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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gcaagcgctttgcttgattggccattcatctccatgactttaggttagttttagatggtttgagtccatgtcaacattaggggccaggaattttctgtctgcatgctaatgctgattcttttaatcatggcagGTGTGGTTTCGTGTTAATGAGCAATTGCCTGCTGCATTACAGAAGTCATTACCTGACAGGCCACCTGGGATGAATCAATCTGCGGCTGATGGGCATGAAG

Basic information

species Vitis vinifera
transcript Vv13s0156g00640.t01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv13s0156g00640.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os09g10720.1 (Oryza sativa), 3'ss of exon 4
gcaagcgctttgcttgattggccattcatctccatgactttaggttagttttagatggtttgagtccatgtcaacattaggggccaggaattttctgtctgcatgctaatgctgattcttttaatcatggcagGTGTGGTTTCGTGTTAATGAGCAATTGCCTGCTGCATTACAGAAGTCATTACCTGACAGGCCACCTGGGATGAATCAA--TCTGCGGCTGATGGGCATGAAG
||||| ||||||||||||||||||||||  ||||||| ||||||||||| |||  | |||   |  |  || ||  | |   |  |    | |||||| |     |||||  |  ||| ||||  ||| | |||||||||| ||||| |||||   | | ||    | | | || |||   ||||||||  |  | ||     || ||||   | || | |  ||     ||| |
gcaagggctttgcttgattggccattcacttccatgaatttaggttagtcttaattagttcatgctc-cgtaaaagtgaaatgtaaaaggtcttctgtttct---ctaattgtatttcattta-ccattgtagGTGTGGTTCCGTGTCAATGAATTACTTCCGTTGGAACTTCAAAAGGACTTACCTGATGGATCTCC--ATCTGGATCAGCTTTTGAGTCGCATATTACTGAGG

upper sequence: Vv13s0156g00640.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os02g37880.3 (Oryza sativa), 3'ss of exon 5
gcaagcgctttgcttgattggccattcatctccatgactttaggttagttttagatggtttgagtccatgtcaacattaggggccaggaa---ttttctgtctgcatgctaatgctgattcttttaatcatggcagGTGTGGTTTCGTGTTAATGAGCAATTGCCTGCTGCATTACAGAAGTCATTACCTGACAGGCCACCTGGGATGAATCAATCTGCGGCTGATGGGCATGAAG
||||| |||||| ||||||||||||||||||||||||   |||||||||  ||||  |||      ||||| | | |||||  |||   |    | | | |||  || || ||| |     || ||    || ||||| ||||||||||| ||||| | | | |||   |  ||||||||     |||| ||  |  |  | |  | | ||     || |  ||   |  ||||||
gcaagagctttgattgattggccattcatctccatgatactaggttagtcatagactgttg-----catgt-agccttaggaaccacataagcatatttttctaaat-ctgatgttagactttgtacatttgacagGTCTGGTTTCGTGTAAATGAACTACTACCTCTCGAGTTACAGAAAAATCTACCCGATGGAGCTTC-GTCAGGCATTTCCATGAGTTTGCAAG--ATGAAG

upper sequence: Vv13s0156g00640.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G416684_T01 (Zea mays), 3'ss of exon 3
-----------------------------------------------------------------------gcaagcgctttgcttgattggccattcatctccatgactttaggttagttttagatggtttgagtccatgtcaacattaggggccaggaattttctgtctgcatgctaatgctgattcttttaatcatggcagGTGTGGTTTCGTGTTAATGAGCAATTGCCTGCTGCATTACAGAAGTCATTACCTGACAGGCCACCTGGGATGAATCA--ATCTGCGGCTGATGGGCATGAAG
                                                                       ||||| ||||||||||||||||||||||  |||||||  ||||||| || |||  | ||       |   | ||    |      ||  || |||||| |  ||| | ||| | | | || |  |      |||||||||| ||| ||||||||  | | ||    |   | || |||   ||||||||  |  | ||     || ||||  || ||   || |          |
gttcttctattacaacacttatcaaagacatgcttaattcttctccagatgccagaccggacatcacacaggcaagggctttgcttgattggccattcacttccatgaacttaggttggtcttaattagtgcatacac-catgaaacgaacacataagagatcttctgtttcaatgttgatgataaatgttctgttt----tagGTGTGGTTCCGTATTAATGAGTTACTTCCATTGGAGCTGCAAAAGGATTTACCTGATGGATCTCC--ATCTGGATCAGCATTTGAATCTCACACTGCCACTG

upper sequence: Vv13s0156g00640.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA08G15920.1 (Glycine max), 3'ss of exon 6
gcaagcgctttgcttgattggccattcatctccatgactttaggttagttttagatggtttgagtccatgtcaacattaggggccaggaattttctgtctgcatgctaatgctgat--tcttttaatcatggcagGTGTGGTTTCGTGTTAATGAGCAATTGCCTGCTGCATTACAGAAGTCATTACCTGACAGGCCACCTGGGATGAATCAATCTGCGGCTGATGGGCATGAAG
                                               ||  |||||  |     || ||  ||    ||||  | || | |        |   | || |   ||    |  ||   |  |||||||| ||||||||||||||||||||| | |||  |   ||||||||||||||||||||||| |||||||   ||     |||    | | |||    ||| |
-----------------------------------------------gtcatagatcatcca--tcaatagcattcataggtactagaattagggcaattaattactgactttggatgttcttccgtggtggcagGTCTGGTTTCGTGTTAATGAGCAACTACCTATTAATTTACAGAAGTCATTACCTGACAGACCACCTGAATTGCCCTCATCCAACGATCATGAAGGTGACG

upper sequence: Vv13s0156g00640.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA15G42460.1 (Glycine max), 3'ss of exon 6
gcaagcgctttgcttgattggccattcatctccatgactttaggttagttttagatggt---ttgagtccatgtcaacattaggggccaggaattttctgtctgcatgctaatgctgattct--tttaatcatggcagGTGTGGTTTCGTGTTAATGAGCAATTGCCTGCTGCATTACAGAAGTCATTACCTGACAGGCCACCTGGGATGAATCAATCTGCGGCTGATGGGCATGAAG
|||||||||||||||||||| |||||||||||||| | |||||||| ||  |||||  |   ||||   ||| |||    || |  | || | |        |   | || |   ||  | |  ||  ||  |||||||| ||||||||||||||||||||| | |||  |   ||||||||||| ||||||||||| |||||||     ||||   || |  || |    |||||||
gcaagcgctttgcttgattgaccattcatctccatcagtttaggttggtcatagatcatccattgatagcat-tcataggtacgtactagaattagggcaattaattactgactttggatgtacttccatggtggcagGTCTGGTTTCGTGTTAATGAGCAACTACCTATTAATTTACAGAAGTCGTTACCTGACAGACCACCTG-----AATCGCCCT-CATCTAACAATCATGAAG

upper sequence: Vv13s0156g00640.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA15G42460.1 (Glycine max), 3'ss of exon 6
gcaagcgctttgcttgattggccattcatctccatgactttaggttagttttagatggt---ttgagtccatgtcaacattaggggccaggaattttctgtctgcatgctaatgctgattct--tttaatcatggcagGTGTGGTTTCGTGTTAATGAGCAATTGCCTGCTGCATTACAGAAGTCATTACCTGACAGGCCACCTGGGATGAATCAATCTGCGGCTGATGGGCATGAAG
|||||||||||||||||||| |||||||||||||| | |||||||| ||  |||||  |   ||||   ||| |||    || |  | || | |        |   | || |   ||  | |  ||  ||  |||||||| ||||||||||||||||||||| | |||  |   ||||||||||| ||||||||||| |||||||     ||||   || |  || |    |||||||
gcaagcgctttgcttgattgaccattcatctccatcagtttaggttggtcatagatcatccattgatagcat-tcataggtacgtactagaattagggcaattaattactgactttggatgtacttccatggtggcagGTCTGGTTTCGTGTTAATGAGCAACTACCTATTAATTTACAGAAGTCGTTACCTGACAGACCACCTG-----AATCGCCCT-CATCTAACAATCATGAAG

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|29786212|gb|CB343818.2|CB343818
EST:     TCAGGGACATGCTGCAAGCTTCTCCAGACAATCGACCAGACATCACGCAG                         GTGTGGTTTCGTGTTAATGAGCAATTGCCTGCTGCATTACAGAAGTCATTA
genomic: TCAGGGACATGCTGCAAGCTTCTCCAGACAATCGACCAGACATCACGCAGgcaagcgctt ... atcatggcagGTGTGGTTTCGTGTTAATGAGCAATTGCCTGCTGCATTACAGAAGTCATTA
EST: gi|110730727|gb|EE108139.1|EE108139
EST:     TCAGGGACATGCTGCAAGCTTCTCCAGACAATCGACCAGACATCACGCAG                         GTGTGGTTTCGTGTTAATGAGCAATTGCCTGCTGCATTACAGAAGTCATTA
genomic: TCAGGGACATGCTGCAAGCTTCTCCAGACAATCGACCAGACATCACGCAGgcaagcgctt ... atcatggcagGTGTGGTTTCGTGTTAATGAGCAATTGCCTGCTGCATTACAGAAGTCATTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aggggccaggaattttctgtctgcatgctaatgctgattcttttaatcatggcagGTGTGGTTTCGTGTTAATGAGCAATTGCCTGCTGCATTACAGAAGTCATTACCTGACAGGCCACCTGGGATGAATCAATCTGCGGCTGATGGGCATGAAG
                                    attcttttaatcat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcaagcgctttgcttgattggccattcatctccatgactttaggttagttttagatggtttgagtccatgtcaacattaggggccaggaattttctgtctgcatgctaatgctgattcttttaatcatggcagGTGTGGTTTCGTGTTAATGAGCAATTGCCTGCTGCATTACAGAAGTCATTACCTGACAGGCCACCTGGGATGAATCAATCTGCGGCTGATGGGCATGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT