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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaattcttagttagtccagttaaaatttataaatgatttcatcattgcaggtgcttagtatctattaattattcattgaacttttgaagGTTGGAGCACAAACTGAGACAGAGCTTAAAGAAAAGAAACTGAGAGTAGAAGACGCTCTCAATGCAACGAAG

Basic information

species Vitis vinifera
transcript Vv06s0004g00240.t01
intron # 9
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 9
lower sequence: LOC_Os02g01280.1 (Oryza sativa), 3'ss of exon 9
-------gtaaattct-tagttagtccagttaaaatttataaatg-atttcatcattgcaggtgcttagtat--ctattaattattcattgaacttttga---agGTTGGAGCACAAACTGAGACAGAGCTTAAAGAAAAGAAACTGAGAGTAGAAGACGCTCTCAATGCAACGAAG
         |  ||||  | ||   ||| |    | || | |||| | | |     ||||  |||  |  ||   | ||    | | |    |||| | |   |||| |||||||| || || || |||||||| |||||||||||||| || ||||| || || |||||||| |||
gtgatctcgatgttctgcaattgaaccaat--gcacttgttaatgtactactaggctgcatttgcagaagataattgttgtgaaatgacgctacttgttatgtagGTAGGAGCACAGACAGAAACTGAGCTTAAGGAAAAGAAACTGAGGGTTGAAGATGCACTGAATGCAACCAAG

upper sequence: Vv06s0004g00240.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA08G18760.1 (Glycine max), 3'ss of exon 8
gtaa-attcttagttagtccagttaaaatttataaatgatttcatcattgcaggtgcttagtatctattaattattcattgaacttttgaagGTTGGAGCACAAACTGAGACAGAGCTTAAAGAAAAGAAACTGAGAGTAGAAGACGCTCTCAATGCAACGAAG
|||| |  || | | |     ||   ||| ||| | |  ||    |  |||| | |  ||  | ||       |||  ||| || | |  ||||||| |||||||||||||||||||| || ||||||||| ||||||| ||||||||||| ||||| || |||
gtaacagactcactgaaat--gtggtaatatattagt--ttggtactctgcaag-gtatatcaacttggggcaattt-ttgtacatatatagGTTGGCGCACAAACTGAGACAGAGCTCAAGGAAAAGAAATTGAGAGTTGAAGACGCTCTTAATGCTACAAAG

upper sequence: Vv06s0004g00240.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA15G40110.1 (Glycine max), 3'ss of exon 8
gtaaattcttagttagtccagttaaa-atttataaatgatttcatcattgcaggtgcttagtatcta-ttaattattcattgaacttttgaagGTTGGAGCACAAACTGAGACAGAGCTTAAAGAAAAGAAACTGAGAGTAGAAGACGCTCTCAATGCAACGAAG
         ||       || | |||   | |||  | | ||    |  || | ||  || |||| | ||    | |  ||| || | || ||||||| |||||||||||||| ||||| || ||||||||| ||||||| ||||| ||||| ||||| || |||
--------gtaacagactcactgaaatggtaatatgttagtttggtac-gccgttgggta-tatcaacttgggcaatttttgtacatgtgtagGTTGGTGCACAAACTGAGACTGAGCTCAAGGAAAAGAAATTGAGAGTTGAAGATGCTCTTAATGCTACAAAG

upper sequence: Vv06s0004g00240.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: AT3G13470.1 (Arabidopsis thaliana), 3'ss of exon 9
gtaaattcttagttagtccagttaaaatttataaatgatttcatcattgcaggtgcttagt-atctattaattattcattgaactt--ttgaagGTTGGAGCACAAACTGAGACAGAGCTTAAAGAAAAGAAACTGAGAGTAGAAGACGCTCTCAATGCAACGAAG
||||| |  || | |       |    | |   | |  | | ||    | |   | | ||| ||||| | |   ||  |  | |||  || ||||||||||| ||||||||||||||||| ||||||||||| |||||||| ||||| ||||| ||||| || |||
gtaaaatagtaatcacatggactt---tcttggatttgtatgatagaagaataagttaagtgatctaattaaagtttttacatcttggttaaagGTTGGAGCTCAAACTGAGACAGAGCTCAAAGAAAAGAAGCTGAGAGTGGAAGATGCTCTTAATGCTACAAAG

upper sequence: Vv06s0004g00240.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: AT5G56500.2 (Arabidopsis thaliana), 3'ss of exon 9
gtaaattcttagttagtccagttaaaatttataaatgatttcatcattgcaggtgcttagtatctattaattattcattgaac-ttttgaagGTTGGAGCACAAACTGAGACAGAGCTTAAAGAAAAGAAACTGAGAGTAGAAGACGCTCTCAATGCAACGAAG
|| |  |  ||   |  | | | | |   |  |||      | |   |  ||||  | || |   || |  ||  | ||  |  || |  ||||||||||||||||||||||||||||||| || |||||| | ||||| ||||| ||||| ||||| || |||
gtgagatactaagaaa-caaatcacatgatgcaaaaag---cgtagcttaaggtaataagaaga-ataatctaaacgttttatattctttagGTTGGAGCACAAACTGAGACAGAGCTTAAGGAGAAGAAATTAAGAGTTGAAGATGCTCTTAATGCTACAAAG

upper sequence: Vv06s0004g00240.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: AT1G55490.2 (Arabidopsis thaliana), 3'ss of exon 9
gtaaattcttagttagtccagttaaaatt-tataaatgatttcatcattgcaggtgcttagtatctattaattattcattgaacttttgaagGTTGGAGCACAAACTGAGACAGAGCTTAAAGAAAAGAAACTGAGAGTAGAAGACGCTCTCAATGCAACGAAG
||||| |   |  || |  ||||    || | | | | |  |     |   || |  | ||| |    |  ||||  ||||     || |||||||||||||||||||||||||| || ||||| |||||  ||||||| ||||| ||||| |||||||| |||
gtaaactaaaaactatttaagtttcctttgtctgattaagatgtgtttcagagatattaagt-taagctcgttatgtattgg----ttaaagGTTGGAGCACAAACTGAGACAGAACTCAAAGAGAAGAAGTTGAGAGTTGAAGATGCTCTTAATGCAACAAAG

upper sequence: Vv06s0004g00240.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: EFJ33580 (Selaginella moellendorffii), 3'ss of exon 8
gtaaattcttagttagtccagttaaaatttataaatgatttcatcattgcag-gtgcttagtatc-tattaattattcattgaacttttgaagGTTGGAGCACAAACTGAGACAGAGCTTAAAGAAAAGAAACTGAGAGTAGAAGACGCTCTCAATGCAACGAAG
                                   | | || ||  ||||||  |  |||| | |  ||   | | |  |       ||||||||||| |||||||||||||||||  | |||||||||||  | ||||| ||||| ||| | ||||| ||||||
----------------------------------gtaagtttatt-ttgcagtatttttagcagcacatctttaacttctctgtaaattgaagGTTGGTGCACAAACTGAGACAGAATTAAAAGAAAAGAAGTTAAGAGTGGAAGATGCTTTGAATGCGACGAAG

upper sequence: Vv06s0004g00240.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: EFJ36935 (Selaginella moellendorffii), 3'ss of exon 8
gtaaattcttagttagtccagttaaaatttataaatgatttcatcattgcag-gtgcttagtatc-tattaattattcattgaacttttgaagGTTGGAGCACAAACTGAGACAGAGCTTAAAGAAAAGAAACTGAGAGTAGAAGACGCTCTCAATGCAACGAAG
                                   | | || ||  ||||||  |  |||| | |  ||   | | |  |       ||||||||||| ||||||||||||||||| || |||||||||||  | ||||| ||||| ||| | ||||||||||||
----------------------------------gtaagtttatt-ttgcagtatttttagcagcacatcgttaacttttctgtaaattgaagGTTGGTGCACAAACTGAGACAGAACTAAAAGAAAAGAAGTTAAGAGTGGAAGATGCTTTGAATGCAACGAAG

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|26259554|gb|CA810617.1|CA810617
EST:     AATTGCAAAA-TGTCAGGTGGTGTTGCTGTGATTCAG                         GTTGGAGCACAAACTGAGACAGAGCTTAAAGAAAAGAAACTGAGAGTAGAA
genomic: AATTGCAAAATTGTCAGGTGGTGTTGCTGTGATTCAGgtaaattctt ... acttttgaagGTTGGAGCACAAACTGAGACAGAGCTTAAAGAAAAGAAACTGAGAGTAGAA
EST: gi|110363904|gb|EC927535.1|EC927535
EST:     AACTTAATGAAAGAATTGCAAAATTGTCAGGTGGTGTTGCTGTGATTCAG                         GTTGGAGCACAAACTGAGACAGAGCTTAAAGAAAAGAAACTGAGAGTAGAA
genomic: AACTTAATGAAAGAATTGCAAAATTGTCAGGTGGTGTTGCTGTGATTCAGgtaaattctt ... acttttgaagGTTGGAGCACAAACTGAGACAGAGCTTAAAGAAAAGAAACTGAGAGTAGAA
EST: gi|351022937|gb|FQ428846.1|FQ428846
EST:     AACTTAATGAAAGAATTGCAAAATTGTCAGGTGGTGTTGCTGTGATTCAG                         GTTGGAGCACAAACTGAGACAGAGCTTAAAGAAAAGAAACTGAGAGTAGAA
genomic: AACTTAATGAAAGAATTGCAAAATTGTCAGGTGGTGTTGCTGTGATTCAGgtaaattctt ... acttttgaagGTTGGAGCACAAACTGAGACAGAGCTTAAAGAAAAGAAACTGAGAGTAGAA
EST: gi|110419196|gb|EC985406.1|EC985406
EST:     AACTTAATGAAAGAATTGCAAAATTGTCAGGTGGTGTTGCTGTGATTCAG                         GTTGGAGCACAAACTGAGACAGAGCTTAAAGAAAAGAAACTGAGAGTAGAA
genomic: AACTTAATGAAAGAATTGCAAAATTGTCAGGTGGTGTTGCTGTGATTCAGgtaaattctt ... acttttgaagGTTGGAGCACAAACTGAGACAGAGCTTAAAGAAAAGAAACTGAGAGTAGAA
EST: gi|37188314|gb|CF607663.1|CF607663
EST:     AACTTAATGAAAGAATTGCAAAATTGTCAGGTGGTGTTGCTGTGATTCAG                         GTTGGAGCACAAACTGAGACAGAGCTTAAAGAAAAGAAACTGAGAGTAGAA
genomic: AACTTAATGAAAGAATTGCAAAATTGTCAGGTGGTGTTGCTGTGATTCAGgtaaattctt ... acttttgaagGTTGGAGCACAAACTGAGACAGAGCTTAAAGAAAAGAAACTGAGAGTAGAA
EST: gi|351036299|gb|FQ458674.1|FQ458674
EST:     AACTTAATGAAAGAATTGCAAAATTGTCAGGTGGTGTTGCTGTGATTCAG                         GTTGGAGCACAAACTGAGACAGAGCTTAAAGAAAAGAAACTGAGAGTAGAA
genomic: AACTTAATGAAAGAATTGCAAAATTGTCAGGTGGTGTTGCTGTGATTCAGgtaaattctt ... acttttgaagGTTGGAGCACAAACTGAGACAGAGCTTAAAGAAAAGAAACTGAGAGTAGAA
EST: gi|34550178|gb|CF518396.1|CF518396
EST:     AACTTAATGAAAGAATTGCAAAATTGTCAGGTGGTGTTGCTGTGATTCAG                         GTTG-ATGCACAAACTGAGACAGAGCTTAAAGAAA-GAAACTG
genomic: AACTTAATGAAAGAATTGCAAAATTGTCAGGTGGTGTTGCTGTGATTCAGgtaaattctt ... acttttgaagGTTGGA-GCACAAACTGAGACAGAGCTTAAAGAAAAGAAACTG
EST: gi|110688028|gb|EE066108.1|EE066108
EST:     AACTTAATGAAAGAATTGCAAAATTGTCAGGTGGTGTTGCTGTGATTCAG                         GTTGGAGCACAAACTGAGACAGAGCTTAAAGAAAAGAAACTGAGAGTAGAA
genomic: AACTTAATGAAAGAATTGCAAAATTGTCAGGTGGTGTTGCTGTGATTCAGgtaaattctt ... acttttgaagGTTGGAGCACAAACTGAGACAGAGCTTAAAGAAAAGAAACTGAGAGTAGAA
EST: gi|349807747|gb|FQ402138.1|FQ402138
EST:     AACTTAATGAAAGAATTGCAAAATTGTCAGGTGGTGTTGCTGTGATTCAG                         GTTGGAGCACAAACTGAGACAGAGCTTAAAGAAAAGAAACTGAGAGTAGAA
genomic: AACTTAATGAAAGAATTGCAAAATTGTCAGGTGGTGTTGCTGTGATTCAGgtaaattctt ... acttttgaagGTTGGAGCACAAACTGAGACAGAGCTTAAAGAAAAGAAACTGAGAGTAGAA
EST: gi|351034062|gb|FQ447979.1|FQ447979
EST:     AACTTAATGAAAGAATTGCAAAATTGTCAGGTGGTGTTGCTGTGATTCAG                         GTTGGAGCACAAACTGAGACAGAGCTTAAAGAAAAGAAACTGAGAGTAGAA
genomic: AACTTAATGAAAGAATTGCAAAATTGTCAGGTGGTGTTGCTGTGATTCAGgtaaattctt ... acttttgaagGTTGGAGCACAAACTGAGACAGAGCTTAAAGAAAAGAAACTGAGAGTAGAA
EST: gi|110362655|gb|EC926202.1|EC926202
EST:     AACTTAATGAAAGAATTGCAAAATTGTCAGGTGGTGTTGCTGTGATTCAG                         GTTGGAGCACAAACTGAGACAGAGCTTAAAGAAAAGAAACTGAGAGTAGAA
genomic: AACTTAATGAAAGAATTGCAAAATTGTCAGGTGGTGTTGCTGTGATTCAGgtaaattctt ... acttttgaagGTTGGAGCACAAACTGAGACAGAGCTTAAAGAAAAGAAACTGAGAGTAGAA
EST: gi|110362851|gb|EC926408.1|EC926408
EST:     AACTTAATGAAAGAATTGCAAAATTGTCAGGTGGTGTTGCTGTGATTCAG                         GTTGGAGCACAAACTGAGACAGAGCTTAAAGAAAAGAAACTGAGAGTAGAA
genomic: AACTTAATGAAAGAATTGCAAAATTGTCAGGTGGTGTTGCTGTGATTCAGgtaaattctt ... acttttgaagGTTGGAGCACAAACTGAGACAGAGCTTAAAGAAAAGAAACTGAGAGTAGAA
EST: gi|34549838|gb|CF518070.1|CF518070
EST:     AACTTAATGAAAGAATTGCAAAATTGTCAGGTGGTGTTGCTGTGATTCAG                         GTTGGAGCACAAACTGAGACAGAGCTTAAAGAAAAGAAACTGAGAGTAGAA
genomic: AACTTAATGAAAGAATTGCAAAATTGTCAGGTGGTGTTGCTGTGATTCAGgtaaattctt ... acttttgaagGTTGGAGCACAAACTGAGACAGAGCTTAAAGAAAAGAAACTGAGAGTAGAA
EST: gi|33401795|gb|CF207422.1|CF207422
EST:     AACTTAATGAAAGAATTGCAAAATTGTCAGGTGGTGTTGCTGTGATTCAG                         GTTGGAGCACAAACTGAGACAGAGCTTAAAGAAAAGAAACTGAGAGTAGAA
genomic: AACTTAATGAAAGAATTGCAAAATTGTCAGGTGGTGTTGCTGTGATTCAGgtaaattctt ... acttttgaagGTTGGAGCACAAACTGAGACAGAGCTTAAAGAAAAGAAACTGAGAGTAGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatttcatcattgcaggtgcttagtatctattaattattcattgaacttttgaagGTTGGAGCACAAACTGAGACAGAGCTTAAAGAAAAGAAACTGAGAGTAGAAGACGCTCTCAATGCAACGAAG
                            tattaat  putative branch site (score: 2)
                                              ctttt  putative PPT
                        tatctattaattattc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaattcttagttagtccagttaaaatttataaatgatttcatcattgcaggtgcttagtatctattaattattcattgaacttttgaagGTTGGAGCACAAACTGAGACAGAGCTTAAAGAAAAGAAACTGAGAGTAGAAGACGCTCTCAATGCAACGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA