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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctgtttttgcttaactcttttgtttggtaaacatgaagaacatagtaatctaaggaaatgataacactgtgtttgttgctaactaagatcattcattcattcagGTGGTAGCAGCTGGTGCAAACCCTGTTCTAATCACTCGAGGCATTGAGAAGACCACAAAATCTCTAGTGGCTGAGCTTAAGCTGATATCAAAAGAG

Basic information

species Vitis vinifera
transcript Vv06s0004g00240.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0004g00240.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA15G40110.1 (Glycine max), 3'ss of exon 3
gtctgtttttgcttaactcttttgtttg-gtaaacatgaagaacatagtaat--ctaaggaaatgataacactgtgtttgttgctaactaagatcattcattcattcagGTGGTAGCAGCTGGTGCAAACCCTGTTCTAATCACTCGAGGCATTGAGAAGACCACAAAATCTCTAGTGGCTGAGCTTAAGCTGATATCAAAAGAG
       |    |||  | || |||||  | |||  |   |  |||| ||||  |||      |    |   |||  ||    || | |       || |||  | ||||| || |||||||| || |||||||| || ||||| || ||||||||||||||  ||||| |||| ||  |||||||||| ||||| |||||||||
------gtaaaattatttgttgtgttttcggaaatgtagtgttcatactaataactactcggttttggattttgtaattaggcctcatttta--tgttaatttttgcagGTTGTTGCAGCTGGGGCCAACCCTGTGCTCATCACCCGGGGCATTGAGAAGACGGCAAAAGCTCTTGTTTCTGAGCTTAAACTGATGTCAAAAGAG

upper sequence: Vv06s0004g00240.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA08G18760.2 (Glycine max), 3'ss of exon 3
gtctgtttttgcttaactcttttgtttggtaaacatgaagaacatagtaatctaaggaaatgataacactgtgtttgttgctaactaaga-tcattc-------attcattcagGTGGTAGCAGCTGGTGCAAACCCTGTTCTAATCACTCGAGGCATTGAGAAGACCACAAAATCTCTAGTGGCTGAGCTTAAGCTGATATCAAAAGAG
       |  | |||  | || | ||     ||  | |    ||||   |  |||  |  || |     | | | |  ||| ||||| |  |||||        |||    ||||| || |||||||| || |||||||| || ||||| || ||||||||||||||  | ||| |||| ||  |||||||||| | ||| |||||||||
------gtaggattatttgttgtcttattggaaatttagtgtcataactaa-taactacttggttttgttttttgtaatgc-aactaggcctcattttatgttaattttcgcagGTTGTTGCAGCTGGGGCCAACCCTGTGCTCATCACACGTGGCATTGAGAAGACAGCGAAAGCTCTTGTATCTGAGCTTAAACAGATGTCAAAAGAG

upper sequence: Vv06s0004g00240.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT1G55490.2 (Arabidopsis thaliana), 3'ss of exon 4
gtctgtttttgcttaactcttttgtttggtaaacatgaagaacatagtaatctaaggaaatgataacactgtgtttgttgctaactaagatcattcattcattcagGTGGTAGCAGCTGGTGCAAACCCTGTTCTAATCACTCGAGGCATTGAGAAGACCACAAAATCTCTAGTGGCTGAGCTTAAGCTGATATCAAAAGAG
       | ||  ||||  | || |||    | | |     |  |   | |  ||  |  |        |||  |  ||      |||||| ||    | |||||||||||||| |||||||||||||||||| | |||||  |||| |||||||||||  ||||  || | ||  | ||||| |||   || || || |||
------gtctgtgtaacattcttctttc---agctttctctatgtgaaacttcaaaaactt-------ttgtactaatt-----ttaagattatc---ttattcagGTGGTAGCTGCTGGTGCAAACCCTGTTTTGATCACCAGAGGTATTGAGAAGACAGCAAAGGCTTTGGTTACCGAGCTCAAGAAAATGTCTAAGGAG

upper sequence: Vv06s0004g00240.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT5G56500.1 (Arabidopsis thaliana), 3'ss of exon 4
gtctgtttttgcttaact-cttttgtttggtaaacatgaagaacatagtaatctaaggaaatgataacactgtgtttgttgctaactaagatc-attcattcattcagGTGGTAGCAGCTGGTGCAAACCCTGTTCTAATCACTCGAGGCATTGAGAAGACCACAAAATCTCTAGTGGCTGAGCTTAAGCTGATATCAAAAGAG
    |||| |  || | |   ||| ||| || ||  ||||  |   |||  | |                |||  ||||||  |  | |  |  ||| | |  |  |||||||||| ||||||||||| |||||| | || ||  |||| |||||||| ||||| ||| |||| ||||||||| | |||   || ||||| |||
----gtttgtaatttattgtctttcttttgtgaatttgaaacaaccagtgtttt---------------ttgttgttgttgtgatatgatgtggattgaattgtgtagGTGGTAGCTGCTGGTGCAAATCCTGTTTTGATTACCAGAGGTATTGAGAAAACCACCAAAGCTCTTGTGGCTGAGTTGAAGAAAATGTCAAAGGAG

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|351017572|gb|FQ435925.1|FQ435925
EST:     CAACAACATCTGTTGTTCTTGCACAAGGGCTTATTGCTGAAGGTGTCAAG                         GTGGTAGCAGCTGGTGCAAACCCTGTTCTAATTACTCGAGGCATTGAGAAG
genomic: CAACAACATCTGTTGTTCTTGCACAAGGGCTTATTGCTGAAGGTGTCAAGgtctgttttt ... attcattcagGTGGTAGCAGCTGGTGCAAACCCTGTTCTAATCACTCGAGGCATTGAGAAG
EST: gi|110685246|gb|EE063449.1|EE063449
EST:     CAACAACATCTGTTGTTCTTGCACAAGGGCTTATTGCTGAAGGTGTCAAG                         GTGGTAGCAGCTGGTGCAAACCCTGTTCTAATCACTCGAGGCATTGAGAAG
genomic: CAACAACATCTGTTGTTCTTGCACAAGGGCTTATTGCTGAAGGTGTCAAGgtctgttttt ... attcattcagGTGGTAGCAGCTGGTGCAAACCCTGTTCTAATCACTCGAGGCATTGAGAAG
EST: gi|110725842|gb|EE102769.1|EE102769
EST:     CAACAACATCTGTTGTTCTTGCACAAGGGCTTATTGCTGAAGGTGTCAAG                         GTGGTAGCAGCTGGTGCAAACCCTGTTCTAATTACTCGAGGCATTGAGAAG
genomic: CAACAACATCTGTTGTTCTTGCACAAGGGCTTATTGCTGAAGGTGTCAAGgtctgttttt ... attcattcagGTGGTAGCAGCTGGTGCAAACCCTGTTCTAATCACTCGAGGCATTGAGAAG
EST: gi|351022807|gb|FQ428716.1|FQ428716
EST:     CAACAACATCTGTTGTTCTTGCACAAGGGCTTATTGCTGAAGGTGTCAAG                         GTGGTAGCAGCTGGTGCAAACCCTGTTCTAATTACTCGAGGCATTGAGAAG
genomic: CAACAACATCTGTTGTTCTTGCACAAGGGCTTATTGCTGAAGGTGTCAAGgtctgttttt ... attcattcagGTGGTAGCAGCTGGTGCAAACCCTGTTCTAATCACTCGAGGCATTGAGAAG
EST: gi|110686609|gb|EE064441.1|EE064441
EST:     CAACAACATCTGTTGTTCTTGCACAAGGGCTTATTGCTGAAGGTGTCAAG                         GTGGTAGCAGCTGGTGCAAACCCTGTTCTAATCACTCGAGGCATTGAGAAG
genomic: CAACAACATCTGTTGTTCTTGCACAAGGGCTTATTGCTGAAGGTGTCAAGgtctgttttt ... attcattcagGTGGTAGCAGCTGGTGCAAACCCTGTTCTAATCACTCGAGGCATTGAGAAG
EST: gi|110699104|gb|EE077129.1|EE077129
EST:     CAACAACATCTGTTGTTCTTGCACAAGGGCTTATTGCTGAAGGTGTCAAG                         GTGGTAGCAGCTGGTGCAAACCCTGTTCTAATCACTCGAGGCATTGAGAAG
genomic: CAACAACATCTGTTGTTCTTGCACAAGGGCTTATTGCTGAAGGTGTCAAGgtctgttttt ... attcattcagGTGGTAGCAGCTGGTGCAAACCCTGTTCTAATCACTCGAGGCATTGAGAAG
EST: gi|351024818|gb|FQ430643.1|FQ430643
EST:     CAACAACATCTGTTGTTCTTGCACAAGGGCTTATTGCTGAAGGTGTCAAG                         GTGGCAGCAGCTGGTGCAAACCCTGTTCTAATTACTCGAGGCATTGAGAAG
genomic: CAACAACATCTGTTGTTCTTGCACAAGGGCTTATTGCTGAAGGTGTCAAGgtctgttttt ... attcattcagGTGGTAGCAGCTGGTGCAAACCCTGTTCTAATCACTCGAGGCATTGAGAAG
EST: gi|349833403|gb|FQ420149.1|FQ420149
EST:     CAACAACATCTGTTGTTCTTGCACAAGGGCTTATTGCTGAAGGTGTCAAG                         GTGGTGGCAGCTGGTGCAAACCCTGTTCTAATTACTCGAGGCATTGAGAAG
genomic: CAACAACATCTGTTGTTCTTGCACAAGGGCTTATTGCTGAAGGTGTCAAGgtctgttttt ... attcattcagGTGGTAGCAGCTGGTGCAAACCCTGTTCTAATCACTCGAGGCATTGAGAAG
EST: gi|29782617|gb|CB348122.2|CB348122
EST:     CAACAACATCTGTTGTTCTTGCACAAGGGCTTATTGCTGAAGGTGTCAAG                         GTGGTAGCAGCTGGTGCAAACCCTGTTCTAATCACTCGAGGCATTGAGAAG
genomic: CAACAACATCTGTTGTTCTTGCACAAGGGCTTATTGCTGAAGGTGTCAAGgtctgttttt ... attcattcagGTGGTAGCAGCTGGTGCAAACCCTGTTCTAATCACTCGAGGCATTGAGAAG
EST: gi|30256253|gb|CB972096.1|CB972096
EST:     CAACAACATCTGTTGTTCTTGCACAAGGGCTTATTGCTGAAGGTGTCAAG                         GTGGTAGCAGCTGGTGCAAACCCTGTTCTAATCACCCGAGGCATTGAGAAG
genomic: CAACAACATCTGTTGTTCTTGCACAAGGGCTTATTGCTGAAGGTGTCAAGgtctgttttt ... attcattcagGTGGTAGCAGCTGGTGCAAACCCTGTTCTAATCACTCGAGGCATTGAGAAG
EST: gi|110713396|gb|EE089279.1|EE089279
EST:     CAACAACATCTGTTGTTCTTGCACAAGGGCTTATTGCTGAAGGTGTCAAG                         GTGGTAGCAGCTGGTGCAAACCCTGTTCTAATCACTCGAGGCATTGAGAAG
genomic: CAACAACATCTGTTGTTCTTGCACAAGGGCTTATTGCTGAAGGTGTCAAGgtctgttttt ... attcattcagGTGGTAGCAGCTGGTGCAAACCCTGTTCTAATCACTCGAGGCATTGAGAAG
EST: gi|110689447|gb|EE065678.1|EE065678
EST:     CAACAACATCTGTTGTTCTTGCACAAGGGCTTATTGCTGAAGGTGTCAAG                         GTGGTAGCAGCTGGTGCAAACCCTGTTCTAATCACTCGAGGCATTGAGAAG
genomic: CAACAACATCTGTTGTTCTTGCACAAGGGCTTATTGCTGAAGGTGTCAAGgtctgttttt ... attcattcagGTGGTAGCAGCTGGTGCAAACCCTGTTCTAATCACTCGAGGCATTGAGAAG
EST: gi|351040630|gb|FQ438174.1|FQ438174
EST:     CAACAACATCTGTTGTTCTTGCACAAGGGCTTATTGCTGAAGGTGTCAAG                         GTGGTAGCAGCTGGTGCAAACCCTGTTCTAATTACTCGAGGCATTGAGAAG
genomic: CAACAACATCTGTTGTTCTTGCACAAGGGCTTATTGCTGAAGGTGTCAAGgtctgttttt ... attcattcagGTGGTAGCAGCTGGTGCAAACCCTGTTCTAATCACTCGAGGCATTGAGAAG
EST: gi|71864487|gb|DT013542.1|DT013542
EST:     CAACAACATCTGTTGTTCTTGCACAAGGGCTTATTGCTGAAGGTGTCAAG                         GTGGTAGCAGCTGGTGCAAACCCTGTTCTAATCACCCGAGGCATTGAGAAG
genomic: CAACAACATCTGTTGTTCTTGCACAAGGGCTTATTGCTGAAGGTGTCAAGgtctgttttt ... attcattcagGTGGTAGCAGCTGGTGCAAACCCTGTTCTAATCACTCGAGGCATTGAGAAG
EST: gi|349815356|gb|FQ400511.1|FQ400511
EST:     CAACAACATCTGTTGTTCTTGCACAAGGGCTTATTGCTGAAGGTGTCAAG                         GTGGTAGCAGCTGGTGCAAACCCTGTTCTAATTACTCGAGGCATTGAGAAG
genomic: CAACAACATCTGTTGTTCTTGCACAAGGGCTTATTGCTGAAGGTGTCAAGgtctgttttt ... attcattcagGTGGTAGCAGCTGGTGCAAACCCTGTTCTAATCACTCGAGGCATTGAGAAG
EST: gi|351025708|gb|FQ426722.1|FQ426722
EST:     CAACAACATCTGTTGTTCTTGCACAAGGGCTTATTGCTGAAGGTGTCAGG                         GTGGTAGCAGCTGGTGCAAACCCTGTTCTAATTACTCGAGGCATTGAGAAG
genomic: CAACAACATCTGTTGTTCTTGCACAAGGGCTTATTGCTGAAGGTGTCAAGgtctgttttt ... attcattcagGTGGTAGCAGCTGGTGCAAACCCTGTTCTAATCACTCGAGGCATTGAGAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctaaggaaatgataacactgtgtttgttgctaactaagatcattcattcattcagGTGGTAGCAGCTGGTGCAAACCCTGTTCTAATCACTCGAGGCATTGAGAAGACCACAAAATCTCTAGTGGCTGAGCTTAAGCTGATATCAAAAGAG
                           tgctaac  putative branch site (score: 1)
                                          ttcattc  putative PPT
      aaatgataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtctgtttttgcttaactcttttgtttggtaaacatgaagaacatagtaatctaaggaaatgataacactgtgtttgttgctaactaagatcattcattcattcagGTGGTAGCAGCTGGTGCAAACCCTGTTCTAATCACTCGAGGCATTGAGAAGACCACAAAATCTCTAGTGGCTGAGCTTAAGCTGATATCAAAAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT