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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctgcaagaaatatcattatagaaattaattgatgggcaaatataggattgaataagaaccctaaattatttcagctctcttggtccatcattgtctgcagCTGGTTTTGTTGGGGGATTCTGGTGTTGGAAAAAGCTGTATTGTTCTTCGTTTTGTTCGTGGCCAGTTTGACCCTACATCCAAG

Basic information

species Vitis vinifera
transcript Vv13s0019g04680.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv13s0019g04680.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os10g30520.1 (Oryza sativa), 3'ss of exon 2
---------------------ctgcaagaaatatcattatagaaattaattgatgggcaaatataggattgaataagaaccctaaa--ttat-ttcagctctcttggtccatcattgtctgcagCTGGTTTTGTTGGGGGATTCTGGTGTTGGAAAAAGCTGTATTGTTCTTCGTTTTGTTCGTGGCCAGTTTGACCCTACATCCAAG
                          | || | |  | |||    | |  |     |   | ||    ||||||  |||    ||   | ||   |  |  | ||  |  | | |  |||| || |||| ||| | || ||||| |||||||| ||||| || ||||||||||| ||||| ||||| ||||||||||| || || |||
gtttggacttactcactagtgtcttcataattcttttaatatttctcatctccattgttgacattaagttgaattggaatgaaaaggttcatgcccttcgtttttattttaccctattctgtagTTGGTATTGCTTGGAGATTCAGGTGTTGGGAAAAGTTGCATTGTTCTTCGCTTTGTCCGTGGTCAGTTTGACCCCACTTCAAAG

upper sequence: Vv13s0019g04680.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os03g05740.1 (Oryza sativa), 3'ss of exon 2
-----ctgcaagaaatatcattatagaaattaattgatgggcaaatataggattgaataagaaccctaaattatttcagctctcttggtccatcattgtctgcagCTGGTTTTGTTGGGGGATTCTGGTGTTGGAAAAAGCTGTATTGTTCTTCGTTTTGTTCGTGGCCAGTTTGACCCTACATCCAAG
     |||||     |  | || ||  | |  | | |||     ||||    || | ||  | |  |       || | |         |  |   ||| || || |||| ||| | || || |||||||| || ||||| || ||||||||||| ||||||||||| |||||||| || || ||||||
gtttactgcacattttgccctt-tattactacaataatgcctctatatcatgtt-actagcagcttt------ctttaacgtgtccatccttttgatgt-tgtagTTGGTATTGCTTGGTGACTCTGGTGTAGGGAAAAGTTGCATTGTTCTTCGCTTTGTTCGTGGTCAGTTTGATCCCACTTCCAAG

upper sequence: Vv13s0019g04680.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G362088_T02 (Zea mays), 3'ss of exon 3
-ctgcaagaaatatcattatagaaattaattgatgggcaaatataggattgaataa--gaaccctaaattatttcagctctcttggtccatcattgtctgcagCTGGTTTTGTTGGGGGATTCTGGTGTTGGAAAAAGCTGTATTGTTCTTCGTTTTGTTCGTGGCCAGTTTGACCCTACATCCAAG
  ||  ||    |||||||          |   |   | | || |    ||||||   ||      | || | | |    | |    |      ||| |  || |||| ||| |||| || || |||||||| ||||| || ||||||||||||||||||||||| |||||||| ||||| ||||||
tatgttaggg-catcattaatagtggctgtgatttatctagta-aaacctgaatacctgattaacgacttttgttaatgttttcaaccttctcatgt-tatagTTGGTATTGCTGGGAGACTCAGGTGTTGGGAAAAGTTGCATTGTTCTTCGTTTTGTTCGTGGTCAGTTTGATCCTACTTCCAAG

upper sequence: Vv13s0019g04680.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA10G35230.3 (Glycine max), 3'ss of exon 2
ctgcaagaaatatcattatagaaattaattgatgggcaaatataggattgaataagaaccctaaattatttcagctct-cttggtccatcattgtctgcagCTGGTTTTGTTGGGGGATTCTGGTGTTGGAAAAAGCTGTATTGTTCTTCGTTTTGTTCGTGGCCAGTTTGACCCTACATCCAAG
 |      || |   || |    ||   ||     || | |||    |||  ||        |    |    | ||   ||| |    ||| ||    ||||| ||| | || || |||||||||||||| ||||||||||||||||| || ||||||||||| |||||||| || ||||| |||
ttaatcacaacagt-ttctgtttatctgttatactgccattattttcttgtttagcctttaaaggaaaccataactaaactttgaatgtcactggaaacagCTTGTTCTCTTAGGTGATTCTGGTGTTGGTAAAAGCTGTATTGTTCTACGATTTGTTCGTGGTCAGTTTGATCCAACATCTAAG

upper sequence: Vv13s0019g04680.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA20G32320.1 (Glycine max), 3'ss of exon 2
ctgcaagaaatatcattatagaaattaattgatgg------gcaaatataggattgaataagaaccctaaattatttcagctctcttggtccatcattgtctgcagCTGGTTTTGTTGGGGGATTCTGGTGTTGGAAAAAGCTGTATTGTTCTTCGTTTTGTTCGTGGCCAGTTTGACCCTACATCCAAG
       |   ||||  | | |   |  |||   |      || | |||    |||  |||       ||   |    | ||  | | |    ||| |     ||||| ||| | || || |||||||||||||| ||||||||||||||||| || ||||||||||| |||||||| || ||||| |||
------aattaatcacaacaaattctgcttgtctgtatactgccattattttcttgtttaaccttgaaaagaaaccataactaaccttgaatgtcacttaaaacagCTTGTTCTCTTAGGTGATTCTGGTGTTGGCAAAAGCTGTATTGTTCTACGATTTGTTCGTGGTCAGTTTGATCCAACATCTAAG

upper sequence: Vv13s0019g04680.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT3G54840.2 (Arabidopsis thaliana), 3'ss of exon 2
ctgcaagaaatatcattatagaaattaattgatgggcaaatatag---gattgaataagaaccc---taaattatttcagctctcttggtccatcattgtctgcagCTGGTTTTGTTGGGGGATTCTGGTGTTGGAAAAAGCTGTATTGTTCTTCGTTTTGTTCGTGGCCAGTTTGACCCTACATCCAAG
        | | || |  |    |  | |   | | ||| | | |    ||||  |   |       |||   ||  ||      || |       |||  ||||| | ||| | || || || ||||||||||| ||||| |||||||| ||||| ||||| ||||| ||||||||| ||||||| |||
------ttattttcttgttgctcagcagtattttgccaagtgtggtataattggtttcaactttgcgtaagacataccactaacttttggattcacttgattgcagTTAGTTCTATTAGGAGACTCTGGTGTTGGTAAAAGTTGTATTGTCCTTCGATTTGTACGTGGTCAGTTTGACGCTACATCTAAG

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|294963923|gb|GW836798.1|GW836798
EST:     TGAATGCTGAGAATGGTGGAGCACCCGATGCAAAAAACCTCCGGGTTAAG                         CTGGTTTTGTTGGGGGATTCTGGTGTTGGAAAAAGCTGTATTGTTCTTCGT
genomic: TGAATGCGGAGAATGGTGGAGCACCCGATGCAAAAAACCTCCGGGTTAAGgtacttaatt ... ttgtctgcagCTGGTTTTGTTGGGGGATTCTGGTGTTGGAAAAAGCTGTATTGTTCTTCGT
EST: gi|351049141|gb|FQ449863.1|FQ449863
EST:     TGAATGCGGAGAATGGTGGAGCACCCGATGCAAAAAACCTCCGGGTTAAG                         CTGGTTTTGTTGGGGGATTCTGGTGTTGGAAAAAGCTGTATTGTTCTTCGT
genomic: TGAATGCGGAGAATGGTGGAGCACCCGATGCAAAAAACCTCCGGGTTAAGgtacttaatt ... ttgtctgcagCTGGTTTTGTTGGGGGATTCTGGTGTTGGAAAAAGCTGTATTGTTCTTCGT
EST: gi|351031329|gb|FQ445354.1|FQ445354
EST:     TGAATGCGGAGAATGGTGGAGCACCCGATGCAAAAAACCTCCGGGTTAAG                         CTGGTTTTGTTGGGGGATTCTGGTGTTGGAAAAAGCTGTATTGTTCTTCGT
genomic: TGAATGCGGAGAATGGTGGAGCACCCGATGCAAAAAACCTCCGGGTTAAGgtacttaatt ... ttgtctgcagCTGGTTTTGTTGGGGGATTCTGGTGTTGGAAAAAGCTGTATTGTTCTTCGT
EST: gi|110378503|gb|EC943640.1|EC943640
EST:     TGAATGCGGAGAATGGTGGAGCACCCGATGCAAAAAACCTCCGGGTTAAG                         CTGGTTTTGTTGGGGGATTCTGGTGTTGGAAAAAGCTGTATTGTTCTTCGT
genomic: TGAATGCGGAGAATGGTGGAGCACCCGATGCAAAAAACCTCCGGGTTAAGgtacttaatt ... ttgtctgcagCTGGTTTTGTTGGGGGATTCTGGTGTTGGAAAAAGCTGTATTGTTCTTCGT
EST: gi|110386522|gb|EC951122.1|EC951122
EST:     GAATGCGGAGAATGGTGGAGCACCCGATGCAAAAAACCTCCGGGTTAAG                         CTGGTTTTGTTGGGGGATTCTGGTGTTGGAAAAAGCTGTATTGTTCTTCGT
genomic: GAATGCGGAGAATGGTGGAGCACCCGATGCAAAAAACCTCCGGGTTAAGgtacttaatt ... ttgtctgcagCTGGTTTTGTTGGGGGATTCTGGTGTTGGAAAAAGCTGTATTGTTCTTCGT
EST: gi|110707796|gb|EE084605.1|EE084605
EST:     TGAATGCGGAGAATGGTGGAGCACCCGATGCAAAAAACCTCCGGGTTAAG                         CTGGTTTTGTTGGGGGATTCTGGTGTTGGAAAAAGCTGTATTGTTCTTCGT
genomic: TGAATGCGGAGAATGGTGGAGCACCCGATGCAAAAAACCTCCGGGTTAAGgtacttaatt ... ttgtctgcagCTGGTTTTGTTGGGGGATTCTGGTGTTGGAAAAAGCTGTATTGTTCTTCGT
EST: gi|351029650|gb|FQ427490.1|FQ427490
EST:     TGAATGCGGAGAATGGTGGAGCACCCGATGCAAAAAACCTCCGGGTTAAG                         CTGGTTTTGTTGGGGGATTCTGGTGTTGGAAAAAGCTGTATTGTTCTTCGT
genomic: TGAATGCGGAGAATGGTGGAGCACCCGATGCAAAAAACCTCCGGGTTAAGgtacttaatt ... ttgtctgcagCTGGTTTTGTTGGGGGATTCTGGTGTTGGAAAAAGCTGTATTGTTCTTCGT
EST: gi|351031354|gb|FQ445379.1|FQ445379
EST:     TGAATGCGGAGAATGGTGGAGCACCCGATGCAAAAAACCTCCGGGTTAAG                         CTGGTTTTGTTGGGGGATTCTGGTGTTGGAAAAAGCTGTATTGTTCTTCGT
genomic: TGAATGCGGAGAATGGTGGAGCACCCGATGCAAAAAACCTCCGGGTTAAGgtacttaatt ... ttgtctgcagCTGGTTTTGTTGGGGGATTCTGGTGTTGGAAAAAGCTGTATTGTTCTTCGT
EST: gi|351036602|gb|FQ457315.1|FQ457315
EST:     TGAATGCGGAGAATGGTGGAGCACCCGATGCAAAAAACCTCCGGGTTAAG                         CTGGTTTTGTTGGGGGATTCTGGTGTTGGAAAAAGCTGTATTGTTCTTCGT
genomic: TGAATGCGGAGAATGGTGGAGCACCCGATGCAAAAAACCTCCGGGTTAAGgtacttaatt ... ttgtctgcagCTGGTTTTGTTGGGGGATTCTGGTGTTGGAAAAAGCTGTATTGTTCTTCGT
EST: gi|110390981|gb|EC955931.1|EC955931
EST:     GAGCACCCGATGCAAAAAACCTCCGGGTTAAG                         CTGGTTTTGTTGGGGGATTCTGGTGTTGGAAAAAGCTGTATTGTTCTTCGT
genomic: GAGCACCCGATGCAAAAAACCTCCGGGTTAAGgtacttaatt ... ttgtctgcagCTGGTTTTGTTGGGGGATTCTGGTGTTGGAAAAAGCTGTATTGTTCTTCGT
EST: gi|351033397|gb|FQ462048.1|FQ462048
EST:     TGAATGCGGAGAATGGTGGAGCACCCGATGCAAAAAACCTCCGGGTTAAG                         CTGGTTTTGTTGGGGGATTCTGGTGTTGGAAAAAGCTGTATTGTTCTTCGT
genomic: TGAATGCGGAGAATGGTGGAGCACCCGATGCAAAAAACCTCCGGGTTAAGgtacttaatt ... ttgtctgcagCTGGTTTTGTTGGGGGATTCTGGTGTTGGAAAAAGCTGTATTGTTCTTCGT
EST: gi|30302011|gb|CB978805.1|CB978805
EST:     TGAATGCGGAGAATGGTGGAGCACCCGATGCAAAAAACCTCCGGGTTAAG                         CTGGTTTTGTTGGGGGATTCTGGTGTTGGAAAAAGCTGTATTGTTCTTCGT
genomic: TGAATGCGGAGAATGGTGGAGCACCCGATGCAAAAAACCTCCGGGTTAAGgtacttaatt ... ttgtctgcagCTGGTTTTGTTGGGGGATTCTGGTGTTGGAAAAAGCTGTATTGTTCTTCGT
EST: gi|349830843|gb|FQ418151.1|FQ418151
EST:     TGAATGCGGAGAATGGTGGAGCACCCGATGCAAAAAACCTCCGGGTTAAG                         CTGGTTTTGTTGGGGGATTCTGGTGTTGGAAAAAGCTGTATTGTTCTTCGT
genomic: TGAATGCGGAGAATGGTGGAGCACCCGATGCAAAAAACCTCCGGGTTAAGgtacttaatt ... ttgtctgcagCTGGTTTTGTTGGGGGATTCTGGTGTTGGAAAAAGCTGTATTGTTCTTCGT
EST: gi|110428129|gb|EC994591.1|EC994591
EST:     TGAATGCGGAGAATGGTGGAGCACCCGATGCAAAAAACCTCCGGGTTAAG                         CTGGTTTTGTTGGGGGATTCTGGTGTTGGAAAAAGCTGTATTGTTCTTCGT
genomic: TGAATGCGGAGAATGGTGGAGCACCCGATGCAAAAAACCTCCGGGTTAAGgtacttaatt ... ttgtctgcagCTGGTTTTGTTGGGGGATTCTGGTGTTGGAAAAAGCTGTATTGTTCTTCGT
EST: gi|351016862|gb|FQ424289.1|FQ424289
EST:     TGAATGCGGAGAATGGTGGAGCACCCGATGCAAAAAACCTCCGGGTTAAG                         CTGGTTTTGTTGGGGGATTCTGGTGTTGGAAAAAGCTGTATTGTTCTTCGT
genomic: TGAATGCGGAGAATGGTGGAGCACCCGATGCAAAAAACCTCCGGGTTAAGgtacttaatt ... ttgtctgcagCTGGTTTTGTTGGGGGATTCTGGTGTTGGAAAAAGCTGTATTGTTCTTCGT
EST: gi|110691925|gb|EE070587.1|EE070587
EST:     TGAATGCGGAGAATGGTGGAGCACCCGATGCAAAAAACCTCCGGGTTAAG                         CTGGTTTTGTTGGGGGATTCTGGTGTTGGAAAAAGCTGTATTGTTCTTCGT
genomic: TGAATGCGGAGAATGGTGGAGCACCCGATGCAAAAAACCTCCGGGTTAAGgtacttaatt ... ttgtctgcagCTGGTTTTGTTGGGGGATTCTGGTGTTGGAAAAAGCTGTATTGTTCTTCGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gattgaataagaaccctaaattatttcagctctcttggtccatcattgtctgcagCTGGTTTTGTTGGGGGATTCTGGTGTTGGAAAAAGCTGTATTGTTCTTCGTTTTGTTCGTGGCCAGTTTGACCCTACATCCAAG
             ccctaaa  putative branch site (score: 3)
                taaattatttca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctgcaagaaatatcattatagaaattaattgatgggcaaatataggattgaataagaaccctaaattatttcagctctcttggtccatcattgtctgcagCTGGTTTTGTTGGGGGATTCTGGTGTTGGAAAAAGCTGTATTGTTCTTCGTTTTGTTCGTGGCCAGTTTGACCCTACATCCAAG

- gcaagaa
- - - - - - - - - - -aaattaa
- - - - - - - - - - - - - - -tgatggg
- - - - - - - - - - - - - - - - - - -aaatata
- - - - - - - - - - - - - - - - - - - - - - - - - - -aagaacc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tccatca