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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaagctgcaaaacaattaatatttatgataaaacttggtttcaaaagagtccagctgaaatttctggtgtgcagTTTGCAACAGAAGCAGCCATAACAATTCTTCGAATTGACGACATGATCAAGCTTGTCAAAGATGAAACTCAGAATGAAGAAGATTAGAGGAGAGCAGCCT

Basic information

species Vitis vinifera
transcript Vv15s0021g02230.t01
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv15s0021g02230.t01 (Vitis vinifera), 3'ss of exon 16
lower sequence: GLYMA08G12970.1 (Glycine max), 3'ss of exon 16
-----------gtaaaagctgcaaaacaattaatatttatgataaaacttggtttcaaaagagt-ccagctgaaatttctggtgtg----cagTTTGCAACAGAAGCAGCCATAACAATTCTTCGAATTGACGACATGATCAAGCTTGTCAAAGATGAAACTCAGAATGAAGAAGATTAGAGGAGAGCAGCCT---
           || |||  | || |    || |  |  || ||| | |||  || || |   |    ||||  || || |  |       ||||||||||| ||||| ||||| || || ||||||||||| ||||||||||||||| |||| ||||||| ||| ||||| ||   ||| || | | | |  |   
gtatgtatttagttaaatat-cacagttgttgacttcaat-atacagcttccttacacagctgcgtgagctagaagtttttttacttccccagTTTGCAACTGAAGCTGCCATTACTATCCTTCGAATTGATGACATGATCAAGCTTATCAAGGATGAAAGTCAAAATGAGGA---TTAAAGTATAACTGAATCTA

upper sequence: Vv15s0021g02230.t01 (Vitis vinifera), 3'ss of exon 16
lower sequence: GLYMA05G29870.1 (Glycine max), 3'ss of exon 16
-----------gtaaaagctgcaaaacaattaatatttatgataaaacttggtttcaaaagag----tccagctgaaatttctggtgtg----cagTTTGCAACAGAAGCAGCCATAACAATTCTTCGAATTGACGACATGATCAAGCTTGTCAAAGATGAAACTCAGAATGAAGAAGATTAGAGGAGAGCAGCCT---
           || |||  |  | |    || |  || | |||| | |||  ||   | | ||       ||||  || || |  | |     ||||||||||| ||||| || || || || ||||||||||| |||||||||||||||||||| ||||||| ||| ||||| ||   ||| || | | | |  |   
gtatgtatttagttaaatatcaacagttgttgac-ttcaagatatagcttccttcttatacagctgtctgagctataagttttatttttttcccagTTTGCAACTGAAGCTGCTATTACCATCCTTCGAATTGATGACATGATCAAGCTTGTCAAGGATGAAAGTCAAAATGAGGA---TTAAAGTATAACTGAATCTA

upper sequence: Vv15s0021g02230.t01 (Vitis vinifera), 3'ss of exon 16
lower sequence: AT3G20050.1 (Arabidopsis thaliana), 3'ss of exon 16
gtaaaag--------ctgcaaaacaattaatat-ttatgataaaacttggtttcaaaagagtccagctgaaatttctggtgtg--cagTTTGCAACAGAAGCAGCCATAACAATTCTTCGAATTGACGACATGATCAAGCTTGTCAAAGATGAAACTCAGAATGAAGAAGATTAGAGGAGAGCAGCCT--
|||||||        ||  | |  || ||  || |||  | |  |  |  | ||  || | |  |   ||  ||| |  ||||  |||||||||||||| ||||||||||| ||||| |||||||||||||||||||| || || || ||||| |  ||    |||||| |  ||   ||  ||||    
gtaaaaggcacttggctttacatgaactagaatattaaaaaatcaagtaatctcttaa-attttaaaggagctttgttttgtgaccagTTTGCAACAGAGGCAGCCATAACGATTCTACGAATTGACGACATGATCAAACTGGTGAAGGATGAGAGCCAAGGCGAAGAATA--AGCAAAGCTCAGCTCCT

upper sequence: Vv15s0021g02230.t01 (Vitis vinifera), 3'ss of exon 16
lower sequence: PP1S200_112V6.2 (Physcomitrella patens), 3'ss of exon 16
-------------------------------------------------------------------------------------gtaaaagctgcaaaacaattaatatttatgataaaacttggtttcaaaagagtccagctgaaatttctgg----tgtgcagTTTGCAACAGAAGCAGCCATAACAATTCTTCGAATTGACGACATGATCAAGCTTGTCAAAGATGAAACTCAGAATGAAGAAGATTAGAGGAG-AGCAGCCT
                                                                                     ||      |         |||||   | || |       ||| | | |  |  || | ||  |  || |     | ||||||||||||| ||||| || || ||||| || |||||||| ||||||||||| ||  |||| || |||  |    ||     | || |     | || ||   
gtaagaaacatgtgcttttgaaagattcccttttaatatatgaagattttttgacagatatgtactgtctcgtttctggatcattgttctttgtatgttgaggttaattgctctggtgtgtgggggtgtaagatcatgcctgatgtgacatcggtattttttgcagTTTGCAACTGAAGCTGCAATTACAATCCTACGAATTGATGACATGATCAAACTGTTCAAGGAGGAAGATGGTGATCGGTGACATCACTTTCGCAGAAGGA-

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|110699451|gb|EE076471.1|EE076471
EST:     TAGAAGCTGGGGTTATTGAACCTGCAATGAGCAAAGTGAAGATCCTACAG                         TTTGCAACAGAAGCAGCCATAACAATTCTTCGAATTGACGACATGATCAAG
genomic: TAGAAGCTGGGGTTATTGAGCCTGCAATGAGCAAAGTGAAGATCCTACAGgtaaaagctg ... tggtgtgcagTTTGCAACAGAAGCAGCCATAACAATTCTTCGAATTGACGACATGATCAAG
EST: gi|110702474|gb|EE081230.1|EE081230
EST:     TAGAAGCTGGGGTTATTGAACCTGCAATGAGCAAAGTGAAGATCCTACAG                         TTTGCAACAGAAGCAGCCATAACAATTCTTCGAATTGACGACATGATCAAG
genomic: TAGAAGCTGGGGTTATTGAGCCTGCAATGAGCAAAGTGAAGATCCTACAGgtaaaagctg ... tggtgtgcagTTTGCAACAGAAGCAGCCATAACAATTCTTCGAATTGACGACATGATCAAG
EST: gi|110732035|gb|EE106967.1|EE106967
EST:     TAGAAGCTGGGGTTATTGAACCTGCAATGAGCAAAGTGAAGATCCTACAG                         TTTGCAACAGAAGCAGCCATAACAATTCTTCGAATTGACGACATGATCAAG
genomic: TAGAAGCTGGGGTTATTGAGCCTGCAATGAGCAAAGTGAAGATCCTACAGgtaaaagctg ... tggtgtgcagTTTGCAACAGAAGCAGCCATAACAATTCTTCGAATTGACGACATGATCAAG
EST: gi|110701345|gb|EE078813.1|EE078813
EST:     TAGAAGCTGGGGTTATTGAACCTGCAATGAGCAAAGTGAAGATCCTACAG                         TTTGCAACAGAAGCAGCCATAACAATTCTTCGAATTGACG
genomic: TAGAAGCTGGGGTTATTGAGCCTGCAATGAGCAAAGTGAAGATCCTACAGgtaaaagctg ... tggtgtgcagTTTGCAACAGAAGCAGCCATAACAATTCTTCGAATTGACG
EST: gi|34545337|gb|CF513569.1|CF513569
EST:     TAGAAGCTGGGGTTATTGAGCCTGCAATGAGCAAAGTGAAGATCCTACAG                         TTTGCAACAGAAGCAGCCATAACAATTCTTCGAATTGACGACATGATCAAG
genomic: TAGAAGCTGGGGTTATTGAGCCTGCAATGAGCAAAGTGAAGATCCTACAGgtaaaagctg ... tggtgtgcagTTTGCAACAGAAGCAGCCATAACAATTCTTCGAATTGACGACATGATCAAG
EST: gi|34545258|gb|CF513490.1|CF513490
EST:     TAGAAGCTGGGGTTATTGAGCCTGCAATGAGCAAAGTGAAGATCCTACAG                         TTTGCAACAGAAGCAGCCATAACAATTCTTCGAATTGACGACATGATCAAG
genomic: TAGAAGCTGGGGTTATTGAGCCTGCAATGAGCAAAGTGAAGATCCTACAGgtaaaagctg ... tggtgtgcagTTTGCAACAGAAGCAGCCATAACAATTCTTCGAATTGACGACATGATCAAG
EST: gi|32272417|gb|CD721576.1|CD721576
EST:     TAGAAGCTGGGGTTATTGAGCCTGCAATGAGCAAAGTGAAGATCCTACAG                         TTTGCAACAGAAGCAGCCATAACAATTCTTCGAATTGACGACATGATCAAG
genomic: TAGAAGCTGGGGTTATTGAGCCTGCAATGAGCAAAGTGAAGATCCTACAGgtaaaagctg ... tggtgtgcagTTTGCAACAGAAGCAGCCATAACAATTCTTCGAATTGACGACATGATCAAG
EST: gi|351026359|gb|FQ428371.1|FQ428371
EST:     TAGAAGCTGGGGTTATTGAGCCTGCAATGAGCAAAGTGAAGATCCTACAG                         TTTGCAACAGAAGCAGCCATAACAATTCTTCGAATTGACGACATGATCAAG
genomic: TAGAAGCTGGGGTTATTGAGCCTGCAATGAGCAAAGTGAAGATCCTACAGgtaaaagctg ... tggtgtgcagTTTGCAACAGAAGCAGCCATAACAATTCTTCGAATTGACGACATGATCAAG
EST: gi|30138039|gb|CB923377.1|CB923377
EST:     TAGAAGCTGGGGTTATTGAGCCTGCAATGAGCAAAGTGAAGATCCTACAG                         TTTGCAACAGAAGCAGCCATAACAATTCTTCGAATTGACGACATGATCAAG
genomic: TAGAAGCTGGGGTTATTGAGCCTGCAATGAGCAAAGTGAAGATCCTACAGgtaaaagctg ... tggtgtgcagTTTGCAACAGAAGCAGCCATAACAATTCTTCGAATTGACGACATGATCAAG
EST: gi|110371042|gb|EC934755.1|EC934755
EST:     TAGAAGCTGGGGTTATTGAGCCTGCAATGAGCAAAGTGAAGATCCTACAG                         TTTGCAACAGAAGCAGCCATAACAATTCTTCGAATTGACGACATGATCAAG
genomic: TAGAAGCTGGGGTTATTGAGCCTGCAATGAGCAAAGTGAAGATCCTACAGgtaaaagctg ... tggtgtgcagTTTGCAACAGAAGCAGCCATAACAATTCTTCGAATTGACGACATGATCAAG
EST: gi|161712591|gb|FC062193.1|FC062193
EST:     TAGAAGCTGGGGTTATTGAGCCTGCAATGAGCAAAGTGAAGATCCTACAG                         TTTGCGACAGAAGCAGCCATAACAATTCTTCGAATTGACGACATGATCAAG
genomic: TAGAAGCTGGGGTTATTGAGCCTGCAATGAGCAAAGTGAAGATCCTACAGgtaaaagctg ... tggtgtgcagTTTGCAACAGAAGCAGCCATAACAATTCTTCGAATTGACGACATGATCAAG
EST: gi|26266195|gb|CA817258.1|CA817258
EST:     TAGAAGCTGGGGTTATTGAGCCTGCAATGAGCAAAGTGAAGATCCTACAG                         TTTGCAACAGAAGCAGCCATAACAATTCTTCGAATTGACGACATGATCAAG
genomic: TAGAAGCTGGGGTTATTGAGCCTGCAATGAGCAAAGTGAAGATCCTACAGgtaaaagctg ... tggtgtgcagTTTGCAACAGAAGCAGCCATAACAATTCTTCGAATTGACGACATGATCAAG
EST: gi|110362101|gb|EC925611.1|EC925611
EST:     TAGAAGCTGGGGTTATTGAGCCTGCAATGAGCAAAGTGAAGATCCTACAG                         TTTGCAACAGAAGCAGCCATAACAATTCTTCGAATTGACGACATGATCAAG
genomic: TAGAAGCTGGGGTTATTGAGCCTGCAATGAGCAAAGTGAAGATCCTACAGgtaaaagctg ... tggtgtgcagTTTGCAACAGAAGCAGCCATAACAATTCTTCGAATTGACGACATGATCAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatttatgataaaacttggtttcaaaagagtccagctgaaatttctggtgtgcagTTTGCAACAGAAGCAGCCATAACAATTCTTCGAATTGACGACATGATCAAGCTTGTCAAAGATGAAACTCAGAATGAAGAAGATTAGAGGAGAGCAGCCT
                                         tttct  CT-rich tract
     atgataaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaaagctgcaaaacaattaatatttatgataaaacttggtttcaaaagagtccagctgaaatttctggtgtgcagTTTGCAACAGAAGCAGCCATAACAATTCTTCGAATTGACGACATGATCAAGCTTGTCAAAGATGAAACTCAGAATGAAGAAGATTAGAGGAGAGCAGCCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG