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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACACAAATATTGAGAGAGAAAAGAACAGAGGAAAAAAGCAGGCATGGGTCAAGCCTTTCGCAAGCTCTTCGATACCTTCTTCGGCAACTCTGAGATGAGGgtacccttttttctctatctttttctttacatacccatttgtattatgtgtttctgtatatgggtttctttttgtttcgtttcaattcatttctttttat...

Basic information

species Vitis vinifera
transcript Vv16s0039g02240.t01
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv16s0039g02240.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: LOC_Os10g42940.1 (Oryza sativa), 5'ss of exon 1
ACACAAATATTGAGAGAGAAAAGAACAGAGGAAAAAAGCAGGCATGGGTCAAGCCTTTCGCAAGCTCTTCGATACCTTCTTCGGCAACTCTGAGATGAGGgtaccct--tttttctctatctttttctttacatacccatttgtattatgtgttt-ctgtatatgggtttctttttgtttcgtttcaattcatttctttttat
    ||   |  |||       |    ||      ||| ||| ||||| || ||||| ||||||||||||||  ||||||||||||||   |||||| ||||||||     |||  |  |||| |   |  | |  |   |||  || ||         |  |||    |  |||||  | |                     
CTGGAAGCTTCTAGATCCGGCCGCTACGATCGGCGAAGAAGGGATGGGGCAGGCCTTCCGCAAGCTCTTCGACGCCTTCTTCGGCAACAAGGAGATGCGGgtaccccaagcttttccactcttgtctgtctcgtctcagattgggttttggacggatcatggatgatggtggttttggctggcag------------------

upper sequence: Vv16s0039g02240.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: GLYMA01G43910.1 (Glycine max), 5'ss of exon 1
ACACAAATATTGAGAGAGAAAAGAACAGAGGAAAAAAGCAGGCATGGGTCAAGCCTTTCGCAAGCTCTTCGATACCTTCTTCGGCAACTCTGAGATGAGGgtacccttttttctctatctttttctttacatacccatttgtattatgtgtttctgtatatgggtttctttttgtttcgtttcaattcatttctttttat
|         |   |         ||   |        | |||||||||||||| ||||| |||||||| || ||||||||||||||| | |||||||||||| | || |   |   | ||   | |||  |    |     | | | |  ||   | |||   || |||  | | |   ||||                
ATTTTTTACCTTTCAATTTTTGATACTCGGACCCGGCACCGGCATGGGTCAAGCTTTTCGAAAGCTCTTTGACACCTTCTTCGGCAACACCGAGATGAGGgtaactttctgcttgcttgttaaacgttaattttttacactcaatttattattaactttattatttccttgatctgtttgttcag---------------

upper sequence: Vv16s0039g02240.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: GLYMA12G02110.1 (Glycine max), 5'ss of exon 1
--ACACAAATATTGAGAGAGAAAAGAACAGAGGAAAAAAGCAGGCATGGGTCAAGCCTTTCGCAAGCTCTTCGATACCTTCTTCGGCAACTCTGAGATGAGGgtacccttttttctctatctttttctttacatacccatttgtattatgtgtttctgtatatgggtttctttttgtttcgtttcaattcatttctttttat----
       | | | ||         || |  |   ||  |  ||||||||||||||| ||||| ||||||||||| ||||||||||||||| | |||||| |||| | |||  |||  | ||  || ||| | |    || |  || ||    |     ||||    ||  |    |  | | |   |||  || |||  ||     
TTTTGTGATTCTCGATTTGATTTGGATCGCACAGAACGA--AGGCATGGGTCAAGCTTTTCGGAAGCTCTTCGACACCTTCTTCGGCAACACCGAGATGCGGgt-ctcttccttccttctccattccttaatagcaacagtcataata---atgataatataataattcttagaagaatagatgtcattttttgcttaataacgct

upper sequence: Vv16s0039g02240.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: GLYMA11G09790.2 (Glycine max), 5'ss of exon 1
-ACACAAATATTGAGAGAGAAAAGAACAGAGGAAAAAAGCAGGCATGGGTCAAGCCTTTCGCAAGCTCTTCGATACCTTCTTCGGCAACTCTGAGATGAGGgtacccttttttctctatctttttctttacatacccatttgtattatgtgtttctgtatatgggtttctttttgtttcgtttcaattcatttctttttat----
   |  | |  |      ||   || | ||  | || || ||||||||||||||| ||||| ||||||||||| ||||||||||||||  | |||||| |||| | |||  |||  | ||  || ||||   |    |||  | || | | |||   |||    | |  |  |  |     |  |||  | ||||    |     
ATAATCAGTTCTCGATTTGATTTGATCGGAACAGAACAG-AGGCATGGGTCAAGCTTTTCGGAAGCTCTTCGACACCTTCTTCGGCAATACCGAGATGCGGgt-ctcttccttccttctccattccttttttttattattattctttt-tcttttaatatcaacggtcataataatgataatataat--aattctaagaagaaga

upper sequence: Vv16s0039g02240.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: GLYMA11G01380.2 (Glycine max), 5'ss of exon 2
ACACAAATATTGAGAGAGAAAAGAACAGAGGAAAAAAGCAGGCATGGGTCAAGCCTTTCGCAAGCTCTTCGATACCTTCTTCGGCAACTCTGAGATGAGGgtacccttttttctctatctttttctttacatacccatttgtattatgtgtttctgt--atatgggtttctttttgtttcgtttcaattcatttctttttat
                               |      | |||||||||||||| ||||| ||||| || || |||||||| |||||| | |||||||||||| | || |        |||  |  ||| ||    |||| ||   |   ||  | |  || |   | | |  ||| |  ||||   ||||           
---------------------------AGACACCGGCACCGGCATGGGTCAAGCTTTTCGGAAGCTATTTGACACCTTCTTTGGCAACACCGAGATGAGGgtaactttctg-------cttgattgttaaatgttaatttttacactcaattattattaattttattatttccttgatctgttt--gttcag----------

upper sequence: Vv16s0039g02240.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: GLYMA11G01380.3 (Glycine max), 5'ss of exon 1
ACACAAATATTGAGAGAGAAAAGAACAGAGGAAAAAA-GCAGGCATGGGTCAAGCCTTTCGCAAGCTCTTCGATACCTTCTTCGGCAACTCTGAGATGAGGgtacccttttttctctatctttttctttacatacccatttgtattatgtgtttctgt--atatgggtttctttttgtttcgtttcaattcatttctttttat
    |  |    |  |    |    |||||  |      | |||||||||||||| ||||| ||||| || || |||||||| |||||| | |||||||||||| | || |        |||  |  ||| ||    |||| ||   |   ||  | |  || |   | | |  ||| |  ||||   ||||           
-TTTATCTTCCAATTGTCTGATACTCAGAGACACCGGCACCGGCATGGGTCAAGCTTTTCGGAAGCTATTTGACACCTTCTTTGGCAACACCGAGATGAGGgtaactttctg-------cttgattgttaaatgttaatttttacactcaattattattaattttattatttccttgatctgttt--gttcag----------

upper sequence: Vv16s0039g02240.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: GLYMA01G43910.2 (Glycine max), 5'ss of exon 2
ACACAAATATTGAGAGAGAAAAGAACAGAGGAAAAAAGCAGGCATGGGTCAAGCCTTTCGCAAGCTCTTCGATACCTTCTTCGGCAACTCTGAGATGAGGgtacccttttttctctatctttttctttacatacccatttgtattatgtgtttctgtatatgggtttctttttgtttcgtttcaattcatttctttttat
                                                     | ||||| |||||||| || ||||||||||||||| | |||||||||||| | || |   |   | ||   | |||  |    |     | | | |  ||   | |||   || |||  | | |   ||||                
-----------------------------------------------------CTTTTCGAAAGCTCTTTGACACCTTCTTCGGCAACACCGAGATGAGGgtaactttctgcttgcttgttaaacgttaattttttacactcaatttattattaactttattatttccttgatctgtttgttcag---------------

upper sequence: Vv16s0039g02240.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: AT3G03120.1 (Arabidopsis thaliana), 5'ss of exon 1
ACACAAATATTGAGAGAGAAAAGAACAGAGGAAAAAAGCAGGCATGGGTCAAGCCTTTCGCAAGCTCTTCGATACCTTCTTCGGCAACTCTGAGATGAGGgtaccctt-ttttctctatctttttctttacatacccatttgt-attatgtgtt--tctgtat-atgggtttctttttgtt--tcgtttcaattcatttctttttat
  | || |  |  | | |     ||              ||  ||||||||| | ||||||||||| |||||||||||||||||||||   ||||||||||||| ||  || |||| ||||| |   ||  ||  |  | | | ||  | |  |   | | ||   | ||| |   | |||  |||||  | |   ||||       
GTAAAATTCGTCTGTGGGGGTTTAAGCTTTTTTGGGGTGAGAGATGGGTCAAACTTTTCGCAAGCTTTTCGATACCTTCTTCGGCAACCAGGAGATGAGGgtactctccttctctccatcttctgtatttgatttctgtatttgatcgtttactggacggaatcgcgtgttacccatcgttaatcgttatactcgctttc-------

upper sequence: Vv16s0039g02240.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: AT5G17060.1 (Arabidopsis thaliana), 5'ss of exon 1
-ACACAAATATTGAGAGAGAAAAGAACAGAGGAAAAAAGCAGGCATGGGTCAAGCCTTTCGCAAGCTCTTCGATACCTTCTTCGGCAACTCTGAGATGAGGgtacccttttttctctatctttttctttacatacccatttgtattatgtgtttctgta--tatgggtttctttttgtttcgtttcaattcatttctttttat
 | || ||| ||   ||||           ||      | ||  ||||||||||| ||||| ||||| |||||||| |||||||||||    || |||||||||  ||  |   ||| || |  | ||||  |         | |  |||  || |||     | | ||| |||| ||||   |   |    ||       ||
AAAACTAATTTTTGAAGAGTTTTTTTTTTTGGGTTTGGG-AGCGATGGGTCAAGCTTTTCGTAAGCTATTCGATACTTTCTTCGGCAATCAAGAAATGAGGgtaatctcatca-tctctcgtgctatttatctggatggg-atctcgtgtaattttgtcatctttgatttgttttggttttagtcatagcttttatcgcccat

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:     AAGCCTTTCGCAAGCTCTTCGATACCTTCTTCGGCAACTCTGAGATGAGG                         GTTGTGATGCTTGGCCTGGATGCAGCTGGTAAAACAACCATACTGTACAAA
genomic: AAGCCTTTCGCAAGCTCTTCGATACCTTCTTCGGCAACTCTGAGATGAGGgtaccctttt ... gttggattagGTTGTGATGCTTGGCCTGGATGCAGCTGGTAAAACAACCATACTGTACAAA
EST: gi|71879757|gb|DT028812.1|DT028812
EST:     GCTCTTCGATACCTTCTTCGGCAACTCTGAGATGAGG                         GTTGTGATGCTTGGCCTGGATGCAGCTGGTAAAACAACCATACTGTACAAA
genomic: GCTCTTCGATACCTTCTTCGGCAACTCTGAGATGAGGgtaccctttt ... gttggattagGTTGTGATGCTTGGCCTGGATGCAGCTGGTAAAACAACCATACTGTACAAA
EST: gi|71880432|gb|DT029487.1|DT029487
EST:     GCTCTTCGATACCTTCTTCGGCAACTCTGAGATGAGG                         GTTGTGATGCTTGGCCTGGATGCAGCTGGTAAAACAACCATACTGTACAAA
genomic: GCTCTTCGATACCTTCTTCGGCAACTCTGAGATGAGGgtaccctttt ... gttggattagGTTGTGATGCTTGGCCTGGATGCAGCTGGTAAAACAACCATACTGTACAAA
EST: gi|71880733|gb|DT029788.1|DT029788
EST:     GCTCTTCCATACCTTCTTCGGCAACTCTGAGATGAGG                         GTTGTGATGCTTGGCCTGGATGCAGCTGGTAAAACAACCATACTGTACAAA
genomic: GCTCTTCGATACCTTCTTCGGCAACTCTGAGATGAGGgtaccctttt ... gttggattagGTTGTGATGCTTGGCCTGGATGCAGCTGGTAAAACAACCATACTGTACAAA
EST: gi|71878380|gb|DT027435.1|DT027435
EST:     GCTCTTCGATACCTTCTTCGGCAACTCTGAGATGAGG                         GTTGTGATGCTTGGCCTGGATGCAGCTGGTAAAACAACCATACTGTACAAA
genomic: GCTCTTCGATACCTTCTTCGGCAACTCTGAGATGAGGgtaccctttt ... gttggattagGTTGTGATGCTTGGCCTGGATGCAGCTGGTAAAACAACCATACTGTACAAA
EST: gi|71880637|gb|DT029692.1|DT029692
EST:     GCTCTTCGATACCTTCTTCGGCAACTCTGAGATGAGG                         GTTGTGATGCTTGGCCTGGATGCAGCTGGTAAAACAACCATACTGTACAAA
genomic: GCTCTTCGATACCTTCTTCGGCAACTCTGAGATGAGGgtaccctttt ... gttggattagGTTGTGATGCTTGGCCTGGATGCAGCTGGTAAAACAACCATACTGTACAAA
EST: gi|30296765|gb|CB973559.1|CB973559
EST:     AAGCCTTTCGCAAGCTCTTCGATACCTTCTTCGGCAACTCTGAGATGAGG                         GTTGTGATGCTCGGCCTGGATGCAGCTGGTAAAACAACCATACTGTACAAA
genomic: AAGCCTTTCGCAAGCTCTTCGATACCTTCTTCGGCAACTCTGAGATGAGGgtaccctttt ... gttggattagGTTGTGATGCTTGGCCTGGATGCAGCTGGTAAAACAACCATACTGTACAAA
EST: gi|294964756|gb|GW838559.1|GW838559
EST:     AAGCCTTTCGCAAGCTCTTCGATACCTTCTTCGGCAACTCTGAGATGAGG                         GTTGTGATGCTTGGCCTGGATGCAGCTGGTAAAACAACCATACTGTACAAA
genomic: AAGCCTTTCGCAAGCTCTTCGATACCTTCTTCGGCAACTCTGAGATGAGGgtaccctttt ... gttggattagGTTGTGATGCTTGGCCTGGATGCAGCTGGTAAAACAACCATACTGTACAAA
EST: gi|71877999|gb|DT027054.1|DT027054
EST:     GCTCTTCGATACCTTCTTCGGCAACTCTGAGATGAGG                         GTTGTGATGCTTGGCCTGGATGCAGCTGGTAAAACAACCATACTGTACAAA
genomic: GCTCTTCGATACCTTCTTCGGCAACTCTGAGATGAGGgtaccctttt ... gttggattagGTTGTGATGCTTGGCCTGGATGCAGCTGGTAAAACAACCATACTGTACAAA
EST: gi|71880723|gb|DT029778.1|DT029778
EST:     GCTCTTCGATACCTTCTTCGGCAACTCTGAGATGAGG                         GTTGTGATGCTTGGCCTGGATGCAGCTGGTAAAACAACCATACTGTACAAA
genomic: GCTCTTCGATACCTTCTTCGGCAACTCTGAGATGAGGgtaccctttt ... gttggattagGTTGTGATGCTTGGCCTGGATGCAGCTGGTAAAACAACCATACTGTACAAA
EST: gi|110729888|gb|EE106340.1|EE106340
EST:     AAGCCTTTCGCAAGCTCTTCGATACCTTCTTCGGCAACTCTGAGATGAGG                         GTTGTGATGCTTGGCCTGGATGCAGCTGGTAAAACAACCATACTGTACAAA
genomic: AAGCCTTTCGCAAGCTCTTCGATACCTTCTTCGGCAACTCTGAGATGAGGgtaccctttt ... gttggattagGTTGTGATGCTTGGCCTGGATGCAGCTGGTAAAACAACCATACTGTACAAA
EST: gi|71878000|gb|DT027055.1|DT027055
EST:     GCTCTTCGATACCTTCTTCGGCAACTCTGAGATGAGG                         GTTGTGATGCTTGGCCTGGATGCAGCTGGTAAAACAACCATACTGTACAAA
genomic: GCTCTTCGATACCTTCTTCGGCAACTCTGAGATGAGGgtaccctttt ... gttggattagGTTGTGATGCTTGGCCTGGATGCAGCTGGTAAAACAACCATACTGTACAAA
EST: gi|71879446|gb|DT028501.1|DT028501
EST:     GCTCTTCGATACCTTCTTCGGCAACTCTGAGATGAGG                         GTTGTGATGCTTGGCCTGGATGCAGCTGGTAAAACAACCATACTGTACAAA
genomic: GCTCTTCGATACCTTCTTCGGCAACTCTGAGATGAGGgtaccctttt ... gttggattagGTTGTGATGCTTGGCCTGGATGCAGCTGGTAAAACAACCATACTGTACAAA
EST: gi|71879383|gb|DT028438.1|DT028438
EST:     GCTCTTCGATACCTTCTTCGGCAACTCTGAGATGAGG                         GTTGTGATGCTTGGCCTGGATGCAGCTGGTAAAACAACCATACTGTACAAA
genomic: GCTCTTCGATACCTTCTTCGGCAACTCTGAGATGAGGgtaccctttt ... gttggattagGTTGTGATGCTTGGCCTGGATGCAGCTGGTAAAACAACCATACTGTACAAA
EST: gi|161707222|gb|FC055589.1|FC055589
EST:     AAGCCTTTCGCAAGCTCTTCGATACCTTCTTCGGCAACTCTGAGATGAGG                         GTTGTGATGCTTGGCCTGGATGCAGCTGGTAAAACAACCATACTGTACAAA
genomic: AAGCCTTTCGCAAGCTCTTCGATACCTTCTTCGGCAACTCTGAGATGAGGgtaccctttt ... gttggattagGTTGTGATGCTTGGCCTGGATGCAGCTGGTAAAACAACCATACTGTACAAA
EST: gi|351036486|gb|FQ457199.1|FQ457199
EST:     AAGCCTTTCGCAAGCTCTTCGATACCTTCTTCGGCAACTCTGAGATGAGG                         GTTGTGATGCTTGGCCTGGATGCAGCTGGTAAAACAACCATACTGTACAAA
genomic: AAGCCTTTCGCAAGCTCTTCGATACCTTCTTCGGCAACTCTGAGATGAGGgtaccctttt ... gttggattagGTTGTGATGCTTGGCCTGGATGCAGCTGGTAAAACAACCATACTGTACAAA
EST: gi|110375930|gb|EC940960.1|EC940960
EST:     AAGCCTTTCGCAAGCTCTTCGATACCTTCTTCGGCAACTCTGAGATGAGG                         GTTGTGATGCTTGGCCTGGATGCAGCTGGTAAAACAACCATACTGTACAAA
genomic: AAGCCTTTCGCAAGCTCTTCGATACCTTCTTCGGCAACTCTGAGATGAGGgtaccctttt ... gttggattagGTTGTGATGCTTGGCCTGGATGCAGCTGGTAAAACAACCATACTGTACAAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACACAAATATTGAGAGAGAAAAGAACAGAGGAAAAAAGCAGGCATGGGTCAAGCCTTTCGCAAGCTCTTCGATACCTTCTTCGGCAACTCTGAGATGAGGgtacccttttttctctatctttttctttacatacccatttgtattatgtgtttctgtatatgggtttctttttgtttcgtttcaattcatttctttttat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG