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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttaatcttatctagaataaatattataaattggtgttgagggtgggggggaaggggggggggtcttggtgaagttctttgtaaactaatagttatcaatcttatgtgtttagAGAGAAGAGCAAATAAGGAAAGAAATGGAAAGGCATGACCGTGAAAGACGGAAGGAAGAAGAGAGGTTGATGCGTGAAAGGCAGCGGGAGGTTGAGAGGT

Basic information

species Vitis vinifera
transcript Vv10s0003g00290.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv10s0003g00290.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G125294_T02 (Zea mays), 3'ss of exon 2
gtttaatcttatctagaataaatattataaattggtgttgagggtgggggggaaggggggggggtcttggtgaagttctttgtaaactaatagttatcaatcttatgtgtttagAGAGAAGAGCAAATAAGGAAAGAAATGGAAAGGCATGACCGTGAAAGACGGAAGGAAGAAGAGAGGTTGATGCGTGAAAGGCAGCGGGAGGTTGAGAGGT
                                    ||      | |         |  |   |  |  |  |     |   | |   | |  | |||  | |  | | |  |||||||||| |||||  ||| ||||||||| || ||||| ||||| ||||| |||||||| |||||||||||||||||||||||| |||| |  ||||  |
------------------------------------gtcttctttagttacactaagaagcatgcatacggcataccttccatgatgcattgctaatctttttcgtatttgcagAGAGAAGAACAAATGCGGAGAGAAATGGAGAGACATGATCGTGAGAGACGTAAGGAAGAGGAGAGGTTGATGCGTGAAAGGCAGAGGGAAGAAGAGAAAT

upper sequence: Vv10s0003g00290.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G122750_T01 (Zea mays), 3'ss of exon 5
gtttaatcttatctagaataaatattataaattggtgttgagggtgggggggaaggggggggggtcttggtgaagttctttgtaaactaatagttatcaatcttatgtgtttagAGAGAAGAGCAAATAAGGAAAGAAATGGAAAGGCATGACCGTGAAAGACGGAAGGAAGAAGAGAGGTTGATGCGTGAAAGGCAGCGGGAGGTTGAGAGGT
                                  || ||     |  |  | |    |   |    |   |    ||| |  |  | || || || |   ||||   | |  |||||||||| |||||   ||  ||||  || || | ||  ||||| ||||| |||||||| |||||||||||||||||||||||| |||| |  ||||  |
----------------------------------gtcttcc---ttagttgcactaagaaagttcatgcatacctttcatgatgcattattattttttcctctt---tctgcagAGAGAAGAACAAATGCAGAGGGAAACAGAGAGACTTGGTCGTGAGAGACGAAAGGAAGAGGAGAGGTTGATGCGTGAAAGGCAGAGGGAAGAAGAGAAAT

upper sequence: Vv10s0003g00290.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA13G30860.1 (Glycine max), 3'ss of exon 5
gtttaatcttatctagaataaatattataaattggtgttgagggtgggggggaaggggggggggtcttggtgaagttctttgtaaactaatagt-tatcaatcttatgtgttt-agAGAGAAGAGCAAATAAGGAAAGAAATGGAAAGGCATGACCGTGAAAGACGGAAGGAAGAAGAGAGGTTGATGCGTGAAAGGCAGCGGGAGGTTGAGAGGT--
      | |||| || ||| ||  ||    | |  ||| |           | |  | |      |    |    |||| ||||    |    | |||    | | |   ||| |||| ||||||| ||| ||||||||||||||||| || || ||||||||| |||||||||||||||||||||||||||| |  || || || |  || || |  
-----gttttat-taaaatgaactttgcctactactgtggcaccatacactgtatagagcttaaacaacatccctttctctgtagctaacccctctattttccctctcccttttagagTGAAGAGCGAATGAGGAAAGAAATGGAAAGACAAGATCGTGAAAGAAGGAAGGAAGAAGAGAGGTTGATGCGTGAGAAACAACGAGAAGAGGAAAGATCA

upper sequence: Vv10s0003g00290.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA07G32180.1 (Glycine max), 3'ss of exon 6
gtttaatcttatctagaataaat-attataaattggtgttgagggtgggggggaaggggggggggtcttggtgaagttctttgtaaactaatagttatcaatcttatgtgtttagAGAGAAGAGCAAATAAGGAAAGAAATGGAAAGGCATGACCGTGAAAGACGGAAGGAAGAAGAGAGGTTGATGCGTGAAAGGCAGCGGGAGGTTGAGAGGT
|||| ||   ||  ||  ||  | || | |||||  | |      | ||||  ||    |     ||  | | |  ||||||   ||||| |   | |    | |   | | ||||| |||||||  | ||| ||||||||||| || || || |||||||||  |||||||||||| |||||||||||||| || ||||| ||||  || ||  
gttttattgaattcagtttagcttatcacaaattttttt-----ataggggttaaaaatgaa---tcacgttcacattctttt--aactattctcttttcccccttcttttgtagAGTGAAGAGCGGACAAGAAAAGAAATGGAGAGACAGGATCGTGAAAGAAAGAAGGAAGAAGAAAGGTTGATGCGTGAGAGACAGCGAGAGGAGGAAAGAG

upper sequence: Vv10s0003g00290.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA13G24370.1 (Glycine max), 3'ss of exon 5
gtttaatcttatctagaataaatattataaattggtgttgagggtgggggggaaggggggggggtcttggtgaagttctttgtaaactaatagttatcaatcttatgtgtttagAGAGAAGAGCAAATAAGGAAAGAAATGGAAAGGCATGACCGTGAAAGACGGAAGGAAGAAGAGAGGTTGATGCGTGAAAGGCAGCGGGAGGTTGAGAGGT
|||| ||  |   |  | | | | |       |       |   |    |||         |  ||    | |  ||||||   ||||| |   | |    | |   | | ||||| |||||||  | ||| ||||||||||| || || || |||||||||  |||||||||||| || ||||||||||| || ||||| ||||  || ||  
gttttattat---tgaattcagtttagcttgctatcacaaaattttataggggttaaaaacgaatcacattcacattctttt--aactattctctttttcccctccttttgtagAGTGAAGAGCGGACAAGAAAAGAAATGGAGAGACAAGATCGTGAAAGAAAGAAGGAAGAAGAAAGATTGATGCGTGAGAGACAGCGAGAGGAGGAAAGAG

upper sequence: Vv10s0003g00290.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT1G28420.1 (Arabidopsis thaliana), 3'ss of exon 5
gtttaatcttatctagaataaatattataaattggtgttgagggtgggggggaaggggggggggtcttggtgaagttctttgtaa-actaatagttatcaat-----cttatgtgtttagAGAGAAGAGCAAATAAGGAAAGAAATGGAAAGGCATGACCGTGAAAGACGGAAGGAAGAAGAGAGGTTGATGCGTGAAAGGCAGCGGGAGGTTGAGAGGT
     || |  |||| | | | |||  |   ||  || | |   | ||   |  |       |   || || |   ||  ||||| |   ||| | || | |     ||| |||  | |||  ||||| |  || || ||||| ||||||||| | || ||||| || || |||||||||||||||||||||||||||||       || |  || ||||
---gtatttgctctacatttattatcctcc-ttactgattat--ttggaaaggtgtcttattgtcttttgttagtatcactgtaacagatatattgatgagttgatgcttgtgtcctcagAATGAAGAACGCATGAGAAAAGAGATGGAAAGGAACGAGCGTGAGAGGCGTAAGGAAGAAGAGAGGTTGATGCGTGAAAGAATAAAAGAAGAGGAAAGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gggggtcttggtgaagttctttgtaaactaatagttatcaatcttatgtgtttagAGAGAAGAGCAAATAAGGAAAGAAATGGAAAGGCATGACCGTGAAAGACGGAAGGAAGAAGAGAGGTTGATGCGTGAAAGGCAGCGGGAGGTTGAGAGGT
                         aactaat  putative branch site (score: 2)
                       taaactaatagttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttaatcttatctagaataaatattataaattggtgttgagggtgggggggaaggggggggggtcttggtgaagttctttgtaaactaatagttatcaatcttatgtgtttagAGAGAAGAGCAAATAAGGAAAGAAATGGAAAGGCATGACCGTGAAAGACGGAAGGAAGAAGAGAGGTTGATGCGTGAAAGGCAGCGGGAGGTTGAGAGGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG