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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgctatgctgttcatttatgacttacacgtgtgcacatatatattacgtttacgcattatagaactgtgtatttactgatattgtataattcctctgtagAGGACAGTTATGGAGGCAGTGACTGCTATACTTGGAGGTGGACTACGTGTCGGTGTGCTTCTTCGAGGCAAGAAGGTTAGGGATGATAGCAAAACCCTGC

Basic information

species Vitis vinifera
transcript Vv06s0004g04940.t01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0004g04940.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os03g16700.4 (Oryza sativa), 3'ss of exon 5
---------------tgctatgctgttcatttatgacttacacgtgtgcacatata--tattacg-----tttacgcattatagaactgtgtatttac-tgatattgtataattcctctgtagAGGACAGTTATGGAGGCAGTGACTGCTATACTTGGAGGTGGACTACGTGTCGGTGTGCTTCTTCGAGGCAAGAAGGTTAGGGATGATAGCAAAACCCTGC
                  | ||||  |  ||| | | | |    |  ||||| | |  | || |      || ||   || | ||    ||| |     |  || | | || ||    || |||  || ||| |||||||||| | ||| |||||||||||||| || |||||||||||||| | ||  || ||||| || || |||||||  |||||| |  
gtacggaaaaagagacattttgctcctgttttctcattaattgatcagcacaaagagatgttgcaagaatttcaccttttgtcga-tgatgtttccgtgttttaatatgtatttataatgcagAAAACTGTTCTGGAGGCAGTAAATGCCATACTTGGAGGTGGTCTGCGTGTCGGTGTGCTCCATCATGGGAAGAAAGTCAGAGATGATAATAAAACCTTAA

upper sequence: Vv06s0004g04940.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G063151_T01 (Zea mays), 3'ss of exon 5
-tgc-tatgctgttcatttatgacttacacgtgtgcacatatatattacgttt-acgcattatagaactgtgtatttactgatattgtataat-------tcctctgtagAGGACAGTTATGGAGGCAGTGACTGCTATACTTGGAGGTGGACTACGTGTCGGTGTGCTTCTTCGAGGCAAGAAGGTTAGGGATGATAGCAAAACCCTGC
 | |  | |   |   |||||   |||   ||    | ||     ||   ||| |    || |    ||   |   |  |  | | || ||||       |||  || |||  || ||| | |||||||||||||| || ||||||||||| |||||||| ||||| ||||  |  || ||||| || || |||||||| |||||  |  
gtacacaagacatctgtttattttttatgtgtaaagatattagagttctttttgattttttttcctgctcaatgggttttcctctcgtttaatcagcatttccaatgcagAAAACTGTTCTCGAGGCAGTGACTGCGATTCTTGGAGGTGGCCTACGTGTTGGTGTTCTTCACCATGGAAAGAAAGTCAGAGATGATAGTAAAACGTTAA

upper sequence: Vv06s0004g04940.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G110309_T01 (Zea mays), 3'ss of exon 6
tgctatgctgttcatttatgacttacacgtgtgcacatatat-attacgtttacgcattatagaactgtgtatttactgat-----attgtataattcctctgtagAGGACAGTTATGGAGGCAGTGACTGCTATACTTGGAGGTGGACTACGTGTCGGTGTGCTTCTTCGAGGCAAGAAGGTTAGGGATGATAGCAAAACCCTGC
   | ||| |  ||||| |   ||     |||| | | | || |     |||  |  ||   |  |  ||  ||| |   |     | | |  | ||||  || |||  || ||| | |||||||||||||| || || |||||||| |||||||| ||||| ||||  |  || ||||| ||||| |||||||  |||||  || 
gtatgtgcaggacatttctttattttttatgtgtaaagagattacagttttttagttttgctgctcaatgggttttccagtcgtttaatctgcatttccaatgcagAAAACTGTTCTCGAGGCAGTGACTGCGATTCTCGGAGGTGGTCTACGTGTTGGTGTTCTTCACCATGGAAAGAAAGTTAGAGATGATAATAAAACGTTGA

upper sequence: Vv06s0004g04940.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA15G04200.1 (Glycine max), 3'ss of exon 6
-----------------------------------------------------------------------------tgctatgctgttcatttatgacttac-acgtgtgcacatatatattacgtttacgcattatagaactgtgtatttactgatattgta-taattc-ctctgtagAGGACAGTTATGGAGGCAGTGACTGCTATACTTGGAGGTGGACTACGTGTCGGTGTGCTTCTTCGAGGCAAGAAGGTTAGGGATGATAGCAAAACCCTGC
                                                                             | || |  |||   ||  || | | |  | |       | |  || |   || |   ||  | |   ||     | | | | ||  |  ||||  ||||| |||||||||| |||||||||||||||||| |||||||||||||| | || || |||||| |||| |  || ||||||||||| ||||| || ||||| || |
gtatgataaaatcctattctgccatacacacaaaaatcctctaccatattcagatgttaatgatgagtggcatctgcttctgta-tgtgtgttcttggcatgctgcatcatttggtgtg-atcattattgcatttttcacataagttgggctgcagctcttacaacaatttgctctgcagAGGACAGTGATGGAGGCAGTGACTGCTGTACTTGGAGGTGGATTGCGCGTGGGTGTGATTCTCCATGGAAAGAAGGTTAGAGATGACAGTAAAACTCTAC

upper sequence: Vv06s0004g04940.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA13G41210.1 (Glycine max), 3'ss of exon 8
-------------------------------------------------tgctatgctgttcatttatgacttacacgtgtgcacatatatattacgtttacgcattatagaactgtgtatttactg------atattgtataattc-----ctctgtagAGGACAGTTATGGAGGCAGTGACTGCTATACTTGGAGGTGGACTACGTGTCGGTGTGCTTCTTCGAGGCAAGAAGGTTAGGGATGATAGCAAAACCCTGC
                                                 |   ||| |  | ||   || | |     | || |  | |   ||      | ||   ||      ||||  | | |       || |   |||| ||     ||||| |||||||||| |||||||||||||||||| |||||||||| ||| | ||||| |||||| |||| |  || ||||||||||| ||||| || ||||| || |
gtatgataaaattctattctgccatacacacaagcatcctctcccatattcagatgttaatgatgggtggcgtctgtttctgtatctgtgagttcgtggcatgctgcatcatgtggtgtgatcattattgcatatttcacataagtcgtttgctctgcagAGGACAGTGATGGAGGCAGTGACTGCTGTACTTGGAGGCGGATTGCGTGTGGGTGTGATTCTCCATGGAAAGAAGGTTAGAGATGACAGTAAAACTCTAC

upper sequence: Vv06s0004g04940.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA12G06680.1 (Glycine max), 3'ss of exon 5
----------------------------------------------------------------tgctatgctgttcatttatgacttacacgtgtgcacatata---tattacgtttacgcat-tatagaactgtgtattta------ctg-atattgtataa----ttcctctgtagAGGACAGTTATGGAGGCAGTGACTGCTATACTTGGAGGTGGACTACGTGTCGGTGTGCTTCTTCGAGGCAAGAAGGTTAGGGATGATAGCAAAACCCTGC
                                                                ||| ||     | |||||| |  | ||  |        |||    ||| | ||| |   | | |   |       || |      ||| || || || ||    ||  |||| |||||||||| ||||| |||||||||||| | |||||||||| | | |   | |||||  |||| |  || || || |||| |||||| || ||||| || |
gtataatagttttatatttttccatccacataccatcctaccttttttagatgttcacaaggaatgccatttgtgtaatttataagctgcatttacattttaataatccattgcatttgcatgtatcttccatcacaagttcagttgagctgtattttttacaacattttggtctgcagAGGACAGTGATGGATGCAGTGACTGCTGTGCTTGGAGGTGAATTGCACATTGGTGTTTTTCTCCAGGGAAAAAAAGTTAAGGATGACAGTAAAACTCTAC

upper sequence: Vv06s0004g04940.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA11G14760.1 (Glycine max), 3'ss of exon 6
-------------------------------------------------------------------tgctatgctgttcatttatgacttacacgtgtg---cacatatatattacgtttacgcat------tatagaactgtgtatttactg-atattgtataa----ttcctctgtagAGGACAGTTATGGAGGCAGTGACTGCTATACTTGGAGGTGGACTACGTGTCGGTGTGCTTCTTCGAGGCAAGAAGGTTAGGGATGATAGCAAAACCCTGC
                                                                   ||  ||     | |||||| | || ||  |      ||   ||  ||| | ||| |   |      ||   || |     |   ||| || || || ||    ||  |||| |||||||||| ||||| |||||||||||| | |||||||||| | | |   | |||||  |||| |  || ||  | |||| |||||| || ||||| || |
gtataatagttttatattttgccattcacataccatcttcttactatttttagatgttcacgaggaatgtcatttgtgtaatttataagttgcatttacatttcaataatccattgcatttgcatgtatcttctactcaagttcagttgggctgtattttttacaacattttggtctgcagAGGACAGTGATGGATGCAGTGACTGCTGTGCTTGGAGGTGAATTGCACATTGGTGTTTTTCTCCAGGGAAAACAAGTTAAGGATGACAGTAAAACTCTAC

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|30302294|gb|CB979088.1|CB979088
EST:     CAGAGCTCTTTATAGAGATTCCAGAAACTGCAACTGTTGGTTCCCTCAAG                         AGGACAGTTATGGAGGCAGTGACTGCTATACTTGGAGGTGGACTACGTGTC
genomic: CAGAGCTCTTTATAGAGATTCCAGAAACTGCAACTGTTGGTTCCCTCAAGgtatattgat ... tcctctgtagAGGACAGTTATGGAGGCAGTGACTGCTATACTTGGAGGTGGACTACGTGTC






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acgtttacgcattatagaactgtgtatttactgatattgtataattcctctgtagAGGACAGTTATGGAGGCAGTGACTGCTATACTTGGAGGTGGACTACGTGTCGGTGTGCTTCTTCGAGGCAAGAAGGTTAGGGATGATAGCAAAACCCTGC
                            tactgat  putative branch site (score: 2)
                                            ttcctctgt  putative PPT
                        tatttactgatattgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgctatgctgttcatttatgacttacacgtgtgcacatatatattacgtttacgcattatagaactgtgtatttactgatattgtataattcctctgtagAGGACAGTTATGGAGGCAGTGACTGCTATACTTGGAGGTGGACTACGTGTCGGTGTGCTTCTTCGAGGCAAGAAGGTTAGGGATGATAGCAAAACCCTGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- ctatgct
- - - - - - - - - - - - -cacgtgt
- - - - - - - - - - - - - - - - gcacata