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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtataataaattgcaggcagtttattgttactatttggttacaatttttctgataatttttaagtacaatatgaacatttaatgttggtattgctttaatttatttttttgaatcaatgtttttcactgaccttttaagtgaaattcctcttcttgtttcttttagGGTGAGGAGGGTTTGGTCCATTTTCAGTGGCTTGATAGAACCAACAATGTCCTTGAAGAT

Basic information

species Vitis vinifera
transcript Vv11s0065g00450.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv11s0065g00450.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AC233870.1_FGT006 (Zea mays), 3'ss of exon 3
gtataataaattgcaggcagtttattgttactatttggttacaatttttctgataatttttaagtacaata-tgaacatttaatgttggtattgctttaatttatttttttgaatcaatgtttttcactgaccttttaagtgaaattcctcttcttgtttcttttagGGTGAGGAGGGTTTGGTCCATTTTCAGTGGCTTGATAGAACCAACAATGTCCTTGAAGAT
                                       ||    |  | | |    |  ||||  ||| | |  |  ||  | | | ||  ||| ||| ||| ||| |||||||        |||||||  |   ||  |  |||  |||||        || |||||||| ||||| || ||||||||||||||||||||  |     | ||  |  ||||||||
--------------------------------------gtatggatactttaacttatactaagctcaacaatagaacttctaagctagt--tgcatta-tttctttctttgaat--------ttcactg--caactatatacaatctctctt--------ttgtagGGTGAAGAGGGATTAGTCCATTTTCAGTGGCTTGACCGTGGACAGAACATAGTTGAAGAT

upper sequence: Vv11s0065g00450.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA08G03080.3 (Glycine max), 3'ss of exon 3
gtataataaattgcaggcagtttattgttactatttggttacaatttttctgataatttttaagtacaatatgaacatttaatgttgg-tattgctttaatt-tatttttttgaatcaatgtttttcactgaccttttaagtgaaattcctcttcttgtttcttttagGGTGAGGAGGGTTTGGTCCATTTTCAGTGGCTTGATAGAACCAACAATGTCCTTGAAGAT
                                                               |||   | | |   ||  |||| |  || | | ||| |  |  | |||| || |  |   |   ||||   ||||||  |  ||| ||       | | ||| ||||||||||||| || ||||||||||||||||||||| | ||  | ||| |  ||||||||
---------------------------------------------------------------gtatggtttaa---ttgcatgtcgaatacttcattattcattgtgttttaaaccctttactgcaactggatttttaaa-gtgattgct-------tctgtttcagGGTGAGGAGGGATTAGTCCATTTTCAGTGGCTTGATCGCACACAAAATATTGTTGAAGAT

upper sequence: Vv11s0065g00450.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA05G36490.1 (Glycine max), 3'ss of exon 3
gtataataaattgcaggcagtttattgttactatttggttacaatttttctgataatttttaagtacaatatgaacatttaatgttggtattgctttaatttatttttttgaatcaatgtttttcactgaccttttaagtgaaattcctcttcttgtttcttttagGGTGAGGAGGGTTTGGTCCATTTTCAGTGGCTTGATAGAACCAACAATGTCCTTGAAGAT
                                                            || |    |  || | || ||||  |  ||||  || | | | ||||    || | | |  |   ||||   ||||||    | |   |  |  ||||||    ||||||||||||| || || |||||||||||||||||| | ||  | |||||  ||||||||
-----------------------------------------------------------gtatggtttacttgcatatctaatactt-tatta-ttcattgtgtttt---aaacccacgactgcaactggatttttaa----agTGTTTGCTTCTGTTTC----AGGGTGAGGAGGGATTAGTACATTTTCAGTGGCTTGATCGCACACAAAATGTTGTTGAAGAT

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|87584845|gb|DY473849.1|DY473849
EST:     GAACAAGAGTCACCCCAGATACACGTAAAGGACTTGTTCGTATTGCAAGG                         GGTGAGGAGGGTTTGGTCCATTTTCAGTGGCTTGATAGAACCAACAATGTC
genomic: GAACAAGAGTCACCCCAGATGCACGTAAAGGACTTGTTCGTATTGCAAAGgtataataaa ... tttcttttagGGTGAGGAGGGTTTGGTCCATTTTCAGTGGCTTGATAGAACCAACAATGTC
EST: gi|294964296|gb|GW838099.1|GW838099
EST:     GAACAAGAGTCACCCCAGATGCACGTAAAGGACTTGTTCGTATTGCAAAG                         GGTGAGGAGGGTTTGGTCCATTTTCAGTGGCTTGATAGAACCAACAATGTC
genomic: GAACAAGAGTCACCCCAGATGCACGTAAAGGACTTGTTCGTATTGCAAAGgtataataaa ... tttcttttagGGTGAGGAGGGTTTGGTCCATTTTCAGTGGCTTGATAGAACCAACAATGTC
EST: gi|33405732|gb|CF211359.1|CF211359
EST:     GAGTCACCCCAGATACACGTAAAGGACTTGTTCGTATTGCAAGG                         GGTGAGGAGGGTTTGGTCCATTTTCAGTGGCTTGATAGAACCAACAATGTC
genomic: GAGTCACCCCAGATGCACGTAAAGGACTTGTTCGTATTGCAAAGgtataataaa ... tttcttttagGGTGAGGAGGGTTTGGTCCATTTTCAGTGGCTTGATAGAACCAACAATGTC
EST: gi|351028718|gb|FQ433148.1|FQ433148
EST:     GAACAAGAGTCACCCCAGATACACGTAAAGGACTTGTTCGTATTGCAAGG                         GGTGAGGAGGGTTTGGTCCATTTTCAGTGGCTTGATAGAACCAACAATGTC
genomic: GAACAAGAGTCACCCCAGATGCACGTAAAGGACTTGTTCGTATTGCAAAGgtataataaa ... tttcttttagGGTGAGGAGGGTTTGGTCCATTTTCAGTGGCTTGATAGAACCAACAATGTC
EST: gi|22011495|gb|BQ796529.1|BQ796529
EST:     GAACAAGAGTCACCCCAGATACACGCAAAGGACTTGTTCGTATTGCAAAG                         GGTGAGGAGGGTTTGGTCCATTTTCAGTGGCTTGATAGAACCAACAATGTC
genomic: GAACAAGAGTCACCCCAGATGCACGTAAAGGACTTGTTCGTATTGCAAAGgtataataaa ... tttcttttagGGTGAGGAGGGTTTGGTCCATTTTCAGTGGCTTGATAGAACCAACAATGTC
EST: gi|110377829|gb|EC942921.1|EC942921
EST:     GAACAAGAGTCACCCCAGATACACGTAAAGGACTTGTTCGTATTGCAAGG                         GGTGAGGAGGGTTTGGTCCATTTTCAGTGGCTTGATAGAACCAACAATGTC
genomic: GAACAAGAGTCACCCCAGATGCACGTAAAGGACTTGTTCGTATTGCAAAGgtataataaa ... tttcttttagGGTGAGGAGGGTTTGGTCCATTTTCAGTGGCTTGATAGAACCAACAATGTC
EST: gi|161716363|gb|FC068095.1|FC068095
EST:     GAACAAGAGTCACCCCAGATACACGTAAAGGACTTGTTCGTATTGCAAGG                         GGTGAGGAGGGTTTGGTCCATTTTCAGTGGCTTGATAGAACCAACAATGTC
genomic: GAACAAGAGTCACCCCAGATGCACGTAAAGGACTTGTTCGTATTGCAAAGgtataataaa ... tttcttttagGGTGAGGAGGGTTTGGTCCATTTTCAGTGGCTTGATAGAACCAACAATGTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatcaatgtttttcactgaccttttaagtgaaattcctcttcttgtttcttttagGGTGAGGAGGGTTTGGTCCATTTTCAGTGGCTTGATAGAACCAACAATGTCCTTGAAGAT
             cactgac  putative branch site (score: 2)
                                 ttcctcttcttgtttc  putative PPT
                     ttttaagtgaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtataataaattgcaggcagtttattgttactatttggttacaatttttctgataatttttaagtacaatatgaacatttaatgttggtattgctttaatttatttttttgaatcaatgtttttcactgaccttttaagtgaaattcctcttcttgtttcttttagGGTGAGGAGGGTTTGGTCCATTTTCAGTGGCTTGATAGAACCAACAATGTCCTTGAAGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA