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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtaaaaatttgttttctcaaaataaagcacatatgtatatatctatctgtaaaaagccatttgaatgttagatgacatagaaaagtgattgtctttgcagGAAGACACTTTCAACCAGAAAAGTAAGTGCAACTAGTGGGGCAGCTTCGGTTCCTGATGAGGTTTTCCACAGAGCCAAAGGGGTCCAGTTGTGCAATACT

Basic information

species Vitis vinifera
transcript Vv08s0007g01660.t01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0007g01660.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM5G892742_T03 (Zea mays), 3'ss of exon 6
gtaaaaatttgttttctcaaa-----ataaagcacatatgtatatatctatctgtaaaaagccatttgaatgttagatgacatagaaaagtgattgtctttgcagGAAGACACTTTCAACCAGAAAAGTAAGTGCAACTAGTGGGGCAGCTTCGGTTCCTGATGAGGTTTTCCACAGAGCCAAAGGGGTCCAGTTGTGCAATACT
 |  | |||| |||| |  ||       ||   |    |  | ||  || | |  |  || ||  |   || |      |  | |||     ||| | ||| ||||||||| || ||| | |||||||| |||||| |||| ||||| || ||||| ||||| || |||||||||||||||||||| || ||| | ||||| |  
-tgtatatttattttatttaatagtttcaagaaatcacttcagattgctgt-tacagtaatcccctgatatatcgatccaactcgaa---ctattctgtttccagGAAGACGCTGTCAGCTAGAAAAGTTAGTGCAGCTAGAGGGGCTGCCTCGGTCCCTGAAGAAGTTTTCCACAGAGCCAAAGGAGTGCAGCTATGCAACATA

upper sequence: Vv08s0007g01660.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA18G41980.1 (Glycine max), 3'ss of exon 4
gtaaaaatttgttttctcaaaa--taaagcacatatgtatata-tctatctg-taaaaagccatttgaatgttagatgacatagaaaagtgattgt---ctttgcagGAAGACACTTTCAACCAGAAAAGTAAGTGCAACTAGTGGGGCAGCTTCGGTTCCTGATGAGGTTTTCCACAGAGCCAAAGGGGTCCAGTTGTGCAATACT
       |||||||     |    ||| |||   |  |  ||  | |   |  ||   |  |  || | ||  |    | |   | | ||| ||||    ||| ||||||||||||||||||  | ||||||| |||||||||||| ||||| || || || |||||||||| ||| ||| |||||||||| || |||||||| |||
-------tttgtttaagagattcctaaggcatccagtttcatggtatgcttaatattgattccctttagtgcaatgctaaaggaacacgtgtttgtgctttttacagGAAGACACTTTCAACTCGGAAAGTAAATGCAACTAGTGGAGCAGCATCAGTACCAGATGAGGTTTCCCATAGATCCAAAGGGGTTCAATTGTGCAACACT

upper sequence: Vv08s0007g01660.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA07G17240.1 (Glycine max), 3'ss of exon 6
-------gtaaaa-atttgttttctcaaaataaagcacatatgtatatatctatctgtaaaaa-gccatttgaatgttagatgacatagaaaagtgattgtctttgcagGAAGACACTTTCAACCAGAAAAGTAAGTGCAACTAGTGGGGCAGCTTCGGTTCCTGATGAGGTTTTCCACAGAGCCAAAGGGGTCCAGTTGTGCAATACT
        |||    |    ||||      | | ||  | || |  ||  || |  || | || || |   |||||        | |      ||    |  ||| ||||||||||||||||||  | ||||||| |||||| ||||| ||||| || || || ||||| |||||||| ||| |||||||||| || |||||||| |||
tagattcataaggcgtccagtttcatgttgttatgctta-atattgattccttttagtgacaatgctaaaggaatg--------cgtgtctgtgtttgcgcttttacagGAAGACACTTTCAACTCGGAAAGTAAATGCAACAAGTGGAGCAGCATCAGTACCGGATGAAGTTTTCCATAGATCCAAAGGGGTTCAATTGTGCAACACT

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|77579124|gb|DV218390.1|DV218390
EST:     TGTCGTGGAGGTGGTTCTCTTTTGACACATGACGTTGCTGTGATTAGATG                         GAAGACACTTTCAACCAGAAAAGTAAGTGCAACTAGTGGGGCAGCTTCGGT
genomic: TGTCGTGGAGGTGGTTCTCTTTTGACACACGATGTTGCTGTGATTAGATGgtacgtatgt ... gtctttgcagGAAGACACTTTCAACCAGAAAAGTAAGTGCAACTAGTGGGGCAGCTTCGGT
EST: gi|34363111|gb|CF404696.1|CF404696
EST:     GTTGCTGTGATTAGATG                         GAAGACNCTTTCACCCAGAAAAGTAAGTGCAACTAGTGGGGCAGCTTCGGT
genomic: GTTGCTGTGATTAGATGgtacgtatgt ... gtctttgcagGAAGACACTTTCAACCAGAAAAGTAAGTGCAACTAGTGGGGCAGCTTCGGT
EST: gi|110418300|gb|EC984441.1|EC984441
EST:     TGTCGTGGAGGTGGTTCTCTTTTGACACACGATGTTGCTGTGATTAGATG                         GAAGACACTTTCAACCAGAAAAGTAAGTGCAACTAGTGGGGCAGCTTCGGT
genomic: TGTCGTGGAGGTGGTTCTCTTTTGACACACGATGTTGCTGTGATTAGATGgtacgtatgt ... gtctttgcagGAAGACACTTTCAACCAGAAAAGTAAGTGCAACTAGTGGGGCAGCTTCGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctgtaaaaagccatttgaatgttagatgacatagaaaagtgattgtctttgcagGAAGACACTTTCAACCAGAAAAGTAAGTGCAACTAGTGGGGCAGCTTCGGTTCCTGATGAGGTTTTCCACAGAGCCAAAGGGGTCCAGTTGTGCAATACT
                                           ttgtcttt  CT-rich tract
             atttgaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaaaatttgttttctcaaaataaagcacatatgtatatatctatctgtaaaaagccatttgaatgttagatgacatagaaaagtgattgtctttgcagGAAGACACTTTCAACCAGAAAAGTAAGTGCAACTAGTGGGGCAGCTTCGGTTCCTGATGAGGTTTTCCACAGAGCCAAAGGGGTCCAGTTGTGCAATACT

gtaaaaa
- - - - - - - - - aaaataa
- - - - - - - - - - - - - gcacata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - ccatttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tagaaaa