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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttttttaggtacctttatgggaaaagatatatttgaatgggaaaaggttttgcatcattatactcactatggcattcttattttctgcctttattttcagGATTGACAATTGGAAACGTGAACATATACTGCAATTCCTGAGAGAGAAGGTCAAGCCTGCTTCATCAGCAATCTAACCAGGCAGTTCAGCAAATAACCAA

Basic information

species Vitis vinifera
transcript Vv05s0094g00490.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0094g00490.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA07G32960.1 (Glycine max), 3'ss of exon 3
---ttttttaggtacctttatgggaaaagatatatttgaatgggaaaaggttttgcatcatt-atactcactatggcattcttattttctgcctttatttt-cagGATTGACAATTGGAAACGTGAACATATACTGCAATTCCTGAGAGAGAAGGTCAAGCCTGCTTCATCAGCAATCTAACCAGGCAGTTCAGCAAATAACCAA---
     ||  |   | || | |         |   |||||| |  |||  |||||   | ||| ||| | |   |      |  |    ||   | | | || ||||||||| |||||||||||||| ||||||||||| |||||  |||||||||| ||||||    | || |     | |        || | | | |  | |    
aggagttaaaataatctctcttttt-----ttcttttgaacgaaaaagagttttattttatttatatttatctttcttcccccaccccctttttgtctcttgcagGATTGATAATTGGAAACGTGAGCATATACTGCAGTTCCTCCGAGAGAAGGTGAAGCCTCTGGCTTCTGA---TTGAGAGAATCTTTGACCCATTCTCTAGCAA

upper sequence: Vv05s0094g00490.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA02G15540.1 (Glycine max), 3'ss of exon 3
ttttttaggtacctttatgggaaaagatatat---ttgaatgggaaaaggttttgcatcattatactcactatggcattcttattttctgcctttatttt-cagGATTGACAATTGGAAACGTGAACATATACTGCAATTCCTGAGAGAGAAGGTCAAGCCTGCTTCATCAGCAATCTAACCAGGCAGTTCAGCAAATAACCAA-
    | |  ||  |||||    |    |   |   |||||||  ||||||||||   |  || |             ||||| ||  ||   | | | || ||| ||||| |||||||||||||| |||||||| || ||||||||||||||||| ||||||    | || | | |   |      |   ||     |  |    
----taaaatatttttatatttattttttcttctcttgaatgaaaaaaggttttaacttgttttttatctctcttttttctttttccctttttgtctgttgcagAATTGATAATTGGAAACGTGAGCATATACTACAGTTCCTGAGAGAGAAGGTGAAGCCTCTAGCGTCTG-ATTGAGAATCTTTAACCCATTCTCTGGCATGC
















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|110706312|gb|EE081730.1|EE081730
EST:     CCAAAATTGATCATGTTGGATGATGATGGCCAACACAAGGAAACCATAAG                         GATTGACAATTGGAAACGTGAACATATACTGCAATTCCTGAGAGAGAAGGT
genomic: CCAAAATTGATCATGTTGGATGATGATGGCCAACACAAGGAAACCATAAGgtgagcctct ... ttattttcagGATTGACAATTGGAAACGTGAACATATACTGCAATTCCTGAGAGAGAAGGT
EST: gi|110692617|gb|EE072063.1|EE072063
EST:     CCAAAATTGATCATGTTGGATGATGATGGCCAACACAAGGAAACCATAAG                         GATTGACAATTGGAAACGTGAACATATACTGCAATTCCTGAGAGAGAAGGT
genomic: CCAAAATTGATCATGTTGGATGATGATGGCCAACACAAGGAAACCATAAGgtgagcctct ... ttattttcagGATTGACAATTGGAAACGTGAACATATACTGCAATTCCTGAGAGAGAAGGT
EST: gi|110692825|gb|EE068530.1|EE068530
EST:     CCAAAATTGATCATGTTGGATGATGATGGCCAACACAAGGAAACCATAAG                         GATTGACAATTGGAAACGTGAACATATACTGCAATTCCTGAGAGAGAAGGT
genomic: CCAAAATTGATCATGTTGGATGATGATGGCCAACACAAGGAAACCATAAGgtgagcctct ... ttattttcagGATTGACAATTGGAAACGTGAACATATACTGCAATTCCTGAGAGAGAAGGT
EST: gi|30129296|gb|CB914635.1|CB914635
EST:     CCAAAATTGATCATGTTGGATGATGATGGCCAACACAAGGAAACCATAAG                         GATTGACAATTGGAAACGTGAACATATACTGCAATTCCTGAGAGAGAAGGT
genomic: CCAAAATTGATCATGTTGGATGATGATGGCCAACACAAGGAAACCATAAGgtgagcctct ... ttattttcagGATTGACAATTGGAAACGTGAACATATACTGCAATTCCTGAGAGAGAAGGT
EST: gi|26265467|gb|CA816530.1|CA816530
EST:     CCAAAATTGATCATGTTGGATGATGATGGCCAACACAAGGAAACCGTAAG                         GATTGACAATTGGAAACGTGAACATATACTGCAATTCCTGAGAGAGAAGGT
genomic: CCAAAATTGATCATGTTGGATGATGATGGCCAACACAAGGAAACCATAAGgtgagcctct ... ttattttcagGATTGACAATTGGAAACGTGAACATATACTGCAATTCCTGAGAGAGAAGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggttttgcatcattatactcactatggcattcttattttctgcctttattttcagGATTGACAATTGGAAACGTGAACATATACTGCAATTCCTGAGAGAGAAGGTCAAGCCTGCTTCATCAGCAATCTAACCAGGCAGTTCAGCAAATAACCAA
               tactcac  putative branch site (score: 1)
                             ttcttattttctgcct  putative PPT
                            attcttatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttttttaggtacctttatgggaaaagatatatttgaatgggaaaaggttttgcatcattatactcactatggcattcttattttctgcctttattttcagGATTGACAATTGGAAACGTGAACATATACTGCAATTCCTGAGAGAGAAGGTCAAGCCTGCTTCATCAGCAATCTAACCAGGCAGTTCAGCAAATAACCAA

- - - - - - - - - gggaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - tgcatca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctcacta