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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagtttcttgtgctagttgtttctgtaaatagactccctgtatataatcatctttttactggtgatcaaatattttatgctatgttcttactgaagGCAAAACTAGGTGAGAAGAATAAATTTTATTATGATGAAAAGCTCAAGCGATGGGTTGAGGAAGGTACTGAACTTCCATCTGAAGAAGCAGCCTTGCCGC

Basic information

species Vitis vinifera
transcript Vv15s0021g02730.t01
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv15s0021g02730.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: LOC_Os02g01490.1 (Oryza sativa), 3'ss of exon 11
gtagtttc-ttgtgctagttgtttctgtaaatagactccctgtatataatcatctttttac-tggtgat-caaatatttt-atgctatgttcttactgaagGCAAAACTAGGTGAGAAGAATAAATTTTATTATGATGAAAAGCTCAAGCGATGGGTTGAGGAAGGTACTGAACTTCCATCTGAAGAAGCAGCCTTGCCGC
||| |||   || |||| |   ||  | |   |  |  | | | |  | |     ||  |  | || |  | |||| |   || ||   |   |  ||||||| ||| ||||  |  | || || ||||| ||||| |||||||| ||||||||||| ||||||||| ||||  ||||  | || ||  |  |  | || |
gtactttaactgagctattgaatt--ggagccactccacttttgttcagtttctcttccatatagtaaagctaatactgagatccttcctatgtcttgaagGCTAAATTAGGGCAACAAAACAAGTTTTACTATGACGAAAAGCTAAAGCGATGGGTGGAGGAAGGTGCTGAGATTCCTGCCGAGGAGCCTCCTCTCCCTC

upper sequence: Vv15s0021g02730.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GRMZM2G163277_T01 (Zea mays), 3'ss of exon 11
gtagtttcttgtgct-agttgt-------ttctgtaaatagactccctgtatataatcatctttttactggtgatcaaatattttatgctatgttcttactgaagGCAAAACTAGGTGAGAAGAATAAATTTTATTATGATGAAAAGCTCAAGCGATGGGTTGAGGAAGGTACTGAACTTCCATCTGAAGAAGCAGCCTTGCCGC
||| |||  | | || |||| |        | | |  |     |  |   || |  ||   | | ||       ||||   |   || |||| |   | |||||||||||| |||| ||  |||| |||||||| |||||||||||| | ||||| ||||| || |||||| |||   ||||  | || ||  |  |  | || |
gtatttttatttactgagttatgaaaagactatctccagttcttttccccatcttgtctcttctatatgcaatgtcaaccttaggatcctatttctgttctgaagGCAAAATTAGGGGATCAGAACAAATTTTACTATGATGAAAAGTTGAAGCGGTGGGTGGAAGAAGGTGCTGTGGTTCCTGCCGAGGAGCCTCCTCTTCCTC

upper sequence: Vv15s0021g02730.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GRMZM2G429241_T01 (Zea mays), 3'ss of exon 11
gtagtttcttgtgctagttgtttctgtaaatagactcc--ctgtatataatcatctttttactggtg-------atcaaatattttatgctatgttcttactgaagGCAAAACTAGGTGAGAAGAATAAATTTTATTATGATGAAAAGCTCAAGCGATGGGTTGAGGAAGGTACTGAACTTCCATCTGAAGAAGCAGCCTTGCCGC
||| ||| ||   || | |  |    |  | |  ||||   | | | |  |||||| ||   |  |          | ||  | | || |||| |   | |||||||||||| |||| ||  |||| |||||||| |||||||||||  | ||||| ||||| ||||||||| |||   ||||  | |||||  |  |  | || |
gtattttttta--ctgggttatgaaatggacaatctccagttttttttcttcatctcttcttttctatatgcaaggccaacttatgatcctatttctgttctgaagGCAAAATTAGGGGATCAGAACAAATTTTACTATGATGAAAAATTGAAGCGGTGGGTGGAGGAAGGTGCTGCTGTTCCTGCCGAAGAGCCTCCTCTTCCTC

upper sequence: Vv15s0021g02730.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA01G41790.1 (Glycine max), 3'ss of exon 15
--gtagtttcttgtgctagttgtttctgtaaatagactccctgtatataatcatctttttactggtgatcaaatattttatgctatgttcttactgaagGCAAAACTAGGTGAGAAGAATAAATTTTATTATGATGAAAAGCTCAAGCGATGGGTTGAGGAAGGTACTGAACTTCCATCTGAAGAAGCAGCCTTGCCGC
   || ||  ||||  || || | | | ||   | |  |  ||  | | ||  |   | |    ||| |      | |||| |||   | |   || |||| ||| | |||||||| || || || ||||||||||| ||||| ||  ||||||| ||||||||| ||||||||||| |||||||||| ||    | ||
gtataattagttgttttattt-tctttatattcacaa-cagtgcttctgattgtgcctgtttaagtggt------tcttattctactctgtatatgtagGCTAAATTGGGTGAGAAAAACAAGTTCTATTATGATGAGAAGCTGAAAAGATGGGTGGAGGAAGGTGCTGAACTTCCAGCTGAAGAAGCTGCTGCTCTGC

upper sequence: Vv15s0021g02730.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA11G03590.1 (Glycine max), 3'ss of exon 17
--gtagtttcttgtgctagttgtttctgtaaatagactccctgtatataatcatctttttactggtgatcaaatattttatgctatgttcttactgaagGCAAAACTAGGTGAGAAGAATAAATTTTATTATGATGAAAAGCTCAAGCGATGGGTTGAGGAAGGTACTGAACTTCCATCTGAAGAAGCAGCCTTGCCGC
   || ||  ||||  || ||  || |        | || |   |  |  |  |  || | |  ||  | ||||  ||  |  | |  |||   || |||| ||| | |||||||| || || || ||||||||||| ||||| ||| ||||||| ||||||||| ||||| ||||| ||||||||||  |    | ||
gtataattagttgttttattttcttttt-------attcaccaca-gtgcttctgattgtgcctgt--ttaaatggttcttattctactctatatgtagGCTAAATTGGGTGAGAAAAACAAGTTCTATTATGATGAGAAGCTGAAGAGATGGGTGGAGGAAGGTGCTGAAGTTCCAGCTGAAGAAGCTTCTGCTCTGC

upper sequence: Vv15s0021g02730.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA11G03580.1 (Glycine max), 3'ss of exon 16
gtagtttcttgtgctagttgtttctgtaaatagactccctgtatataatcat-ctttttactgg---tgatcaaatattttatgctatgttcttactgaagGCAAAACTAGGTGAGAAGAATAAATTTTATTATGATGAAAAGCTCAAGCGATGGGTTGAGGAAGGTACTGAACTTCCATCTGAAGAAGCAGCCTTGCCGC
          ||   | | |||  | ||  |   ||   | |  | ||   | ||| | ||||    || ||||||  ||  || | |   ||   || |||| ||| | ||||| || ||||| || ||||||||||| ||||| ||| ||||||| ||||||||| ||||| ||||| |||||||||| ||    | | 
----------gtataattagttgttttatttt--ctttttattcacaacagtgcttctgactgtgcctgttcaaatggttcttgttctacactatatgtagGCTAAATTGGGTGACAAAAATAAGTTCTATTATGATGAGAAGCTGAAGAGATGGGTGGAGGAAGGTGCTGAAGTTCCAGCTGAAGAAGCTGCTGCTCTGA

upper sequence: Vv15s0021g02730.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA01G41800.1 (Glycine max), 3'ss of exon 13
gtagtttcttgtgctagttgtttctgtaaatagactccctgtatataatcat-ctttttactg---gtgatcaaatattt-tatgctatgttcttactgaagGCAAAACTAGGTGAGAAGAATAAATTTTATTATGATGAAAAGCTCAAGCGATGGGTTGAGGAAGGTACTGAACTTCCATCTGAAGAAGCAGCCTTGCCGC
          ||   | |  ||  | ||  |   ||   | |  | ||   | ||| | ||||    || ||||||  || | |  | |  |||   || |||| ||| | |||||||| || || || ||||||||||| ||||| ||| ||||||| || |||||| ||||||||||| |||||||||| ||    | ||
----------gtataattaattgttttatttt--ctttttattcacaacagtgcttctgactgtgcatggtcaaatggttatttattctactctatatgtagGCTAAATTGGGTGAGAAAAACAAGTTCTATTATGATGAGAAGCTGAAGAGATGGGTGGAAGAAGGTGCTGAACTTCCAGCTGAAGAAGCTGCTGCTCTGC

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|33402931|gb|CF208558.1|CF208558
EST:     TATTCCAAAAGACTGTGGGGTTGGTCTTAAGATCCCGCCCTGACCGGCAG                         GCAAAACTAGGTGAGAAGAATAAATTTTATTATGATGAAAAGCTCAAGCGA
genomic: TATTCCAAAAGACTGTGGGGTTGGTCTTAAGATCCCGCCCTGACCGGCAGgtagtttctt ... cttactgaagGCAAAACTAGGTGAGAAGAATAAATTTTATTATGATGAAAAGCTCAAGCGA
EST: gi|351019051|gb|FQ426550.1|FQ426550
EST:     TATTCCAAAAGACTGTGGGGTTGGTCTTAAGATCCCGCCCTGACCGGCAG                         GCAAAACTAGGTGAGAAGAATAAATTTTATTATGATGAAAAGCTCAAGCGA
genomic: TATTCCAAAAGACTGTGGGGTTGGTCTTAAGATCCCGCCCTGACCGGCAGgtagtttctt ... cttactgaagGCAAAACTAGGTGAGAAGAATAAATTTTATTATGATGAAAAGCTCAAGCGA
EST: gi|349827257|gb|FQ421530.1|FQ421530
EST:     TATTCCAAAAGACTGTGGGGTTGGTCTTAAGATCCCGCCCTGACCGGCAG                         GCAAAACTAGGTGAGAAGAATAAATTTTATTATGATGAAAAGCTCAAGCGA
genomic: TATTCCAAAAGACTGTGGGGTTGGTCTTAAGATCCCGCCCTGACCGGCAGgtagtttctt ... cttactgaagGCAAAACTAGGTGAGAAGAATAAATTTTATTATGATGAAAAGCTCAAGCGA
EST: gi|351049265|gb|FQ429008.1|FQ429008
EST:     TATTCCAAAAGACTGTGGGGTTGGTCTTAAGATCCCGCCCTGACCGGCAG                         GCAAAACTAGGTGAGAAGAATAAATTTTATTATGATGAAAAGCTCAAGCGA
genomic: TATTCCAAAAGACTGTGGGGTTGGTCTTAAGATCCCGCCCTGACCGGCAGgtagtttctt ... cttactgaagGCAAAACTAGGTGAGAAGAATAAATTTTATTATGATGAAAAGCTCAAGCGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atataatcatctttttactggtgatcaaatattttatgctatgttcttactgaagGCAAAACTAGGTGAGAAGAATAAATTTTATTATGATGAAAAGCTCAAGCGATGGGTTGAGGAAGGTACTGAACTTCCATCTGAAGAAGCAGCCTTGCCGC
                                           ttcttac  putative branch site (score: 2)
                                           ttcttact  CT-rich tract
                     tgatcaaatattttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagtttcttgtgctagttgtttctgtaaatagactccctgtatataatcatctttttactggtgatcaaatattttatgctatgttcttactgaagGCAAAACTAGGTGAGAAGAATAAATTTTATTATGATGAAAAGCTCAAGCGATGGGTTGAGGAAGGTACTGAACTTCCATCTGAAGAAGCAGCCTTGCCGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC