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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcatatagatcaaactaattgcgtgtatatcatctcaactgaatgcagtaacatttgatgatcttttgtttgtttgtatttcacagACTCTTCGTAGGCTTGCTCAAAATCGTGAAGCTGCACGAAAAAGCCGATTGAGAAAGAAA

Basic information

species Vitis vinifera
transcript Vv13s0084g00660.t01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv13s0084g00660.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os03g20310.2 (Oryza sativa), 3'ss of exon 4
---gtcatatagatcaaactaattgcg---tgtatatcatctcaactgaatgcagtaacatttgatgatcttttgtttgtttgtatttcacagACTCTTCGTAGGCTTGCTCAAAATCGTGAAGCTGCACGAAAAAGCCGATTGAGAAAGAAA
    | || ||  ||  | |  ||| |   ||    | |||    || ||||   |   ||||    |   | ||||||||   |||    ||    | ||  ||||||||||||||||||| |||||| ||||||| ||  ||||||| || 
gtgttaatttatctcctatttcttgtgcagtgctacttatcctttcttaatg--atggtatttaggaag--tatgtttgtt---attctgtagGTGTTACGCCGGCTTGCTCAAAATCGTGAGGCTGCAAGAAAAAGTCGGCTGAGAAAAAAG

upper sequence: Vv13s0084g00660.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA20G39050.2 (Glycine max), 3'ss of exon 4
-----------gtcatatagatcaaact-aattgcgtgtatatcatctcaa-ctgaatgcagtaacatttgatgatcttttgtttgtttgtatttcacagACTCTTCGTAGGCTTGCTCAAAATCGTGAAGCTGCACGAAAAAGCCGATTGAGAAAGAAA
            |  | ||  | ||| |   ||  | |  ||  |||| ||  |  |    |||    ||       | ||| || |||   | |  |||||||| || ||||||||||| |||||||| || ||| ||||||| || ||||||||||||
aaaacaaatgtttactctattttaaatttggttatgcggttaatatctaaaattttaaatggtatttgttacgtgattattgattttttaattattgcagACTCTCCGAAGGCTTGCTCAGAATCGTGAGGCAGCAAGAAAAAGTCGGTTGAGAAAGAAA

upper sequence: Vv13s0084g00660.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA13G26280.1 (Glycine max), 3'ss of exon 6
gtcatatagatca-aactaattgc--gtgtatatcatctcaactgaatgcagtaacatt-tgatgatcttttgtttgtttgtatttcacagACTCTTCGTAGGCTTGCTCAAAATCGTGAAGCTGCACGAAAAAGCCGATTGAGAAAGAAA
||   ||| || | || | || |    | | ||  ||   || ||      |  ||||  |||| || ||||       | | | |   ||||||| || ||||||||||| || |||||||||||  |||||||||| ||| ||||||||
gttgaatatattataaattatggataatatctagaattcaaagtggtatttgctacatcatgataatttttttaaaaaatat-tattgtagACTCTCCGCAGGCTTGCTCAGAACCGTGAAGCTGCCAGAAAAAGCCGCTTGCGAAAGAAA

upper sequence: Vv13s0084g00660.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA15G37220.1 (Glycine max), 3'ss of exon 2
gtcatatagatcaaa---ctaattgcgtgtatatcatctc-aactgaatgcagtaacatttg----atgatcttttgtttgtttgtatt-tcacagACTCTTCGTAGGCTTGCTCAAAATCGTGAAGCTGCACGAAAAAGCCGATTGAGAAAGAAA
||   ||| || | |    | ||| | || |||  ||||  || | ||    |||    ||     |||||  ||| |||     |||| |   ||||||| || ||||||||||| || |||||||||||  |||||||||| ||| ||||||||
gttgaatatattataaatttcattacatggataatatctagaattcaaaatggtatttgttacatcatgataattt-tttaaaaatattattgtagACTCTCCGCAGGCTTGCTCAGAACCGTGAAGCTGCCAGAAAAAGCCGCTTGCGAAAGAAA

upper sequence: Vv13s0084g00660.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA10G44270.1 (Glycine max), 3'ss of exon 4
-----------gtcatatagatcaaacta-attgcgtgtatatcatctcaa-ctgaatgcagtaac-atttgatgatcttttgtttgtttgtatttcacagACTCTTCGTAGGCTTGCTCAAAATCGTGAAGCTGCACGAAAAAGCCGATTGAGAAAGAAA
            |  | ||  | ||| |   ||  | |  |||||||| ||  |  |    |||    ||  |||||| ||  ||| ||  | | |  |||| ||| || ||||||||||| ||||| || |||||| ||||||| || ||||||||||||
aaaacaaatgtttactctattttaaattttgttatgcggttatcatctaaaattttaaatggtatttgttacatgatcattgattttttaat-tattgcagAGTCTCCGGAGGCTTGCTCAGAATCGCGAGGCTGCAAGAAAAAGTCGGTTGAGAAAGAAA

upper sequence: Vv13s0084g00660.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: AT3G12250.5 (Arabidopsis thaliana), 3'ss of exon 4
--------gtcatatagatcaaactaattgcgtgtatatcatctcaactgaatgcagtaacatttgatgatcttttgtttgtttgtatttcacagACTCTTCGTAGGCTTGCTCAAAATCGTGAAGCTGCACGAAAAAGCCGATTGAGAAAGAAA
         |||| |   |  | | | | || | | | | || | |     ||||| |||  | |  || |   || || |||| |  | || |||| |||||||||||||||||||||||||| || ||| |||||||| ||||||| ||||| 
gtgatagattcatctctgtggatcaactagcatctgtgt-atattacgcatatgca-taatctgttttgtttcctt-ttcgttt-tgatccatagACCCTTCGTAGGCTTGCTCAAAATCGTGAGGCAGCAAGAAAAAGCAGATTGAGGAAGAAG

upper sequence: Vv13s0084g00660.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: AT5G06950.3 (Arabidopsis thaliana), 3'ss of exon 4
gtcatatagatcaaactaattgcgtgtatatcatctcaactga-atgcagt-aacatttgatgatcttttgtttgtttgtattt-----cacagACTCTTCGTAGGCTTGCTCAAAATCGTGAAGCTGCACGAAAAAGCCGATTGAGAAAGAAA
        ||     | |  |  ||  |||  ||| |   |   || |||  ||  | | ||    ||||||||  || |||||     || ||||||||||||||||||||||||| ||||| || ||| | |||||| ||||||| ||||| 
------gtgacatgtccatctctgtagataagatcactgtttttattcagccaatttataatctctttttgtttccttatattttgatccatagACTCTTCGTAGGCTTGCTCAAAACCGTGAGGCAGCAAGGAAAAGCAGATTGAGGAAGAAG

upper sequence: Vv13s0084g00660.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: AT5G06960.1 (Arabidopsis thaliana), 3'ss of exon 3
gtca-tatagatcaaactaatt-gcgtgtatatcatctcaactgaatgcagtaacatttgatgatcttttgtttgtt--tgtatttcacagACTCTTCGTAGGCTTGCTCAAAATCGTGAAGCTGCACGAAAAAGCCGATTGAGAAAGAAA
|| | |||| |     ||| || ||  |  | |  | |             |  || ||     | | |||||||||  |||| |  |||||| ||||||||||| |||||||| ||||| |||||| | |||||| ||||||| ||||||
gtgaatataaacatctctattttgcaagagtttggtttttgtcattgagcctttcagttatgtttttcttgtttgttgttgtaatcaacagACGCTTCGTAGGCTCGCTCAAAACCGTGAGGCTGCAAGGAAAAGCAGATTGAGGAAGAAA

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|26257000|gb|CA808063.1|CA808063
EST:     ATATGGCTTCTGATTCCAGCGACAGGTCAAAGGATAAAAATGATCAGAAG                         ACTCTTCGTAGGCTTGCTCAAAATCGTGAAGCTGCACGAAAAAGCCGATTG
genomic: ATATGGCTTCTGATTCCAGCGACAGATCAAAGGATAAAAATGATCAGAAGgtcatataga ... tatttcacagACTCTTCGTAGGCTTGCTCAAAATCGTGAAGCTGCACGAAAAAGCCGATTG
EST: gi|156737550|gb|EV241663.1|EV241663
EST:     ATATGGCTTCTGATTCCAGCGACAGATCAAAGGATAAAAATGATCAGAAG                         ACTCTTCGTAGGCTTGCTCAAAATCGTGAAGCTGCACGAAAAAGCCGATTG
genomic: ATATGGCTTCTGATTCCAGCGACAGATCAAAGGATAAAAATGATCAGAAGgtcatataga ... tatttcacagACTCTTCGTAGGCTTGCTCAAAATCGTGAAGCTGCACGAAAAAGCCGATTG
EST: gi|110687850|gb|EE065730.1|EE065730
EST:     ATATGGCTTCTGATTCCAGCGACAGATCAAAGGATAAAAATGATCAGAAG                         ACTCTTCGTAGGCTTGCTCAAAATCGTGAAGCTGCACGAAAAAGCCGATTG
genomic: ATATGGCTTCTGATTCCAGCGACAGATCAAAGGATAAAAATGATCAGAAGgtcatataga ... tatttcacagACTCTTCGTAGGCTTGCTCAAAATCGTGAAGCTGCACGAAAAAGCCGATTG
EST: gi|30301282|gb|CB978076.1|CB978076
EST:     ATATGGCTTCTGATTCCAGCGACGGATCAAAGGAT-AAAATGATCAGAAG                         ACTCTTCGTAGGCTTGCTCAAAATCGTGAAGCTGCACGAAAAAACCGATTG
genomic: ATATGGCTTCTGATTCCAGCGACAGATCAAAGGATAAAAATGATCAGAAGgtcatataga ... tatttcacagACTCTTCGTAGGCTTGCTCAAAATCGTGAAGCTGCACGAAAAAGCCGATTG
EST: gi|77583990|gb|DV221036.1|DV221036
EST:     ATATGGCTTCTGATTCCAGCGACAGATCAAAGGATAAAAATGATCAGAAG                         ACTCTTCGTAGGCTTGCTCAAAATCGTGAAGCTGCACGAAAAAGCCGATTG
genomic: ATATGGCTTCTGATTCCAGCGACAGATCAAAGGATAAAAATGATCAGAAGgtcatataga ... tatttcacagACTCTTCGTAGGCTTGCTCAAAATCGTGAAGCTGCACGAAAAAGCCGATTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atctcaactgaatgcagtaacatttgatgatcttttgtttgtttgtatttcacagACTCTTCGTAGGCTTGCTCAAAATCGTGAAGCTGCACGAAAAAGCCGATTGAGAAAGAAA
                                         tttgtattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcatatagatcaaactaattgcgtgtatatcatctcaactgaatgcagtaacatttgatgatcttttgtttgtttgtatttcacagACTCTTCGTAGGCTTGCTCAAAATCGTGAAGCTGCACGAAAAAGCCGATTGAGAAAGAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA