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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtccaaaagtatcctccttgaccaaatgattatatcctgacctctgtgacttctgtttgaaagcttattgtaagtgaaattgttgggaaatggtctctagGTGTGGAAGAAAGTGGTATATGTTGACCGACTCATGCAGCTGTTCAGATACGTTCCACGTGAGCAGTTGACAATCCCCGACTTTGTGTTTCA

Basic information

species Vitis vinifera
transcript Vv01s0011g00870.t01
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv01s0011g00870.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: LOC_Os03g05660.1 (Oryza sativa), 3'ss of exon 12
gtaagtccaaaagtatcctccttgaccaaatgattatatcctgacctctgtgacttctgtttgaaagcttattgtaagtgaaattgttgggaaatggtctc---tagGTGTGGAAGAAAGTGGTATATGTTGACCGACTCATGCAGCTGTTCAGATACGTTCCACGTGAGCAGTTGACAATCCCCGACTTTGTGTTTCA
|||  | | |  | | ||  || |  |      ||   |||  |  ||| ||||   | |       ||| || ||| |  |     |      | |||||   ||||| |||||||||||  | ||||| ||| ||||  ||||||||||||||||||| |||||||| ||  ||||||| || || ||||| || ||
gtacttgctattgcagccatctcgctcg-----tttcctccccaattctttgacacattt-------ctttttctaattttagcatcttcctttttgtctcaattagGTCTGGAAGAAAGTTATCTATGTCGACAGACTTGTGCAGCTGTTCAGATACGTACCACGTGAACAACTGACAATTCCTGATTTTGTCTTCCA

upper sequence: Vv01s0011g00870.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GRMZM2G100707_T01 (Zea mays), 3'ss of exon 12
gtaagtccaaaagtatcctccttgaccaaatgattatatcctgacctctgtgacttc-tgtttgaaagcttattgtaagtgaaattgttgggaaatggtctctagGTGTGGAAGAAAGTGGTATATGTTGACCGACTCATGCAGCTGTTCAGATACGTTCCACGTGAGCAGTTGACAATCCCCGACTTTGTGTTTCA
            |||  | |||||     |     | | | |    | ||   || | || ||||||  |   | |  ||    |||||   |         ||||| ||||||||||| |||||||| ||| ||||  ||||||| |||||||| || |||||||| ||| | || || || || |||||||| ||
------------gtactcaccttgcagctaaaccaaaaacattctttgtgctgctccgtgcttgaaatttctgttttggt----ttgtttcaa--------ttagGTCTGGAAGAAAGTTGTATATGTCGACAGACTTGTGCAGCTATTCAGATATGTACCACGTGAACAGCTCACCATTCCTGATTTTGTGTTCCA

upper sequence: Vv01s0011g00870.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GRMZM5G836588_T01 (Zea mays), 3'ss of exon 12
gtaagtccaaaagtatcctccttgaccaaatgattatatcctgacctctgtgacttctgtttgaaagcttattgtaagtgaaattgttgggaaatggtctctagGTGTGGAAGAAAGTGGTATATGTTGACCGACTCATGCAGCTGTTCAGATACGTTCCACGTGAGCAGTTGACAATCCCCGACTTTGTGTTTCA
            ||| |||||| |  || |   || |   |||  ||   |||  |||  | | |  ||| ||                     |  ||| ||||| ||||||||||| |||||||| ||  | ||  |||||||||||||||| || ||||| |||||  | ||||| || |||||||| |||||
------------gta-cctcctagttcagacatttcttcactgtgcttcatgagatct--tagcatccttttt---------------------tcctctatagGTCTGGAAGAAAGTTGTATATGTGGATAGGCTTGTGCAGCTGTTCAGATATGTACCACGCGAGCAACTTACAATTCCTGACTTTGTTTTTCA

upper sequence: Vv01s0011g00870.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA20G03330.1 (Glycine max), 3'ss of exon 13
gtaagtccaaaagtatcctccttgaccaaatgattatatcctgacctctgtgacttctgtttgaaagcttattgtaagtgaaattgttgggaaatggtctctagGTGTGGAAGAAAGTGGTATATGTTGACCGACTCATGCAGCTGTTCAGATACGTTCCACGTGAGCAGTTGACAATCCCCGACTTTGTGTTTCA
            |||   |  | ||    |||  ||| |  |||||||    |  | |||||| |   || |           || ||   |  ||   |  |||| ||||||||||||||||||||||| || ||  ||||||| ||||||||||| || ||||| |||||||| ||||| || |||||||||||
------------gtacagtagtagaatttatgcatatttaatgacctcat--atgtgtgtttgtatatttgt----------gttattaaaagttgactttcagGTTTGGAAGAAAGTGGTATATGTTGATCGCCTTCTGCAGCTCTTCAGATACGTACCTCGTGAACAGTTGACCATCCCAGATTTTGTGTTTCA

upper sequence: Vv01s0011g00870.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA07G35280.2 (Glycine max), 3'ss of exon 13
gtaagtccaaaagtatcctccttgaccaaatgattatatcctgacctctgtgacttctgtttgaaagcttattgtaagtgaaattgttgggaaatggtctctagGTGTGGAAGAAAGTGGTATATGTTGACCGACTCATGCAGCTGTTCAGATACGTTCCACGTGAGCAGTTGACAATCCCCGACTTTGTGTTTCA
            |||   |  |  |   || |  ||| |  |||||||    |  | ||| || |    | ||||        || ||   |  |    |  |||| ||||||||||||||||||| ||| |||||  ||||||| ||||||||| | || ||||| |||||||| ||||| || |||||||||||
------------gtacagtattgaaatcaaagcatatttaatgacctc----atatgtgtatgtatatat-ttgtg-------ttattaaaagttaactttcagGTTTGGAAGAAAGTGGTATATGCTGATCGACTTCTGCAGCTCTTCAGATACATACCTCGTGAACAGTTGACCATCCCAGATTTTGTGTTTCA

upper sequence: Vv01s0011g00870.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA07G35280.1 (Glycine max), 3'ss of exon 13
gtaagtccaaaagtatcctccttgaccaaatgattatatcctgacctctgtgacttctgtttgaaagcttattgtaagtgaaattgttgggaaatggtctctagGTGTGGAAGAAAGTGGTATATGTTGACCGACTCATGCAGCTGTTCAGATACGTTCCACGTGAGCAGTTGACAATCCCCGACTTTGTGTTTCA--------
            |||   |  |  |   || |  ||| |  |||||||    |  | ||| || |    | ||||        || ||   |  |    |  |||| ||||||||||||||||||| ||| |||||  ||||||| ||||||||| | || ||||| |||||||| ||||| || |||||||||||        
------------gtacagtattgaaatcaaagcatatttaatgacctc----atatgtgtatgtatatat-ttgtg-------ttattaaaagttaactttcagGTTTGGAAGAAAGTGGTATATGCTGATCGACTTCTGCAGCTCTTCAGATACATACCTCGTGAACAGTTGACCATCCCAGATTTTGTGTTTCAGTTGAGTC

upper sequence: Vv01s0011g00870.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA01G06730.1 (Glycine max), 3'ss of exon 14
gtaagtccaaaagtatcctccttgaccaaatg-attatatcctgacctctgtgacttctgtttgaaagcttattgtaagtgaaattgt---tgggaaatggtctctagGTGTGGAAGAAAGTGGTATATGTTGACCGACTCATGCAGCTGTTCAGATACGTTCCACGTGAGCAGTTGACAATCCCCGACTTTGTGTTTCA
                  | | | |  || || ||| |||    |  | || |||  || ||| |   | | || ||  ||  ||| |   ||   | |    | ||||| |||||||||||||||||||||||  ||||  | ||||| |||||||| || || ||||| || ||||| ||||| || ||||| |||||
-----------------gtgcgttatgaattggattttattaacagatttg-gac--ctatttaaggacatcttatatatgttattatcaatgacgattaacttttagGTTTGGAAGAAAGTGGTATATGTTGATAGACTACTCCAGCTCTTCAGATATGTACCCCGTGAACAATTGACCATCCCAGATTTTGTCTTTCA

upper sequence: Vv01s0011g00870.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA02G12670.1 (Glycine max), 3'ss of exon 13
gtaagtccaaaagtatcctccttgaccaaatgattatatcctgacctctgtgacttctgtttgaaagcttattgtaagtg---aaattgttgggaaatggtctctagGTGTGGAAGAAAGTGGTATATGTTGACCGACTCATGCAGCTGTTCAGATACGTTCCACGTGAGCAGTTGACAATCCCCGACTTTGTGTTTCA
               | |    |||   |  ||||  ||  | ||   | | |   || ||| |   | | || ||  ||     ||  |||   | |    | ||||| |||||||||||||||||||||||  ||||  | ||||| || |||||| | || ||||| || ||||| ||||| || || || |||||
--------------gtgcgttatgaatca--gatttcat--taacagatttaaac-ctatttaaggacatcttatacatgttcttatcattgacgattaacttttagGTTTGGAAGAAAGTGGTATATGTTGATAGACTACTACAGCTCTTTAGATACATACCCCGTGAACAATTGACCATCCCAGATTTCGTCTTTCA

upper sequence: Vv01s0011g00870.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: AT1G69340.1 (Arabidopsis thaliana), 3'ss of exon 13
gtaa-gtccaaaagtatcctccttgaccaaatgattatatcctgacctctgtgacttctgtttgaaagcttattgtaagtgaaattgttg---------ggaaatggtctctagGTGTGGAAGAAAGTGGTATATGTTGACCGACTCATGCAGCTGTTCAGATACGTTCCACGTGAGCAGTTGACAATCCCCGACTTTGTGTTTCA
|||| ||||  || |||         ||||    ||    |   |     | | | |      |||  || |||    || |  || |||         | |||        |||| ||||||||||| |||||||  ||||||||  |||||||||||| ||||||||| ||||||||| |||||||||| |||||||| || ||
gtaaagtcctgaattatttcaaagtcccaaccttttccgccgatagactcgagtcattctaaagaagtctaatttgctgtcattttcttgttccatttcgaaaaatccgataagGTATGGAAGAAAGTTGTATATGCAGACCGACTTCTGCAGCTGTTCAAATACGTTCCTCGTGAGCAGCTGACAATCCCAGACTTTGTTTTCCA

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|77580521|gb|DV219155.1|DV219155
EST:     CTGGATTGAAGGCTGCAGTTTTTGCTCTGCAATTGTTTGTAGATAATGTG                         GTGTGGAAGAAAGTGGTATATGTTGACCGACTCATGCAGCTGTTCAGATAC
genomic: TTGGATTGAAGGCTGCAGTTTTTGCTCTGCAATTGTTTGTAGATAATGTGgtaagtccaa ... tggtctctagGTGTGGAAGAAAGTGGTATATGTTGACCGACTCATGCAGCTGTTCAGATAC
EST: gi|45368236|gb|CK906595.1|CK906595
EST:     TTGGATTGAAGGCTGCAGTTTTTGCTCTGCAATTGTTTGTAGATAATGTG                         GTGTGGAAGAAAGTGGTATATGTTGACCGACTCATGCAGCTGTTCAGATAC
genomic: TTGGATTGAAGGCTGCAGTTTTTGCTCTGCAATTGTTTGTAGATAATGTGgtaagtccaa ... tggtctctagGTGTGGAAGAAAGTGGTATATGTTGACCGACTCATGCAGCTGTTCAGATAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgacttctgtttgaaagcttattgtaagtgaaattgttgggaaatggtctctagGTGTGGAAGAAAGTGGTATATGTTGACCGACTCATGCAGCTGTTCAGATACGTTCCACGTGAGCAGTTGACAATCCCCGACTTTGTGTTTCA
                                                tctct  CT-rich tract
                   ttattgtaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtccaaaagtatcctccttgaccaaatgattatatcctgacctctgtgacttctgtttgaaagcttattgtaagtgaaattgttgggaaatggtctctagGTGTGGAAGAAAGTGGTATATGTTGACCGACTCATGCAGCTGTTCAGATACGTTCCACGTGAGCAGTTGACAATCCCCGACTTTGTGTTTCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG