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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtcagacctcatgggtggtaattgtaattcgtcctttttataagagacctgattacttttctttgtggtgctaatgttaactaaaatcttattttgcagTGCCGTGTTGGATGAGGTAGATATACTACTAAATGATGAAGATTTTGAGCTAGCGCTGCAGACTTTAATTAATTCTTCCCCTGTTACCATGCAATATCTC

Basic information

species Vitis vinifera
transcript Vv05s0020g01130.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0020g01130.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA06G00480.1 (Glycine max), 3'ss of exon 1
tgtcagacctcatgggtggtaattgtaattcgtcctttttataagagacctgattacttttc----tttgtggtgctaatgttaactaaaatcttattttgcagTGCCGTGTTGGATGAGGTAGATATACTACTAAATGATGAAGATTTTGAGCTAGCGCTGCAGACTTTAATTAATTCTTCCCCTGTTACCATGCAATATCTC
   ||  |    |   |  | | |||  || |||   ||| || || |  | ||       |      ||||    | || ||||| | |||  | | ||||||||| |||||||||||||||||||||||  |   |||||| || || ||  | || || ||  | || || ||||| || || |||  ||  || ||| | 
--ccatgctctttccttcctcactgtggtt-gtctccttt-taggatattttatccacccacaccgactgtgaaatttatcttaacaacaataatttgttgcagTGCTGTGTTGGATGAGGTAGATATACTCTTTGGTGATGAGGACTTCGAAGTGGCTCTTCAATCCTTGATCAATTCATCACCAGTTGACACACAGTATTTA
















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|351019641|gb|FQ439458.1|FQ439458
EST:     TTTATGTTCCTAATTAAAGAAGGCTTCTTGCAGTTAACAAATCTTAGATG                         TGCCGTGTTGGATGAGGTAGATATACTACTAAATGATGAAGATTTTGAGCT
genomic: TTTATGTTCCTAATTAAAGAAGGCTTCTTGCAGTTAACAAATCTTAGATGgtaacctata ... tattttgcagTGCCGTGTTGGATGAGGTAGATATACTACTAAATGATGAAGATTTTGAGCT
EST: gi|351015573|gb|FQ426815.1|FQ426815
EST:     TTTATGTTCCTAATTAAAGAAGGCTTCTTGCAGTTAACAAATCTTAGATG                         TGCCGTGTTGGATGAGGTAGATATACTACTAAATGATGAAGATTTTGAGCT
genomic: TTTATGTTCCTAATTAAAGAAGGCTTCTTGCAGTTAACAAATCTTAGATGgtaacctata ... tattttgcagTGCCGTGTTGGATGAGGTAGATATACTACTAAATGATGAAGATTTTGAGCT
EST: gi|349826150|gb|FQ415955.1|FQ415955
EST:     TTTATGTTCCTAATTAAAGAAGGCTTCTTGCAGTTAACAAATCTTAGATG                         TGCCGTGTTGGATGAGGTAGATATACTACTAAATGATGAAGATTTTGAGCT
genomic: TTTATGTTCCTAATTAAAGAAGGCTTCTTGCAGTTAACAAATCTTAGATGgtaacctata ... tattttgcagTGCCGTGTTGGATGAGGTAGATATACTACTAAATGATGAAGATTTTGAGCT
EST: gi|351022470|gb|FQ445245.1|FQ445245
EST:     TTTATGTTCCTAATTAAAGAAGGCTTCTTGCAGTTAACAAATCTTAGATG                         TGCCGTGTTGGATGAGGTAGATATACTACTAAATGATGAAGATT
genomic: TTTATGTTCCTAATTAAAGAAGGCTTCTTGCAGTTAACAAATCTTAGATGgtaacctata ... tattttgcagTGCCGTGTTGGATGAGGTAGATATACTACTAAATGATGAAGATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agacctgattacttttctttgtggtgctaatgttaactaaaatcttattttgcagTGCCGTGTTGGATGAGGTAGATATACTACTAAATGATGAAGATTTTGAGCTAGCGCTGCAGACTTTAATTAATTCTTCCCCTGTTACCATGCAATATCTC
                                  aactaaa  putative branch site (score: 2)
                                          tcttatttt  CT-rich tract
                           taatgttaactaaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgtcagacctcatgggtggtaattgtaattcgtcctttttataagagacctgattacttttctttgtggtgctaatgttaactaaaatcttattttgcagTGCCGTGTTGGATGAGGTAGATATACTACTAAATGATGAAGATTTTGAGCTAGCGCTGCAGACTTTAATTAATTCTTCCCCTGTTACCATGCAATATCTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - -cctcatg
- - - - - - - - - - - - - - - - - - - - -taagaga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gctaatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aactaaa