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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcactaacatgatggcctgttggctaccgtggtattgttttcatgccacactgcaggaattgattaaatgttccttttttcttttctttttttttcactatttcagAACCTCTATTGGGCTGATAGTGGGGATTTGGTGGCCATTGCCAGTGATACATCATTTTACATCCTGAAGTACAAT

Basic information

species Vitis vinifera
transcript Vv09s0002g04810.t01
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: LOC_Os02g11830.2 (Oryza sativa), 3'ss of exon 13
gtaagcactaacatgatggcctgttggctaccgtggtattgttttcatgccacactgcaggaattgatta-aatgttccttttttcttttctttttttttcactattt-cagAACCTCTATTGGGCTGATAGTGGGGATTTGGTGGCCATTGCCAGTGATACATCATTTTACATCCTGAAGTACAAT
                      ||  |  |   || |  ||  || |        |    |  |   ||  ||| ||    |  |   |    | |  ||   |||||  |||| ||||||||||| |||||||| ||||| ||| | ||||| ||||| || ||||| |||||  |||||||||||
----------------------gtgagtaattttgttcctggatttaaatttttttttgcgtgtcatttggaatattatgatgctaaataggatctgctttcttatttgtagAATCTCTATTGGGCCGATAGTGGTGATTTAGTGACAATTGCAAGTGACACCTCATTCTACATTTTGAAGTACAAT

upper sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: LOC_Os02g11840.2 (Oryza sativa), 3'ss of exon 4
gtaagcactaacatgatggcctgttggctaccgtggtattgttttcatgccacactgcaggaattgatta-aatgttccttttttcttttctttttttttcactattt-cagAACCTCTATTGGGCTGATAGTGGGGATTTGGTGGCCATTGCCAGTGATACATCATTTTACATCCTGAAGTACAAT
                      ||  |  |   || |  ||  ||||      | |    |  |   ||  ||| ||    |  |   |    |    ||   |||||  |||| ||||||||||| |||||||| ||||| ||| | ||||| ||||| || ||||| |||||  |||||||||||
----------------------gtgagtaattttgttcatggattcaaatt-tattttgcgtgtcatttggaatattatgatgctaaataggatccgctttcttatttgtagAATCTCTATTGGGCCGATAGTGGTGATTTAGTGACAATTGCAAGTGACACCTCATTCTACATTTTGAAGTACAAT

upper sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: LOC_Os06g05180.2 (Oryza sativa), 3'ss of exon 13
gtaagcactaacatgatggcctgttggctaccgtggtattgttttcatgccacactgcaggaattgattaaatgttccttttttcttttctttttttttcactatttcagAACCTCTATTGGGCTGATAGTGGGGATTTGGTGGCCATTGCCAGTGATACATCATTTTACATCCTGAAGTACAAT
|| ||  | || || ||   || |||       | |  |  |  |  |  |  | | ||     |  | ||||      ||||     | | |||||           ||||||| |||||||||||||| || ||  | || || || || |||||||||||||| ||||| ||||||||||| 
gtgagt-caaatattat---ctattgatatttatagattgatacttttaacgaatttca-----tactgaaataactagttttgtcactgtattttt-----------agAACCTTTATTGGGCTGATAGCGGTGACCTAGTTGCAATAGCAAGTGATACATCATTCTACATACTGAAGTACAAC

upper sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GRMZM2G000645_T01 (Zea mays), 3'ss of exon 13
gtaagcactaacatgatggcctgttggctaccgtggtattgttttcatgccacactgcaggaattgattaaatgttccttttttcttttctttttttttcac-tattt-cagAACCTCTATTGGGCTGATAGTGGGGATTTGGTGGCCATTGCCAGTGATACATCATTTTACATCCTGAAGTACAAT
                      ||  |  |     ||||| ||||  | |     || |    |||  |  |||    |  | |      ||| ||| |||  | |||  ||||  | || |||||||||||||| ||  | || || || || |||||||||||||| |||||||| |||||||||
----------------------gtgagtca--aaagtattatttt--tccttgggtggaaattttgtatgtatgagtttaatattaaccttttgtttatcatgtgtttatagAATGTTTACTGGGCTGATAGTGGTGACCTAGTTGCAATAGCAAGTGATACATCATTCTACATCCTCAAGTACAAT

upper sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GRMZM2G095348_T02 (Zea mays), 3'ss of exon 12
gtaagcactaacatgatggcctgttggctaccgtggtattgttttcatgccacactgcaggaattgattaaatgttccttttttcttttctttttttttcactatttcagAACCTCTATTGGGCTGATAGTGGGGATTTGGTGGCCATTGCCAGTGATACATCATTTTACATCCTGAAGTACAAT
|| |   | |  || ||    | ||||     |||| | | |||  |||  | | || | || || | ||         ||   ||||||||| |  | || |  |  ||||| | || |||||||||||||| ||  | || || || || |||||||||||||| |||||||| |||||||||
gtgaat-caagtattattttttcttgg-----gtggaaat-tttgtatgtaaaa-tgtatgagtttacta---------ttaaccttttctttatcatgcatt--tatagAACGTTTACTGGGCTGATAGTGGTGACCTAGTTGCAATAGCAAGTGATACATCATTCTACATCCTCAAGTACAAT

upper sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GLYMA07G03890.2 (Glycine max), 3'ss of exon 2
gtaagcactaacatgatggcctgttggctaccgtggtattgttttcatgccacactgcaggaattgattaaatgttccttttttcttttctttttttttcactatttcagAACCTCTATTGGGCTGATAGTGGGGATTTGGTGGCCATTGCCAGTGATACATCATTTTACATCCTGAAGTACAAT
|||||  ||  ||||| |     |  |||  |       || ||| ||  |    | |              |||| ||| ||  |||| ||    |||   | | |||||||||||| |||||||||||||| ||| | ||| | ||||| |||||||||||||| || |||||||||||||||
gtaagtgcttgcatgaggtgacatcagctttc-------tgcttttatttcttcttac--------------tgtttcttgttaattttgttaaaattttcttgtgtcagAACCTCTACTGGGCTGATAGTGGTGATCTAGTGACGATTGCTAGTGATACATCATTCTATATCCTGAAGTACAAT

upper sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GLYMA15G01680.1 (Glycine max), 3'ss of exon 13
gtaagcactaacatgatggcctgttggctaccgtggtattgttttcatgccacactgcaggaattgattaaatgttccttttttcttttctttttttttcactatttcagAACCTCTATTGGGCTGATAGTGGGGATTTGGTGGCCATTGCCAGTGATACATCATTTTACATCCTGAAGTACAAT
              |   |    |||  ||  |||  ||  |  | || |  | ||        | |||   ||||   |||   |||  | ||| | |   | | |||||||||||| |||||||| ||||| ||| | ||  | ||||| |||||||||||||| ||||| ||||||||||||
--------------gtaagtactttgattag-gtgacatc-tagttat-ctgctcttttccttcttattcgttgtttaatttaattttgttatttatct---tgtgtcagAACCTCTACTGGGCTGACAGTGGTGATCTAGTAACAATTGCTAGTGATACATCATTCTACATTCTGAAGTACAAT

upper sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GLYMA08G22140.1 (Glycine max), 3'ss of exon 13
gtaagcactaacatgatggcctgttggctaccgtggtattgttttcatgccacactgcaggaattgattaaatgttccttttttcttttctttttttttcactatttcagAACCTCTATTGGGCTGATAGTGGGGATTTGGTGGCCATTGCCAGTGATACATCATTTTACATCCTGAAGTACAAT
|||||  ||  ||||| |     |  |||  |       || ||| ||  |    | |              |||| ||| ||| | ||   ||||| |   | | ||||||||| || ||||||||||| || ||||| ||| | ||||| |||||||||||||| || ||||| |||||||||
gtaagtgcttgcatgaggtggcatcagctttc-------tgcttttatttcttcttac--------------tgtttcttatttttgttaaatttttct---tgtgtcagAACCTGTACTGGGCTGATAGCGGTGATTTAGTGACGATTGCTAGTGATACATCATTCTATATCCTTAAGTACAAT

upper sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GLYMA13G43680.2 (Glycine max), 3'ss of exon 13
gtaagcactaacatgatggcctgttggctaccgtggtattgttttcatgccacactgcaggaattgattaaatgttccttttttcttttctttttttttcactatttcagAACCTCTATTGGGCTGATAGTGGGGATTTGGTGGCCATTGCCAGTGATACATCATTTTACATCCTGAAGTACAAT
              |   |    |||  ||  |||  ||| |  | || |  | ||        | ||| | ||||   | |   |||  | ||  | |   | | |||||||||||| |||||||| ||||| ||| | ||  | ||||| || ||||||||||| ||||| ||||||||||||
--------------gtaagtactttgattag-gtgacatt-tagttat-ctgctcttttccttcttattcattgtttaatataattttgttattaatct---tgtgtcagAACCTCTACTGGGCTGACAGTGGTGATCTAGTAACAATTGCTAGCGATACATCATTCTACATTCTGAAGTACAAT

upper sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: AT3G15980.2 (Arabidopsis thaliana), 3'ss of exon 13
------------------------gtaagca-ctaacatg-atggcctgttggctaccgtggtattgt-tttcatgccacactgcagg--aattgattaaatgttccttttttcttttctttttttttcactattt-cagAACCTCTATTGGGCTGATAGTGGGGATTTGGTGGCCATTGCCAGTGATACATCATTTTACATCCTGAAGTACAAT
                        || || |  || |||  ||  | | ||  | |   ||   ||   ||| ||       || | |       | | | |||   |  |  || ||   |    |  |  |||| ||||| || ||||||||||| ||||| ||||| || |||||||| |||||||| ||||| |||||| |||||||||||
gtatccaattaccttgtctctgttgtgagaagttagcattcatcacttttttccaattctgtcgttacattttattttcagttgaaagttgtcccaattagtgtctttactaactctttactcccatgaaaaatttgcagAATCTTTATTGGGCTGAAAGTGGTGATTTAGTAGCCATTGCTAGTGATACGTCATTCTACATCTTGAAGTACAAT

upper sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: AT1G79990.1 (Arabidopsis thaliana), 3'ss of exon 17
---------------------------------------------------------------gtaagcactaacatgatggcctgttggctaccgtggtattgttttcatgccac---actgcaggaattgattaaa----------tgttccttttttcttttctttttttttcactatttcagAACCTCTATTGGGCTGATAGTGGGGATTTGGTGGCCATTGCCAGTGATACATCATTTTACATCCTGAAGTACAAT
                                                               ||   || ||| ||  |     |     |||    |  ||  ||   ||  |    |  |||  |   ||||             | |||  ||||    || || ||| |||| | |||||||| || |||||||| || ||||| ||| | || || |||||||||||||||||||| |||||||| |||| ||||
gtaagtgcttatataccagaagtagatccattagtttctacaagaaaatagtttataggttacgttttcagtaatatttttattggagaaatacaaaagagttccttatctgaaatttaaacgcaaaagcagattggtactgctcgcttattcacttttaacgtttttgtttattcaatgtttcagAATCTTTATTGGGCGGACAGTGGTGATCTAGTTGCAATTGCCAGTGATACATCATTCTACATCCTTAAGTTCAAT

upper sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: AT1G52360.2 (Arabidopsis thaliana), 3'ss of exon 13
-----------------------------gtaagca-ctaacatgatggcctgttggctaccgtgg----tattgttttcatgccacactgcaggaattgattaaatgttccttttttcttttct--ttttttttcacta---tttcagAACCTCTATTGGGCTGATAGTGGGGATTTGGTGGCCATTGCCAGTGATACATCATTTTACATCCTGAAGTACAAT
                             ||||| |  | || | | | | | || |  |  ||||    || | |  |          |  |||  ||  |    |||| ||| | |  ||| |  | ||  | ||  |   || ||||| || ||||||||||| ||||| ||||| || |||||||| ||||| |||||||| |||||| |||| | ||| 
gtatcccagttaacttggctcagtttattgtaagaagtttacttcaagacatatttggaatagtggaaactaatatcattgccttcagtttgaggttttcctcgtttgtttcttctctaatttgtagtgttgctacataacgtttgcagAATCTATATTGGGCTGACAGTGGTGATTTAGTAGCCATTGCTAGTGACACATCATTCTACATCTTGAAATTCAAC

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|351030017|gb|FQ430759.1|FQ430759
EST:     ATGACTGGGCTGAATGCAGGCTGATTCGACGAATTGATGTTAATGTCAAA                         AACCTCTATTGGGCTGATAGTGGGGATTTGGTGGCCATTGCCAGTGATACA
genomic: ATGACTGGGCTGAATGCAGGCTGATTCGACGAATTGATGTTAATGTCAAAgtaagcacta ... actatttcagAACCTCTATTGGGCTGATAGTGGGGATTTGGTGGCCATTGCCAGTGATACA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcaggaattgattaaatgttccttttttcttttctttttttttcactatttcagAACCTCTATTGGGCTGATAGTGGGGATTTGGTGGCCATTGCCAGTGATACATCATTTTACATCCTGAAGTACAAT
      aattgat  putative branch site (score: 4)
                 tgttccttttttcttt  putative PPT
                       ttttttcttttctttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagcactaacatgatggcctgttggctaccgtggtattgttttcatgccacactgcaggaattgattaaatgttccttttttcttttctttttttttcactatttcagAACCTCTATTGGGCTGATAGTGGGGATTTGGTGGCCATTGCCAGTGATACATCATTTTACATCCTGAAGTACAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG