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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...caatgatcagttgagcggatttttgcagttctaaaaatagattgtgacataagtgcatttataatcgacaattttatcgatttctaatttgtggttgcagGAGAAATTTGCTTCAATGATCGCAAATGCAGGGTTTCAGAAGGTTGAATATGAAAATCTTGTTGGTGGGGTGGTGGCAATCCATTCTGGGTTGAAATTTT

Basic information

species Vitis vinifera
transcript Vv16s0039g01590.t01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv16s0039g01590.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA07G03210.2 (Glycine max), 3'ss of exon 6
---caatgatcagttgagcggatttttgcagttctaaaaatagattgtgacataagtgcatttataatcgacaattttatcgatttctaatttgtgg-ttgcagGAGAAATTTGCTTCAATGATCGCAAATGCAGGGTTTCAGAAGGTTGAATATGAAAATCTTGTTGGTGGGGTGGTGGCAATCCATTCTGGGTTGAAATTTT
   | || |    |  |     |  || ||  |       |   | |   ||||||   |||   ||| |   | || ||| |||  |||||  ||| |||||||| |||||||| || ||||| ||  |||||||||||||||| || || ||||| ||||| ||||  || ||||| || |||||||| ||||| ||| | |
tatctataaatgatGAAAAATTTGCTTACATATGCTTCTTTGCTTGGCATCATAAGA--ATTGCCAATTGTTGACTT-ATCTATTG-TAATTGATGGATTGCAGGAAAAATTTGCATCGATGATTGCGGATGCAGGGTTTCAGAAAGTAGAGTATGAGAATCTAGTTGCGGGAGTGGTTGCTATCCATTCAGGGTTAAAAATCT

upper sequence: Vv16s0039g01590.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: AT5G57300.3 (Arabidopsis thaliana), 3'ss of exon 8
--caatgatcagttgagcggatttttgcagttctaaaaatagattgtgacataagt-gcatttataatcgacaattttatcgatttctaatttgtggttgcagGAGAAATTTGCTTCAATGATCGCAAATGCAGGGTTTCAGAAGGTTGAATATGAAAATCTTGTTGGTGGGGTGGTGGCAATCCATTCTGGGTTGAAATTTT
    |  |||   || | |      ||  ||       |||    ||    | ||| | |   ||  |    |||    | |||   | |  || |  ||||||||  |||||| |||||||||||| ||||||| ||| ||||||| || || || || ||||||||||| || || || || || ||||   | ||  | |
tatgagcatcgtgtgtgtgatcaggtgatgtctagtctataagacgtttttttagtcggaagcatgttttgtaatcac-tagatgcatgaaatgag--tgcagGAGCGATTTGCATCAATGATCGCAGATGCAGGATTTGAGAAGGTGGAGTACGAGAACCTTGTTGGTGGAGTTGTCGCCATTCACTCTGCCATAAAGCTCT
















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|30328508|gb|CD011770.1|CD011770
EST:     GGGCATCGTACCAGTATTTAGTTGAGAGTATTCGCCGTTTTCCACCGCAG                         GAGAAATTTGCTTCAATGATCGCAAATGCAGGGTTTCAGAAGGTTGAATAT
genomic: GGGCATCGTACCAGTATTTAGTTGAGAGTATTCGCCGTTTTCCACCGCAGgtttcaatcc ... gtggttgcagGAGAAATTTGCTTCAATGATCGCAAATGCAGGGTTTCAGAAGGTTGAATAT
EST: gi|83274635|gb|DV938731.1|DV938731
EST:     GGGCATCGTACCAATATTTAGTTGAGAGTATTCGCCGTTTTCCACCGCAG                         GAGAAATTTGCTTCAATGATCGCAAATGCAGGGTTTCAGAAGGTTGAATAT
genomic: GGGCATCGTACCAGTATTTAGTTGAGAGTATTCGCCGTTTTCCACCGCAGgtttcaatcc ... gtggttgcagGAGAAATTTGCTTCAATGATCGCAAATGCAGGGTTTCAGAAGGTTGAATAT
EST: gi|27580065|gb|CB002760.1|CB002760
EST:     GGGCATCGTACCAGTATTTAGTTGAGAGTATTCGCCGTTTTCCACCGCAG                         GAGAAATTTGCTTCAATGATCGCAAATGCAGGGTTTCAGAAGGTTGAATAT
genomic: GGGCATCGTACCAGTATTTAGTTGAGAGTATTCGCCGTTTTCCACCGCAGgtttcaatcc ... gtggttgcagGAGAAATTTGCTTCAATGATCGCAAATGCAGGGTTTCAGAAGGTTGAATAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gacataagtgcatttataatcgacaattttatcgatttctaatttgtggttgcagGAGAAATTTGCTTCAATGATCGCAAATGCAGGGTTTCAGAAGGTTGAATATGAAAATCTTGTTGGTGGGGTGGTGGCAATCCATTCTGGGTTGAAATTTT
                                    ttctaat  putative branch site (score: 2)
           atttataatcgacaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
caatgatcagttgagcggatttttgcagttctaaaaatagattgtgacataagtgcatttataatcgacaattttatcgatttctaatttgtggttgcagGAGAAATTTGCTTCAATGATCGCAAATGCAGGGTTTCAGAAGGTTGAATATGAAAATCTTGTTGGTGGGGTGGTGGCAATCCATTCTGGGTTGAAATTTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - -tgcagtt
- - - - - - - - - - - - - - - - aaaaata
- - - - - - - - - - - - - - - - - - - - - - - - - - gtgcatt