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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attccatgcaatttaataatatacctttacctgaagttcattgtgctttcatgcatcatttggttcatatgtcaagtcataatactctttggtggttcagGGCCCAAGGGTGATTGTTGTTGGACCTGTAGATTCCGGAAAGAGTACACTGTCAAGGATGCTTCTTAGTTGGTCTGCTAAGCAGGGTTGGAAGCCTACTT

Basic information

species Vitis vinifera
transcript Vv14s0066g02630.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0066g02630.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA10G43930.1 (Glycine max), 3'ss of exon 3
----attccatgcaatttaataatatacctttacctgaagttcattgtgctttcatgcatcat--ttggttcatatgtcaagtcataatactctttggtggttcagGGCCCAAGGGTGATTGTTGTTGGACCTGTAGATTCCGGAAAGAGTACACTGTCAAGGATGCTTCTTAGTTGGTCTGCTAAGCAGGGTTGGAAGCCTACTT
    |||    | || ||      | |   ||     ||  |  |  |  | ||||  ||  |  |    |  ||||| || |      |   |||||| | ||||||||| ||||| |||||||| ||||||   ||||| |||||||||||  ||||||||||||||||||||||| | ||||| || |||||||| ||||| |
ctttattttgcgtaagttgtgccaagagacttg---aaaacttgtgattttatcatagattgtcgtcttgtggtatgtgaattttgtgaa---tttggttggtcagGGCCCTAGGGTCATTGTTGTAGGACCTACTGATTCTGGAAAGAGTACCTTGTCAAGGATGCTTCTTAGTTGGGCAGCTAAACAAGGTTGGAAACCTACCT

upper sequence: Vv14s0066g02630.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA20G38670.1 (Glycine max), 3'ss of exon 3
attccatgcaatttaataatatacctttacctgaagttcattgtgctttcatgcatcatttggttcatatgtcaagtcataatactc--tttggtggttcagGGCCCAAGGGTGATTGTTGTTGGACCTGTAGATTCCGGAAAGAGTACACTGTCAAGGATGCTTCTTAGTTGGTCTGCTAAGCAGGGTTGGAAGCCTACTT
|   | ||  |||| || ||| |   | |  ||  |||  ||    |    || |   | |    | | ||  | || |   |  |   |||||| | ||||||||| ||||| |||||||| ||||||   ||||| |||||||||||  |||| |||||||||||||||||| | ||||| || |||||||||||||| |
aaagcttgtgattttatcatagattgtca--tgttgttactttctttcatttgtaagctctaaagcttgtggtatgtgaattttgtgaatttggttggtcagGGCCCTAGGGTCATTGTTGTAGGACCTACTGATTCTGGAAAGAGTACCTTGTCGAGGATGCTTCTTAGTTGGGCAGCTAAACAAGGTTGGAAGCCTACCT

upper sequence: Vv14s0066g02630.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA09G07820.1 (Glycine max), 3'ss of exon 4
---attccatgcaatttaataatatacctttacctgaagttcattgtgctttcatgcatcatttggttcatatgtcaagtcataatactctttggtggttcagGGCCCAAGGGTGATTGTTGTTGGACCTGTAGATTCCGGAAAGAGTACACTGTCAAGGATGCTTCTTAGTTGGTCTGCTAAGCAGGGTTGGAAGCCTACTT
       | ||  |||| || ||| |   | |  | |  ||| ||    | | |    | |  |   |  ||||| || |      |   |||||| | ||||||||| ||||| |||||||| ||||||   ||||| |||||||||||  |||| ||||||||||||||| || | | ||| || |||||||||||||| |
ttggaagcttgtgattttatcatagattgtcatgttattttctttcatttgtaagctctaaagtttgtggtatgtgaattttgtgaa---tttggttggtcagGGCCCTAGGGTCATTGTTGTAGGACCTACTGATTCTGGAAAGAGTACCTTGTCGAGGATGCTTCTTAGTAGGGCAGTTAAACAAGGTTGGAAGCCTACCT

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|351053969|gb|FQ441735.1|FQ441735
EST:     GAAGAAATCGTGCCAAAGCCTCTTCATCTGGTGATGCTGAAGCTTCTCAG                         GGCCCAAGGGTGATTGTTGTTGGACCTGTAGATTCCGGAAAGAGTACACGG
genomic: GAAGAAATCGTGCCAAAGCCTCTTCATCTGGTGATGCTGAAGCTTCTCAGgtatttcttt ... ggtggttcagGGCCCAAGGGTGATTGTTGTTGGACCTGTAGATTCCGGAAAGAGTACACTG
EST: gi|351048068|gb|FQ441240.1|FQ441240
EST:     GAAGAAATCGTGCCAAAGCCTCTTCATCTGGTGATGCTGAAGCTTCTCAG                         GGCCCAAGGGTGATTGTTGTTGGACCTGTAGATTCCGGAAAGAGTACACTG
genomic: GAAGAAATCGTGCCAAAGCCTCTTCATCTGGTGATGCTGAAGCTTCTCAGgtatttcttt ... ggtggttcagGGCCCAAGGGTGATTGTTGTTGGACCTGTAGATTCCGGAAAGAGTACACTG
EST: gi|351037774|gb|FQ464215.1|FQ464215
EST:     GAAGAAATCGTGCCAAAGCCTCTTCATCTGGTGATGCTGAAGCTTCTCAG                         GGCCCAAGGGTGATTGTTGTTGGACCTGTAGATTCCGGAAAGAGTACACTG
genomic: GAAGAAATCGTGCCAAAGCCTCTTCATCTGGTGATGCTGAAGCTTCTCAGgtatttcttt ... ggtggttcagGGCCCAAGGGTGATTGTTGTTGGACCTGTAGATTCCGGAAAGAGTACACTG
EST: gi|22013971|gb|BQ799005.1|BQ799005
EST:     GAAGAAATCGTGCCAAAGCCTCTTCATCTGGTGATGCTGAAGCTTCTCAG                         GGCCCAAGGGTGATTGTTGTTGGACCTGTAGATTCCGGAAAGAGTACACTG
genomic: GAAGAAATCGTGCCAAAGCCTCTTCATCTGGTGATGCTGAAGCTTCTCAGgtatttcttt ... ggtggttcagGGCCCAAGGGTGATTGTTGTTGGACCTGTAGATTCCGGAAAGAGTACACTG
EST: gi|71862039|gb|DT011094.1|DT011094
EST:     GAAGAAATCGTGCCAAAGCCTCTTCATCTGGTGATGCTGAAGCTTCTCAG                         GGCCCAAGGGTGATTGTTGTTGGACCTGTAGATTCCGGAAAGAGTACACTG
genomic: GAAGAAATCGTGCCAAAGCCTCTTCATCTGGTGATGCTGAAGCTTCTCAGgtatttcttt ... ggtggttcagGGCCCAAGGGTGATTGTTGTTGGACCTGTAGATTCCGGAAAGAGTACACTG
EST: gi|352791526|gb|FQ481105.1|FQ481105
EST:     GAAGAAATCGTGCCAAAGCCTCTTCATCTGGTGATGCTGAAGCTTCTCAG                         GGCCCAAGGGTGATTGTTGTTGGACCTGTAGATTCCGGAAAGAGTACACTG
genomic: GAAGAAATCGTGCCAAAGCCTCTTCATCTGGTGATGCTGAAGCTTCTCAGgtatttcttt ... ggtggttcagGGCCCAAGGGTGATTGTTGTTGGACCTGTAGATTCCGGAAAGAGTACACTG
EST: gi|351044652|gb|FQ443183.1|FQ443183
EST:     GAAGAAATCGTGCCAAAGCCTCTTCATCTGGTGATGCTGAAGCTTCTCAG                         GGCCCAAGGGTGATTGTTGTTGGACCTGTAGATTCCGGAAAGAGTACACTG
genomic: GAAGAAATCGTGCCAAAGCCTCTTCATCTGGTGATGCTGAAGCTTCTCAGgtatttcttt ... ggtggttcagGGCCCAAGGGTGATTGTTGTTGGACCTGTAGATTCCGGAAAGAGTACACTG
EST: gi|351053260|gb|FQ459128.1|FQ459128
EST:     GAAGAAATCGTGCCAAAGCCTCTTCATCTGGTGATGCTGAAGCTTCTCAG                         GGCCCAAGGGTGATTGTTGTTGGACCTGTAGATTCCGGAAAGAGTACACTG
genomic: GAAGAAATCGTGCCAAAGCCTCTTCATCTGGTGATGCTGAAGCTTCTCAGgtatttcttt ... ggtggttcagGGCCCAAGGGTGATTGTTGTTGGACCTGTAGATTCCGGAAAGAGTACACTG
EST: gi|161715992|gb|FC068763.1|FC068763
EST:     GAAGAAATCGTGCCAAAGCCTCTTCATCTGGTGATGCTGAAGCTTCTCAG                         GGCCCAAGGGTGATTGTTGTTGGACCTGTAGATTCCGGAAAGAGTACACTG
genomic: GAAGAAATCGTGCCAAAGCCTCTTCATCTGGTGATGCTGAAGCTTCTCAGgtatttcttt ... ggtggttcagGGCCCAAGGGTGATTGTTGTTGGACCTGTAGATTCCGGAAAGAGTACACTG
EST: gi|110422874|gb|EC989207.1|EC989207
EST:     GAAGAAATCGTGCCAAAGCCTCTTCATCTGGTGATACTGAAGCTTCTCAG                         GGCCCAAGGGTGATTGTTGTTGGACCTGTAGATTCCGGAAAGAGTACACTG
genomic: GAAGAAATCGTGCCAAAGCCTCTTCATCTGGTGATGCTGAAGCTTCTCAGgtatttcttt ... ggtggttcagGGCCCAAGGGTGATTGTTGTTGGACCTGTAGATTCCGGAAAGAGTACACTG
EST: gi|352789973|gb|FQ479583.1|FQ479583
EST:     GAAGAAATCGTGCCAAAGCCTCTTCATCTGGTGATGCTGAAGCTTCTCAG                         GGCCCAAGGGTGATTGTTGTTGGACCTGTAGATTCCGGAAAGAGTACACTG
genomic: GAAGAAATCGTGCCAAAGCCTCTTCATCTGGTGATGCTGAAGCTTCTCAGgtatttcttt ... ggtggttcagGGCCCAAGGGTGATTGTTGTTGGACCTGTAGATTCCGGAAAGAGTACACTG
EST: gi|351046157|gb|FQ442535.1|FQ442535
EST:     GAAGAAATCGTGCCAAAGCCTCTTCATCTGGTGATGCTGAAGCTTCTCAG                         GGCCCAAGGGTGATTGTTGTTGGACCTGTAGATTCCGGAAAGAGTACACTG
genomic: GAAGAAATCGTGCCAAAGCCTCTTCATCTGGTGATGCTGAAGCTTCTCAGgtatttcttt ... ggtggttcagGGCCCAAGGGTGATTGTTGTTGGACCTGTAGATTCCGGAAAGAGTACACTG
EST: gi|351037634|gb|FQ462618.1|FQ462618
EST:     GAAGAAATCGTGCCAAAGCCTCTTCATCTGGTGATGCTGAAGCTTCTCAG                         GGCCCAAGGGTGATTGTTGTTGGACCTGTAGATTCCGGAAAGAGTACACTG
genomic: GAAGAAATCGTGCCAAAGCCTCTTCATCTGGTGATGCTGAAGCTTCTCAGgtatttcttt ... ggtggttcagGGCCCAAGGGTGATTGTTGTTGGACCTGTAGATTCCGGAAAGAGTACACTG
EST: gi|351039234|gb|FQ457909.1|FQ457909
EST:     GAAGAAATCGTGCCAAAGCCTCTTCATCTGGTGATGCTGAAGCTTCTCAG                         GGCCCAAGGGTGATTGTTGTTGGACCTGTAGATTCCGGAAAGAGTACACTG
genomic: GAAGAAATCGTGCCAAAGCCTCTTCATCTGGTGATGCTGAAGCTTCTCAGgtatttcttt ... ggtggttcagGGCCCAAGGGTGATTGTTGTTGGACCTGTAGATTCCGGAAAGAGTACACTG
EST: gi|351042381|gb|FQ442848.1|FQ442848
EST:     GAAGAAATCGTGCCAAAGCCTCTTCATCTGGTGATGCTGAAGCTTCTCAG                         GGCCCAAGGGTGATTGTTGTTGGACCTGTAGATTCCGGAAAGAGTACACTG
genomic: GAAGAAATCGTGCCAAAGCCTCTTCATCTGGTGATGCTGAAGCTTCTCAGgtatttcttt ... ggtggttcagGGCCCAAGGGTGATTGTTGTTGGACCTGTAGATTCCGGAAAGAGTACACTG
EST: gi|351056907|gb|FQ443534.1|FQ443534
EST:     GAAGAAATCGTGCCAAAGCCTCTTCATCTGGTGATGCTGAAGCTTCTCAG                         GGCCCAAGGGTGATTGTTGTTGGACCTGTAGATTCCGGAAAGAGTACACTG
genomic: GAAGAAATCGTGCCAAAGCCTCTTCATCTGGTGATGCTGAAGCTTCTCAGgtatttcttt ... ggtggttcagGGCCCAAGGGTGATTGTTGTTGGACCTGTAGATTCCGGAAAGAGTACACTG
EST: gi|110731309|gb|EE105610.1|EE105610
EST:     GAAGAAATCGTGCCAAAGCCTCTTCATCTGGTGATACTGAAGCTTCTCAG                         GGCCCAAGGGTGATTGTTGTTGGACCTGTAGATTCTGGAAAGAGTACACTG
genomic: GAAGAAATCGTGCCAAAGCCTCTTCATCTGGTGATGCTGAAGCTTCTCAGgtatttcttt ... ggtggttcagGGCCCAAGGGTGATTGTTGTTGGACCTGTAGATTCCGGAAAGAGTACACTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctttcatgcatcatttggttcatatgtcaagtcataatactctttggtggttcagGGCCCAAGGGTGATTGTTGTTGGACCTGTAGATTCCGGAAAGAGTACACTGTCAAGGATGCTTCTTAGTTGGTCTGCTAAGCAGGGTTGGAAGCCTACTT
                                       ctctttg  CT-rich tract
                               tcataata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attccatgcaatttaataatatacctttacctgaagttcattgtgctttcatgcatcatttggttcatatgtcaagtcataatactctttggtggttcagGGCCCAAGGGTGATTGTTGTTGGACCTGTAGATTCCGGAAAGAGTACACTGTCAAGGATGCTTCTTAGTTGGTCTGCTAAGCAGGGTTGGAAGCCTACTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- -ccatgca
- - - - - - - - - - - - - - acctgaa
- - - - - - - - - - - - - - - - - - - - - - - - tcatgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tcaagtc