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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttatcagttggatcagtcaagtaaaccattaaatgtttagtaacccataaagctgtcttggcttgatttctaatcatattagtattgttatttgctacagTCTCTAGAGCTTTGGAACATGAGCGAGAACAAGACAATGACTCTTTCAGCTCATGATGGACTAATAGCTGCCTTGGCTGTATCAACTGTGTCTGGCTTGG

Basic information

species Vitis vinifera
transcript Vv04s0008g04910.t01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0008g04910.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA06G07580.1 (Glycine max), 3'ss of exon 17
--ttatcagttggatcagtcaagtaaaccattaaatgtttagtaacccataaagc-tgtcttggctt-gatttctaat-catattagtattgttatttgctacagTCTCTAGAGCTTTGGAACATGAGCGAGAACAAGACAATGACTCTTTCAGCTCATGATGGACTAATAGCTGCCTTGGCTGTATCAACTGTGTCTGGCTTGG
  || |   |||    |||  | |      |   |  |   | || ||||| | | |||  |   || ||  ||| || | |  ||   ||  | ||   |  ||||  | ||| | ||||||||||||||||||||||| |||||||| || ||||||||||| || ||  || |||||||||| ||||||||   ||| ||||
ggttgtattttgtcctagttgaatggtgagtagtacat---gcaatccatacatcctgttgtaattttgacatcttatgcttggtaaatttaatgttg--tgtagTCATTGGAGTTGTGGAACATGAGCGAGAACAAGACGATGACTCTGTCTGCTCATGATGGTCTCATTACTTCCTTGGCTGTTTCAACTGTAAATGGTTTGG

upper sequence: Vv04s0008g04910.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA04G07460.1 (Glycine max), 3'ss of exon 17
ttatcagttggatcagtcaagta--aaccattaaatgtttagtaacccataaagctgtcttggcttgatttctaat-catattag---tattgttatttg-ctacagTCTCTAGAGCTTTGGAACATGAGCGAGAACAAGACAATGACTCTTTCAGCTCATGATGGACTAATAGCTGCCTTGGCTGTATCAACTGTGTCTGGCTTGG
  ||   |||     ||  | |    |  | ||||||   |   |  || || | |||  |   ||||  ||| |  | | |||    || |||| | |  ||  ||||  | ||||| ||||| |||||||||||||||||||||||||| || ||||||||||| || ||  || ||||||| || ||||||||   ||| ||||
--att--ttgtccttgttgaatggtgagtaataaatgca-atccatacacaatgttgtaat--tttgacatcttacgcttgttaaatttaatgttgtgtaactgtagTCATTGGAGCTGTGGAATATGAGCGAGAACAAGACAATGACTCTGTCTGCTCATGATGGTCTCATTACTTCCTTGGCGGTTTCAACTGTAAATGGTTTGG

upper sequence: Vv04s0008g04910.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA14G16040.1 (Glycine max), 3'ss of exon 17
----ttatcagttggatcagtcaagtaaaccattaaatgtttagtaacccataa--agctgtcttggcttgatttctaatcatattagtattgttatttgctacagTCTCTAGAGCTTTGGAACATGAGCGAGAACAAGACAATGACTCTTTCAGCTCATGATGGACTAATAGCTGCCTTGGCTGTATCAACTGTGTCTGGCTTGG
    ||||   ||   |    |     ||  | ||| | | |   ||   ||||  || | | |    |||     | || ||  | |||   | || |||   ||||  | ||||| ||||||||||  ||||||||||| |||||||| || |||||||| || || || || || ||||| || || |||||   ||| ||||
ctgattatattttactttctccctaacaaatagtaattatatc-caatttataattagatttgtaattttggcccgttataat--tggtaccatgatctgc---agTCATTGGAGCTCTGGAACATGACTGAGAACAAGACGATGACTCTATCTGCTCATGAAGGTCTTATTGCGGCATTGGCGGTTTCTACTGTAAATGGTTTGG

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|71881075|gb|DT030130.1|DT030130
EST:     GTGTTTTTCACCCAACATATTCGTCATTGCTGGTCATCGGTTGTTACCAG                         TCTCTAGAGCTTTGGAACATGAGCGAGAACAAGACAATGACTCTTTCAGCT
genomic: GTGTTTTTCACCCAACATATTCGTCATTGCTGGTCATCGGTTGTTACCAGgcaagtcatt ... tttgctacagTCTCTAGAGCTTTGGAACATGAGCGAGAACAAGACAATGACTCTTTCAGCT
EST: gi|110690242|gb|EE067180.1|EE067180
EST:     GTGTTTTTCACCCAACATATTCGTCATTGCTGGTCATCGGTTGTTACCAG                         TCTCTAGAGCTTTGGAACATGAGCGAGAACAAGACAATGACTCTTTCAGCT
genomic: GTGTTTTTCACCCAACATATTCGTCATTGCTGGTCATCGGTTGTTACCAGgcaagtcatt ... tttgctacagTCTCTAGAGCTTTGGAACATGAGCGAGAACAAGACAATGACTCTTTCAGCT
EST: gi|34545176|gb|CF513408.1|CF513408
EST:     GTGTTTTTCACCCAACATATTCGTCATTGCTGGTCATCGGTTGTTACCAG                         TCTCTAGAGCTTTGGAACATGAGCGAGAACAAGACAATGACTCTTTCAGCT
genomic: GTGTTTTTCACCCAACATATTCGTCATTGCTGGTCATCGGTTGTTACCAGgcaagtcatt ... tttgctacagTCTCTAGAGCTTTGGAACATGAGCGAGAACAAGACAATGACTCTTTCAGCT
EST: gi|34546171|gb|CF514403.1|CF514403
EST:     TGTTTTTCACCCAACATATTCGTCATTGCTGGTCATCGGGTNGT-ACCAG                         TCTCTAGAGCTTTGGAACATG
genomic: TGTTTTTCACCCAACATATTCGTCATTGCTGGTCATCGGTT-GTTACCAGgcaagtcatt ... tttgctacagTCTCTAGAGCTTTGGAACATG
EST: gi|110699780|gb|EE077080.1|EE077080
EST:     GTGTTTTTCACCCAACATATTCGTCATTGCTGGTCATCGGTTGTTACCAG                         TCTCTAGAGCTTTGGAACATGAGCGAGAACAAGACAATGACTCTTTCAGCT
genomic: GTGTTTTTCACCCAACATATTCGTCATTGCTGGTCATCGGTTGTTACCAGgcaagtcatt ... tttgctacagTCTCTAGAGCTTTGGAACATGAGCGAGAACAAGACAATGACTCTTTCAGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cataaagctgtcttggcttgatttctaatcatattagtattgttatttgctacagTCTCTAGAGCTTTGGAACATGAGCGAGAACAAGACAATGACTCTTTCAGCTCATGATGGACTAATAGCTGCCTTGGCTGTATCAACTGTGTCTGGCTTGG
                      ttctaat  putative branch site (score: 2)
                    atttctaatcatatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttatcagttggatcagtcaagtaaaccattaaatgtttagtaacccataaagctgtcttggcttgatttctaatcatattagtattgttatttgctacagTCTCTAGAGCTTTGGAACATGAGCGAGAACAAGACAATGACTCTTTCAGCTCATGATGGACTAATAGCTGCCTTGGCTGTATCAACTGTGTCTGGCTTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - cagttgg
- - - - - - - - - - - aaaccat
- - - - - - - - - - - - - - - - - - - - taaccca