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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agtgattttgcattctcatattttgagttagtaaatcttatacaaatttggctgctactcgaagttttgccccttatcaatatccatttttacattatagGTTTGCAAGACGGCGGATGTGGCAAGCAGGGTTGAGAGCCAGGTTAAACTTGTGATCAGGCCTATGTTTTCAAACCCACCCATTCATGGTGCATCTATCG

Basic information

species Vitis vinifera
transcript Vv04s0008g03770.t01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0008g03770.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: LOC_Os01g55540.2 (Oryza sativa), 3'ss of exon 8
agtgattttgcattctcatattttgagttagta---aatcttatacaaatttggctgctactcgaagttttgccccttatcaatatccatttttacattatagGTTTGCAAGACGGCGGATGTGGCAAGCAGGGTTGAGAGCCAGGTTAAACTTGTGATCAGGCCTATGTTTTCAAACCCACCCATTCATGGTGCATCTATCG
  |||  ||  ||| | ||  | | ||||  |    |  |  |||  ||| |      || | | | |       || | |   ||  |  |||  |||  |||||||    |  || ||||| ||   ||||||||| || ||  |||| ||||| || |||||||||| ||||||||| || |||||||||||||||||||
gttgaaattaaattttgat--tctaagttgatgccgacccagataataatatcctatttagttgca-tagaaaaactgaacggaatgtaactttgtatttcagGTTTGTGGAAGTGCTGATGTAGCTGTCAGGGTTGAAAGTCAACTTAAGCTTGTAATTAGGCCTATGTATTCAAACCCTCCTATTCATGGTGCATCTATCG

upper sequence: Vv04s0008g03770.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GRMZM2G094712_T04 (Zea mays), 3'ss of exon 6
agtgattttgcattctcatattttgagttagtaaatcttatacaaatttggctgctactcgaagtttt---gccccttatcaatatccatttttacattatagGTTTGCAAGACGGCGGATGTGGCAAGCAGGGTTGAGAGCCAGGTTAAACTTGTGATCAGGCCTATGTTTTCAAACCCACCCATTCATGGTGCATCTATCG
  | || |   |   | ||  | | | ||     |  |||| |   ||||     |  |  | | |     |   | |||  |||   | | |||  ||  |||| || || |  || ||||| ||    |||||||| || ||  | |||||||| ||||||||||||| ||||||||| ||  |||||||||| |||||||
--ttatctgttaaa-tgatgatgttatttctcctacattatgcccttttgaacagtcttttaggctgcagagtgtcctattcatagtaactcttatgtttcagGTATGTAAAAGTGCCGATGTAGCTGTTAGGGTTGAAAGTCAACTCAAACTTGTCATCAGGCCTATGTATTCAAACCCTCCTCTTCATGGTGCCTCTATCG
















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|110399226|gb|EC965723.1|EC965723
EST:     ATGCCAAGAACATGGGGCTCTACGGGGAACGTGTTGGTGCACTGAGCATT                         GTTTGCAAGACGGCGGATGTGGCAAGCAGGGTTGAGAGCCAGGTTAAACTT
genomic: ATGCCAAGAACATGGGGCTCTACGGGGAACGTGTTGGTGCACTGAGCATTgtaagagacc ... tacattatagGTTTGCAAGACGGCGGATGTGGCAAGCAGGGTTGAGAGCCAGGTTAAACTT
EST: gi|110404843|gb|EC970367.1|EC970367
EST:     ATGCCAAGAACATGGGGCTCTACGGGGAACGTGTTGGTGCACTGAGCATT                         GTTTGCAAGACGGCGGATGTGGCAAGCAGGGTTGAGAGCCAGGTTAAACTT
genomic: ATGCCAAGAACATGGGGCTCTACGGGGAACGTGTTGGTGCACTGAGCATTgtaagagacc ... tacattatagGTTTGCAAGACGGCGGATGTGGCAAGCAGGGTTGAGAGCCAGGTTAAACTT
EST: gi|30306097|gb|CB982891.1|CB982891
EST:     GGGGAACGTGTTGGGTGNACTGAGCATT                         GTTTGCAAGACGGCGGATGTGGCAAGCAGGGTTGAGAGCCAGGTTAAACTT
genomic: GGGGAACGTGTT-GGTGCACTGAGCATTgtaagagacc ... tacattatagGTTTGCAAGACGGCGGATGTGGCAAGCAGGGTTGAGAGCCAGGTTAAACTT
EST: gi|161716869|gb|FC068115.1|FC068115
EST:     ATGCCAAGAACATGGGGCTCTACGGGGAACGTGTTGGTGCACTGAGCATT                         GTTTGCAAGACGGCGGATGTGGCAAGCAGGGTTGAGAGCCAGGTTAAACTA
genomic: ATGCCAAGAACATGGGGCTCTACGGGGAACGTGTTGGTGCACTGAGCATTgtaagagacc ... tacattatagGTTTGCAAGACGGCGGATGTGGCAAGCAGGGTTGAGAGCCAGGTTAAACTT
EST: gi|352776804|gb|FQ472691.1|FQ472691
EST:     ATGCCAAGAACATGGGGCTCTTCGGGGAACGTGTTGGTGCACTGAGCATT                         GTTTGCAAGACGGCGGATGTGGCAAGCAGGGTTGAGAGCCAGGTTAAACTT
genomic: ATGCCAAGAACATGGGGCTCTACGGGGAACGTGTTGGTGCACTGAGCATTgtaagagacc ... tacattatagGTTTGCAAGACGGCGGATGTGGCAAGCAGGGTTGAGAGCCAGGTTAAACTT
EST: gi|110368860|gb|EC932986.1|EC932986
EST:     ATGCCAAGAACATGGGGCTCTACGGGGAACGTGTTGGTGCACTGAGCATT                         GTTTGCAAGACGGCGGATGTGGCAAGCAGGGTTGAGAGCCAGGTTAAACTT
genomic: ATGCCAAGAACATGGGGCTCTACGGGGAACGTGTTGGTGCACTGAGCATTgtaagagacc ... tacattatagGTTTGCAAGACGGCGGATGTGGCAAGCAGGGTTGAGAGCCAGGTTAAACTT
EST: gi|110388301|gb|EC953036.1|EC953036
EST:     ATGCCAAGAACATGGGGCTCTACGGGGAACGTGTTGGTGCACTGAGCATT                         GTTTGCAAGACGGCGGATGTGGCAAGCAGGGTTGAGAGCCAGGTTAAACTA
genomic: ATGCCAAGAACATGGGGCTCTACGGGGAACGTGTTGGTGCACTGAGCATTgtaagagacc ... tacattatagGTTTGCAAGACGGCGGATGTGGCAAGCAGGGTTGAGAGCCAGGTTAAACTT
EST: gi|110372200|gb|EC936351.1|EC936351
EST:     ATGCCAAGAACATGGGGCTCTACGGGGAACGTGTTGGTGCACTGAGCATT                         GTTTGCAAGACGGCGGATGTGGCAAGCAGGGTTGAGAGCCAGGTTAAACTA
genomic: ATGCCAAGAACATGGGGCTCTACGGGGAACGTGTTGGTGCACTGAGCATTgtaagagacc ... tacattatagGTTTGCAAGACGGCGGATGTGGCAAGCAGGGTTGAGAGCCAGGTTAAACTT
EST: gi|33402663|gb|CF208290.1|CF208290
EST:     GGGGAACGTGTTGGTGCACTGAGCATT                         GTTTGCAAGACGGCGGATGTGGCAAGCAGGGTTGAGAGCCAGGTTAAACTA
genomic: GGGGAACGTGTTGGTGCACTGAGCATTgtaagagacc ... tacattatagGTTTGCAAGACGGCGGATGTGGCAAGCAGGGTTGAGAGCCAGGTTAAACTT
EST: gi|33402572|gb|CF208199.1|CF208199
EST:     ATGCCAAGAACATGGGGCTCTACGGGGAACGTGTTGGTGCACTGAGCATT                         GTTTGCAAGACGGCGGATGTGGCAAGCAGGGTTGAGAGCCAGGGAAAACTA
genomic: ATGCCAAGAACATGGGGCTCTACGGGGAACGTGTTGGTGCACTGAGCATTgtaagagacc ... tacattatagGTTTGCAAGACGGCGGATGTGGCAAGCAGGGTTGAGAGCCAGGTTAAACTT
EST: gi|29783123|gb|CB349091.2|CB349091
EST:     ATGCCAAGAACATGGGGCTCTACGGGGAACGTGTTGGTGCACTGAGCATT                         GTTTGCAAGACGGCGGATGTGGCAAGCAGGGTTGAGAGCCAGGTTAAACTA
genomic: ATGCCAAGAACATGGGGCTCTACGGGGAACGTGTTGGTGCACTGAGCATTgtaagagacc ... tacattatagGTTTGCAAGACGGCGGATGTGGCAAGCAGGGTTGAGAGCCAGGTTAAACTT
EST: gi|30306242|gb|CB983036.1|CB983036
EST:     ATGCCAAGAACATGGGGCTCTACGGGGAACGTGTTGGTGCACTGAGCATT                         GTTTGCAAGACGGC
genomic: ATGCCAAGAACATGGGGCTCTACGGGGAACGTGTTGGTGCACTGAGCATTgtaagagacc ... tacattatagGTTTGCAAGACGGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttggctgctactcgaagttttgccccttatcaatatccatttttacattatagGTTTGCAAGACGGCGGATGTGGCAAGCAGGGTTGAGAGCCAGGTTAAACTTGTGATCAGGCCTATGTTTTCAAACCCACCCATTCATGGTGCATCTATCG
                                     tccattttt  CT-rich tract
                                 aatatccatttttaca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agtgattttgcattctcatattttgagttagtaaatcttatacaaatttggctgctactcgaagttttgccccttatcaatatccatttttacattatagGTTTGCAAGACGGCGGATGTGGCAAGCAGGGTTGAGAGCCAGGTTAAACTTGTGATCAGGCCTATGTTTTCAAACCCACCCATTCATGGTGCATCTATCG

- - - - -gcattct
- - - - - - - - - - - - - - - - - - - -atacaaa
- - - - - - - - - - - - - - - - - - - - - - - - - -ctgctac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccatttt