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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attgttataaaatttatgtttaatttgaacacactgtttcaaaattttgttccctacacaatgttcattgatttacaaacaatcattcaatttttaccagATTATAAATGCAGTCATGAGTGGAAGGGATGTTCTGGTGATCATGGCTGCAGGTGGTGGTAAGAGCCTTTGTTACCAGCTTCCAGCTATACTTCGTGATG

Basic information

species Vitis vinifera
transcript Vv02s0087g00070.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv02s0087g00070.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os11g48090.3 (Oryza sativa), 3'ss of exon 3
attgttataaaatttatgtttaatttgaacacactgtttcaaaattttgttccctacacaatgttcattgatttacaaacaatcattcaattt-----ttaccagATTATAAATGCAGTCATGAGTGGAAGGGATGTTCTGGTGATCATGGCTGCAGGTGGTGGTAAGAGCCTTTGTTACCAGCTTCCAGCTATACTTCGTGATG
  |  | |  |   ||    ||  | | ||| ||     |||  |  | | |     ||| | ||| ||  ||| ||  |  | |  ||  ||      | |||||| || |||||  ||||||||||||| ||||| ||||| || |||||||| ||||| || |||||||| || || || || || ||| |||||| |||||
ggtactgttgagcctagccctagat-gtacatacca---caacttgctatactgcttacagt-ttctttattttgcatccttttaagcatattgcaaccttccagATAATCAATGCCATCATGAGTGGAAGAGATGTACTGGTCATAATGGCTGCTGGTGGAGGGAAGAGCCTCTGCTATCAACTACCTGCTGTACTTCATGATG

upper sequence: Vv02s0087g00070.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G451856_T02 (Zea mays), 3'ss of exon 3
-attgttataaaatttatgtttaatttgaacacactgtttcaaaattttgttccctacacaatgttcattgatttacaaacaatcattcaatttttacc---agATTATAAATGCAGTCATGAGTGGAAGGGATGTTCTGGTGATCATGGCTGCAGGTGGTGGTAAGAGCCTTTGTTACCAGCTTCCAGCTATACTTCGTGATG
 | | |  | |     |     ||      |    | ||  | | |||  |  | |  ||| | | |  | ||||   | | || |  ||  || | |    |||| || |||||||||||||||||||| ||||||||||| || ||||| || ||||| || ||||| || ||||||||||| |||||| ||||||||||||
aactttagtcaggggaac--caaacacccccttcgtattgtacagtttcct--cttgtacagtttcctctcattttgcacccattaaacatattctgcttatagATAATTAATGCAGTCATGAGTGGAAGAGATGTTCTGGTCATAATGGCAGCTGGTGGAGGGAAGAGTCTATGTTACCAGCTCCCAGCTGTACTTCGTGATG

upper sequence: Vv02s0087g00070.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA09G34860.1 (Glycine max), 3'ss of exon 2
---attgttataaaattta-tgtttaatttgaacacactgtttcaaaattttgttccctacacaatgttcattgatttacaaacaatcattcaatttttaccagATTATAAATGCAGTCATGAGTGGAAGGGATGTTCTGGTGATCATGGCTGCAGGTGGTGGTAAGAGCCTTTGTTACCAGCTTCCAGCTATACTTCGTGATG
   ||  | |     |||| | | | ||||        | | |  |    ||||  | |          | ||| || ||||  | | ||    |   |  ||||| || |||||  | ||||||||||| |||||||||||||| ||||||||||||||||| |||||||| || ||||||||||| ||| | ||||||||||
atcataatcaagggctttagtttatgatttttttttggtatatatagggattgtgacttttgggtaaaactttg-ttaacaagtagtaat---gtcgatgacagATAATTAATGCCATTATGAGTGGAAGAGATGTTCTGGTGATTATGGCTGCAGGTGGTGGCAAGAGCCTCTGCTACCAGCTTCCTGCTGTTCTTCGTGATG

upper sequence: Vv02s0087g00070.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT1G31360.2 (Arabidopsis thaliana), 3'ss of exon 2
attgttataaaatttatgtttaatttgaac----acactgtttcaaaattt-tgttccctacacaat-gttcattgatttacaaac--aatcattcaat--ttttaccagATTATAAATGCAGTCATGAGTGGAAGGGATGTTCTGGTGATCATGGCTGCAGGTGGTGGTAAGAGCCTTTGTTACCAGCTTCCAGCTATACTTCGTGATG-----------------------------------------------
   || |   | ||| ||| |  | ||| |    | |   ||      |    |||  ||| | | | |||   || |  |       | || || |||  | |  | ||||||| || ||  | ||||  ||||| ||||| |||||||||||||| ||||||||||| ||||| ||||| || || ||||||||||| ||||||| ||                                               
---gtaagtgactttctgtattttctgatcctaaatatgattcttgtgtccgcgtttgctagaaattcgtttgatgttccatttgttgattctttgaatgatatgtcaagattattaacgctataatgacgggaagagatgtcctggtgatcatggcagCAGGTGGTGGGAAGAGTCTTTGCTATCAACTTCCAGCTATGCTTCGTGGTGGGACAACTCTTGTTGTCAGTCCTCTACTTTCACTGATTCAGGATCAG

upper sequence: Vv02s0087g00070.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT1G31360.1 (Arabidopsis thaliana), 3'ss of exon 2
attgttataaaatttatgtttaatttgaac----acactgtttcaaaattt-tgttccctacacaat-gttcattgatttacaaac--aatcattcaat--ttttaccagATTATAAATGCAGTCATGAGTGGAAGGGATGTTCTGGTGATCATGGCTGCAGGTGGTGGTAAGAGCCTTTGTTACCAGCTTCCAGCTATACTTCGTGATG
   || |   | ||| ||| |  | ||| |    | |   ||      |    |||  ||| | | | |||   || |  |       | || || |||  | |  | ||||||| || ||  | ||||  ||||| ||||| |||||||||||||| ||||||||||| ||||| ||||| || || ||||||||||| ||||||| ||
---gtaagtgactttctgtattttctgatcctaaatatgattcttgtgtccgcgtttgctagaaattcgtttgatgttccatttgttgattctttgaatgatatgtcaagATTATTAACGCTATAATGACGGGAAGAGATGTCCTGGTGATCATGGCAGCAGGTGGTGGGAAGAGTCTTTGCTATCAACTTCCAGCTATGCTTCGTGGTG

upper sequence: Vv02s0087g00070.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: PP1S93_66V6.1 (Physcomitrella patens), 3'ss of exon 3
attgttataaaatttatgtttaatttga-acacactgtttcaaaattttgttccctacacaatgttca-ttgatttacaaacaatcattcaatttttaccagATTATAAATGCAGTCATGAGTGGAAGGGATGTTCTGGTGATCATGGCTGCAGGTGGTGGTAAGAGCCTTTGTTACCAGCTTCCAGCTATACTTCGTGATG
 |||| |   || | ||   ||    |  ||    | |||    | || ||| ||      |  || |  | |          ||  ||    | |  |||||| ||||||||||| |||||||||||||||||  | || || ||||| ||||||||||| ||||| ||||| |||||||| ||||||||  | |||  ||
-ttgtaaatcaagtgatagctatcacggtacttgatatttgtgtacttggtttccgcttttaaattaaacttaaccgtggtatattttttggctgt-gccagATCATAAATGCAGTAATGAGTGGAAGGGATGTAATCGTAATAATGGCAGCAGGTGGTGGGAAGAGTCTTTGCTACCAGCTCCCAGCTATGTTACGTACTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgttccctacacaatgttcattgatttacaaacaatcattcaatttttaccagATTATAAATGCAGTCATGAGTGGAAGGGATGTTCTGGTGATCATGGCTGCAGGTGGTGGTAAGAGCCTTTGTTACCAGCTTCCAGCTATACTTCGTGATG
                    cattgat  putative branch site (score: 4)
                                             tttttacc  putative PPT
                                   aatcattcaattttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attgttataaaatttatgtttaatttgaacacactgtttcaaaattttgttccctacacaatgttcattgatttacaaacaatcattcaatttttaccagATTATAAATGCAGTCATGAGTGGAAGGGATGTTCTGGTGATCATGGCTGCAGGTGGTGGTAAGAGCCTTTGTTACCAGCTTCCAGCTATACTTCGTGATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - ataaaat
- - - - - - - - - - - - - -aacacac
- - - - - - - - - - - - - - - - - - -ttcaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - cacaatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaacaat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cattcaa