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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acttttcacgtggaatttggaagtgatagaaatggatattccttctgtgttagatttggtcattttttactgtttattgtgctttgttttgactctttagGTGTAATCGAGATACTGATAAACAGTGGAAGGCAAATTGATGCTGTTAACCTGGCTTTTGCATTTGAGCTCACAGAGCAGTTCTCACCTGTGCCTTTGCT

Basic information

species Vitis vinifera
transcript Vv07s0151g00650.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv07s0151g00650.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA03G23740.1 (Glycine max), 3'ss of exon 2
----actttt-cacgtgga--atttggaagtgatagaaatggatattccttctgtgttagatttggtcattttttactgtttattgtgctttgttttgactctttagGTGTAATCGAGATACTGATAAACAGTGGAAGGCAAATTGATGCTGTTAACCTGGCTTTTGCATTTGAGCTCACAGAGCAGTTCTCACCTGTGCCTTTGCT
    |||||  ||  || |  |||   |       | ||   |  |   || | ||||   |||    |||||| |   || ||| | |||| | |||    |  |||||| || ||  |  || | || |||||  |||||||||||||||||||| |||||||||||||||| || ||||| || || |||||  | ||||| ||
aatgactttagcatctgtattattcaaagagtgaggtaactaaagtattttatctgtttatttta---atttttaatgattcattttactttttcttg----tgcagGTGTCATTGAAGTTTTGGTGAATAGTGGGCGGCAAATTGATGCTGTTAACTTGGCTTTTGCATTTGATCTTACAGAACAATTTTCACCCATTCCTTTACT

upper sequence: Vv07s0151g00650.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA16G08590.1 (Glycine max), 3'ss of exon 1
acttttcacgtggaatttggaagtgatag-aaatggatattccttctgtgttagatttgg--tcattttttactgtttattgtgctttgttttgactctttagGTGTAATCGAGATACTGATAAACAGTGGAAGGCAAATTGATGCTGTTAACCTGGCTTTTGCATTTGAGCTCACAGAGCAGTTCTCACCTGTGCCTTTGCT
   |    | || ||| | | |||  ||  || |  | | |    |  |   |   |||      ||| ||    |   |  |  |  ||||||  | |  |||||| || | | |  || | ||||||||  | |||||||||||||||||| |||||||||||||||| || || || || || |  |||||  |||| ||
---tcatgcatgaaatctagcagttgtatcaattacagagtaaagcaataaaactattgcatctgtttgttttaatgcttcattttacgttttggatatacagGTGTTATTGGGGTTTTGGTGAACAGTGGGCGACAAATTGATGCTGTTAACTTGGCTTTTGCATTTGATCTTACTGAACAATTTTGTCCTGTTTCTTTACT

upper sequence: Vv07s0151g00650.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA03G23760.1 (Glycine max), 3'ss of exon 3
acttttcacgtggaatttggaagtgatag-aaatggatattccttctgtgttagatttgg--tcattttttactgtttattgtgctttgttttgactctttagGTGTAATCGAGATACTGATAAACAGTGGAAGGCAAATTGATGCTGTTAACCTGGCTTTTGCATTTGAGCTCACAGAGCAGTTCTCACCTGTGCCTTTGCT
   |   || || ||| | | |||  ||  || |  | | |    |  |   |   |||      ||| ||    |   |  |  ||  |||||  | |  ||||||||| ||| |  || | ||||||||  | |||||||||||||||||| |||||||||||||||| || || || ||||| |  |||||  |||| ||
---tcatacatgaaatctagcagttgtatcaattacagagtgaagcaataaaactattgcatctgtttgttttaatgcttcatttttctttttggatatgcagGTGTAATTGAGGTTTTGGTGAACAGTGGGCGACAAATTGATGCTGTTAACTTGGCTTTTGCATTTGATCTTACTGAACAGTTTTGTCCTGTTTCTTTACT

upper sequence: Vv07s0151g00650.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT5G48385.1 (Arabidopsis thaliana), 3'ss of exon 3
-acttttcacgtg-gaatttggaagtgatagaaatggatattccttctgtgttagatttggtcattttttactgtttattgtgctttgttttgactcttt-agGTGTAATCGAGATACTGATAAACAGTGGAAGGCAAATTGATGCTGTTAACCTGGCTTTTGCATTTGAGCTCACAGAGCAGTTCTCACCTGTGCCTTTGCT
 |   |  |  |  |  |||     || |     |  |      |||| |     ||    | || || |    |||| |||||  || |     | ||  |||||| || ||  | ||  | ||||||||||  || |||||||| |||||| |||| ||||| ||||| |||||||| ||||||||||||||  | || ||
catggtggatatctgtgtttttccttgtttagtttacacccagattctctaccttatcccttgatcttatc---tttaatgtgcactgctccttttattccagGTGTGATTGAAGTTCTCGTGAACAGTGGAAAACAGATTGATGCGGTTAACTTGGCATTTGCGTTTGAACTCACAGAACAGTTCTCACCTGTCTCATTACT

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|34543121|gb|CF511353.1|CF511353
EST:     CCAAACAGCTGATTTATGTCGCTCCCTTGGGCTGTCAGAGAAAATGCCAG                         GTGTAATCGAGATACTGATAAACAGTGGAAGGCAAATTGATGCTGTTAACC
genomic: CCAAACAGCTGATTTATGTCGCTCCCTTGGGCTGTCAGAGAAAATGCCAGgttagtcttt ... gactctttagGTGTAATCGAGATACTGATAAACAGTGGAAGGCAAATTGATGCTGTTAACC
EST: gi|110686773|gb|EE064797.1|EE064797
EST:     CCAAACAGCTGATTTATGTCGCTCCCTTGGGCTGTCAGAGAAAATGCCAG                         GTGTAATCGAGATACTGATAAACAGTGGAAGGCAAATTGATGCTGTTAACC
genomic: CCAAACAGCTGATTTATGTCGCTCCCTTGGGCTGTCAGAGAAAATGCCAGgttagtcttt ... gactctttagGTGTAATCGAGATACTGATAAACAGTGGAAGGCAAATTGATGCTGTTAACC
EST: gi|110700228|gb|EE078024.1|EE078024
EST:     CCAAACAGCTGATTTATGTCGCTCCCTTGGGCTGTCAGAGAAAATGCCAG                         GTGTAATCGAGATACTGATAAACAGTGGAAGGCAAATTGATGCTGTTAACC
genomic: CCAAACAGCTGATTTATGTCGCTCCCTTGGGCTGTCAGAGAAAATGCCAGgttagtcttt ... gactctttagGTGTAATCGAGATACTGATAAACAGTGGAAGGCAAATTGATGCTGTTAACC
EST: gi|294966891|gb|GW839766.1|GW839766
EST:     CCAAACAGCTGATTTATGTCGCTCCCTTGGGCTGTCAGAGAAAATGCCAG                         GTGTAATCGAGATACTGATAAACAGTGGAAGGCAAATTGATGCTGTTAACC
genomic: CCAAACAGCTGATTTATGTCGCTCCCTTGGGCTGTCAGAGAAAATGCCAGgttagtcttt ... gactctttagGTGTAATCGAGATACTGATAAACAGTGGAAGGCAAATTGATGCTGTTAACC
EST: gi|110374525|gb|EC939343.1|EC939343
EST:     CCAAACAGCTGATTTATGTCGCTCCCTTGGGCTGTCAGAGAAAATGCCAG                         GTGTAATCGAGATACTGATAAACAGTGGAAGGCAAATTGATGCTGTTAACC
genomic: CCAAACAGCTGATTTATGTCGCTCCCTTGGGCTGTCAGAGAAAATGCCAGgttagtcttt ... gactctttagGTGTAATCGAGATACTGATAAACAGTGGAAGGCAAATTGATGCTGTTAACC
EST: gi|30256284|gb|CB972127.1|CB972127
EST:     CCAAACAGCTGATTTATGTCGCTCCCTTGGGCTGTCAGAGAAAATGCCAG                         GTGTAATCGAGATACTGATAAACAGTGGAAGGCAAATTGATGCTGTTAACC
genomic: CCAAACAGCTGATTTATGTCGCTCCCTTGGGCTGTCAGAGAAAATGCCAGgttagtcttt ... gactctttagGTGTAATCGAGATACTGATAAACAGTGGAAGGCAAATTGATGCTGTTAACC
EST: gi|110397256|gb|EC962986.1|EC962986
EST:     CCAAACAGCTGATTTATGTCGCTCCCTTGGGCTGTCAGAGAAAATGCCAG                         GTGTAATCGAGATACTGATAAACAGTGGAAGGCAAATTGATGCTGTTAACC
genomic: CCAAACAGCTGATTTATGTCGCTCCCTTGGGCTGTCAGAGAAAATGCCAGgttagtcttt ... gactctttagGTGTAATCGAGATACTGATAAACAGTGGAAGGCAAATTGATGCTGTTAACC
EST: gi|30253383|gb|CB970934.1|CB970934
EST:     CCAAACAGCTGATTTATGTCGCTCCCTTGGGCTGTCAGAGAAAATGCCAG                         GTGTAATCGAGATACTGATAAACAGTGGAAGGCAAATTGATGCTGTTAACC
genomic: CCAAACAGCTGATTTATGTCGCTCCCTTGGGCTGTCAGAGAAAATGCCAGgttagtcttt ... gactctttagGTGTAATCGAGATACTGATAAACAGTGGAAGGCAAATTGATGCTGTTAACC
EST: gi|34544630|gb|CF512862.1|CF512862
EST:     CCAAACAGCTGATTTATGTCGCTCCCTTGGGCTGTCAGAGAAAATGCCAG                         GTGTAATCGAGATACTGATAAACAGTGGAAGGCAAATTGATGCTGTTAACC
genomic: CCAAACAGCTGATTTATGTCGCTCCCTTGGGCTGTCAGAGAAAATGCCAGgttagtcttt ... gactctttagGTGTAATCGAGATACTGATAAACAGTGGAAGGCAAATTGATGCTGTTAACC
EST: gi|110702624|gb|EE078760.1|EE078760
EST:     CCAAACAGCTGATTTATGTCGCTCCCTTGGGCTGTCAGAGAAAATGCCAG                         GTGTAATCGAGATACTGATAAACAGTGGAAGGCAAATTGATGCTGTTAACC
genomic: CCAAACAGCTGATTTATGTCGCTCCCTTGGGCTGTCAGAGAAAATGCCAGgttagtcttt ... gactctttagGTGTAATCGAGATACTGATAAACAGTGGAAGGCAAATTGATGCTGTTAACC
EST: gi|110374716|gb|EC939639.1|EC939639
EST:     CCAAACAGCTGATTTATGTCGCTCCCTTGGGCTGTCAGAGAAAATGCCAG                         GTGTAATCGAGATACTGATAAACAGTGGAAGGCAAATTGATGCTGTTAACC
genomic: CCAAACAGCTGATTTATGTCGCTCCCTTGGGCTGTCAGAGAAAATGCCAGgttagtcttt ... gactctttagGTGTAATCGAGATACTGATAAACAGTGGAAGGCAAATTGATGCTGTTAACC
EST: gi|34543204|gb|CF511436.1|CF511436
EST:     CCAAACAGCTGATTTATGTCGCTCCCTTGGGCTGTCAGAGAAAATGCCAG                         GTGTAATCGAGATACTGATAAACAGTGGAAGGCAAATTGATGCTGTTAACC
genomic: CCAAACAGCTGATTTATGTCGCTCCCTTGGGCTGTCAGAGAAAATGCCAGgttagtcttt ... gactctttagGTGTAATCGAGATACTGATAAACAGTGGAAGGCAAATTGATGCTGTTAACC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtgttagatttggtcattttttactgtttattgtgctttgttttgactctttagGTGTAATCGAGATACTGATAAACAGTGGAAGGCAAATTGATGCTGTTAACCTGGCTTTTGCATTTGAGCTCACAGAGCAGTTCTCACCTGTGCCTTTGCT
                                         ttttgac  putative branch site (score: 3)
                                               ctcttt  CT-rich tract
                attttttactgtttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acttttcacgtggaatttggaagtgatagaaatggatattccttctgtgttagatttggtcattttttactgtttattgtgctttgttttgactctttagGTGTAATCGAGATACTGATAAACAGTGGAAGGCAAATTGATGCTGTTAACCTGGCTTTTGCATTTGAGCTCACAGAGCAGTTCTCACCTGTGCCTTTGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - cacgtgg
- - - - - - - - - - - - -atagaaa
- - - - - - - - - - - - - - - - - - - -tccttct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgctttg