACCATGTCTGAAGAAAA

upper sequence: Vv17s0000g04680.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA05G07540.1 (Glycine max), 3'ss of exon 3
aatagaagatgatcttttaaaattggatcactgtgtgagaggagttgtctttattttggtttctctgactgaagtggagtggcttcaaattgtt-----ttgtagGTGTTTTTGAGAAAGTAGGAATTGAACCACAAGTGCAAAGGATTGGTAAATACAAAAGTGCAGGGGATCAACTTACACGCAAAACGATGTCTGAAGAAAA---------
      | |  |  || | ||||   ||       ||        | |  ||| | | |||   || |   || |    |   ||  | |||||     |  || ||||| | |||||  | |||||||||||| ||||| |||||||||| |||||||||||||  || ||||| ||||| || ||||| |||||||||||  |         
------aaaacactttctcaaatcacatagacccttgtt-----ctttgattactatagttagcctaa---aactattttttttttcatttgttaattctcttatgtgttctagAGAATCTTGGAATTGAACCAGAAGTGGAAAGGATTGGCAAATACAAAAGTGTTGGAGATCAGCTTACCCGTAAAACCATGTCTGAAGATCATCATGAGAT

upper sequence: Vv17s0000g04680.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT1G73990.1 (Arabidopsis thaliana), 3'ss of exon 3
------aatagaagatgatcttttaaaattggatcactgtg--tgagaggagttgtctttattttggtttctctgactgaagtggagtggcttcaaattgttttgtagGTGTTTTTGAGAAAGTAGGAATTGAACCACAAGTGCAAAGGATTGGTAAATACAAAAGTGCAGGGGATCAACTTACACGCAAAACGATGTCTGAAGAAAA
       ||  ||| |  |   |   | ||  || | |     |      ||  ||  ||       ||| ||    |||| | |      ||||||      ||||||||| || || ||||| || |||||||| ||||| ||||||||||| |||||||||||||| || ||||| ||| | |||||||  || ||||| |||||
tctcgttatcaaaggtccttaatcggatttcaataattacaattttacaaagcagtaattggcaca-tttatcg---tgaactagttatttttcaaaaa----tgtagGTGTCTTCGAAAAAGTGGGGATTGAACCTCAAGTACAAAGGATTGGAAAATACAAAAGTGCTGGAGATCAGCTTTCTCGCAAAAGTATATCTGAGGAAAA

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|33405039|gb|CF210666.1|CF210666
EST:     TGCATATTTTTCTTTATATGGTCTGACTGTTCAAGCATCCTTTCTTGGAG                         GTGTTTTTGAGAAAGTAGGAATTGAACCCCAAGTGCAAAGGATTGGTAAAT
genomic: TGCATATTTTTCTTTATATGGTCTGACTGTTCAAGCATCCTTTCTTGGAGgtaagttagt ... tgttttgtagGTGTTTTTGAGAAAGTAGGAATTGAACCACAAGTGCAAAGGATTGGTAAAT
EST: gi|29784686|gb|CB345736.2|CB345736
EST:     TGCATATTTTTCTTTATATGGTCTGACTGTTCAAGCATCCTTTCTTGGAG                         GTGTTTTTGAGNAAGTAGGAATTGAACCACGATTGCAAAGGATTGNTGATT
genomic: TGCATATTTTTCTTTATATGGTCTGACTGTTCAAGCATCCTTTCTTGGAGgtaagttagt ... tgttttgtagGTGTTTTTGAGAAAGTAGGAATTGAACCACAAGTGCAAAGGATTGGTAAAT
EST: gi|28966758|gb|CB345791.1|CB345791
EST:     TGCATATTTTTCTTTATATGGTCTGACTGTTCAAGCATCCTTTCTTGGAG                         GTGTTTTTGAGAAAGTAGGAATTGAACCCCAAGTGCAAAGGATTGGTAAAT
genomic: TGCATATTTTTCTTTATATGGTCTGACTGTTCAAGCATCCTTTCTTGGAGgtaagttagt ... tgttttgtagGTGTTTTTGAGAAAGTAGGAATTGAACCACAAGTGCAAAGGATTGGTAAAT
EST: gi|33404955|gb|CF210582.1|CF210582
EST:     TGCATATTTTTCTTTATATGGTCTGACTGTTCAAGCATCCTTTCTTGGAG                         GTGTTTTTGAGAAAGTAGGAATTGAACCACAAGTGCAAAGGATTGGTAAAT
genomic: TGCATATTTTTCTTTATATGGTCTGACTGTTCAAGCATCCTTTCTTGGAGgtaagttagt ... tgttttgtagGTGTTTTTGAGAAAGTAGGAATTGAACCACAAGTGCAAAGGATTGGTAAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtctttattttggtttctctgactgaagtggagtggcttcaaattgttttgtagGTGTTTTTGAGAAAGTAGGAATTGAACCACAAGTGCAAAGGATTGGTAAATACAAAAGTGCAGGGGATCAACTTACACGCAAAACGATGTCTGAAGAAAA
                 ctctgac  putative branch site (score: 3)
                                            ttgtttt  putative PPT
                                         aaattgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aatagaagatgatcttttaaaattggatcactgtgtgagaggagttgtctttattttggtttctctgactgaagtggagtggcttcaaattgttttgtagGTGTTTTTGAGAAAGTAGGAATTGAACCACAAGTGCAAAGGATTGGTAAATACAAAAGTGCAGGGGATCAACTTACACGCAAAACGATGTCTGAAGAAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
aatagaa
- - - - - - - - - aaaattg
- - - - - - - - - - - - - - - -tgtgtga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgactga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tggcttc