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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TAGGTTTGGAACCATTTCAACCACTTGGCTTCTTGGAAACTTCCTTCAATCCTTCCTACAAAGTTCTGGTGCTTTTGAAGTGTACTGCAATGGTGAATTGgtaaagtcttatctttgcttagctatttcttttttctttttgttctttttatataaattaagaggttactactcagcagggtgctacttagtaaggaaaa...

Basic information

species Vitis vinifera
transcript Vv08s0105g00440.t01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0105g00440.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: LOC_Os05g39110.1 (Oryza sativa), 5'ss of exon 3
TAGGTTTGGAACCATTTCAACCACTTGGCTTCTTGGAAACTTCCTTCAATCCTTCCTACAAAGTTCTGGTGCTTTTGAAGTGTACTGCAATGGTGAATTGgtaaagtcttatctttgcttagctatttcttttttctttttgttctttttatataaattaagaggttactac-tcagcagggtgctacttagtaaggaaaa
||| |||||||||||  |||| |  |||||  |||| || ||    ||||| |||||||||||||||||||| |||||||| ||||||||||| || ||||||   | |     |     |    | |     |||||||| |      | | || |||| | | | | |   |    ||| |   ||  | |||  |   
TAGATTTGGAACCATGGCAACAATCTGGCTATTTGGCAATTTTGCGCAATCTTTCCTACAAAGTTCTGGTGCCTTTGAAGTTTACTGCAATGGAGATTTGgtatgctttctatgtcagacacacctgtaaaacttctttttatctgccatttttacattacgggctaattttatttctaggattaaaccaattaaaaatt-

upper sequence: Vv08s0105g00440.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: LOC_Os01g61580.2 (Oryza sativa), 5'ss of exon 4
TAGGTTTGGAACCATTTCAACCACTTGGCTTCTTGGAAACTTCCTTCAATCCTTCCTACAAAGTTCTGGTGCTTTTGAAGTGTACTGCAATGGTGAATTGgtaaagtcttatctttgcttagctatttcttttttctttttgttctttttatataaattaagaggttactactcagc---agggtgctacttagtaaggaaaa--
||| |||||||| ||  |||| |  |||||  |||| || |||   || || || ||||||||||||||||| |||||||| |||||||||||  ||||||||   | ||   | ||| ||   ||   ||||||   |    |  ||   ||  | ||  |    |  ||   |     ||  | |  |         ||||  
TAGATTTGGAACAATGGCAACAATCTGGCTGTTTGGCAATTTCGCCCAGTCATTTCTACAAAGTTCTGGTGCCTTTGAAGTTTACTGCAATGGACAATTGgta---tgtttgttatgcata--catccttttttttgctgcagtggttcagtagtacttttgcttgtgttatgtaatgttagaatcccccccccccccaaaaaaa

upper sequence: Vv08s0105g00440.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GRMZM2G173874_T01 (Zea mays), 5'ss of exon 3
TAGGTTTGGAACCATTTCAACCACTTGGCTTCTTGGAAACTTCCTTCAATCCTTCCTACAAAGTTCTGGTGCTTTTGAAGTGTACTGCAATGGTGAATTGgtaaagt-cttatctttgct-tagctatttcttttttctttt-tgttctttttatataaattaagaggttactactcagcagggtgctacttagtaaggaaaa
||| || ||||||||  |||| |  |||||  |||| |||||   ||| ||||| |||||||| |||||||| |||||||| ||||||||||| || ||||||   | | ||| || | |  | |  | ||||||||||||| ||||  ||| ||  ||| |      |||    |||| || |  ||   |  | |   |  
TAGATTCGGAACCATGGCAACAATCTGGCTATTTGGCAACTTTGCTCAGTCCTTTCTACAAAGCTCTGGTGCCTTTGAAGTTTACTGCAATGGAGATTTGgtatgcttcctatgttagatgcaaccttatcttttttcttttgtgttgatttgatgcaaaatgct---ttatatatcaggagtgccctctgttttgaaatagg

upper sequence: Vv08s0105g00440.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA14G37390.1 (Glycine max), 5'ss of exon 3
TAGGTTTGGAACCATTTCAACCACTTGGCTTCTTGGAAACTTCCTTCAATCCTTCCTACAAAGTTCTGGTGCTTTTGAAGTGTACTGCAATGGTGAATTGgt-aaagtcttatctttgcttagct---atttcttttttctttttgttctttttatataaattaagaggttactactcagcagggtgctacttagtaaggaaaa
|||||||||||||||| |||  |||||||||||||| ||   | | || || ||| |||| || ||||| ||||| ||||| |||| |||||||||| ||||    | |||   | ||  |  ||   |||| ||  |     ||  | |  |  |  |   |  ||  || ||   | | | | |  | |    |  |     
TAGGTTTGGAACCATTGCAAGTACTTGGCTTCTTGGGAATGCCTTGCAGTCATTCTTACAGAGCTCTGGGGCTTTCGAAGTTTACTTCAATGGTGAACTGgttggtgccttccttctgtctttcttacatttattagtaaacatttctttgctagttgagcatctgatctttctctccggtaagctaatgcaagttttgt----

upper sequence: Vv08s0105g00440.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: AT3G47300.1 (Arabidopsis thaliana), 5'ss of exon 3
TAGGTTTGGAACCATTTCAACCACTTGGCTTCTTGGAAACTTCCTTCAATCCTTCCTACAAAGTTCTGGTGCTTTTGAAGTGTACTGCAATGGTGAATTGgtaaagtcttatctttgcttagc-tatttcttttttctttttgttctttttatataaattaagaggttactactcagcagggtgctacttagtaaggaaaa
||| || ||  ||||  |  |||||||||||||||| |||||| | || || ||  | |||||||||||||||||||||||   ||||||||| |||||||| |  |||| | | |  |  || |  ||    | || | |    || |     |    |||     | | |        | ||| |              
TAGATTCGGGTCCATGGCTTCCACTTGGCTTCTTGGTAACTTCTTGCAGTCTTTTTTGCAAAGTTCTGGTGCTTTTGAAGTTAGCTGCAATGGAGAATTGgtcagttcttttttctcttatgcatggttgcagtatcatatcacactctcggctttggctaatcaaatccaatgttttgtgttgccag-------------

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|27586821|gb|CB009516.1|CB009516
EST:     CCTTCCTACAAAGTTCTGGTGCTTTTGAAGTGTACTGCAATGGTGAATTG                         GTTTTCTCTAAGCTGAAGCAGCAAAGGTTCCCTGGGGAAATCGAGTTAAAG
genomic: CCTTCCTACAAAGTTCTGGTGCTTTTGAAGTGTACTGCAATGGTGAATTGgtaaagtctt ... accattttagGTTTTCTCTAAGCTGAAGCAGCAAAGGTTCCCTGGGGAAATCGAGTTAAAG
EST: gi|110372028|gb|EC936170.1|EC936170
EST:     CCTTCCTACAAAGTTCCGGTGCTTTTGAAGTGTACTGCAATGGTGAATTG                         GTTTTCTTTAAGCTGAAGCAGCAAAGGTTCCCTGGGGAAATCGAGTTAAAG
genomic: CCTTCCTACAAAGTTCTGGTGCTTTTGAAGTGTACTGCAATGGTGAATTGgtaaagtctt ... accattttagGTTTTCTCTAAGCTGAAGCAGCAAAGGTTCCCTGGGGAAATCGAGTTAAAG
EST: gi|351022500|gb|FQ447022.1|FQ447022
EST:     CCTTCCTACAAAGTTCTGGTGCTTTTGAAGTGTACTGCAATGGTGAATTG                         GTTTTCTCTAAGCTGAAGCAGCAAAAGTTCCCTGGGGGAAATCGAGTTAAA
genomic: CCTTCCTACAAAGTTCTGGTGCTTTTGAAGTGTACTGCAATGGTGAATTGgtaaagtctt ... accattttagGTTTTCTCTAAGCTGAAGCAGCAAAGGTTCCCTGGGG-AAATCGAGTTAAA
EST: gi|46910851|gb|CN546226.1|CN546226
EST:     CCTTCCTACAAAGTTCCGGTGCTTTTGAAGTGTACTGCAATGGTGAATTG                         GTTTTCTCTAAGCTGAAGCAGCAAAGGTTCCCTGGGGAAATCGAGTTAAAG
genomic: CCTTCCTACAAAGTTCTGGTGCTTTTGAAGTGTACTGCAATGGTGAATTGgtaaagtctt ... accattttagGTTTTCTCTAAGCTGAAGCAGCAAAGGTTCCCTGGGGAAATCGAGTTAAAG
EST: gi|110424174|gb|EC990530.1|EC990530
EST:     CCTTCCTACAAAGTTCCGGTGCTTTTGAAGTGTACTGCAATGGTGAATTG                         GTTTTCTCTAAGCTGAAGCAGCAAAGGTTCCCTGGGGAAATCGAGTTAAAG
genomic: CCTTCCTACAAAGTTCTGGTGCTTTTGAAGTGTACTGCAATGGTGAATTGgtaaagtctt ... accattttagGTTTTCTCTAAGCTGAAGCAGCAAAGGTTCCCTGGGGAAATCGAGTTAAAG
EST: gi|34415650|gb|CF414404.1|CF414404
EST:     CTTCCTACAAAGTTCCGGTGC-TTTGAANGTGTACTGCAATGGTGAATTG                         GTTTTCTCTAAGCTGAAGCAGCAAAGGTTCCCTGGGGAAATCGAGTTAAAG
genomic: CTTCCTACAAAGTTCTGGTGCTTTTGAA-GTGTACTGCAATGGTGAATTGgtaaagtctt ... accattttagGTTTTCTCTAAGCTGAAGCAGCAAAGGTTCCCTGGGGAAATCGAGTTAAAG
EST: gi|22012759|gb|BQ797793.1|BQ797793
EST:     CCTTCCTACAAAGTTCTGGTGCTTTTGAAGTGTACTGCAATGGTGAATTG                         GTTTTCTCTAAGCTGAAGCAGCAAAGGTTCCCTGGGGAAATCGAGTTAAAG
genomic: CCTTCCTACAAAGTTCTGGTGCTTTTGAAGTGTACTGCAATGGTGAATTGgtaaagtctt ... accattttagGTTTTCTCTAAGCTGAAGCAGCAAAGGTTCCCTGGGGAAATCGAGTTAAAG
EST: gi|34321032|gb|CF373786.1|CF373786
EST:     CCTTCCTACAAAGTTCCGGTGCTTTTGAAGTGTACTGCAATGGTGAATTG                         GTTTTCTCTAAGCTGAAGCAGCAAAGGTTCCCTGGGGAAATCGAGTTAAAG
genomic: CCTTCCTACAAAGTTCTGGTGCTTTTGAAGTGTACTGCAATGGTGAATTGgtaaagtctt ... accattttagGTTTTCTCTAAGCTGAAGCAGCAAAGGTTCCCTGGGGAAATCGAGTTAAAG
EST: gi|110717602|gb|EE093600.1|EE093600
EST:     GGTGCTTTTGAAGTGTACTGCAATGGTGAATTG                         GTTTTCTCTAAGCTGAAGCAGCAAAGGTTCCCTGGGGAAATCGAGTTAAAG
genomic: GGTGCTTTTGAAGTGTACTGCAATGGTGAATTGgtaaagtctt ... accattttagGTTTTCTCTAAGCTGAAGCAGCAAAGGTTCCCTGGGGAAATCGAGTTAAAG
EST: gi|351024908|gb|FQ433325.1|FQ433325
EST:     CCTTCCTACAAAGTTCTGGTGCTTTTGAAGTGTACTGCAATGGTGAGTTG                         GTTTTCTCTAAGCTGAAGCAGCAAAGGTTCCCTGGGGAAATCGAGTTAAAG
genomic: CCTTCCTACAAAGTTCTGGTGCTTTTGAAGTGTACTGCAATGGTGAATTGgtaaagtctt ... accattttagGTTTTCTCTAAGCTGAAGCAGCAAAGGTTCCCTGGGGAAATCGAGTTAAAG
EST: gi|22013113|gb|BQ798147.1|BQ798147
EST:     CCTTCCTACAAAGTTCTGGTGCTTTTGAAGTGTACTGCAATGGTGAATTG                         GTTTTCTCTAAGCTGAAGCAGCAAAGGTTCCCTGGGGAAATCGAGTTAAAG
genomic: CCTTCCTACAAAGTTCTGGTGCTTTTGAAGTGTACTGCAATGGTGAATTGgtaaagtctt ... accattttagGTTTTCTCTAAGCTGAAGCAGCAAAGGTTCCCTGGGGAAATCGAGTTAAAG
EST: gi|110702346|gb|EE080958.1|EE080958
EST:     CCTTCCTACAAAGTTCCGGTGCTTTTGAAGTGTACTGCAATGGTGAATTG                         GTTTTCTCTAAGCTGAAGCAGCAAAGGTTCCCTGGGGAAATCGAGTTAAAG
genomic: CCTTCCTACAAAGTTCTGGTGCTTTTGAAGTGTACTGCAATGGTGAATTGgtaaagtctt ... accattttagGTTTTCTCTAAGCTGAAGCAGCAAAGGTTCCCTGGGGAAATCGAGTTAAAG
EST: gi|34319244|gb|CF371998.1|CF371998
EST:     CCTTCCTACAAAGTTCCGGTGCTTTTGAAGTGTACTGCAATGGTGAATTG                         GTTTTCTCTAAGCTGAAGCAGCAAAGGTTCCCTGGGGAAATCGAGTTAAAG
genomic: CCTTCCTACAAAGTTCTGGTGCTTTTGAAGTGTACTGCAATGGTGAATTGgtaaagtctt ... accattttagGTTTTCTCTAAGCTGAAGCAGCAAAGGTTCCCTGGGGAAATCGAGTTAAAG
EST: gi|46911248|gb|CN546623.1|CN546623
EST:     AAAGTTCCGGTGCTTTTGAAGTGTACTGCAATGGTGAATTG                         GTTTTCTTTAAGCTGAAGCAGCAAAGGTTCCCTGGGGAAATCGAGTTAAAG
genomic: AAAGTTCTGGTGCTTTTGAAGTGTACTGCAATGGTGAATTGgtaaagtctt ... accattttagGTTTTCTCTAAGCTGAAGCAGCAAAGGTTCCCTGGGGAAATCGAGTTAAAG
EST: gi|46910972|gb|CN546347.1|CN546347
EST:     CCTTCCTACAAAGTTCCGGTGCTTTTGAAGTGTACTGCAATGGTGAATTG                         GTTTTCTCTAAGCTGAAGCAGCAAAGGTTCCCTGGGGAAATCGAGTTAAAG
genomic: CCTTCCTACAAAGTTCTGGTGCTTTTGAAGTGTACTGCAATGGTGAATTGgtaaagtctt ... accattttagGTTTTCTCTAAGCTGAAGCAGCAAAGGTTCCCTGGGGAAATCGAGTTAAAG
EST: gi|46910624|gb|CN545999.1|CN545999
EST:     CCTTCCTACAAAGTTCCGGTGCTTTTGAAGTGTACTGCAATGGTGAATTG                         GTTTTCTCTATGCTGAAGCAGCAAAGGTTCCCTGGGGAAATCGAGTTAAAG
genomic: CCTTCCTACAAAGTTCTGGTGCTTTTGAAGTGTACTGCAATGGTGAATTGgtaaagtctt ... accattttagGTTTTCTCTAAGCTGAAGCAGCAAAGGTTCCCTGGGGAAATCGAGTTAAAG
EST: gi|27580321|gb|CB003016.1|CB003016
EST:     CCTTCCTACAAAGTTCTGGTGCTTTTGAAGTGTACTGCAATGGTGAATTG                         GTTTTCTCTAAGCTGAAGCAGCAAAGGTTCCCTGGGGAAATCGAGTTAAAG
genomic: CCTTCCTACAAAGTTCTGGTGCTTTTGAAGTGTACTGCAATGGTGAATTGgtaaagtctt ... accattttagGTTTTCTCTAAGCTGAAGCAGCAAAGGTTCCCTGGGGAAATCGAGTTAAAG
EST: gi|46919677|gb|CN549006.1|CN549006
EST:     CCTTCCTACAAAGTTCTGGTGCTTTTGAAGTGTACTGCAATGGTGAATTG                         GTTTTCTCTAAGCTGAAGCAGCAAAGGTTCCCTGGGGAAATCGAGTTAAAG
genomic: CCTTCCTACAAAGTTCTGGTGCTTTTGAAGTGTACTGCAATGGTGAATTGgtaaagtctt ... accattttagGTTTTCTCTAAGCTGAAGCAGCAAAGGTTCCCTGGGGAAATCGAGTTAAAG
EST: gi|22013003|gb|BQ798037.1|BQ798037
EST:     CCTTCCTACAAAGTTCTGGTGCTTTTGAAGTGTACTGCAATGGTGAATTG                         GTTTTCTCTAAGCTGAAGCAGCAAAGGTTCCCTGGGGAAATCGAGTTAAAG
genomic: CCTTCCTACAAAGTTCTGGTGCTTTTGAAGTGTACTGCAATGGTGAATTGgtaaagtctt ... accattttagGTTTTCTCTAAGCTGAAGCAGCAAAGGTTCCCTGGGGAAATCGAGTTAAAG
EST: gi|71888556|gb|DT037611.1|DT037611
EST:     CCTTCCTACAAAGTTCCGGTGCTTTTGAAGTGTACTGCAATGGTGAATTG                         GTTTTCTCTAAGCTGAAGCAGCAAAGGTTCCCTGGGGAAATCGAGTTAAAG
genomic: CCTTCCTACAAAGTTCTGGTGCTTTTGAAGTGTACTGCAATGGTGAATTGgtaaagtctt ... accattttagGTTTTCTCTAAGCTGAAGCAGCAAAGGTTCCCTGGGGAAATCGAGTTAAAG
EST: gi|27578480|gb|CB001175.1|CB001175
EST:     CCTTCCTACAAAGTTCTGGTGCTTTTGAAGTGTACTGCAATGGTGAATTG                         GTTTTCTCTAAGCTGAAGCAGCAAAGGTTCCCTGGGGAAATCGAGTTAAAG
genomic: CCTTCCTACAAAGTTCTGGTGCTTTTGAAGTGTACTGCAATGGTGAATTGgtaaagtctt ... accattttagGTTTTCTCTAAGCTGAAGCAGCAAAGGTTCCCTGGGGAAATCGAGTTAAAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TAGGTTTGGAACCATTTCAACCACTTGGCTTCTTGGAAACTTCCTTCAATCCTTCCTACAAAGTTCTGGTGCTTTTGAAGTGTACTGCAATGGTGAATTGgtaaagtcttatctttgcttagctatttcttttttctttttgttctttttatataaattaagaggttactactcagcagggtgctacttagtaaggaaaa

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaattaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaggaaa