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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taatgtccttgtttatatgtgtgtgtgtgtgtgtacacttatgcttggacagtaatttaaatttcttcccgaggtatttaattttggagttgaaatgcagGATTCAATTCAACATTGCGCCAAGGGAATGTTACTCATCATGAATATATTCAG

Basic information

species Vitis vinifera
transcript Vv06s0004g01200.t01
intron # 36
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0004g01200.t01 (Vitis vinifera), 3'ss of exon 36
lower sequence: GLYMA10G44150.1 (Glycine max), 3'ss of exon 39
-----taatgtccttgtttatatgtgtgtgtgtgtgtgtacacttatgcttggacagtaatttaaatttcttcccgaggtatttaattttggagttgaaatgcagGATTCAATTCAACATTGCGCCAAGGGAATGTTACTCATCATGAATATATTCAG
       | |  ||| ||  |||   |||       |||    || |  |||     | ||||     ||| ||     | ||| || ||   ||| |   ||||||||||||||||| || || ||||| ||| |||| ||||||||||||||||||
ttctaagaagctcttatt-gtattgctgttcaaaattgtgt-tttctatttgcc---tcatttttccctctgccactctttttttatattcttgttcattcgcagGATTCAATTCAACCTTACGTCAAGGAAATATTACACATCATGAATATATTCAG

upper sequence: Vv06s0004g01200.t01 (Vitis vinifera), 3'ss of exon 36
lower sequence: GLYMA10G44150.2 (Glycine max), 3'ss of exon 39
-----taatgtccttgtttatatgtgtgtgtgtgtgtgtacacttatgcttggacagtaatttaaatttcttcccgaggtatttaattttggagttgaaatgcagGATTCAATTCAACATTGCGCCAAGGGAATGTTACTCATCATGAATATATTCAG-----------------------------------------------
       | |  ||| ||  |||   |||       |||    || |  |||     | ||||     ||| ||     | ||| || ||   ||| |   ||||||||||||||||| || || ||||| ||| |||| ||||||||||||||||||                                               
ttctaagaagctcttatt-gtattgctgttcaaaattgtgt-tttctatttgcc---tcatttttccctctgccactctttttttatattcttgttcattcgcagGATTCAATTCAACCTTACGTCAAGGAAATATTACACATCATGAATATATTCAGGTGAGACTTGTTGTTTATTGATCCCTCTACAACAAATCGTTTTCTAA

upper sequence: Vv06s0004g01200.t01 (Vitis vinifera), 3'ss of exon 36
lower sequence: GLYMA20G38860.1 (Glycine max), 3'ss of exon 41
-----taatgtccttgtttatatgtgtgtgtgtgtgtgtacacttatgcttggacagtaatttaaatttcttcccgaggtatttaattttggagttgaaatgcagGATTCAATTCAACATTGCGCCAAGGGAATGTTACTCATCATGAATATATTCAG
     |||  || |  |||||   ||| ||    |||||   |||    |||    |   ||     |||| | |    | ||| || ||   ||| |    |||||||||||||||| || || ||||| ||| |||| ||||||||||||||||||
tggcttaagctcttattttattgctgtttgaaattgtgttttctt---tttgcctcgcttttccctcttctgctctt--ttttttatattcttgttaattcacagGATTCAATTCAACCTTACGTCAAGGAAATATTACACATCATGAATATATTCAG

upper sequence: Vv06s0004g01200.t01 (Vitis vinifera), 3'ss of exon 36
lower sequence: AT3G07160.1 (Arabidopsis thaliana), 3'ss of exon 38
------------------------------------------taatgtcctt-gtttatatgtgtgtgtgtgtg-tgtacact--tatgcttggacagt----aatttaaatttcttcc-----cgaggtat-ttaattttggagtt----gaaatgcagGATTCAATTCAACATTGCGCCAAGGGAATGTTACTCATCATGAATATATTCAG
                                            ||||  |  |  ||||        ||  |  || | | |   || ||  | || |    |||   ||||||||||      || | |  || ||| |     |    |   | |||| |||||  ||||  | || ||||||||||||||||||||||| |||||||||
gtaaatttgattttttaattgacagttaccttcaaaactgttcgatgttttaagaatataaaaacacatgaataatgaaaagtgcaattctgagccattttttaataccaatttcttccacacatgatggacgttgattatatgcctctacggtttccagGTTTCAACACAACTCTACGTCAAGGGAATGTTACTCATCATGAGTATATTCAG

upper sequence: Vv06s0004g01200.t01 (Vitis vinifera), 3'ss of exon 36
lower sequence: PP1S160_88V6.1 (Physcomitrella patens), 3'ss of exon 39
taatgtccttgtttatatgtgtg-tgtgtgtgtgtacacttatgcttggacag-taatttaaatttcttcccgaggtatttaattttggagttgaaatgc-agGATTCAATTCAACATTGCGCCAAGGGAATGTTACTCATCATGAATATATTCAG
   | |  ||| ||  || ||   | |  | |||| ||  |    |     || | ||||  ||    |  | |   |   ||  ||   ||  || |   |||||||||  | ||  |  | ||||| ||||| |||||||||||||||||||||
gtttttttttgattgaatctgcaattttcgagtgtccaactgatttaatgtagctgatttggatgatgttacta---aaccaaactttatgtcaaattattagGATTCAACACTACTCTTAGGCAAGGCAATGTCACTCATCATGAATATATTCAG

upper sequence: Vv06s0004g01200.t01 (Vitis vinifera), 3'ss of exon 36
lower sequence: PP1S13_132V6.1 (Physcomitrella patens), 3'ss of exon 38
taatgtccttgtttatatgtgtgtgtgtgtgtgtacacttatgcttggacagtaatttaaatttcttcccgaggtatttaattttgg-agttgaaatgcagGATTCAATTCAACATTGCGCCAAGGGAATGTTACTCATCATGAATATATTCAG
| |    | |   | |||| |  |   |     |     | |   |   |  ||   |   ||           |  | || |||   | ||    |||||| |||||||| || || || | ||||||| |||||||||||||||||||||||
tgagagtcctccctctatg-gcatactttacgttgtctgtgtctgtcatcgatagcatgttttctagtttataatgataaactttctcacttcttttgcagGGTTCAATTCCACTTTACGACTAGGGAATATTACTCATCATGAATATATTCAG

upper sequence: Vv06s0004g01200.t01 (Vitis vinifera), 3'ss of exon 36
lower sequence: PP1S67_234V6.1 (Physcomitrella patens), 3'ss of exon 40
taatgtccttgtttatatgtgtgtgtgtgtgtgtacacttatgcttggacagtaatt-taaatttcttcccgaggtatttaattttggagttgaaatgcagGATTCAATTCAACATTGCGCCAAGGGAATGTTACTCATCATGAATATATTCAG
|    || | ||||| |  | ||      ||      ||| |     || ||  | |   ||| |  |       ||||   ||||  | |     |||||| || ||||||||||| || | ||| ||| ||||||| |||||||||||||||
tggcatcat-gtttaaaaatttggcaacttgctgctgcttgttaagagaaagggagtaccaatgttctttaagcttattcccttttctaatccttttgcagGTTTTAATTCAACATTACGACGAGGAAATATTACTCACCATGAATATATTCAG

upper sequence: Vv06s0004g01200.t01 (Vitis vinifera), 3'ss of exon 36
lower sequence: PP1S145_49V6.1 (Physcomitrella patens), 3'ss of exon 37
taatgtccttgtttatatgtgtgtgtgtgtgtgtacacttatgcttggacagtaatttaaatttcttcccga--ggtatttaattttggagttgaaatgcagGATTCAATTCAACATTGCGCCAAGGGAATGTTACTCATCATGAATATATTCAG
 ||||   |  | | |||   |   |||   |      | ||  |||    | || || |   |||   |       |   |  | |   | |    ||||||||||||||| || || || | |||||||||||| ||||||||||| ||||||
-aatgagttcatgt-tattaatcgttgttaatcgttgttaatcgttgttatggaactttatcctctggtcagctacaaccaagctctattgcttttctgcagGATTCAATTCTACTTTACGACTAGGGAATGTTACCCATCATGAATACATTCAG

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|30252507|gb|CB970058.1|CB970058
EST:     TATCAGCAAGGCCTCTCGAGTTATCAACATTAGTGAAGATATATATGCTG                         GATTCAATTCAACATTGCGCCAAGGGAATGTTACTCATCATGAATATATTC
genomic: TATCAGCAAGGCCTCTCGAGTTATCAACATTAGTGAAGATATATATGCTGgtatgattgt ... tgaaatgcagGATTCAATTCAACATTGCGCCAAGGGAATGTTACTCATCATGAATATATTC






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggacagtaatttaaatttcttcccgaggtatttaattttggagttgaaatgcagGATTCAATTCAACATTGCGCCAAGGGAATGTTACTCATCATGAATATATTCAG
                              atttaat  putative branch site (score: 4)
     agtaatttaaatttct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taatgtccttgtttatatgtgtgtgtgtgtgtgtacacttatgcttggacagtaatttaaatttcttcccgaggtatttaattttggagttgaaatgcagGATTCAATTCAACATTGCGCCAAGGGAATGTTACTCATCATGAATATATTCAG

-aatgtcc
- - - - - - - - - gtgtgtg
- - - - - - - - - - - - - - - - - - -cttatgc