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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTCAAAGTGATCATTTTGAGGAATTTTTTGCCCCAGAGCTGGACAAACATGGATATCAAGCACTTTACAAGAGAAAAACAAACGAGgtacatgatgaatttctttgcattatgatagtagcttctgaaattctgtatgttattaatcctttgatcttgttgactttttgcag

Basic information

species Vitis vinifera
transcript Vv08s0007g07020.t01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0007g07020.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: LOC_Os03g07080.3 (Oryza sativa), 5'ss of exon 4
ATTCAAAGTGATCATTTTGAGGAATTTTTTGCCCCAGAGCTGGACAAACATGGATATCAAGCACTTTACAAGAGAAAAACAAACGAGgtacatgatgaatttc---tttgcattatgatagtagcttctgaaattctgtatgttattaatcctttgatcttgttgactttttgcag--------------
 | |||||| | || ||||| ||||| ||||| || ||||| ||||||||||||||||| ||||| | ||||| ||  ||||  ||||||     |  ||||     ||| || |  |   | || |   |  || | |   ||  ||||  ||   |  ||     ||| ||||               
GTACAAAGTAACCACTTTGAAGAATTCTTTGCACCGGAGCTTGACAAACATGGATATCAGGCACTGTTCAAGAAAAGGACAACTGAGgtatgccttttattttgtggttggataaacaacttggcatactattttgtttgacttcgtaattattgcttgatgcgttgtttgtgcatcaattatgtaatag

upper sequence: Vv08s0007g07020.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: LOC_Os10g27230.1 (Oryza sativa), 5'ss of exon 4
ATTCAAAGTGATCATTTTGAGGAATTTTTTGCCCCAGAGCTGGACAAACATGGATATCAAGCACTTTACAAGAGAAAAACAAACGAGgtacat---gatgaatttctttgcattatgatagtagcttctgaaattctgtatgttattaatcctttgatcttgttgactttttgcag
 | |||    | || || || || |||||| | || ||||| || |||||||||||||| ||||||||||||| ||  ||||  |||||| ||     || || |  ||  ||||| |||     || |    |||  | | |||||      |   || ||||     |||  ||
GTGCAACTGAACCACTTCGAAGATTTTTTTTCACCCGAGCTTGATAAACATGGATATCAGGCACTTTACAAGAAAAGGACAACAGAGgtatatttgactgcatctggttctattataatacgcatttatacgcttcaatttcttatttgattctgcttcatgtt-----tttaaag

upper sequence: Vv08s0007g07020.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GRMZM2G118467_T03 (Zea mays), 5'ss of exon 4
ATTCAAAGTGATCATTTTGAGGAATTTTTTGCCCCAGAGCTGGACAAACATGGATATCAAGCACTTTACAAGAGAAAAACAAACGAGgtacatgatgaatttctttgcattatgatagtagcttctgaaattctgtatgttattaatcctttgatcttgttgactttttgcag---
 | |||    | ||||| || || |||||| | || ||||| ||||||||||||||||| || |||||||||| ||  ||||  |||||| |   ||| || ||||  | |  | || ||   | ||  ||  | |    |  ||    ||||||  || |   || |||      
GTACAAGTAAACCATTTCGAAGATTTTTTTTCACCTGAGCTTGACAAACATGGATATCAGGCGCTTTACAAGAAAAGGACAACAGAGgta-actttgagttgcttt-tacttggctaatatgatttggtatcttttgctgtccta----tttgatactgctcctttgttgtcacag

upper sequence: Vv08s0007g07020.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA09G15980.2 (Glycine max), 5'ss of exon 3
ATTCAAAGTGATCATTTTGAGGAATTTTTTGCCCCAGAGCTGGACAAACATGGATATCAAGCACTTTACAAGAGAAAAACAAACGAGgtacatgatgaatttctttgcattatgatagtagcttctgaaattctgtatgttattaatcctttgatcttgttgactttttgcag
 ||||||| ||||||| ||| ||||| ||| | || || || ||||||||||||||||| |  |||||||||||||||||||| |||||   |    |  ||||   | || ||||  ||   | | ||| | | |  | |  ||| |  || ||  ||  |  ||   |   
GTTCAAAGCGATCATTATGACGAATTCTTTTCTCCTGAACTAGACAAACATGGATATCATGGTCTTTACAAGAGAAAAACAAATGAGgt-tgttgcaatattctggtccttgtgatcataaacttttaaagtattttagatgctaacctgtttattatg--ggtttacag---

upper sequence: Vv08s0007g07020.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA03G36550.1 (Glycine max), 5'ss of exon 3
ATTCAAAGTGATCATTTTGAGGAATTTTTTGCCCCAGAGCTGGACAAACATGGATATCAAGCACTTTACAAGAGAAAAACAAACGAGgtacatgatgaatttctttgcattatgatagtagcttctgaaattctgtatgttattaatcct-ttgatc---ttgttgactttttgcag
 ||||||||||||||| ||| ||||||||| | || || |||||||||||||| ||| | |  |||||||| |  |||||||| |||||   |   | |||    |  |||||  |  |||  ||  || || |  ||||||||  |  | || | |   || | |    ||  |||
GTTCAAAGTGATCATTATGAAGAATTTTTTTCTCCTGAACTGGACAAACATGGTTATTATGGTCTTTACAAAAAGAAAACAAATGAGgttgttacagtattcagatttattatagttttagtctcataatttttaaatgttattttttttgttaagcggtttatggtgggttcacag

upper sequence: Vv08s0007g07020.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA02G26620.1 (Glycine max), 5'ss of exon 3
ATTCAAAGTGATCATTTTGAGGAATTTTTTGCCCCAGAGCTGGACAAACATGGATATCAAGCACTTTACAAGAGAAAAACAAACGAGgtacatgatgaatttctttgcattatgatagtagcttctgaaattctgtatgttattaatcctttgatcttgttgactttttgcag
 ||||||| ||||||| ||| ||||||||| | || ||  | ||||||||||||||| | |  |||||||||||||||      |||||   |    |  ||||     || ||||  ||   | | ||| | |    | |  ||| |  || ||  ||| |  ||    |||
GTTCAAAGCGATCATTATGACGAATTTTTTTCTCCCGAATTAGACAAACATGGATATTATGGTCTTTACAAGAGAAAA------GAGgt-tgttgcaatattctggttcttgtgatcataaactttaaaaatattctagatggtaacctgtttat--tgtgggtttacaacag

upper sequence: Vv08s0007g07020.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: AT3G58580.1 (Arabidopsis thaliana), 5'ss of exon 3
ATTCAAAGTGATCATTTTGAGGAATTTTTTGCCCCAGAGCTGGACAAACATGGATATCAAGCACTTTACAAGAGAAAAACAAACGAGgtacatgatgaatttctttgcattatgatagtagcttctgaaattctgtatgttattaatcctttgatcttgttgactttttgcag----
 | ||||||||||||||  | ||| ||||||| || ||| |||| || ||||| |||||||| ||||||||||| || || || |||||   || | |||   |   ||       | |   | ||  | |  | |||||| | ||  || | | |      | || |||  |    
GTACAAAGTGATCATTTCCATGAAATTTTTGCTCCTGAGTTGGATAAGCATGGGTATCAAGCTCTTTACAAGAGGAAGACTAATGAGgtt--tggtcaatgattccacac------actccttccttcagtgatttatgttttaaaatctattaacc-acaaatttcttgttgctag

upper sequence: Vv08s0007g07020.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: AT3G58560.1 (Arabidopsis thaliana), 5'ss of exon 3
ATTCAAAGTGATCATTTTGAGGAATTTTTTGCCCCAGAGCTGGACAAACATGGATATCAAGCACTTTACAAGAGAAAAACAAACGAGgtacat---gatgaatttctttgcattatgatagtagcttc-tgaaattctgtatgtta---ttaatcctttgatcttgttgactttttgcag--------
 | || | ||||||||||||||| ||||||   || |||||||| ||||| ||||| ||||  ||||  ||||| |||||||| |||||        | | ||  | |||   |   ||      ||| ||      | | ||  |    ||       ||   | |||| |   || |         
GTACAGAATGATCATTTTGAGGAGTTTTTTCTTCCTGAGCTGGATAAACACGGATACCAAGGTCTTTTTAAGAGGAAAACAAATGAGgtttgcttcaacgcatccccttgatcttccattaccttttcgtggtcacttatctgcaagatgtaccaaccagaaaatattgattcactggataattttag

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|349808434|gb|FQ405578.1|FQ405578
EST:     CAAGCACTTTACAAGAGAAAAACAAACGAG                         GTTTACACTGGTAATATCCATACAATTGATGGTTGTGCAACATTTTTTCGC
genomic: CAAGCACTTTACAAGAGAAAAACAAACGAGgtacatgatg ... ctttttgcagGTTTACACTGGTAATATCCATACAATTGATGGTTGTGCAACATTTTTTCGC
EST: gi|351051864|gb|FQ455278.1|FQ455278
EST:     CAAACATGGATATCAAGCACTTTACAAGAGAAAAACAAACGAG                         GTTTACACTGGTAATATCCATACAATTGATGGTTGTGCAACATTTTTTCGC
genomic: CAAACATGGATATCAAGCACTTTACAAGAGAAAAACAAACGAGgtacatgatg ... ctttttgcagGTTTACACTGGTAATATCCATACAATTGATGGTTGTGCAACATTTTTTCGC
EST: gi|351052763|gb|FQ456490.1|FQ456490
EST:     CAAACATGGATATCAAGCACTTTACAAGAGAAAAACAAACGAG                         GTTTACACTGGTAATATCCATACAATTGATGGTTGTGCAACATTTTTTCGC
genomic: CAAACATGGATATCAAGCACTTTACAAGAGAAAAACAAACGAGgtacatgatg ... ctttttgcagGTTTACACTGGTAATATCCATACAATTGATGGTTGTGCAACATTTTTTCGC
EST: gi|294965969|gb|GW839308.1|GW839308
EST:     AGCTGGACAAACATGGATATCAAGCACTTTACAAGAGAAAAACAAACGAG                         GTTTACACTGGTAATATCCATACAATTGATGGTTGTGCAACATTTTTTCGC
genomic: AGCTGGACAAACATGGATATCAAGCACTTTACAAGAGAAAAACAAACGAGgtacatgatg ... ctttttgcagGTTTACACTGGTAATATCCATACAATTGATGGTTGTGCAACATTTTTTCGC
EST: gi|351044388|gb|FQ452940.1|FQ452940
EST:     CAAACATGGATATCCAGCACTTTACAAGAGAAAAACAAACGAG                         GTTTACACTGGTAATATCCATACAATTGATGGTTGTGCAACATTTTTTCGC
genomic: CAAACATGGATATCAAGCACTTTACAAGAGAAAAACAAACGAGgtacatgatg ... ctttttgcagGTTTACACTGGTAATATCCATACAATTGATGGTTGTGCAACATTTTTTCGC
EST: gi|351048297|gb|FQ449389.1|FQ449389
EST:     CAAACATGGATATCAAGCACTTTACAAGAGAAAAACAAACGAG                         GTTTACACTGGTAATATCCATACAATTGATGGTTGTGCAACATTTTTTCGC
genomic: CAAACATGGATATCAAGCACTTTACAAGAGAAAAACAAACGAGgtacatgatg ... ctttttgcagGTTTACACTGGTAATATCCATACAATTGATGGTTGTGCAACATTTTTTCGC
EST: gi|349810776|gb|FQ403019.1|FQ403019
EST:     CAAACATGGATATCAAGCACTTTACAAGAGAAAAACAAACGAG                         GTTTACACTGGTAATATCCATACAATTGATGGTTGTGCAACATTTTTTCGC
genomic: CAAACATGGATATCAAGCACTTTACAAGAGAAAAACAAACGAGgtacatgatg ... ctttttgcagGTTTACACTGGTAATATCCATACAATTGATGGTTGTGCAACATTTTTTCGC
EST: gi|351037882|gb|FQ465120.1|FQ465120
EST:     CAAACATGGATATCAAGCACTTTACAAGAGAAAAACAAACGAG                         GTTTACACTGGTAATATCCATACAATTGATGGTTGTGCAACATTTTTTCGC
genomic: CAAACATGGATATCAAGCACTTTACAAGAGAAAAACAAACGAGgtacatgatg ... ctttttgcagGTTTACACTGGTAATATCCATACAATTGATGGTTGTGCAACATTTTTTCGC
EST: gi|351054602|gb|FQ456799.1|FQ456799
EST:     CAAACATGGATATCAAGCACTTTACAAGAGAAAAACAAACGAG                         GTTTACACTGGTAATATCCATACAATTGATGGTTGTGCAACATTTTTTCGC
genomic: CAAACATGGATATCAAGCACTTTACAAGAGAAAAACAAACGAGgtacatgatg ... ctttttgcagGTTTACACTGGTAATATCCATACAATTGATGGTTGTGCAACATTTTTTCGC
EST: gi|349813262|gb|FQ411502.1|FQ411502
EST:     CAAACATGGATATCAAGCACTTTACAAGAGAAAAACAAACGAG                         GTTTACACTGGTAATATCCATACAATTGATGGTTGTGCAACATTTTTTCGC
genomic: CAAACATGGATATCAAGCACTTTACAAGAGAAAAACAAACGAGgtacatgatg ... ctttttgcagGTTTACACTGGTAATATCCATACAATTGATGGTTGTGCAACATTTTTTCGC
EST: gi|351039176|gb|FQ457851.1|FQ457851
EST:     CAAACATGGATATCAAGCACTTTACAAGAGAAAAACAAACGAG                         GTTTACACTGGTAATATCCATACAATTGATGGTTGTGCAACATTTTTTCGC
genomic: CAAACATGGATATCAAGCACTTTACAAGAGAAAAACAAACGAGgtacatgatg ... ctttttgcagGTTTACACTGGTAATATCCATACAATTGATGGTTGTGCAACATTTTTTCGC
EST: gi|351048422|gb|FQ448696.1|FQ448696
EST:     CAAACATGGATATCAAGCACTTTACAAGAGAAAAACAAACGAG                         GTTTACACTGGTAATATCCATACAATTGATGGTTGTGCAACATTTTTTCGC
genomic: CAAACATGGATATCAAGCACTTTACAAGAGAAAAACAAACGAGgtacatgatg ... ctttttgcagGTTTACACTGGTAATATCCATACAATTGATGGTTGTGCAACATTTTTTCGC
EST: gi|351047379|gb|FQ451891.1|FQ451891
EST:     CAAACATGGATATCAAGCACTTTACAAGAGAAAAACAAACGAG                         GTTTACACTGGTAATATCCATACAATTGATGGTTGTGCAACATTTTTTCGC
genomic: CAAACATGGATATCAAGCACTTTACAAGAGAAAAACAAACGAGgtacatgatg ... ctttttgcagGTTTACACTGGTAATATCCATACAATTGATGGTTGTGCAACATTTTTTCGC
EST: gi|349815100|gb|FQ410323.1|FQ410323
EST:     CAAACATGGATATCAAGCACTTTACAAGAGAAAAACAAACGAG                         GTTTACACTGGTAATATCCATACAATTGATGGTTGTGCAACATTTTTTCGC
genomic: CAAACATGGATATCAAGCACTTTACAAGAGAAAAACAAACGAGgtacatgatg ... ctttttgcagGTTTACACTGGTAATATCCATACAATTGATGGTTGTGCAACATTTTTTCGC
EST: gi|110697952|gb|EE075410.1|EE075410
EST:     AGCTGGACAAACATGGATATCAAGCACTTTACAAGAGAAAAACAAACGAG                         GTTTACACTGGTAATATCCATACAATTGATGGTTGTGCAACATTTTTTCGC
genomic: AGCTGGACAAACATGGATATCAAGCACTTTACAAGAGAAAAACAAACGAGgtacatgatg ... ctttttgcagGTTTACACTGGTAATATCCATACAATTGATGGTTGTGCAACATTTTTTCGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATTCAAAGTGATCATTTTGAGGAATTTTTTGCCCCAGAGCTGGACAAACATGGATATCAAGCACTTTACAAGAGAAAAACAAACGAGgtacatgatgaatttctttgcattatgatagtagcttctgaaattctgtatgttattaatcctttgatcttgttgactttttgcag

- - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA