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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acacagccatgacattgtgataattgttgatttgctttgatttgattagtatgtccttgatacaatttgatagttaatcctttgtctttctcctgttcagAAAGGTGCAATGACGCCAATGGAAGTATGTGAAGGATTAGGTCTCTATGATCTCAAGAACCGAAAATGGCATATACAAGGAACTTGCGCTCTGAAGGGAG

Basic information

species Vitis vinifera
transcript Vv16s0039g02240.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv16s0039g02240.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA12G02110.1 (Glycine max), 3'ss of exon 5
acacagccatgacattgtgataattgttgatttgctttgatttgattagtatgtccttga-tacaatt-tgatagttaatcctttgtctttctcctgttcagAAAGGTGCAATGACGCCAATGGAAGTATGTGAAGGATTAGGTCTCTATGATCTCAAGAACCGAAAATGGCATATACAAGGAACTTGCGCTCTGAAGGGAG
|  |       | |  ||  |     |  |      |  ||    ||    | ||||  | |  | || | || ||||||  |||  | || || |   |||||||| |||||| | |||| |||| ||||||||||||||||||||| ||||||||||||| |||| ||||| |||||||| ||||| |||||   |||||
attctttttgaataaagtactctccttcaaacaatatatatagttttgtcttatcctcaagtctagttataattgttaatgtttt--ccttttctttaccagAAAGGAGCAATGTCACCAAGGGAAATATGTGAAGGATTAGGTCTCTTTGATCTCAAGAACAGAAAGTGGCACATACAAGGCACTTGTGCTCTTCGGGGAG

upper sequence: Vv16s0039g02240.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA01G43910.2 (Glycine max), 3'ss of exon 6
acacagccatgacattgtgataattgttgatttgctttgatttgattagtat-gt-ccttgatacaatt-tgatagttaatcctttgtctttctcctgttcagAAAGGTGCAATGACGCCAATGGAAGTATGTGAAGGATTAGGTCTCTATGATCTCAAGAACCGAAAATGGCATATACAAGGAACTTGCGCTCTGAAGGGAG
 || |    |    |||  | || | ||    |      ||  | || | || || |  |  |    || | || |||||   ||| | |||||  |||  ||| ||| |||||||||||||||||||| ||||||||| ||||||||| |||||| |||||  |||||||||| |||||||| ||||| || || |||||||
-catacttttcctcttgaaaaaaatattctcctcaaacaatgagttttgcattgtgctctagtgtggttataattgttaacattttctttttcttttgt--agAGAGGGGCAATGACGCCAATGGAAGTGTGTGAAGGACTAGGTCTCTTTGATCTAAAGAATAGAAAATGGCACATACAAGGCACTTGTGCACTTAAGGGAG

upper sequence: Vv16s0039g02240.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA11G01380.2 (Glycine max), 3'ss of exon 6
----acacagccatgacattgtgataattgttgatttgctttgatttgattagtatgtccttgatacaatttgatagttaatcctttgtctttctcctgttcagAAAGGTGCAATGACGCCAATGGAAGTATGTGAAGGATTAGGTCTCTATGATCTCAAGAACCGAAAATGGCATATACAAGGAACTTGCGCTCTGAAGGGAG
           | ||| |   | ||        |    ||  | ||||  |  | ||  || | |    | | || ||| ||  ||  | |||||  |||  ||| ||| || ||||||||||||||||||||||||||| ||||||||| |||||| |||||  |||||||||| ||||| || ||||| || || |||||||
agacttttcctcttgaaaaaataatctccacaaacaatctgaggtttgcct--tgtgctctagtttggttataattgttgatatttcctttttcttttgt--agAGAGGGGCGATGACGCCAATGGAAGTATGTGAAGGACTAGGTCTCTTTGATCTAAAGAATAGAAAATGGCACATACATGGCACTTGTGCACTCAAGGGAG

upper sequence: Vv16s0039g02240.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA11G09790.3 (Glycine max), 3'ss of exon 4
---acacagccatgacattgtgataattgttgatttgctttga-tttgattagtatgtccttgatacaatttgatagttaatcctttgtctttctcctgttcagAAAGGTGCAATGACGCCAATGGAAGTATGTGAAGGATTAGGTCTCTATGATCTCAAGAACCGAAAATGGCATATACAAGGAACTTGCGCTCTGAAGGGAG
     | |  | | ||||    |  | |   | | ||| |    ||  |  |     |   ||  |   | | || ||||||  |||   |||||       ||||||| |||||| | |||| |||| ||||||||||||||||||||| ||||||||||||  |||| ||||| |||||||| ||||| |||||   |||||
tagttatattctt-acatgtataccactcgagttctgcatgatcttccacaaaagcatgactgcca-gttataattgttaatatttttcttttcttta--caagAAAGGAGCAATGTCACCAAGGGAAATATGTGAAGGATTAGGTCTCTTTGATCTCAAGAATAGAAAGTGGCACATACAAGGCACTTGTGCTCTTCGGGGAG

upper sequence: Vv16s0039g02240.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA11G09790.2 (Glycine max), 3'ss of exon 5
acacagccatgacattgtgataattgttgatttgctttga-tttgattagtatgtccttgatacaatttgatagttaatcctttgtctttctcctgttcagAAAGGTGCAATGACGCCAATGGAAGTATGTGAAGGATTAGGTCTCTATGATCTCAAGAACCGAAAATGGCATATACAAGGAACTTGCGCTCTGAAGGGAG----
  | |  | | ||||    |  | |   | | ||| |    ||  |  |     |   ||  |   | | || ||||||  |||   |||||       ||||||| |||||| | |||| |||| ||||||||||||||||||||| ||||||||||||  |||| ||||| |||||||| ||||| |||||   |||||    
-tatattctt-acatgtataccactcgagttctgcatgatcttccacaaaagcatgactgcca-gttataattgttaatatttttcttttcttta--caagaaagGAGCAATGTCACCAAGGGAAATATGTGAAGGATTAGGTCTCTTTGATCTCAAGAATAGAAAGTGGCACATACAAGGCACTTGTGCTCTTCGGGGAGATGG

upper sequence: Vv16s0039g02240.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT5G17060.1 (Arabidopsis thaliana), 3'ss of exon 5
acacagccatgacattgtgataattgttgatttgctttgatttgattagtatgtccttgatacaatttgatagttaatcctttgtctttctcctgttcagAAAGGTGCAATGACGCCAATGGAAGTATGTGAAGGATTAGGTCTCTATGATCTCAAGAACCGAAAATGGCATATACAAGGAACTTGCGCTCTGAAGGGAG
         | |     |  |   | ||| |||   ||  |||   | || ||| |||   |    |  ||  | | | ||||    | ||     | ||| ||| || ||| | || |  |||||||||||||| |||||  | | ||||||||||||| | |||||||| |||||||| ||||| |||||    ||||
--------gtaattcgatattttcttttggtttttgtttgttt--ctcgtctgtgcttataattcctcaat--tcacttctttactctgctggatattagAGAGGAGCCATGTCACCGAGAGAAGTATGTGAAGGGTTAGGCTTATTTGATCTCAAGAACAGGAAATGGCACATACAAGGTACTTGTGCTCTTCGTGGAG

upper sequence: Vv16s0039g02240.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT3G03120.1 (Arabidopsis thaliana), 3'ss of exon 5
acacagccatgacattgtgataattgttga--tttgctttgatttgattagtatgtccttgatacaatttg--atagttaatcctttgtctttctcctgttcagAAAGGTGCAATGACGCCAATGGAAGTATGTGAAGGATTAGGTCTCTATGATCTCAAGAACCGAAAATGGCATATACAAGGAACTTGCGCTCTGAAGGGAG
                || | | ||  |    | |   ||   ||  ||  ||| |  | | |   ||||   | | ||  ||     ||||| |    |||||| ||| || ||| | ||    ||||||||||||||  | ||  |   ||||||||||||| | ||||||||||||||||| || || |||||  | ||||
----------------gtaaaagttcataggctctagctttccttatttcatattttttcgttctcatttaccaaaattcgtctgaactctttatgaatttcagAGAGGAGCCATGTCTCCTCGAGAAGTATGTGAAGGGCTTGGCTTACTTGATCTCAAGAACAGGAAATGGCATATACAAGGCACATGTGCTCTTCAAGGAG

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|26264563|gb|CA815626.1|CA815626
EST:     CATTTATGCTGAACAGCGTCATCTTGATTTTTGCAAACAAACAGGACATG                         AAAGGTGCAATGACGCCAATGGAAGTATGTGAAGGATTAGGTCTCTATGAT
genomic: CATTTATGCTGAACAGCGTCATCTTGATTTTTGCAAACAAACAGGACATGgtatgttgca ... tcctgttcagAAAGGTGCAATGACGCCAATGGAAGTATGTGAAGGATTAGGTCTCTATGAT
EST: gi|30296696|gb|CB973490.1|CB973490
EST:     CATTTATGCTGAACAGCGTCATCTTGATTTTTGCAAACAAACAGGACATG                         AAAGGTGCAATGACGCCAATGGAAGTATGTGAAGGATTAGGTCTCTATGAT
genomic: CATTTATGCTGAACAGCGTCATCTTGATTTTTGCAAACAAACAGGACATGgtatgttgca ... tcctgttcagAAAGGTGCAATGACGCCAATGGAAGTATGTGAAGGATTAGGTCTCTATGAT
EST: gi|71879757|gb|DT028812.1|DT028812
EST:     CATTTATGCTGAACAGCGTCATCTTGATTTTTGCAAACAAACAGGACATG                         AAAGGTGCAATGACGCCAATGGAAGTATGTGAAGGATTAGGTCTCTATGAT
genomic: CATTTATGCTGAACAGCGTCATCTTGATTTTTGCAAACAAACAGGACATGgtatgttgca ... tcctgttcagAAAGGTGCAATGACGCCAATGGAAGTATGTGAAGGATTAGGTCTCTATGAT
EST: gi|71880432|gb|DT029487.1|DT029487
EST:     CATTTATGCTGAACAGCGTCATCTTGATTTTTGCAAACAAACAGGACATG                         AAAGGTGCAATGACGCCAATGGAAGTATGTGAAGGATTAGGTCTCTATGAT
genomic: CATTTATGCTGAACAGCGTCATCTTGATTTTTGCAAACAAACAGGACATGgtatgttgca ... tcctgttcagAAAGGTGCAATGACGCCAATGGAAGTATGTGAAGGATTAGGTCTCTATGAT
EST: gi|71880733|gb|DT029788.1|DT029788
EST:     CATTTATGCTGAACAGCGTCATCTTGATTTTTGCAAACAAACAGGACATG                         AAAGGTGCAATGACGCCAATGGAAGTATGTGAAGGATTAGGTCTCTATGAT
genomic: CATTTATGCTGAACAGCGTCATCTTGATTTTTGCAAACAAACAGGACATGgtatgttgca ... tcctgttcagAAAGGTGCAATGACGCCAATGGAAGTATGTGAAGGATTAGGTCTCTATGAT
EST: gi|71878380|gb|DT027435.1|DT027435
EST:     CATTTATGCTGAACAGCGTCATCTTGATTTTTGCAAACAAACAGGACATG                         AAAGGTGCAATGACGCCAATGGAAGTATGTGAAGGATTAGGTCTCTATGAT
genomic: CATTTATGCTGAACAGCGTCATCTTGATTTTTGCAAACAAACAGGACATGgtatgttgca ... tcctgttcagAAAGGTGCAATGACGCCAATGGAAGTATGTGAAGGATTAGGTCTCTATGAT
EST: gi|71880637|gb|DT029692.1|DT029692
EST:     CATTTATGCTGAACAGCGTCATCTTGATTTTTGCAAACAAACAGGACATG                         AAAGGTGCAATGACGCCAATGGAAGTATGTGAAGGATTAGGTCTCTATGAT
genomic: CATTTATGCTGAACAGCGTCATCTTGATTTTTGCAAACAAACAGGACATGgtatgttgca ... tcctgttcagAAAGGTGCAATGACGCCAATGGAAGTATGTGAAGGATTAGGTCTCTATGAT
EST: gi|30296765|gb|CB973559.1|CB973559
EST:     CATTTATGCTGAACAGCGTCATCTTGATTTTTGCAAACAAACAGGACATG                         AAAGGTGCAATGACGCCAATGGAAGTATGTGAAGGATTAGGTCTCTATGAT
genomic: CATTTATGCTGAACAGCGTCATCTTGATTTTTGCAAACAAACAGGACATGgtatgttgca ... tcctgttcagAAAGGTGCAATGACGCCAATGGAAGTATGTGAAGGATTAGGTCTCTATGAT
EST: gi|71877999|gb|DT027054.1|DT027054
EST:     CATTTATGCTGAACAGCGTCATCTTGATTTTTGCAAACAAACAGGACATG                         AAAGGTGCAATGACGCCAATGGAAGTATGTGAAGGATTAGGTCTCTATGAT
genomic: CATTTATGCTGAACAGCGTCATCTTGATTTTTGCAAACAAACAGGACATGgtatgttgca ... tcctgttcagAAAGGTGCAATGACGCCAATGGAAGTATGTGAAGGATTAGGTCTCTATGAT
EST: gi|110430069|gb|EC996597.1|EC996597
EST:     CATTTATGCTGAACAGCGTCATCTTGATTTTTGCAAACAAACAGGGCATG                         AAAGGTGCAATGACGCCAATGGAAGTATGTGAAGGATTAGGTCTCTATGAT
genomic: CATTTATGCTGAACAGCGTCATCTTGATTTTTGCAAACAAACAGGACATGgtatgttgca ... tcctgttcagAAAGGTGCAATGACGCCAATGGAAGTATGTGAAGGATTAGGTCTCTATGAT
EST: gi|110716367|gb|EE091287.1|EE091287
EST:     CATTTATGCTGAACAGCGTCATCTTGATTTTTGCAAACAAACAGGACATG                         AAAGGTGCAATGACGCCAATGGAAGTATGTGAAGGATTAGGTCTCTATGAT
genomic: CATTTATGCTGAACAGCGTCATCTTGATTTTTGCAAACAAACAGGACATGgtatgttgca ... tcctgttcagAAAGGTGCAATGACGCCAATGGAAGTATGTGAAGGATTAGGTCTCTATGAT
EST: gi|71880723|gb|DT029778.1|DT029778
EST:     CATTTATGCTGAACAGCGTCATCTTGATTTTTGCAAACAAACAGGACATG                         AAAGGTGCAATGACGCCAATGGAAGTATGTGAAGGATTAGGTCTCTATGAT
genomic: CATTTATGCTGAACAGCGTCATCTTGATTTTTGCAAACAAACAGGACATGgtatgttgca ... tcctgttcagAAAGGTGCAATGACGCCAATGGAAGTATGTGAAGGATTAGGTCTCTATGAT
EST: gi|33409512|gb|CF215139.1|CF215139
EST:     CATTTATGCTGAACAGCGTCATCTTGATTTTTGCAAACAAACAGGACATG                         AAAGGTGCAATGACGCCAATGGAAGTATGTGAAGGATTAGGTCTCTATGAT
genomic: CATTTATGCTGAACAGCGTCATCTTGATTTTTGCAAACAAACAGGACATGgtatgttgca ... tcctgttcagAAAGGTGCAATGACGCCAATGGAAGTATGTGAAGGATTAGGTCTCTATGAT
EST: gi|110729888|gb|EE106340.1|EE106340
EST:     CATTTATGCTGAACAGCGTCATCTTGATTTTTGCAAACAAACAGGACATG                         AAAGGTGCAATGACGCCAATGGAAGTATGTGAAGGATTAGGTCTCTATGAT
genomic: CATTTATGCTGAACAGCGTCATCTTGATTTTTGCAAACAAACAGGACATGgtatgttgca ... tcctgttcagAAAGGTGCAATGACGCCAATGGAAGTATGTGAAGGATTAGGTCTCTATGAT
EST: gi|71878000|gb|DT027055.1|DT027055
EST:     CATTTATGCTGAACAGCGTCATCTTGATTTTTGCAAACAAACAGGACATG                         AAAGGTGCAATGACGCCAATGGAAGTATGTGAAGGATTAGGTCTCTATGAT
genomic: CATTTATGCTGAACAGCGTCATCTTGATTTTTGCAAACAAACAGGACATGgtatgttgca ... tcctgttcagAAAGGTGCAATGACGCCAATGGAAGTATGTGAAGGATTAGGTCTCTATGAT
EST: gi|71879446|gb|DT028501.1|DT028501
EST:     CATTTATGCTGAACAGCGTCATCTTGATTTTTGCAAACAAACAGGACATG                         AAAGGTGCAATGACGCCAATGGAAGTATGTGAAGGATTAGGTCTCTATGAT
genomic: CATTTATGCTGAACAGCGTCATCTTGATTTTTGCAAACAAACAGGACATGgtatgttgca ... tcctgttcagAAAGGTGCAATGACGCCAATGGAAGTATGTGAAGGATTAGGTCTCTATGAT
EST: gi|71879383|gb|DT028438.1|DT028438
EST:     CATTTATGCTGAACAGCGTCATCTTGATTTTTGCAAACAAACAGGACATG                         AAAGGTGCAATGACGCCAATGGAAGTATGTGAAGGATTAGGTCTCTATGAT
genomic: CATTTATGCTGAACAGCGTCATCTTGATTTTTGCAAACAAACAGGACATGgtatgttgca ... tcctgttcagAAAGGTGCAATGACGCCAATGGAAGTATGTGAAGGATTAGGTCTCTATGAT
EST: gi|351036486|gb|FQ457199.1|FQ457199
EST:     CATTTATGCTGAACAGCGTCATCTTGATTTTTGCAAACAAGCAGGACATG                         AAAGGTGCAATGACGCCNATGGAAGTATGTGAAGGATTAGGTCTCTATGAT
genomic: CATTTATGCTGAACAGCGTCATCTTGATTTTTGCAAACAAACAGGACATGgtatgttgca ... tcctgttcagAAAGGTGCAATGACGCCAATGGAAGTATGTGAAGGATTAGGTCTCTATGAT
EST: gi|110375930|gb|EC940960.1|EC940960
EST:     CATTTATGCTGAACAGCGTCATCTTGATTTTTGCAAACAAACAGGACATG                         AAAGGTGCAATGACGCCAATGGAAGTATGTGAAGGATTAGGTCTCTATGAT
genomic: CATTTATGCTGAACAGCGTCATCTTGATTTTTGCAAACAAACAGGACATGgtatgttgca ... tcctgttcagAAAGGTGCAATGACGCCAATGGAAGTATGTGAAGGATTAGGTCTCTATGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttagtatgtccttgatacaatttgatagttaatcctttgtctttctcctgttcagAAAGGTGCAATGACGCCAATGGAAGTATGTGAAGGATTAGGTCTCTATGATCTCAAGAACCGAAAATGGCATATACAAGGAACTTGCGCTCTGAAGGGAG
                          agttaat  putative branch site (score: 4)
                                tcctttgtctttctcc  CT-rich tract
                  aatttgatagttaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acacagccatgacattgtgataattgttgatttgctttgatttgattagtatgtccttgatacaatttgatagttaatcctttgtctttctcctgttcagAAAGGTGCAATGACGCCAATGGAAGTATGTGAAGGATTAGGTCTCTATGATCTCAAGAACCGAAAATGGCATATACAAGGAACTTGCGCTCTGAAGGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - ccatgac
- - - - - - - - - - - - - - - - tgctttg
- - - - - - - - - - - - - - - - - - - - - - - - gtatgtc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - gatacaa