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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatagatatctatatatatctgtgtgtgtgtgtgtgtgtgtgtgtgtaaactgttgttgggttaattaaattatattcctgcatttgattagATTCTTCAAGAAGAAATTGGAGGTGTGAAAGGGCACTTTGGACCTATAAATGCTTTAGCATTCAACCCTGATGGAAAGAG

Basic information

species Vitis vinifera
transcript Vv01s0011g06630.t01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv01s0011g06630.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA01G03610.1 (Glycine max), 3'ss of exon 6
----gtaatagatatctatatatatctgtgtgtgtgtgtgtgtgtgtgtgtgtaaactg-ttgttgggttaattaaattatattcctg---catttgattagATTCTTCAAGAAGAAATTGGAGGTGTGAAAGGGCACTTTGGACCTATAAATGCTTTAGCATTCAACCCTGATGGAAAGAG
    ||  |   | | | |   |  || ||| |   | | |     | |||   | ||  || ||  | |  |||  | |||||  |    ||||||||||||||||||||||||||||||| ||||| |||||||| |||||||| || ||||| || || || |||||||||||||| ||
gtaagttttttttttttttcctttactatgtttagttctctaatgatatgtaacatctacttattttgctttttatttcatatttgttattcatttgattagATTCTTCAAGAAGAAATTGGGGGTGTAAAAGGGCATTTTGGACCAATTAATGCATTGGCTTTTAACCCTGATGGAAAAAG

upper sequence: Vv01s0011g06630.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA12G00510.1 (Glycine max), 3'ss of exon 3
gtaatagatatctatatatatctgtgtgtg-tgtgtgtgtgtg-tgtgtgtaaactgt-tgttgggttaattaaatta---tattcctgcatttgattagATTCTTCAAGAAGAAATTGGAGGTGTGAAAGGGCACTTTGGACCTATAAATGCTTTAGCATTCAACCCTGATGGAAAGAG
    ||  | | | |   | |||   |    | ||| |||||  ||||   | | ||  |||    ||| ||   ||    | ||  | ||||||||||||||||||||||||||||||| ||||||||||| || |||||||| || ||||| || || || |||||||||||||| ||
---gtaagtttgtttgcttttcttcctagactatgt-tgtgtactgtgatgatattgaatgtctacttattttgcttccttttttttttcatttgattagATTCTTCAAGAAGAAATTGGGGGTGTGAAAGGCCATTTTGGACCAATTAATGCATTGGCTTTTAACCCTGATGGAAAAAG

upper sequence: Vv01s0011g06630.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA01G03610.2 (Glycine max), 3'ss of exon 6
gtaatagatatctatatatatctgtgtgtgtgtgtgtgtgtgtgtgtgtaaactg-ttgttgggttaattaaattatattcct---gcatttgattagATTCTTCAAGAAGAAATTGGAGGTGTGAAAGGGCACTTTGGACCTATAAATGCTTTAGCATTCAACCCTGATGGAAAGAG
||  |   | | | |   |  || ||| |   | | |     | |||   | ||  || ||  | |  |||  | |||||  |    ||||||||||||||||||||||||||||||| ||||| |||||||| |||||||| || ||||| || || || |||||||||||||| ||
gttttttttttttttcctttactatgtttagttctctaatgatatgtaacatctacttattttgctttttatttcatatttgttattcatttgattagATTCTTCAAGAAGAAATTGGGGGTGTAAAAGGGCATTTTGGACCAATTAATGCATTGGCTTTTAACCCTGATGGAAAAAG

upper sequence: Vv01s0011g06630.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA09G36870.1 (Glycine max), 3'ss of exon 3
gtaatagatatctatatatatctgtgtgtgtgtgtgtgtgtgtgtgtgtaa-actgttgttgggttaattaaattatattcctgcatttgattagATTCTTCAAGAAGAAATTGGAGGTGTGAAAGGGCACTTTGGACCTATAAATGCTTTAGCATTCAACCCTGATGGAAAGAG
    ||| | | | | |   ||  | |   | | ||| || || | |||||   | |||   |  || |||  ||    |  |  |||| ||||||||||||||||||||||||| ||||||||||| ||||||||||| || ||||| || || || |||||||||||||| ||
---gtaggtttttttttccttcc-tatac-tatatgt-tgagt-tctgtaatggtattgaatgtctactta--tttcgcttttttatttcattagATTCTTCAAGAAGAAATTGGGGGTGTGAAAGGCCACTTTGGACCAATTAATGCATTGGCTTTTAACCCTGATGGAAAAAG

upper sequence: Vv01s0011g06630.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA09G36870.2 (Glycine max), 3'ss of exon 3
gtaatagatatctatatatatctgtgtgtgtgtgtgtgtgtgtgtgtgtaa-actgttgttgggttaattaaattatattcctgcatttgattagATTCTTCAAGAAGAAATTGGAGGTGTGAAAGGGCACTTTGGACCTATAAATGCTTTAGCATTCAACCCTGATGGAAAGAG----
    ||| | | | | |   ||  | |   | | ||| || || | |||||   | |||   |  || |||  ||    |  |  |||| ||||||||||||||||||||||||| ||||||||||| ||||||||||| || ||||| || || || |||||||||||||| ||    
---gtaggtttttttttccttcc-tatac-tatatgt-tgagt-tctgtaatggtattgaatgtctactta--tttcgcttttttatttcattagATTCTTCAAGAAGAAATTGGGGGTGTGAAAGGCCACTTTGGACCAATTAATGCATTGGCTTTTAACCCTGATGGAAAAAGGTAT

upper sequence: Vv01s0011g06630.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: AT2G46280.3 (Arabidopsis thaliana), 3'ss of exon 5
gtaatagatatctatatatatctgtgtgt-gtgtgtgtgtgtgtg-tgtgtaaactgttgttgggttaattaaattatattcctgcatttgat--------tagATTCTTCAAGAAGAAATTGGAGGTGTGAAAGGGCACTTTGGACCTATAAATGCTTTAGCATTCAACCCTGATGGAAAGAG
    |   | | |||| |||   |||| |    ||      |||    || ||| |     |   | ||| |   | |||   ||  |||| |        |||||||| ||||| |||||||| ||||||||||| || |||||||||||||||||||| |||||||| |||||||| |||||
---gttagtgtttata-ataagagtgttttacttggaaacatgtaacctggaaaatacacatatttaaataaccgtgtatcattgtgtttggtataatatatagATTCTGCAAGAGGAAATTGGTGGTGTGAAAGGTCATTTTGGACCTATAAATGCTTTGGCATTCAATCCTGATGGGAAGAG

upper sequence: Vv01s0011g06630.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: AT2G46290.1 (Arabidopsis thaliana), 3'ss of exon 7
gtaatagatatctatatatatctgtgtgtgtgtgtgtgtgtgtg-tgtgtaaactgttgttgggttaattaaattatattcctgcatttgattagATTCTTCAAGAAGAAATTGGAGGTGTGAAAGGGCACTTTGGACCTATAAATGCTTTAGCATTCAACCCTGATGGAAAGAG
    |   | |     || | | || | | | |       |||    || |||  | | |     |   ||   | |  || |  | |  || ||||||| ||||| |||||||| || |||||||| || ||||||||||| |||||||| |||||||  |||||||| |||||
---gttagtgttgcagtaaaacagttt-tatttaaaaacttgtaacctggaaagagatatgtaactgtgta---tttggtcttataatatat-agATTCTGCAAGAGGAAATTGGTGGCGTGAAAGGTCATTTTGGACCTATTAATGCTTTGGCATTCAGTCCTGATGGGAAGAG

upper sequence: Vv01s0011g06630.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: PP1S65_136V6.1 (Physcomitrella patens), 3'ss of exon 5
--gtaatagatatctatatatatctgtgtgtgtgtgtgtgtgtgtgtgtgtaaactgttgttgggttaattaaattatattcctgcatt--tgat-----tagATTCTTCAAGAAGAAATTGGAGGTGTGAAAGGGCACTTTGGACCTATAAATGCTTTAGCATTCAACCCTGATGGAAAGAG
    | | ||| | |  |   ||   | |  |  ||| |   | | | | |  ||||      ||| | | ||      |||  |  ||  ||||      ||||| || | ||||| ||||| |||||||| || ||||||||||||||||||||  | || || || || || || |  ||
gctaagttgatgtttgcaggcattcttcttagcttgtttacttctttat-tccactgcaa--aggtcactgaatccgcgttcacgatttcctgatgtctgcagATTTTTGAGGAAGAGATTGGGGGTGTGAAGGGTCACTTTGGACCTATAAATGCCCTGGCTTTTAATCCGGACGGTAGAAG

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|29783544|gb|CB349778.2|CB349778
EST:     CAACAACTGATCATCGTGCTGGAAAGTTTGAGGCAAAATTCTATGATAAG                         ATTCTTCAAGAAGAAATTGGAGGTGTGAAAGGGCACTTTGGACCTATAAAT
genomic: CAACAACTGATCATCGTGCTGGAAAGTTTGAGGCAAAATTCTATGATAAGgtaatagata ... atttgattagATTCTTCAAGAAGAAATTGGAGGTGTGAAAGGGCACTTTGGACCTATAAAT
EST: gi|351036544|gb|FQ457257.1|FQ457257
EST:     CAACAACTGATCATCGTGCTGGGAAGTTTGAGGCAAAATTCTATGATAAG                         ATTCCTTCA-GAAAAAATTGG
genomic: CAACAACTGATCATCGTGCTGGAAAGTTTGAGGCAAAATTCTATGATAAGgtaatagata ... atttgattagATTC-TTCAAGAAGAAATTGG
EST: gi|110697326|gb|EE074214.1|EE074214
EST:     CAACAACTGATCATCGTGCTGGAAAGTTTGAGGCAAAATTCTATGATAAG                         ATTCTTCAAGAAGAAATTGGAGGTGTGAAAGGGCACTTTGGACCTATAAAT
genomic: CAACAACTGATCATCGTGCTGGAAAGTTTGAGGCAAAATTCTATGATAAGgtaatagata ... atttgattagATTCTTCAAGAAGAAATTGGAGGTGTGAAAGGGCACTTTGGACCTATAAAT
EST: gi|110380898|gb|EC946200.1|EC946200
EST:     CAACAACTGATCATCGTGCTGGAAAGTTTGAGGCAAAATTCTATGATAAG                         ATTCTTCAAGAAGAAATTGGAGGTGTGAAAGGGCACTTTGGACCTATAAAT
genomic: CAACAACTGATCATCGTGCTGGAAAGTTTGAGGCAAAATTCTATGATAAGgtaatagata ... atttgattagATTCTTCAAGAAGAAATTGGAGGTGTGAAAGGGCACTTTGGACCTATAAAT
EST: gi|110411322|gb|EC977030.1|EC977030
EST:     CAACAACTGATCATCGTGCTGGAAAGTTTGAGGCAAAATTCTATGATAAG                         ATTCTTCAAGAAGAAATTGGAGGTGTGAAAGGGCACTTTGGACCTATAAAT
genomic: CAACAACTGATCATCGTGCTGGAAAGTTTGAGGCAAAATTCTATGATAAGgtaatagata ... atttgattagATTCTTCAAGAAGAAATTGGAGGTGTGAAAGGGCACTTTGGACCTATAAAT
EST: gi|110369193|gb|EC933345.1|EC933345
EST:     CAACAACTGATCATCGTGCTGGAAAGTTTGAGGCAAAATTCTATGATAAG                         ATTCTTCAAGAAGAAATTGGAGGTGTGAAAGGGCACTTTGGACCTATAAAT
genomic: CAACAACTGATCATCGTGCTGGAAAGTTTGAGGCAAAATTCTATGATAAGgtaatagata ... atttgattagATTCTTCAAGAAGAAATTGGAGGTGTGAAAGGGCACTTTGGACCTATAAAT
EST: gi|110420350|gb|EC986622.1|EC986622
EST:     CAACAACTGATCATCGTGCTGGAAAGTTTGAGGCAAAATTCTATGATAAG                         ATTCTTCAAGAAGAAATTGGAGGTGTGAAAGGGCACTTTGGACCTATAAAT
genomic: CAACAACTGATCATCGTGCTGGAAAGTTTGAGGCAAAATTCTATGATAAGgtaatagata ... atttgattagATTCTTCAAGAAGAAATTGGAGGTGTGAAAGGGCACTTTGGACCTATAAAT
EST: gi|349810075|gb|FQ401521.1|FQ401521
EST:     CAACAACTGATCATCGTGCTGGAAAGTTTGAGGCAAAATTCTATGATAAG                         ATTCTTCAAGAAGAAATTGGAGGTGTGAAAGGGCACTTTGGACCTATAAAT
genomic: CAACAACTGATCATCGTGCTGGAAAGTTTGAGGCAAAATTCTATGATAAGgtaatagata ... atttgattagATTCTTCAAGAAGAAATTGGAGGTGTGAAAGGGCACTTTGGACCTATAAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgtgtgtgtaaactgttgttgggttaattaaattatattcctgcatttgattagATTCTTCAAGAAGAAATTGGAGGTGTGAAAGGGCACTTTGGACCTATAAATGCTTTAGCATTCAACCCTGATGGAAAGAG
                      ggttaat  putative branch site (score: 4)
                   ttgggttaattaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatagatatctatatatatctgtgtgtgtgtgtgtgtgtgtgtgtgtaaactgttgttgggttaattaaattatattcctgcatttgattagATTCTTCAAGAAGAAATTGGAGGTGTGAAAGGGCACTTTGGACCTATAAATGCTTTAGCATTCAACCCTGATGGAAAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA