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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaaatattatattatttctatgttggagacttggctggtaattttgttataaagcaaaaatgttaacttgatgtctgtcttttttgttctttaatgtaagGTGCGAATAATGCGTAGATTACGTCATCCAAATGTTGTTCTTTTTATGGGTGCTGTTACTCGCCCTCCAAACCTCTCTATCATCACTGAGTTTCTTCCAA

Basic information

species Vitis vinifera
transcript Vv14s0030g01440.t01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0030g01440.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os03g06410.1 (Oryza sativa), 3'ss of exon 6
-------aaaatat-tatattatttctatgttggagacttggctggtaattttgt-----tataaagcaaaaatgttaacttgatgtctgtc----ttttttg-------------ttctttaatgtaagGTGCGAATAATGCGTAGATTACGTCATCCAAATGTTGTTCTTTTTATGGGTGCTGTTACTCGCCCTCCAAACCTCTCTATCATCACTGAGTTTCTTCCAA
       ||| ||| |||||| | | ||| || ||| |||  ||||  ||   ||      ||  |      || || | ||||| | ||      | |||||             ||  ||  |  |||||||| || |||||| || | |||||||||||| ||||||| || ||||||||||||||||| ||||||||| | |||||  |  |||||| ||||||||
gtaggtgaaactatatatattttatatatcttagag-ctttactggctatagcgtggattcatttatttgtcatttttaattgatttttgctgcaatgttttgatttgccatatactttctttttacaagGTGCGGATTATGCGTCGACTGCGTCATCCAAATATTGTTCTCTTCATGGGTGCTGTTACTCGTCCTCCAAACTTATCTATTGTATCTGAGTATCTTCCAA

upper sequence: Vv14s0030g01440.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G175563_T01 (Zea mays), 3'ss of exon 6
------aaaatattatattatttctatgttggagactt--------ggctggt-aattttg----ttataaagcaaaaatgttaacttgatgtctgtctttt--ttgttctttaatgtaagGTGCGAATAATGCGTAGATTACGTCATCCAAATGTTGTTCTTTTTATGGGTGCTGTTACTCGCCCTCCAAACCTCTCTATCATCACTGAGTTTCTTCCAA
       || | ||||  | ||||||| ||||||  ||          ||  | ||||||     |||   ||   || |||| | ||  ||| ||   |     | | ||||     ||||| ||||| |||||| |  | || ||||||||| ||||||| ||||||||||||||||| |||||||| ||| | |||||  |  |||| | ||||||||
gtaggtgaacttttat-ctgtttctatcttggagttttcctaaataaactattcaattttcatatttactcagttcaattgttgatttattgtttgatatacggatatactttttgacaagGTTCGAATTATGCGTCGGCTGCGCCATCCAAATATTGTTCTCTTTATGGGTGCTGTTACACGCCCTCCGAACTTATCTATTGTATCTGAATATCTTCCAA

upper sequence: Vv14s0030g01440.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G038982_T01 (Zea mays), 3'ss of exon 6
------aaaatattatattatttctatgttggagacttggctggtaatt-------ttgttata------aagcaaaaatgttaacttgatgtctgtcttttt--tgttctttaat--gtaagGTGCGAATAATGCGTAGATTACGTCATCCAAATGTTGTTCTTTTTATGGGTGCTGTTACTCGCCCTCCAAACCTCTCTATCATCACTGAGTTTCTTCCAA
       || | ||||  | ||||||| ||||||  || |    ||| |       || | |||       ||   |  ||||   ||  ||| ||   |     ||| |||||      ||||| ||||| |||||| |  | || ||||||||| ||||||| ||||||||||||||||| |||||||| ||| | |||||  |  |||| |  |||||||
gtaggtgaacttttat-ctgtttctatcttggagttttcgtaaataaataattcaattatcatatttactcagtccagttgttgctttattgtttgatatacggatgtactttatctgacaagGTCCGAATTATGCGTCGGCTGCGCCATCCAAATATTGTTCTCTTTATGGGTGCTGTTACACGCCCTCCGAACTTATCTATTGTATCTGAATACCTTCCAA

upper sequence: Vv14s0030g01440.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA20G37330.1 (Glycine max), 3'ss of exon 7
aaaatattatattatttctatgttggagacttggctggtaattttgttataaagcaaaaatgttaa--cttgatgtctgtcttttttgt-tctttaatgtaagGTGCGAATAATGCGTAGATTACGTCATCCAAATGTTGTTCTTTTTATGGGTGCTGTTACTCGCCCTCCAAACCTCTCTATCATCACTGAGTTTCTTCCAA
 ||| |  |||  | ||    |   | |  ||   |||||    |     |     |   |  |||      |      ||| |||| | | |||  || ||||| || ||||||||||| ||||||||||||||| |||||||||||||||||||||||||||| ||||| || ||||| |||||  | |||| ||| ||||
-aaaaagaata--agttgacagacagtggtttcattggtagaggtccaccatcattatcttcctaaaggccaaaactaatctgttttatctttttgctgaaagGTACGGATAATGCGTAGGTTACGTCATCCAAATATTGTTCTTTTTATGGGTGCTGTTACTCGTCCTCCCAATCTCTCAATCATTTCAGAGTATCTACCAA

upper sequence: Vv14s0030g01440.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA10G30070.1 (Glycine max), 3'ss of exon 7
-aaaatattatattatttctatgttggagacttggctggtaattttgttataaagcaaaaatgttaa--cttgatgtctgtcttttttgttctttaa-tgtaagGTGCGAATAATGCGTAGATTACGTCATCCAAATGTTGTTCTTTTTATGGGTGCTGTTACTCGCCCTCCAAACCTCTCTATCATCACTGAGTTTCTTCCAA
 |||| | ||  ||        |   | || ||    |||||   |     |     |   | ||||      |  |   ||| |||  | ||||   || |||||||| |||||||||||  |||||||||||||| |||||||||||||||||||||||||||| ||||| || || || |||||  | |||| ||| ||||
gaaaagaataagttgaca----ggcagtgatttcatgggtaagggtccaccatgattatcttcttaaaggccaaaattaatctgtttaatccttttgctgcaagGTGCGGATAATGCGTAGGCTACGTCATCCAAATATTGTTCTTTTTATGGGTGCTGTTACTCGTCCTCCCAATCTGTCAATCATTTCAGAGTATCTACCAA

upper sequence: Vv14s0030g01440.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: AT1G08720.1 (Arabidopsis thaliana), 3'ss of exon 6
--------------------------------aaaatattatattatt--tctatgttggagacttggctggtaattttgttataaagcaaaaatgttaac--ttgatgtctgtcttttttg----ttctttaatgtaagGTGCGAATAATGCGTAGATTACGTCATCCAAATGTTGTTCTTTTTATGGGTGCTGTTACTCGCCCTCCAAACCTCTCTATCATCACTGAGTTTCTTCCAA
                                |  ||| |    ||    | ||| ||   |  |   |        ||    |  |||  |  || |  |  ||||  ||   || | ||     |||  ||    ||||| || || ||||| ||||| |||||||||||||||||  | ||  | || ||||||||||| |||||||| || || ||| |||| |||||||| || |
gtaagccataagttcacttgcgtttatttactagtatacttagctacccatttatttttttggttgaacccaatggcttacgttgcagcttatttgcttgcctttgaattcccactctattaatatttccctatctgaagGTACGGATTATGCGAAGATTGCGTCATCCAAATGTTGTATTCTTCCTTGGGGCTGTTACTCGTCCTCCAAATCTTTCCATCGTCACAGAGTTTCTGCCTA

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|30303225|gb|CB980019.1|CB980019
EST:     TCTTGGACCAGGATTTCTCAGGTGCTGCTTTGGCCGAGTTCAAAAGAGAA                         GTGCGAATAATGCGTAGATTACGTCATCCAAATGTTGTTCTTTTTATGGGT
genomic: TCTTGGACCAGGATTTCTCAGGTGCTGCTTTGGCCGAGTTCAAAAGAGAAgtaagcaccg ... ttaatgtaagGTGCGAATAATGCGTAGATTACGTCATCCAAATGTTGTTCTTTTTATGGGT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttataaagcaaaaatgttaacttgatgtctgtcttttttgttctttaatgtaagGTGCGAATAATGCGTAGATTACGTCATCCAAATGTTGTTCTTTTTATGGGTGCTGTTACTCGCCCTCCAAACCTCTCTATCATCACTGAGTTTCTTCCAA
                          tgtctgtcttttttgt  CT-rich tract
                                  ttttttgttctttaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaaatattatattatttctatgttggagacttggctggtaattttgttataaagcaaaaatgttaacttgatgtctgtcttttttgttctttaatgtaagGTGCGAATAATGCGTAGATTACGTCATCCAAATGTTGTTCTTTTTATGGGTGCTGTTACTCGCCCTCCAAACCTCTCTATCATCACTGAGTTTCTTCCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT
aaaatat
- - - - - - - - - - tgttgga
- - - - - - - - - - - - - - - -tggctgg
- - - - - - - - - - - - - - - - - - - - - - - - - aaagcaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cttgatg