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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tattttcagttgaaagcatgttaaagagaagtcaaaatttgtgaacagaatcctaagttgacattgctgtttttatgtaactgtttctcttaccttacagATGTTGATGAATGCAAAGAAAAGAAAGCCTGTCAGTGCCCTGAATGCAGCTGCAAAAACACATGGGGTAGCTACGAGTGCACTTGCAGTGGGGATCTTTT

Basic information

species Vitis vinifera
transcript Vv03s0091g00740.t01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv03s0091g00740.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GRMZM2G303631_T01 (Zea mays), 3'ss of exon 9
-----tattttcagttgaaagcatgttaaagagaagtcaaaatttgtgaacagaatcctaagttgacattgctgtttttatgtaactgtttctcttaccttacagATGTTGATGAATGCAAAGAAAAGAAAGCCTGTCAGTGCCCTGAATGCAGCTGCAAAAACACATGGGGTAGCTACGAGTGCACTTGCAGTGGGGATCTTTT
     |||    || |       ||||      |  |  |   |  ||||    ||  | |||   || ||| |    ||  |  ||   |||  | | || ||||  ||||||| ||||| || || ||||| |||||||| |||||||||| ||||||| | ||||||||| |||| || |||||||||||||| || |||||
acacatatacatagattttgtactgttggtagtatttacatggtaatgaagtagatatttagt--gcaatgcagaaaatacatctct---tctaattcattgcagACATTGATGAGTGCAAGGAGAAAAAAGCTTGTCAGTGTCCTGAATGCAACTGCAAAGATACATGGGGTGGCTATGACTGCACTTGCAGTGGTGACCTTTT

upper sequence: Vv03s0091g00740.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA20G27000.1 (Glycine max), 3'ss of exon 9
--tattttcagttgaaagcatgttaaagagaagtcaaaatttgtgaacagaatcctaagttgacattgctgtttttatgtaactgtttctctt-accttacagATGTTGATGAATGCAAAGAAAAGAAAGCCTGTCAGTGCCCTGAATGCAGCTGCAAAAACACATGGGGTAGCTACGAGTGCACTTGCAGTGGGGATCTTTT
  || |           ||||  | ||  || |   | || | ||||     || | |      |  ||    | | || |    |||  ||| ||||| ||||  |||||||||||||||| |||||||| ||||||||||||||||| |||||||| || || ||||| ||||| || |||||||||||||||||||||||
attaatcctttgccttggcattgttaattgatg---atatctttgaatgttttcatcataactaaaagccaaatatctgaactccttttgcttcacctttcagACATTGATGAATGCAAAGAGAAGAAAGCTTGTCAGTGCCCTGAATGTAGCTGCAAGAATACTTGGGGAAGCTATGACTGCACTTGCAGTGGGGATCTTTT

upper sequence: Vv03s0091g00740.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA10G40340.1 (Glycine max), 3'ss of exon 9
---tattttcagttgaaagcat--gttaaagagaagtcaaaatttgtgaacagaatcctaagttgacattgctgtttttatgtaactgtttctcttaccttacagATGTTGATGAATGCAAAGAAAAGAAAGCCTGTCAGTGCCCTGAATGCAGCTGCAAAAACACATGGGGTAGCTACGAGTGCACTTGCAGTGGGGATCTTTT
   |  |||   |||  |   |   || | || |  |   ||| | |  |    | |  ||    | ||  |||   |  | |     || |     |||| ||||  |||| ||||||||||| |||||||| ||||||||||||||||| |||||||| || || ||||| ||||| || |||||||||||||||||||||||
taatcctttgccttggcattgttaattgatgatacctttgaatcttttcatcataactaaaagcaaaatatctgaactctttt-----ttgcctcatcctttcagACATTGACGAATGCAAAGAGAAGAAAGCTTGTCAGTGCCCTGAATGTAGCTGCAAGAATACTTGGGGAAGCTATGACTGCACTTGCAGTGGGGATCTTTT

upper sequence: Vv03s0091g00740.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA11G00370.1 (Glycine max), 3'ss of exon 9
tattttcagttgaaagcatgttaaagagaagtcaaaatttgtgaacagaatcctaagttgacattgctgtttttatgtaactgtttctcttaccttacagATGTTGATGAATGCAAAGAAAAGAAAGCCTGTCAGTGCCCTGAATGCAGCTGCAAAAACACATGGGGTAGCTACGAGTGCACTTGCAGTGGGGATCTTTT
 || |   | |   | || ||       |  | |  ||   |    ||         |  ||||  |   |   |   ||||  |  |    | |||||||| |||||||||||||||| ||||| || ||||||||||||||||| |||||||| || || ||||| ||||| || |||| ||| ||||| |||||| |
aatctgtgggtttgaacaagtattgcgaacttgatgatacatacctagtgattgttttccacataacaagtgaaactgaacttatgtttcatctttacagATATTGATGAATGCAAAGAGAAGAAGGCTTGTCAGTGCCCTGAATGTAGCTGCAAGAATACGTGGGGAAGCTATGACTGCAGTTGTAGTGGAGATCTTCT

upper sequence: Vv03s0091g00740.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA01G45380.1 (Glycine max), 3'ss of exon 9
tattttcagttgaaagcatgttaaagagaagtcaaaatttgtgaacagaatcctaagtt---gacattgctgtttttatgtaactgtttctcttaccttacagATGTTGATGAATGCAAAGAAAAGAAAGCCTGTCAGTGCCCTGAATGCAGCTGCAAAAACACATGGGGTAGCTACGAGTGCACTTGCAGTGGGGATCTTTT
| || ||| |     |   |||  |   |   | || ||  |||     |    | |||    ||||  |   |   ||  ||||  |  |    |  ||||||| | |||||||||||||| ||||| || |||||||||||||| || |||||||| || || ||||| ||||| || |||| ||| ||||| |||||| |
tcttctcaatccgtgg---gtttgaagtattgcgaacttgatgatacctagtgaatgttttccacataacacgtgaaattgaacttatgtttcatctatacagATATAGATGAATGCAAAGAGAAGAAGGCTTGTCAGTGCCCTGACTGTAGCTGCAAGAATACTTGGGGAAGCTATGACTGCAGTTGTAGTGGAGATCTTCT

upper sequence: Vv03s0091g00740.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: AT2G14740.2 (Arabidopsis thaliana), 3'ss of exon 9
tattttcagttgaaagcatgttaaagagaagtcaaaatttgtgaacagaatcctaagttgacattgctgtttttatgtaactgtttctcttacctta--cagATGTTGATGAATGCAAAGAAAAGAAAGCCTGTCAGTGCCCTGAATGCAGCTGCAAAAACACATGGGGTAGCTACGAGTGCACTTGCAGTGGGGATCTTTT
           |  ||    |   | | || |  || |     |  |  |   |    |     |  |  | ||||     | ||  |  | |||    ||||  || |||| |||||||| |||||||| || |||||||| || || |||||||| ||||||||||| ||||| |||||| |||| || ||||| ||| |
-----------gttagaccctctgaaaaaacttgaattac---agtactactttgttctagttctaatcatcttataaggattttcgtgcttcctgcaccagACATTAATGAGTGCAAAGAGAAGAAAGCATGCCAGTGCCCAGAGTGTAGCTGCAAGAACACATGGGGAAGCTATGAGTGCTCTTGTAGCGGGGACCTTCT

upper sequence: Vv03s0091g00740.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: AT2G14720.2 (Arabidopsis thaliana), 3'ss of exon 10
tattttcagttgaaagcatgttaaagagaagtcaaaatttgtgaacagaatcctaagttgacattgctgtttttatgtaactgtttctcttaccttac-agATGTTGATGAATGCAAAGAAAAGAAAGCCTGTCAGTGCCCTGAATGCAGCTGCAAAAACACATGGGGTAGCTACGAGTGCACTTGCAGTGGGGATCTTTT
        |||  |    ||| |||     |   |    | |        || ||  || | |    | || ||| | |  | |    ||| | | || |||  |  |||| |||||||| |||||||| ||||||||||| ||||| ||||| || ||||| ||||| ||||| |||||| |||| || ||||| ||| |
--------gttagacctctgtcaaaactttggttac-cctattttttttgtcttac-ttcataaacatcttcttaaggatttttcatacttccttcactagACATCAATGAGTGCAAAGAGAAGAAAGCATGTCAGTGCCCGGAATGTAGCTGTAAGAACACCTGGGGAAGCTATGAGTGCTCTTGTAGCGGGGACCTTCT

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|71888433|gb|DT037488.1|DT037488
EST:     ATGTGAGTGTCCTCCAGGGTTTAAAGGTGATGGTGTCAAGAGTTGTAAAG                         ATGTTGATGAATGCAAAGAAAAGAAAGCCTGTCAGTGCCCTGAATGCAGCT
genomic: ATGTGAGTGTCCTCCAGGGTTTAAAGGTGATGGTGTTAAGAGTTGTAAAGgtaagagatg ... taccttacagATGTTGATGAATGCAAAGAAAAGAAAGCCTGTCAGTGCCCTGAATGCAGCT
EST: gi|110363399|gb|EC926982.1|EC926982
EST:     ATGTGAGTGTCCTCCAGGGTTTAAAGGTGATGGTGTCAAGAGTTGTAAAG                         ATGTTGATGAATGCAAAGACAAGAAAGCCTGTCAGTGCCCTGAATGCAGCT
genomic: ATGTGAGTGTCCTCCAGGGTTTAAAGGTGATGGTGTTAAGAGTTGTAAAGgtaagagatg ... taccttacagATGTTGATGAATGCAAAGAAAAGAAAGCCTGTCAGTGCCCTGAATGCAGCT
EST: gi|110359067|gb|EC919937.1|EC919937
EST:     ATGTGAGTGTCCTCCAGGGTTTAAAGGTGATGGTGTCAAGAGTTGTAAAG                         ATGTTGATGAATGCAAAGAAAAGAAAGCCTGTCAGTGCCCTGAATGCAGCT
genomic: ATGTGAGTGTCCTCCAGGGTTTAAAGGTGATGGTGTTAAGAGTTGTAAAGgtaagagatg ... taccttacagATGTTGATGAATGCAAAGAAAAGAAAGCCTGTCAGTGCCCTGAATGCAGCT
EST: gi|110718216|gb|EE094793.1|EE094793
EST:     ATGTGAGTGTCCTCCAGGGTTTAAAGGTGATGGTGTCAAGAGTTGTAAAG                         ATGTTGATGAATGCAAAGAAAAGAAAGCCTGTCAGTGCCCTGAATGCAGCT
genomic: ATGTGAGTGTCCTCCAGGGTTTAAAGGTGATGGTGTTAAGAGTTGTAAAGgtaagagatg ... taccttacagATGTTGATGAATGCAAAGAAAAGAAAGCCTGTCAGTGCCCTGAATGCAGCT
EST: gi|349830520|gb|FQ416830.1|FQ416830
EST:     ATGTGAGTGTCCTCCAGGGTTTAAAGGTGATGGTGTCAAGAGTTGTAAAG                         ATGTTGATGAATGCAAAGACAAGAAAGCCTGTCAGTGCCCTGAATGCAGCT
genomic: ATGTGAGTGTCCTCCAGGGTTTAAAGGTGATGGTGTTAAGAGTTGTAAAGgtaagagatg ... taccttacagATGTTGATGAATGCAAAGAAAAGAAAGCCTGTCAGTGCCCTGAATGCAGCT
EST: gi|26262131|gb|CA813194.1|CA813194
EST:     ATGTGAGTGTCCTCCAGGGTTTAAAGGTGATGGTGTCAAGAGTTGTAAAG                         ATGTTGATGAATGCAAAGACAAGAAAGCCTGTCAGTGCCCTGAATGCAGCT
genomic: ATGTGAGTGTCCTCCAGGGTTTAAAGGTGATGGTGTTAAGAGTTGTAAAGgtaagagatg ... taccttacagATGTTGATGAATGCAAAGAAAAGAAAGCCTGTCAGTGCCCTGAATGCAGCT
EST: gi|30296650|gb|CB973444.1|CB973444
EST:     ATGTGAGTGTCCTCCAGGGTTTAAAGGTGATGGTGTCAAGAGTTGTAAAG                         ATGTTGATGAATGCAAAGACAAGAAAGCCTGTCAGTGCCCTGAATGCAGCT
genomic: ATGTGAGTGTCCTCCAGGGTTTAAAGGTGATGGTGTTAAGAGTTGTAAAGgtaagagatg ... taccttacagATGTTGATGAATGCAAAGAAAAGAAAGCCTGTCAGTGCCCTGAATGCAGCT
EST: gi|110692278|gb|EE071340.1|EE071340
EST:     ATGTGAGTGTCCTCCAGGGTTTAAAGGTGATGGTGTCAAGAGTTGTAAAG                         ATGTTGATGAATGCAAAGAAAAGAAAGCCTGTCAGTGCCCTGAATGCAGCT
genomic: ATGTGAGTGTCCTCCAGGGTTTAAAGGTGATGGTGTTAAGAGTTGTAAAGgtaagagatg ... taccttacagATGTTGATGAATGCAAAGAAAAGAAAGCCTGTCAGTGCCCTGAATGCAGCT
EST: gi|110403004|gb|EC964013.1|EC964013
EST:     ATGTGAGTGTCCTCCAGGGTTTAAAGGTGATGGTGTCAAGAGTTGTAAAG                         ATGTTGATGAATGCAAAGACAAGAAAGCCTGTCAGTGCCCTGAATGCAGCT
genomic: ATGTGAGTGTCCTCCAGGGTTTAAAGGTGATGGTGTTAAGAGTTGTAAAGgtaagagatg ... taccttacagATGTTGATGAATGCAAAGAAAAGAAAGCCTGTCAGTGCCCTGAATGCAGCT
EST: gi|30300932|gb|CB977726.1|CB977726
EST:     ATGTGAGTGTCCTCCAGGGTTTAAAGGTGATGGTGTCAAGAGTTGTAAAG                         ATGTTGATGAATGCAAAGACAAGAAAGCCTGTCAGTGCCCTGAATGCAGCT
genomic: ATGTGAGTGTCCTCCAGGGTTTAAAGGTGATGGTGTTAAGAGTTGTAAAGgtaagagatg ... taccttacagATGTTGATGAATGCAAAGAAAAGAAAGCCTGTCAGTGCCCTGAATGCAGCT
EST: gi|30296719|gb|CB973513.1|CB973513
EST:     ATGTGAGTGTCCTCCAGGGTTTAAAGGTGATGGTGTCAAGAGTTGTAAAG                         ATGTTGATGAATGCAAAGACAAGAAAGCCTGTCAGTGCCCTGAATGCAGCT
genomic: ATGTGAGTGTCCTCCAGGGTTTAAAGGTGATGGTGTTAAGAGTTGTAAAGgtaagagatg ... taccttacagATGTTGATGAATGCAAAGAAAAGAAAGCCTGTCAGTGCCCTGAATGCAGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cagaatcctaagttgacattgctgtttttatgtaactgtttctcttaccttacagATGTTGATGAATGCAAAGAAAAGAAAGCCTGTCAGTGCCCTGAATGCAGCTGCAAAAACACATGGGGTAGCTACGAGTGCACTTGCAGTGGGGATCTTTT
                                         ctcttac  putative branch site (score: 3)
                                   ctgtttctcttacctt  CT-rich tract
                        tttttatgtaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tattttcagttgaaagcatgttaaagagaagtcaaaatttgtgaacagaatcctaagttgacattgctgtttttatgtaactgtttctcttaccttacagATGTTGATGAATGCAAAGAAAAGAAAGCCTGTCAGTGCCCTGAATGCAGCTGCAAAAACACATGGGGTAGCTACGAGTGCACTTGCAGTGGGGATCTTTT

- - - - - -gaaagca
- - - - - - - - - - - -aagagaa
- - - - - - - - - - - - - - - -tcaaaat
- - - - - - - - - - - - - - - - - - - - - -aacagaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cattgct