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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attcctttattctttccacatctctcaattttcattttagtggttttatttttcctcaattacgcagaatgatatttttctttacatctgtcttacacagCTTTGGAGATTGAGTTCACAAGATCTCAGATCGTTGCAGCAATACCAGGGACCTTTTTCTGTGCATGGTATGCTTCCCAGAAGCATTGGCTAGCCAACAA

Basic information

species Vitis vinifera
transcript Vv06s0009g03520.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0009g03520.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA06G08620.3 (Glycine max), 3'ss of exon 5
attcctttattctttccacatctctcaattttcattttagtggttttatttttcctcaattacgcagaatgatat---ttttctttacatctgtcttacacagCTTTGGAGATTGAGTTCACAAGATCTCAGATCGTTGCAGCAATACCAGGGACCTTTTTCTGTGCATGGTATGCTTCCCAGAAGCATTGGCTAGCCAACAA
  |  | | ||  ||  |  | | |  | ||  || | | ||   |||  || | |  || ||||||||||||||   ||| ||| |||  | |||||||||||||||||||||||||| ||||  || ||| ||||||| | ||| || ||||| ||||| ||||||||||||||||  | ||||||||||||||| || ||
--tgttctgttacttttagctgtttgcacttg-atctaattgacattaacttgcttgtatcacgcagaatgatatacttttgcttaacaattttcttacacagCTTTGGAGATTGAGTTTACAAAGTCACAGGTCGTTGCTGGAATCCCTGGGACTTTTTTTTGTGCATGGTATGCTTTGCGGAAGCATTGGCTAGCAAATAA

upper sequence: Vv06s0009g03520.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA04G08510.1 (Glycine max), 3'ss of exon 5
attcctttattctttccacatctctcaattttcattttagtggttttatttttcctcaattacgcagaatgatat--ttttctttacatctgtcttacacagCTTTGGAGATTGAGTTCACAAGATCTCAGATCGTTGCAGCAATACCAGGGACCTTTTTCTGTGCATGGTATGCTTCCCAGAAGCATTGGCTAGCCAACAA
 ||  | | ||  ||  |  | | |  | ||  || |   ||   |||  || | |  || | ||||||||||||  ||||  |||||  | ||||||||||| |||||||||||||| ||||  || ||| ||||||| | ||| || ||||| ||||| ||||| ||||||||||  ||||||||||||||||| || ||
-ttgttctgttacttttagctgtttgcacttg-atctagttgacattaacttgcttgtatcatgcagaatgatatacttttgcttacaattttcttacacagCATTGGAGATTGAGTTTACAAAGTCACAGGTCGTTGCTGGAATCCCTGGGACATTTTTTTGTGCCTGGTATGCTTTGCAGAAGCATTGGCTAGCAAATAA
















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|71877015|gb|DT026070.1|DT026070
EST:     AAAGCATTGGAATGATGACCCTATCATCTGGCATTTTCCATATTTTCGCT                         CTTTGGAGATTGAGTTCACAAGATCTCAGATCGTTGCAGCAATACCAGGGA
genomic: AAAGCATTGGAATGATGACCCTATCATCTGGCATTTTCCATATTTTCGCTgtatgatgtg ... tcttacacagCTTTGGAGATTGAGTTCACAAGATCTCAGATCGTTGCAGCAATACCAGGGA
EST: gi|27579299|gb|CB001994.1|CB001994
EST:     AAAGCATTGGAATGATGACCCTATCATCTGGCATTTTCCATATTTTCGCT                         CTTTGGAGATTGAGTTCACAAGATCTCAGATCGTTGCAGCAATACCAGGGA
genomic: AAAGCATTGGAATGATGACCCTATCATCTGGCATTTTCCATATTTTCGCTgtatgatgtg ... tcttacacagCTTTGGAGATTGAGTTCACAAGATCTCAGATCGTTGCAGCAATACCAGGGA
EST: gi|351030693|gb|FQ438531.1|FQ438531
EST:     AAGCATTGGAATGATGACCCTATCATCTGGCATTTTCCATATTTTTCGCT                         CTTTGGAGATTGAGTTCACAAGATCTCAGATCGTTGCAGCAATACCAGGG
genomic: AAGCATTGGAATGATGACCCTATCATCTGGCATTTTCCATATTTT-CGCTgtatgatgtg ... tcttacacagCTTTGGAGATTGAGTTCACAAGATCTCAGATCGTTGCAGCAATACCAGGG
EST: gi|22010806|gb|BQ795840.1|BQ795840
EST:     AAAGCATTGGAATGATGACCCTATCATCTGGCATTTTCCATATTTTCGCT                         CTTTGGAGATTGAGTTCACAAGATCTCAGATCGTTGCAGCAATACCAGGGA
genomic: AAAGCATTGGAATGATGACCCTATCATCTGGCATTTTCCATATTTTCGCTgtatgatgtg ... tcttacacagCTTTGGAGATTGAGTTCACAAGATCTCAGATCGTTGCAGCAATACCAGGGA
EST: gi|77579348|gb|DV218502.1|DV218502
EST:     AAAGCATTGGAATGATGACCCTATCATCTGGCATTTTCCATATTTTCGCT                         CTTTGGAGATTGAGTTCACAAGATCTCAGATCGTTGCAGCAATACCAGGGA
genomic: AAAGCATTGGAATGATGACCCTATCATCTGGCATTTTCCATATTTTCGCTgtatgatgtg ... tcttacacagCTTTGGAGATTGAGTTCACAAGATCTCAGATCGTTGCAGCAATACCAGGGA
EST: gi|161717568|gb|FC066896.1|FC066896
EST:     AAAGCATTGGAATGATGACCCTATCATCTGGCATTTTCCATATTTTCGCT                         CTTTGGAGATTGAGTTCACAAGATCTCAGATCGTTGCAGCAATACCAGGGA
genomic: AAAGCATTGGAATGATGACCCTATCATCTGGCATTTTCCATATTTTCGCTgtatgatgtg ... tcttacacagCTTTGGAGATTGAGTTCACAAGATCTCAGATCGTTGCAGCAATACCAGGGA
EST: gi|349812621|gb|FQ409780.1|FQ409780
EST:     AAAGCATTGGAATGATGACCCTATCATCTGGCATTTTCCATATTTTCGCT                         CTTTGGAGATTGAGTTCACAAGATCTCAGATCGTTGCAGCAATACCAGGGA
genomic: AAAGCATTGGAATGATGACCCTATCATCTGGCATTTTCCATATTTTCGCTgtatgatgtg ... tcttacacagCTTTGGAGATTGAGTTCACAAGATCTCAGATCGTTGCAGCAATACCAGGGA
EST: gi|110730433|gb|EE107509.1|EE107509
EST:     AAAGCATTGGAATGATGACCCTATCATCTGGCATTTTCCATATTTTCGCT                         CTTTGGAGATTGAGTTCACAAGATCTCAGATCGTTGCAGCAATACCAGGGA
genomic: AAAGCATTGGAATGATGACCCTATCATCTGGCATTTTCCATATTTTCGCTgtatgatgtg ... tcttacacagCTTTGGAGATTGAGTTCACAAGATCTCAGATCGTTGCAGCAATACCAGGGA
EST: gi|110708740|gb|EE086629.1|EE086629
EST:     AAAGCATTGGAATGATGACCCTATCATCTGGCATTTTCCATATTTTCGCT                         CTTTGGAGATTGAGTTCACAAGATCTCAGATCGTTGCAGCAATACCAGGGA
genomic: AAAGCATTGGAATGATGACCCTATCATCTGGCATTTTCCATATTTTCGCTgtatgatgtg ... tcttacacagCTTTGGAGATTGAGTTCACAAGATCTCAGATCGTTGCAGCAATACCAGGGA
EST: gi|71874644|gb|DT023699.1|DT023699
EST:     AAAGCATTGGAATGATGACCCTATCATCTGGCATTTTCCATATTTTCGCT                         CTTTGGAGATTGAGTTCACAAGATCTCAGATCGTTGCAGCAATACCAGGGA
genomic: AAAGCATTGGAATGATGACCCTATCATCTGGCATTTTCCATATTTTCGCTgtatgatgtg ... tcttacacagCTTTGGAGATTGAGTTCACAAGATCTCAGATCGTTGCAGCAATACCAGGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttatttttcctcaattacgcagaatgatatttttctttacatctgtcttacacagCTTTGGAGATTGAGTTCACAAGATCTCAGATCGTTGCAGCAATACCAGGGACCTTTTTCTGTGCATGGTATGCTTCCCAGAAGCATTGGCTAGCCAACAA
                                            gtcttac  putative branch site (score: 3)
                                         tctgtctt  CT-rich tract
                      aatgatatttttcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attcctttattctttccacatctctcaattttcattttagtggttttatttttcctcaattacgcagaatgatatttttctttacatctgtcttacacagCTTTGGAGATTGAGTTCACAAGATCTCAGATCGTTGCAGCAATACCAGGGACCTTTTTCTGTGCATGGTATGCTTCCCAGAAGCATTGGCTAGCCAACAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - -ccacatc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cagaatg