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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgaggaagagattggtggcagatgataaattgttgggaagctagaatgattgcttcaatttgtttaattttttattcttattttttatttatacatgcagTGAGACTTGCAATTTTTGGTGCTTTATGGATAATTCTTGGAAAGCGGGTCTGGTTTTTCCCTAACATCCTTGTAGAGGAAGTAACACTACGAGAATTATT

Basic information

species Vitis vinifera
transcript Vv06s0004g02280.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0004g02280.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA08G45020.1 (Glycine max), 3'ss of exon 3
tga--ggaagagattggtggcagatgataaattgttgggaagctagaatgattgcttcaat--ttgtttaattttttattcttattttttatttatacatgcagTGAGACTTGCAATTTTTGGTGCTTTATGGATAATTCTTGGAAAGCGGGTCTGGTTTTTCCCTAACATCCTTGTAGAGGAAGTAACACTACGAGAATTATT
|||   || | |  |  | |      |||   |  |     ||   |     ||||||| |  ||  ||     |    | |||| |||||   |||  || ||| |||  | |||| ||||| |||||||  || ||||||||||||||  ||||||||||||||||||||||||  ||||||| |||||| || || || ||
tgattagaggtggctaattgtctgaaatatgcttattaagtgcaccacatcctgcttcagtgcttccttgggcctcatgttttatgtttta---atat-tgtagTAAGAGGTACAATATTTGGCGCTTTATATATTATTCTTGGAAAGCGAATCTGGTTTTTCCCTAACATCCTTGCCGAGGAAGCAACACTGCGGGAGTTGTT

upper sequence: Vv06s0004g02280.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA18G07900.1 (Glycine max), 3'ss of exon 3
tgaggaagagattggtggcagatgataaattgttgggaagc-tagaatgat-tgcttcaat-ttgtttaattttttattcttattttttatttatacatgcagTGAGACTTGCAATTTTTGGTGCTTTATGGATAATTCTTGGAAAGCGGGTCTGGTTTTTCCCTAACATCCTTGTAGAGGAAGTAACACTACGAGAATTATT
    || | |  |  | |      |||   | ||   ||    |  |   | ||||||| |  | | |      | ||| || |||||||  |||   || ||| |||  | |||| |||||||||||||  ||  | |||||||||||  ||||||||||||| ||||||||||  ||||||| ||| || || || || ||
attagaggtggctaattgtctgaaatatgctcttattaaatgcaccacattctgcttcagtgctttcttgggcctcattttttttttttaaatat---tgtagTAAGAGGTACAATATTTGGTGCTTTATATATTGTACTTGGAAAGCGAATCTGGTTTTTCCCCAACATCCTTGCCGAGGAAGCAACTCTGCGGGAGTTGTT
















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|110711779|gb|EE088644.1|EE088644
EST:     ACTATATACATGTGCTGGTGTTCTACTACTCATACTCTCCCTGCTATTAT                         TGAGACTTGCAATTTTTGGTGCTTTATGGATAATTCTTGGGAAGCGGGTCG
genomic: ACTATATACATGTGCTGGTGTTCTACTACTCATACTCTCCCTGCTATTATgtaagttctg ... atacatgcagTGAGACTTGCAATTTTTGGTGCTTTATGGATAATTCTTGGAAAGCGGGTCT
EST: gi|110712755|gb|EE088078.1|EE088078
EST:     ACTATATACATGTGCTGGTGTTCTACTACTCATACTCTCCCTGCTATTAT                         TGAGACTTGCAATTTTTGGTGCTTTATGGATAATTCTTGGAAAGCGGGTCT
genomic: ACTATATACATGTGCTGGTGTTCTACTACTCATACTCTCCCTGCTATTATgtaagttctg ... atacatgcagTGAGACTTGCAATTTTTGGTGCTTTATGGATAATTCTTGGAAAGCGGGTCT
EST: gi|161713701|gb|FC062841.1|FC062841
EST:     ACTATATACATGTGCTGGTGTTCTACTACTCATACTCTCCCTGCTATTAT                         TGAGACTTGCAATTTTTGGTGCTTTATGGATAATTCTTGGAAAGCGGGTCT
genomic: ACTATATACATGTGCTGGTGTTCTACTACTCATACTCTCCCTGCTATTATgtaagttctg ... atacatgcagTGAGACTTGCAATTTTTGGTGCTTTATGGATAATTCTTGGAAAGCGGGTCT
EST: gi|110711813|gb|EE088718.1|EE088718
EST:     ACTGTATACATGTGCTGGTGTTCTACTACTCATACTCTCCCTGCTATTAT                         TGAGACTTGCAATTTTTGGTGCTTTATGGATAATTCNTGGAAAGCGGGTCT
genomic: ACTATATACATGTGCTGGTGTTCTACTACTCATACTCTCCCTGCTATTATgtaagttctg ... atacatgcagTGAGACTTGCAATTTTTGGTGCTTTATGGATAATTCTTGGAAAGCGGGTCT
EST: gi|33406482|gb|CF212109.1|CF212109
EST:     ACTATATACATGTGCTGGTGTTCTACTACTCATACTCTCCCTGCTATTAT                         TGAGACTTGCAATTTTTGGTGCTTTATGGATAATTCTTGGAAAGCGGGTCT
genomic: ACTATATACATGTGCTGGTGTTCTACTACTCATACTCTCCCTGCTATTATgtaagttctg ... atacatgcagTGAGACTTGCAATTTTTGGTGCTTTATGGATAATTCTTGGAAAGCGGGTCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgattgcttcaatttgtttaattttttattcttattttttatttatacatgcagTGAGACTTGCAATTTTTGGTGCTTTATGGATAATTCTTGGAAAGCGGGTCTGGTTTTTCCCTAACATCCTTGTAGAGGAAGTAACACTACGAGAATTATT
                gtttaat  putative branch site (score: 4)
        ttcaatttgtttaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgaggaagagattggtggcagatgataaattgttgggaagctagaatgattgcttcaatttgtttaattttttattcttattttttatttatacatgcagTGAGACTTGCAATTTTTGGTGCTTTATGGATAATTCTTGGAAAGCGGGTCTGGTTTTTCCCTAACATCCTTGTAGAGGAAGTAACACTACGAGAATTATT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- aggaaga
- - - - - - tggtggc
- - - - - - - - - - - - - - - tgttggg
- - - - - - - - - - - - - - - - - - - - - - - tgattgc