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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcttgctctttctctcacattgatgcacttaaatacaactcaagttactgtgttataaataaagatatatatttattaattcttaaattatgtgaaacagGTGGTGGAAGCATTCAAAATATTGACTGCTGATGATAAGGTCAAAGCAATTTTAGTGAACATTTTTGGAGGAATAATGAAATGTGACATAATAGCAAGTG

Basic information

species Vitis vinifera
transcript Vv07s0005g03790.t01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv07s0005g03790.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: LOC_Os02g40830.1 (Oryza sativa), 3'ss of exon 9
tcttgctctttctctcacattgatgcacttaaatacaactcaagttac-tgtgttataaataaagatata--tatttattaa-ttcttaaattatgtgaaa-cagGTGGTGGAAGCATTCAAAATATTGACTGCTGATGATAAGGTCAAAGCAATTTTAGTGAACATTTTTGGAGGAATAATGAAATGTGACATAATAGCAAGTG
      ||| | | |   | |      || || |   | |    ||     ||||||   |     | |    |||||| || || ||| || |  || |  ||||| ||||||||||| || || |||||| | |||||||  || || || ||| |||||||||||||||| || || |||||||||||  | ||||||||||
----aatctgtttgttggaatc-catgctaaattgttattttgtttttgcatgttatgcttcccagtttggtcatttataaactttttatataacttgtattcagGTTGTGGAAGCATTTAAGATTTTGACTTCCGATGATAGAGTGAAGGCTATTCTAGTGAACATTTTTGGTGGTATCATGAAATGTGATGTGATAGCAAGTG

upper sequence: Vv07s0005g03790.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GRMZM2G064695_T01 (Zea mays), 3'ss of exon 9
--------------------------------------------tcttgctctttctctcacattgatgcacttaaatacaactcaagttactgtgttataaataaagatat-----atatttattaattcttaaa----ttatgtgaaacagGTGGTGGAAGCATTCAAAATATTGACTGCTGATGATAAGGTCAAAGCAATTTTAGTGAACATTTTTGGAGGAATAATGAAATGTGACATAATAGCAAGTG
                                            |||   ||  | |   ||  ||| ||  ||    |||    |  ||| | ||    |     | ||       | | |  |||  |  ||||     |||   |  ||||| |||||||| || || ||| ||||| | |||||||  || || |||||| |||||||||||||||| || || |||||||||||  | ||||||||||
gtataaattggttgccgttttagcgttacttgaatgtttgaccttctctatccatgttaaaccctgacgccattttg-acattgtagcttaatttgccgcaggcgcatatgcctttgacagtgcttatcttgtaaaatttctattctatccagGTTGTGGAAGCTTTTAAGATACTGACTTCAGATGATAGAGTGAAGGCAATTCTAGTGAACATTTTTGGTGGCATTATGAAATGTGATGTGATAGCAAGTG

upper sequence: Vv07s0005g03790.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA13G18730.1 (Glycine max), 3'ss of exon 9
tcttgctctttctctcacattgatgcacttaaatacaactcaagttact--gtgttataaataaagatatatatttattaattcttaa----attatgtgaaacagGTGGTGGAAGCATTCAAAATATTGACTGCTGATGATAAGGTCAAAGCAATTTTAGTGAACATTTTTGGAGGAATAATGAAATGTGACATAATAGCAAGTG
         || | | | |||  | |  |||  |    ||  | |   |   || | || ||      || | ||| || |   ||||    ||||||| || |||||||| || ||||| |||||||||||||||||||| || || || |||||||| || ||||||||||| || |||||||| |||||  | ||||||||||
-----aagattatattaaattttt-cttttagtttttgctagattccttcaatgatctacatgttatgatgtttttgttcacatttaatgcaattatgtaaatcagGTGGTTGAGGCATTTAAAATATTGACTGCTGATGACAAAGTGAAGGCAATTTTGGTTAACATTTTTGGGGGTATAATGAAGTGTGATGTTATAGCAAGTG

upper sequence: Vv07s0005g03790.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA10G04480.1 (Glycine max), 3'ss of exon 9
tcttgctctttctctcacattgatgcacttaaatacaactcaagttactgtgttataaataaagatatatatttattaattcttaa----attatgtgaaacagGTGGTGGAAGCATTCAAAATATTGACTGCTGATGATAAGGTCAAAGCAATTTTAGTGAACATTTTTGGAGGAATAATGAAATGTGACATAATAGCAAGTG
    | |  |  |   | | |  |  | ||   | | |   |  ||    |||| |  ||      || | ||| || ||  ||||    ||||||| || ||||| || || ||||| |||||||||||||||||||| || || || |||||||| || ||||||||||| || |||||||| |||||  | ||||||||||
---agattatattaaaaaaattgtatagttttttcctagatacctt-taatgttctccatgttatgatgtttttgttcatatttaatgcaattatgtaaatcagGTTGTTGAGGCATTTAAAATATTGACTGCTGATGACAAAGTGAAGGCAATTTTGGTTAACATTTTTGGTGGTATAATGAAGTGTGATGTTATAGCAAGTG

upper sequence: Vv07s0005g03790.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: AT2G20420.1 (Arabidopsis thaliana), 3'ss of exon 9
tcttgctctttctctcacattgatgcacttaaatacaactcaagttactgtgttataaataaagatatatatttattaattcttaaattatgtgaaacagGTGGTGGAAGCATTCAAAATATTGACTGCTGATGATAAGGTCAAAGCAATTTTAGTGAACATTTTTGGAGGAATAATGAAATGTGACATAATAGCAAGTG
              | | |   |    |||   | |  | |   |     |  |   ||| || |   || || ||  |   ||   | |    | | ||||||||||||| || || ||| ||||  | || ||||| || |||||||| || |||||||| ||||| || ||||||||||||||  | || || ||||
-------------gtaaaaggaaccttctttctttcttcacttttgggaatcattggaatgaaaaccaattttaatagaggtttgtgtcaaaaaata-agGTGGTGGAAGCGTTTAAGATACTGACATCGGACGATAAAGTGAAAGCAATCTTGGTGAACATATTTGGTGGGATAATGAAATGTGATGTGATTGCTAGTG

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|32458077|gb|CD799251.1|CD799251
EST:     AATTTTCTAGATGTTGGAGGGAATGCTTCTGAAAGTCAG                         GTGGTGGAAGCACATTCAAAATATTGACTGCTGATGATAAGGTCAAAGCAA
genomic: AATTTTCTAGATGTTGGAGGAAATGCTTCTGAAAGTCAGgtaatgcgaa ... tgtgaaacagGTGGTGGAAG--CATTCAAAATATTGACTGCTGATGATAAGGTCAAAGCAA
EST: gi|34545859|gb|CF514091.1|CF514091
EST:     GAACTCCTGCCAATTTTCTAGATGTTGGAGGAAATGCTTCTGAAAGTCAG                         GTGGTGGAAGCATTCAAAATATTGACTGCTGATGATAAGGTCAAAGCAATT
genomic: GAACTCCTGCCAATTTTCTAGATGTTGGAGGAAATGCTTCTGAAAGTCAGgtaatgcgaa ... tgtgaaacagGTGGTGGAAGCATTCAAAATATTGACTGCTGATGATAAGGTCAAAGCAATT
EST: gi|34545781|gb|CF514013.1|CF514013
EST:     GAACTCCTGCCAATTTTCTAGATGTTGGAGGAAATGCTTCTGAAAGTCAG                         GTGGTGGAAGCATTCAAAATATTGACTGCTGATGATAAGGTCAAAGCAATT
genomic: GAACTCCTGCCAATTTTCTAGATGTTGGAGGAAATGCTTCTGAAAGTCAGgtaatgcgaa ... tgtgaaacagGTGGTGGAAGCATTCAAAATATTGACTGCTGATGATAAGGTCAAAGCAATT
EST: gi|71881691|gb|DT030746.1|DT030746
EST:     GAACTCCTGCCAATTTTCTAGATGTTGGAGGAAATGCTTCTGAAAGTCAG                         GTGGTGGAAGCATTCAAAATATTGACTGCTGATGATAAGGTCAAAGCAATT
genomic: GAACTCCTGCCAATTTTCTAGATGTTGGAGGAAATGCTTCTGAAAGTCAGgtaatgcgaa ... tgtgaaacagGTGGTGGAAGCATTCAAAATATTGACTGCTGATGATAAGGTCAAAGCAATT
EST: gi|110379096|gb|EC944270.1|EC944270
EST:     GAACTCCTGCCAATTTTCTAGATGTTGGAGGAAATGCTTCTGAAAGTCAG                         GTGGTGGAAGCATTCAAAATATTGACTGCTGATGATAAGGTCAAAGCAATT
genomic: GAACTCCTGCCAATTTTCTAGATGTTGGAGGAAATGCTTCTGAAAGTCAGgtaatgcgaa ... tgtgaaacagGTGGTGGAAGCATTCAAAATATTGACTGCTGATGATAAGGTCAAAGCAATT
EST: gi|30255821|gb|CB971953.1|CB971953
EST:     GAACTCCTGCCAATTTTCTAGATGTTGGAGGAAATGCTTCTGAAAGTCAG                         GTGGTGGAAGCATTCAAAATATTGACTGCTGATGATAAGGTCAAAGCAATT
genomic: GAACTCCTGCCAATTTTCTAGATGTTGGAGGAAATGCTTCTGAAAGTCAGgtaatgcgaa ... tgtgaaacagGTGGTGGAAGCATTCAAAATATTGACTGCTGATGATAAGGTCAAAGCAATT
EST: gi|110390462|gb|EC955371.1|EC955371
EST:     GAACTCCTGCCAATTTTCTAGATGTTGGAGGAAATGCTTCTGAAAGTCAG                         GTGGTGGAAGCATTCAAAATATTGACTGCTGATGATAAGGTCAAAGCAATT
genomic: GAACTCCTGCCAATTTTCTAGATGTTGGAGGAAATGCTTCTGAAAGTCAGgtaatgcgaa ... tgtgaaacagGTGGTGGAAGCATTCAAAATATTGACTGCTGATGATAAGGTCAAAGCAATT
EST: gi|110428351|gb|EC994820.1|EC994820
EST:     GAACTCCTGCCAATTTTCTAGATGTTGGAGGAAATGCTTCTGAAAGTCAG                         GTGGTGGAAGCATTCAAAATATTGACTGCTGATGATAAGGTCAAAGCAATT
genomic: GAACTCCTGCCAATTTTCTAGATGTTGGAGGAAATGCTTCTGAAAGTCAGgtaatgcgaa ... tgtgaaacagGTGGTGGAAGCATTCAAAATATTGACTGCTGATGATAAGGTCAAAGCAATT
EST: gi|110688710|gb|EE067574.1|EE067574
EST:     GAACTCCTGCCAATTTTCTAGATGTTGGAGGAAATGCTTCTGAAAGTCAG                         GTGGTGGAAGCATTCAAA
genomic: GAACTCCTGCCAATTTTCTAGATGTTGGAGGAAATGCTTCTGAAAGTCAGgtaatgcgaa ... tgtgaaacagGTGGTGGAAGCATTCAAA
EST: gi|110702283|gb|EE080823.1|EE080823
EST:     GAACTCCTGCCAATTTTCTAGATGTTGGAGGAAATGCTTCTGAAAGTCAG                         GTGGTGGAAGCATTCAAAATATTGACTGCTGATGATAAGGTCAAAGCAATT
genomic: GAACTCCTGCCAATTTTCTAGATGTTGGAGGAAATGCTTCTGAAAGTCAGgtaatgcgaa ... tgtgaaacagGTGGTGGAAGCATTCAAAATATTGACTGCTGATGATAAGGTCAAAGCAATT
EST: gi|22007633|gb|BQ792667.1|BQ792667
EST:     GAACTCCTGCCAATTTTTTAGATGTTGGAGGAAATGCTTTTGAAAGTCAG                         GTGGTGGAAGCATTCAAAATATTGACTGCTGATGATAAGGTCAAAGCAATT
genomic: GAACTCCTGCCAATTTTCTAGATGTTGGAGGAAATGCTTCTGAAAGTCAGgtaatgcgaa ... tgtgaaacagGTGGTGGAAGCATTCAAAATATTGACTGCTGATGATAAGGTCAAAGCAATT
EST: gi|30256178|gb|CB972021.1|CB972021
EST:     GAACTCCTGCCAATTTTCTAGATGTTGGAGGAAATGCTTCTGAAAGTCAG                         GTGGTGGAAGCATTCAAAATATTGACTGCTGATGATAAGGTCAAAGCAATT
genomic: GAACTCCTGCCAATTTTCTAGATGTTGGAGGAAATGCTTCTGAAAGTCAGgtaatgcgaa ... tgtgaaacagGTGGTGGAAGCATTCAAAATATTGACTGCTGATGATAAGGTCAAAGCAATT
EST: gi|71883833|gb|DT032888.1|DT032888
EST:     GAACTCCTGCCAATTTTCTAGATGTTGGAGGAAATGCTTCTGAAAGTCAG                         GTGGTGGAAGCATTCAAAATATTGACTGCTGATGATAAGGTCAAAGCAATT
genomic: GAACTCCTGCCAATTTTCTAGATGTTGGAGGAAATGCTTCTGAAAGTCAGgtaatgcgaa ... tgtgaaacagGTGGTGGAAGCATTCAAAATATTGACTGCTGATGATAAGGTCAAAGCAATT
EST: gi|30256398|gb|CB972241.1|CB972241
EST:     GAACTCCTGCCAATTTTCTAGATGTTGGAGGAAATGCTTCTGAAAGTCAG                         GTGGTGGAAGCATTCAAAATATTGACTGCTGATGATAAGGTCAAAGCAATT
genomic: GAACTCCTGCCAATTTTCTAGATGTTGGAGGAAATGCTTCTGAAAGTCAGgtaatgcgaa ... tgtgaaacagGTGGTGGAAGCATTCAAAATATTGACTGCTGATGATAAGGTCAAAGCAATT
EST: gi|110714835|gb|EE092196.1|EE092196
EST:     GAACTCCTGCCAATTTTCTAGATGTTGGAGGAAATGCTTCTGAAAGTCAG                         GTGGTGGAAGCATTCAAAATATTGACTGCTGATGATAAGGTCAAAGCAATT
genomic: GAACTCCTGCCAATTTTCTAGATGTTGGAGGAAATGCTTCTGAAAGTCAGgtaatgcgaa ... tgtgaaacagGTGGTGGAAGCATTCAAAATATTGACTGCTGATGATAAGGTCAAAGCAATT
EST: gi|30305949|gb|CB982743.1|CB982743
EST:     GAACTCCTGCCAATTTTCTAGATGTTGGAGGAAATGCTTCTGAAAGTCAG                         GTGGTGGAAGCATTCAAAATATTGACTGCTGATGATAAGGTCAAAGCAATT
genomic: GAACTCCTGCCAATTTTCTAGATGTTGGAGGAAATGCTTCTGAAAGTCAGgtaatgcgaa ... tgtgaaacagGTGGTGGAAGCATTCAAAATATTGACTGCTGATGATAAGGTCAAAGCAATT
EST: gi|110362830|gb|EC926386.1|EC926386
EST:     GAACTCCTGCCAATTTTCTAGATGTTGGAGGAAATGCTTCTGAAAGTCAG                         GTGGTGGAAGCATTCAAAATATTGACTGCTGATGATAAGGTCAAAGCAATT
genomic: GAACTCCTGCCAATTTTCTAGATGTTGGAGGAAATGCTTCTGAAAGTCAGgtaatgcgaa ... tgtgaaacagGTGGTGGAAGCATTCAAAATATTGACTGCTGATGATAAGGTCAAAGCAATT
EST: gi|30256478|gb|CB972321.1|CB972321
EST:     GAACTCCTGCCAATTTTCTAGATGTTGGAGGAAATGCTTCTGAAAGTCAG                         GTGGTGGAAGCATTCAAAATATTGACTGCTGATGATAAGGTCAAAGCAATT
genomic: GAACTCCTGCCAATTTTCTAGATGTTGGAGGAAATGCTTCTGAAAGTCAGgtaatgcgaa ... tgtgaaacagGTGGTGGAAGCATTCAAAATATTGACTGCTGATGATAAGGTCAAAGCAATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tactgtgttataaataaagatatatatttattaattcttaaattatgtgaaacagGTGGTGGAAGCATTCAAAATATTGACTGCTGATGATAAGGTCAAAGCAATTTTAGTGAACATTTTTGGAGGAATAATGAAATGTGACATAATAGCAAGTG
                            tattaat  putative branch site (score: 2)
       ttataaataaagatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcttgctctttctctcacattgatgcacttaaatacaactcaagttactgtgttataaataaagatatatatttattaattcttaaattatgtgaaacagGTGGTGGAAGCATTCAAAATATTGACTGCTGATGATAAGGTCAAAGCAATTTTAGTGAACATTTTTGGAGGAATAATGAAATGTGACATAATAGCAAGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
-cttgctc
- - - - - -ctctcac
- - - - - - - - - - -gatgcac
- - - - - - - - - - - - - - - - - -caactca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - aaataaa