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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACTGATGGACAGGATTTCTTCACATCTTATGATGAGGTTTATGATAGTTTTGATTCTATGGGTTTGCAAGAGAATCTTCTCAGAGGCATTTATGCATATGgtagaccaatcatgtttcaatattattttctttctaggtttttttattatgatgtatgattgcttgaaatctcttgcttccatgatcaatcaatggttta...

Basic information

species Vitis vinifera
transcript Vv11s0016g01920.t01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv11s0016g01920.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GLYMA15G18760.1 (Glycine max), 5'ss of exon 3
ACTGATGGACAGGATTTCTTCACATCTTATGATGAGGTTTATGATAGTTTTGATTCTATGGGTTTGCAAGAGAATCTTCTCAGAGGCATTTATGCATATGgtagacc-aatcatgtttcaatattat-tttctttctaggtttttttattatgatgtatgattgcttgaaatctcttgcttccatgatcaatcaatggttta----------------------------------------------------------------------------------------------
 |||||||||||||||| |||||||||||||||||||||||||| ||||||||| ||||||| |||||||||||||| || ||||||||||||||||||||||||   ||   | |||   |  | | || |||| |   |||| || ||   |   |   ||  ||   || |  |      ||||  | |  ||  |||                                                                                               
TCTGATGGACAGGATTTTTTCACATCTTATGATGAGGTTTATGACAGTTTTGATGCTATGGGCTTGCAAGAGAATCTCCTGAGAGGCATTTATGCATATGgtagatttaactttctttatgtcctctattacttttttaattttgtttttcaaaccaagagttattttgtattt--tatcgtgatgacaattgtattttttgttatttgttatgtttttattggactgtgaaatttcattttttattggtatcaatctttaactatacatttaaacttgtttgatttgtgttttag

upper sequence: Vv11s0016g01920.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GLYMA09G07530.3 (Glycine max), 5'ss of exon 3
ACTGATGGACAGGATTTCTTCACATCTTATGATGAGGTTTATGATAGTTTTGATTCTATGGGTTTGCAAGAGAATCTTCTCAGAGGCATTTATGCATATGgtagaccaatcatgtttcaatattattttctttctaggtttttttattatgatgtatgattgcttgaaatctcttgcttccatgatcaat-caatggttta-
 | ||||| ||||||||||||||||| || |||||||||||||| ||||||||| ||||||| |||||||||||||| || ||||||||||||||||||||||||   | | |  || |       || |||| |   |||| || |    |   |   ||  ||   || |  |      ||||  | |  |||  |||  
TCCGATGGTCAGGATTTCTTCACATCCTACGATGAGGTTTATGACAGTTTTGATGCTATGGGCTTGCAAGAGAATCTCCTGAGAGGCATTTATGCATATGgtagatttaactttctttatgtcctcttacttttttaattttattttccaaaccaagagttattttgtattt--tatcgtgatgacaattgtaatttttttt

upper sequence: Vv11s0016g01920.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GLYMA13G16570.1 (Glycine max), 5'ss of exon 3
ACTGATGGACAGGATTTCTTCACATCTTATGATGAGGTTTATGATAGTTTTGATTCTATGGGTTTGCAAGAGAATCTTCTCAGAGGCATTTATGCATATGgtagaccaatcatgtttcaatattattttctttctaggtttttttattatgatgtatgattgcttgaaatctcttgcttccatgatcaatcaatggttta-
 ||||||||||||| ||||||||||| ||||| ||||||||||||||||||||  ||||||||||||| || ||||||||||| || ||||| ||||||||||    ||  ||  |||  |||   || |  |    ||||  || || |    |       |    ||| |  | ||   || ||  | || |   | | 
TCTGATGGACAGGACTTCTTCACATCCTATGACGAGGTTTATGATAGTTTTGACGCTATGGGTTTGCAGGAAAATCTTCTCAGGGGAATTTACGCATATGgtattttaaatattcttcc-tatggattgccattggtgtttcattgttttttaatgaataaaccaccaattttgtcctcaaattattgaacagtctctaac

upper sequence: Vv11s0016g01920.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GLYMA17G06110.1 (Glycine max), 5'ss of exon 3
ACTGATGGACAGGATTTCTTCACATCTTATGATGAGGTTTATGATAGTTTTGATTCTATGGGTTTGCAAGAGAATCTTCTCAGAGGCATTTATGCATATGgtagaccaatcatgtttcaatattattttctttctaggtttttttattatgatgtatgattgcttgaaatctcttgcttccatgatcaatcaatggttta
 ||||||||||||| ||||||||||| ||||| ||||||||||||||||||||  ||||||||||||| |||||||||||||| || ||||| ||||| ||||     |  ||  ||   |   |||| |  |    ||||| || || |    |       |    ||| |  | ||   |  ||  |  |    |   
TCTGATGGACAGGACTTCTTCACATCCTATGACGAGGTTTATGATAGTTTTGACGCTATGGGTTTGCAGGAGAATCTTCTCAGGGGAATTTACGCATACGgtatttttaatattctttcttgggatttgccattggtgttttattgttttttaatgaataaaccaccaattttgtcctcaaactattgagtatctatcag

upper sequence: Vv11s0016g01920.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: AT3G13920.4 (Arabidopsis thaliana), 5'ss of exon 3
-ACTGATGGACAGGAT---TTCTTCACATCTTATGATGAGGTTTATGATAGTTTTGATTCTATGGGTTTGCAAGAGAATCTTCTCAGAGGCATTTATGCATATGgtagaccaatcatgtttcaatattattttctttctaggtttttttattatgatgtatgattgcttgaaatctcttgcttccatgatcaatcaatggttta
   ||| ||||| |||   ||||||||||| |||||||| ||| |||| || |||||| | |||||| | |||||||| |||||||| || |||||||| |||||||      |      |  | |    | |||||   | ||| | | |||   |  |  |||   | |     | ||||||  |  |   | |        
ACTTGAGGGACAAGATGAGTTCTTCACATCCTATGATGATGTTCATGAGAGCTTTGATGCCATGGGTCTTCAAGAGAACCTTCTCAGGGgtatttatgcttatggtatgtgtgtaggaacttgaaaaagctatcttttgtgatttatgtcttagattagaacattatctcatg---cgtgcttctgttttttcttag-------

upper sequence: Vv11s0016g01920.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: AT3G13920.2 (Arabidopsis thaliana), 5'ss of exon 3
ACTGATGGACAGGAT---TTCTTCACATCTTATGATGAGGTTTATGATAGTTTTGATTCTATGGGTTTGCAAGAGAATCTTCTCAGAGGCATTTATGCATATGgtagaccaatcatgtttcaatattattttctttctaggtttttttattatgatgtatgattgcttgaaatctcttgcttccatgatcaatcaatggttta
   || ||||| |||   ||||||||||| |||||||| ||| |||| || |||||| | |||||| | |||||||| |||||||| || |||||||| |||||||      |      |  | |    | |||||   | ||| | | |||   |  |  |||   | |     | ||||||  |  |   | |        
---GAGGGACAAGATGAGTTCTTCACATCCTATGATGATGTTCATGAGAGCTTTGATGCCATGGGTCTTCAAGAGAACCTTCTCAGGGGTATTTATGCTTATGgtatgtgtgtaggaacttgaaaaagctatcttttgtgatttatgtcttagattagaacattatctcatg---cgtgcttctgttttttcttag-------

upper sequence: Vv11s0016g01920.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: AT1G54270.2 (Arabidopsis thaliana), 5'ss of exon 3
-ACTGATGGACAGGAT---TTCTTCACATCTTATGATGAGGTTTATGATAGTTTTGATTCTATGGGTTTGCAAGAGAATCTTCTCAGAGGCATTTATGCATATGgtagaccaatcatgtttcaatattattttctttctaggtttttttattatgatgtatgattgcttgaaatct-cttgcttccatgatcaatcaatggttta--------
    ||||||||||||   |||||||| || |||||||||||  |||| || |||||| | ||||||||||||||||||||||| || || || ||||| || ||||    ||  | |||| || |        ||| |  ||| | ||   ||      | | |   |   || | ||   | |  ||||  ||   | | ||         
TCTCGATGGACAGGATGAGTTCTTCACCTCATATGATGAGGTCCATGAGAGCTTTGATGCCATGGGTTTGCAAGAGAATCTTCTTAGGGgtatctatgcttacggtaagtgaagaaggtttaaagaaacaaccttttgtttgttatgttgggattcctattaactttatcgtatgtgctctttcctgtgattgattggttgatttttttctag

upper sequence: Vv11s0016g01920.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: AT1G54270.1 (Arabidopsis thaliana), 5'ss of exon 3
ACTGATGGACAGGAT---TTCTTCACATCTTATGATGAGGTTTATGATAGTTTTGATTCTATGGGTTTGCAAGAGAATCTTCTCAGAGGCATTTATGCATATGgtagaccaatcatgtttcaatattattttctttctaggtttttttattatgatgtatgattgcttgaaatct-cttgcttccatgatcaatcaatggttta--------
   ||||||||||||   |||||||| || |||||||||||  |||| || |||||| | ||||||||||||||||||||||| || || || ||||| || ||||    ||  | |||| || |        ||| |  ||| | ||   ||      | | |   |   || | ||   | |  ||||  ||   | | ||         
---GATGGACAGGATGAGTTCTTCACCTCATATGATGAGGTCCATGAGAGCTTTGATGCCATGGGTTTGCAAGAGAATCTTCTTAGGGGTATCTATGCTTACGgtaagtgaagaaggtttaaagaaacaaccttttgtttgttatgttgggattcctattaactttatcgtatgtgctctttcctgtgattgattggttgatttttttctag

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|110702274|gb|EE080798.1|EE080798
EST:     TGATTCTATGGGTTTGCAAGAGAATCTTCTCAGAGGCATTTATGCATATG                         GTTTTGAAAAACCTTCTGCAATTCAGCAAAGAGGAATTGTTCCCTTTTGCA
genomic: TGATTCTATGGGTTTGCAAGAGAATCTTCTCAGAGGCATTTATGCATATGgtagaccaat ... cttcgtgtagGTTTTGAAAAACCTTCTGCAATTCAGCAAAGAGGAATTGTTCCCTTTTGCA
EST: gi|30301294|gb|CB978088.1|CB978088
EST:     TTTATGCATAGAN                         GTTTTGAAAAACCTTCTGCAACCCTTCAAAGAGGAATTGTTCCCTTTTGC
genomic: TTTATGCATA-TGgtagaccaat ... cttcgtgtagGTTTTGAAAAACCTTCTGCAATTCAGCAAAGAGGAATTGTTCCCTTTTGC
EST: gi|110723538|gb|EE100968.1|EE100968
EST:     TGATTCTATGGGTTTGCAAGAGAATCTTCTCAGAGGCATTTATGCATATG                         GTTTTGAAAAACCTTCTGCAATTCAGCAAAGAGGAATTGTTCCCTTTTGCA
genomic: TGATTCTATGGGTTTGCAAGAGAATCTTCTCAGAGGCATTTATGCATATGgtagaccaat ... cttcgtgtagGTTTTGAAAAACCTTCTGCAATTCAGCAAAGAGGAATTGTTCCCTTTTGCA
EST: gi|110370832|gb|EC934384.1|EC934384
EST:     TGATTCTATGGGTTTGCAAGAGAATCTTCTCAGAGGCATTTATGCATATG                         GTTTTGAAAAACCTTCTGCAATTCAGCAAAGAGGAATTGTTCCCTTTTGCA
genomic: TGATTCTATGGGTTTGCAAGAGAATCTTCTCAGAGGCATTTATGCATATGgtagaccaat ... cttcgtgtagGTTTTGAAAAACCTTCTGCAATTCAGCAAAGAGGAATTGTTCCCTTTTGCA
EST: gi|110696480|gb|EE072635.1|EE072635
EST:     CTCAGAGGCATTTATGCATATG                         GTTTTGAAAAACCTTCTGCAATTCAGCAAAGAGGAATTGTTCCCTTTTGCA
genomic: CTCAGAGGCATTTATGCATATGgtagaccaat ... cttcgtgtagGTTTTGAAAAACCTTCTGCAATTCAGCAAAGAGGAATTGTTCCCTTTTGCA
EST: gi|37190367|gb|CF609716.1|CF609716
EST:     TGATTCTATGGGTTTGCAAGAGAATCTTCTCAGAGGCATTTATGCATATG                         GTTTTGAAAAACCTTCTGCAATTCAGCAAAGAGGAATTGTTCCCTTTTGCA
genomic: TGATTCTATGGGTTTGCAAGAGAATCTTCTCAGAGGCATTTATGCATATGgtagaccaat ... cttcgtgtagGTTTTGAAAAACCTTCTGCAATTCAGCAAAGAGGAATTGTTCCCTTTTGCA
EST: gi|110712119|gb|EE089376.1|EE089376
EST:     GGGTTTGCAAGAGAATCTTCTCAGAGGCATTTATGCATATG                         GTTTTGAAAAACCTTCTGCAATTCAGCAAAGAGGAATTGTTCCCTTTTGCA
genomic: GGGTTTGCAAGAGAATCTTCTCAGAGGCATTTATGCATATGgtagaccaat ... cttcgtgtagGTTTTGAAAAACCTTCTGCAATTCAGCAAAGAGGAATTGTTCCCTTTTGCA
EST: gi|110696050|gb|EE074763.1|EE074763
EST:     TGATTCTATGGGTTTGCAAGAGAATCTTCTCAGAGGCATTTATGCATATG                         GTTTTGAAAAACCTTCTGCAATTCAGCAAAGAGGAATTGTTCCCTTTTGCA
genomic: TGATTCTATGGGTTTGCAAGAGAATCTTCTCAGAGGCATTTATGCATATGgtagaccaat ... cttcgtgtagGTTTTGAAAAACCTTCTGCAATTCAGCAAAGAGGAATTGTTCCCTTTTGCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACTGATGGACAGGATTTCTTCACATCTTATGATGAGGTTTATGATAGTTTTGATTCTATGGGTTTGCAAGAGAATCTTCTCAGAGGCATTTATGCATATGgtagaccaatcatgtttcaatattattttctttctaggtttttttattatgatgtatgattgcttgaaatctcttgcttccatgatcaatcaatggttta

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA