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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctacattgaggataatgttgatcctaaagcataatcttgatattgttacttaaagtgatctttgaattttctttcccatgatgcgtttccattttgcagCTTGTAGGGACTGATCATTGTGCCTTCAATTCCACACAGAAAGCTTTTGGAATTGATGATTTCCGAAAAATTCCTAATGGTGTCAATG

Basic information

species Vitis vinifera
transcript Vv06s0009g02790.t01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0009g02790.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: LOC_Os01g59340.2 (Oryza sativa), 3'ss of exon 11
--------------------------------------------------------------------------tctacattg-aggataatgttgatcctaaagcataatcttgatattgttacttaa-agtgatctttgaat---tttctttcccatgatgcgtttccattttgcagCTTGTAGGGACTGATCATTGTGCCTTCAATTCCACACAGAAAGCTTTTGGAATTGATGATTTCCGAAAAATTCCTAATGGTGTCAATG
                                                                             | |||  |||       || |          ||  |  |  ||| ||      ||  | |||   ||   |  || ||  |     | |      | ||||||||||||| |||||||||||  ||||||| ||||||||||||||||| ||   |||||||||| |||| |||||||||||||| ||||
gtgatacttttcataccctcagtttgacatcacggagttactttttcatcttagctaatatttggaggtcagttagcaaattataggggcgcactgtttgcttgcagaaacttataccttgctaaggggtagaaaacttcacatggatgactatctaactgctcttcatttctatgcagCTTGTAGGAACTGATCATTGCACCTTCAACTCCACACAGAAAGCTTTCGGCTCTGATGATTTCAGAAAGATTCCTAATGGTGTTAATG

upper sequence: Vv06s0009g02790.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GRMZM2G020002_T03 (Zea mays), 3'ss of exon 8
tctacattgaggataatgttgatcctaaagcataatcttgatattgttacttaaagtg-atctttga-attttctttcccatgatgcgtttccattttgcagCTTGTAGGGACTGATCATTGTGCCTTCAATTCCACACAGAAAGCTTTTGGAATTGATGATTTCCGAAAAATTCCTAATGGTGTCAATG
  |  ||||  || |       |   |   | |  | | || |  |  |||||   || || ||| | | || | |   ||     |  | |  | |||||||||||||| |||||||| ||  | ||||| ||||||||||||||||||||   ||||||||| || || ||||| |||||||| ||||
--ttaattgctgagaggcaatgttacattacctgctatggagaaggaaacttatgttgcatttttcatagttacataaacacctaactgtactttgttgcagCTTGTAGGTACTGATCACTGCACATTCAACTCCACACAGAAAGCTTTTGGTTCTGATGATTTTCGGAAGATTCCCAATGGTGTAAATG

upper sequence: Vv06s0009g02790.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA15G06100.1 (Glycine max), 3'ss of exon 8
----tctacattgaggataatgttg-atccta-aagcataatcttgatattgttacttaaagtgatctttgaattttctttcccatgatgcgtttccattttgcagCTTGTAGGGACTGATCATTGTGCCTTCAATTCCACACAGAAAGCTTTTGGAATTGATGATTTCCGAAAAATTCCTAATGGTGTCAATG
    |||    |  | || || |   | |||    ||  |||       || ||||| | | ||||  ||  |       | || |      || | |  || ||||| ||||| ||||||||||||||||| |||||||| ||||||||| ||||||||||||| ||||| ||||||||||||||||||||||
tgtttctgagctctgtattatctaataccctgtgtgctcaattaattcttttttactaagactgattatttgaccaagggtaccgt------ttacaacctttcagCTGGTAGGAACTGATCATTGTGCCTTTAATTCCACCCAGAAAGCTCTTGGAATTGATGACTTCCGGAAAATTCCTAATGGTGTCAATG

upper sequence: Vv06s0009g02790.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA08G18920.1 (Glycine max), 3'ss of exon 9
tctacattgaggataatgttgatcctaaagcataatcttgatattgttacttaaagtgatctttgaattttctttcccatgatgcgttt--ccattttgcagCTTGTAGGGACTGATCATTGTGCCTTCAATTCCACACAGAAAGCTTTTGGAATTGATGATTTCCGAAAAATTCCTAATGGTGTCAATG
| |  |||    |    ||     |||| ||    |  | |  |  ||  ||  | | |   |   ||| | |  || | | | | |||  | | ||||||||| ||||| |||||||  |||||||| |||||||| ||||||||| ||||||||||||| ||||  ||||||||||||||||||||||
tatgtattatctaatgagtaatgactaatgccctgtgctcaattaattctttttactaagact--gattatttgaccaagggtaccttttacaactttgcagCTGGTAGGAACTGATCGGTGTGCCTTTAATTCCACCCAGAAAGCTCTTGGAATTGATGACTTCCAGAAAATTCCTAATGGTGTCAATG

upper sequence: Vv06s0009g02790.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA14G04030.1 (Glycine max), 3'ss of exon 8
---------------------------------------------------tctacattg---aggataatgttgatcctaaagcataatcttgatattgtt----acttaaagtgatc--tttgaattttctttcccat----------gatgcgtttcc--attttgcagCTTGTAGGGACTGATCATTGTGCCTTCAATTCCACACAGAAAGCTTTTGGAATTGATGATTTCCGAAAAATTCCTAATGGTGTCAATG
                                                   | |   ||    |||||| | |      | ||  | |  ||| |   |        || ||  | ||   ||| | ||  |||    ||          ||| | |||    | ||||||||| ||||| ||||||||||||||||| |||||||| || ||||||  |||||| ||||| ||||| ||||| ||||||||||||||||
gtttcacattatgattcaggcttaggttcaataaccaattaaagatgagggtttgagtttctcaggatagtctcagctatgaaatacacccttcaagcttccctcagctcaattttattcgttttacttagcttgtttatttgaccaaaggatacctttttgaaatttgcagCTGGTAGGAACTGATCATTGTGCCTTTAATTCCACCCAAAAAGCTCGTGGAATCGATGACTTCCGGAAAATGCCTAATGGTGTCAATG

upper sequence: Vv06s0009g02790.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA02G44690.1 (Glycine max), 3'ss of exon 8
tctacattgaggataatgttgatcctaaagcataatcttgatattgttacttaaagtgatctttgaattttctttcccatgatgcgtttccat-tttgcagCTTGTAGGGACTGATCATTGTGCCTTCAATTCCACACAGAAAGCTTTTGGAATTGATGATTTCCGAAAAATTCCTAATGGTGTCAATG
     |||   ||| |   |   |  |  |  | | ||  || || ||  ||  | | |  || |  | ||    |  | ||| | |||  |  ||||||||| ||||| ||||||||||||||||| |||||||| || ||||||  |||||| ||||| ||||| ||||| ||||||||||||||||
caattatttctgatcaatattccctcagcggctcagctcaattttattggttttacttagatt-gtttatttgaccaaaggataccttttaaaatttgcagCTGGTAGGAACTGATCATTGTGCCTTTAATTCCACCCAAAAAGCTCGTGGAATCGATGACTTCCGTAAAATGCCTAATGGTGTCAATG

upper sequence: Vv06s0009g02790.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: AT5G12200.1 (Arabidopsis thaliana), 3'ss of exon 8
-------tctacattgaggataatgttgatcctaaagcataatct-tgatattgttac-ttaaagtgatctttg-aattttctttcccatgatgcgtttccattttgcagCTTGTAGGGACTGATCATTGTGCCTTCAATTCCACACAGAAAGCTTTTGGAATTGATGATTTCCGAAAAATTCCTAATGGTGTCAATG
       ||  |  || | ||||  | ||   |   |||| | || |   ||    |  ||||  |  |||    |  ||| | |||  | ||  |  |    | ||||||||||||| |||||||| ||  | |||||||| ||||| |||||| | ||| ||||||||||||| | ||| ||||||||||| ||||
gtttctttcctcgctgtgcataaactagagaatt--gcatgacctgtagcatcaaaatgttaagatcttctaaacacctttttctccttttattgggataatctctgcagCTTGTAGGAACTGATCACTGCACTTTCAATTCTACACAAAAAGCTCTAGGACTTGATGATTTCCGCAGAATACCTAATGGTGTTAATG

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|30137635|gb|CB922973.1|CB922973
EST:     TGGGACATGACAAGGCCCTTCAAGCTGCTCTTTCAACTGGAAATCTGCAG                         CTTGTAGGGACTGATCATTGTGCCTTCAATTCCACACAGAAAGCTTTTGGA
genomic: TGGGACATGACAAGGCCCTTCAAGCTGCTCTTTCAACTGGAAATCTGCAGgttttttctc ... cattttgcagCTTGTAGGGACTGATCATTGTGCCTTCAATTCCACACAGAAAGCTTTTGGA
EST: gi|30131395|gb|CB916734.1|CB916734
EST:     TGGGACATGACAAGGCCCTTCAAGCTGCTCTTTCAACTGGAAATCTGCAG                         CTTGTAGGGACTGATCATTGTGCCTTCAATTCCACACAGAAAGCTTTTGGA
genomic: TGGGACATGACAAGGCCCTTCAAGCTGCTCTTTCAACTGGAAATCTGCAGgttttttctc ... cattttgcagCTTGTAGGGACTGATCATTGTGCCTTCAATTCCACACAGAAAGCTTTTGGA
EST: gi|30295952|gb|CB972746.1|CB972746
EST:     TGGGACATGACAAGGCCCTTCAAGCTGCTCTTTCAACTGGAAATCTGCAG                         CTTGTAGGGACTGATCATTGTGCCTTCAATTCCACACAGAAAGCTTTTGGA
genomic: TGGGACATGACAAGGCCCTTCAAGCTGCTCTTTCAACTGGAAATCTGCAGgttttttctc ... cattttgcagCTTGTAGGGACTGATCATTGTGCCTTCAATTCCACACAGAAAGCTTTTGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttacttaaagtgatctttgaattttctttcccatgatgcgtttccattttgcagCTTGTAGGGACTGATCATTGTGCCTTCAATTCCACACAGAAAGCTTTTGGAATTGATGATTTCCGAAAAATTCCTAATGGTGTCAATG
                                         tttccatttt  CT-rich tract
                tttgaattttcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tctacattgaggataatgttgatcctaaagcataatcttgatattgttacttaaagtgatctttgaattttctttcccatgatgcgtttccattttgcagCTTGTAGGGACTGATCATTGTGCCTTCAATTCCACACAGAAAGCTTTTGGAATTGATGATTTCCGAAAAATTCCTAATGGTGTCAATG

- - - - -aggataa
- - - - - - - - - - - - -taaagca
- - - - - - - - - - - - - - - - - - - - - - - - - - aaagtga