Skip to another splice site:
1  
 5'  3'   
2  
 5'  3'   
3  
 5'  3'   
4  
 5'  3'   
5  
 5'  3'   
6  
 5'  3'   
7  
 5'  3'   
8  
 5'  3'   
9  
 5'  3'   
10  
 5'  3'   
11  
 5'  3'   
12  
 5'  3'   
13  
 5'  3'   
14  
 5'  3'   
15  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttgtttaaatcatttatctatttgtccgctcccacgtaaagagacatatttctgaacaccaactttatttaaagcttatttatttattttttttggcagTCAATGTGCAGTCATTATCTGGATCCCCTGCCAACTTTCAAGCTTACACGGCATTATTAAAACCTCATGAGAGAATCATGGCACTTGATCTTCCTCATGG

Basic information

species Vitis vinifera
transcript Vv18s0001g07960.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0001g07960.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os03g52840.2 (Oryza sativa), 3'ss of exon 5
-tttgtttaaatcatttatctatt-tgtccgctcccacgtaaagagacatatttctgaacaccaactttatttaaagcttatttatttattttt--tttggcagTCAATGTGCAGTCATTATCTGGATCCCCTGCCAACTTTCAAGCTTACACGGCATTATTAAAACCTCATGAGAGAATCATGGCACTTGATCTTCCTCATGG
| | |||||| ||||||| | || || || | ||||| | | ||| || ||| | |||| | | ||||| |||||||| | |||| || || ||||||||||| || | |||||| || |||| ||||| ||||||||||||||||| | ||||||||||||||
ttgtacttaaat---ttatctagaatacttattctcaaaattttagttttctttctccaaaaaggtggcattctaa-cttgacaaccaatttctacctctgcagTGAATGTGCAACCTCTATCAGGGTCACCTGCCAACTTCCATGTTTACACTGCCCTATTGAAACCACATGAGAGAATCATGGCTTTGGATCTTCCTCATGG

upper sequence: Vv18s0001g07960.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA02G38160.2 (Glycine max), 3'ss of exon 5
tttgtttaaatcatttatctat--ttgtccgctcccacgtaaagagacatatttctgaacaccaactttatttaaagcttatttatt-tattttttttggcagTCAATGTGCAGTCATTATCTGGATCCCCTGCCAACTTTCAAGCTTACACGGCATTATTAAAACCTCATGAGAGAATCATGGCACTTGATCTTCCTCATGG
||| | || || ||||| || ||| | | || | | ||| | || ||| | |||| || | | | | || | | |||||| ||||||||||||| |||||||||||||||||| | ||||| |||| |||||| || ||||| ||||||||||||||||| ||||||||||||||||| |||||
---gttcatatgtcttttctattattttcctccacaacttgggggaacaaaattttgagaatgtgctttcttggagaatcttatgttctctgctttttgacagTCAATGTGCAATCATTATCTGGATCCCCTTCTAACTTCCAAGTTTACACTGCTTTATTGAAACCTCATGAGAGAATTATGGCACTTGATCTTCCCCATGG

upper sequence: Vv18s0001g07960.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA14G36280.2 (Glycine max), 3'ss of exon 5
tttgtttaaatcatttatctat--ttgtccgctcccacgtaaagagacatatttctgaacaccaactttatttaaagcttatttatt-tattttttttggcagTCAATGTGCAGTCATTATCTGGATCCCCTGCCAACTTTCAAGCTTACACGGCATTATTAAAACCTCATGAGAGAATCATGGCACTTGATCTTCCTCATGG
||| | || || ||||| || ||| | | | | | ||| | || ||| | |||| || | | | | || | | ||||| ||||||||||||| |||||||||||||||||| | ||||| |||| |||||| || ||||| ||||||||||||||||| ||||||||||||||||| |||||
---gttcatatgtcttttctattattttcctccacagcttgggggaacaaaattttgataatgtgctttcttggagaatcttatgttctctgcattttgacagTCAATGTGCAATCATTATCTGGATCCCCTTCTAACTTCCAAGTTTACACTGCTTTATTGAAACCTCATGAGAGAATTATGGCACTTGATCTTCCCCATGG

upper sequence: Vv18s0001g07960.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT5G26780.1 (Arabidopsis thaliana), 3'ss of exon 5
tttgtttaaatcatttatctatttgtccgctcccacgtaaagagacatatttctgaacaccaactttatttaaagcttatttatttattttttttggcagTCAATGTGCAGTCATTATCTGGATCCCCTGCCAACTTTCAAGCTTACACGGCATTATTAAAACCTCATGAGAGAATCATGGCACTTGATCTTCCTCATGG
||| ||| | || | | | |||||| | | | || | ||||| |||| | | | | | || || ||||| ||||||||||||||| ||||| ||||| || || || || |||| |||||| ||||| || || |||||||| |||||||||||||||||| | ||||||||
-gtgtgctaattacatactttcgttgtgaattgtgattaaagaaa--tcctactagaaaccaaatttactaatgg---agacacttgttcattttg-tagTCAATGTGCAGTCTTTATCAGGATCACCAGCTAATTTCCAAGTTTACACTGCATTGTTGAAGCCTCATGAAAGAATCATGGCACTTGATTTACCTCATGG

upper sequence: Vv18s0001g07960.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: EFJ16660 (Selaginella moellendorffii), 3'ss of exon 5
tttgtttaaatcatttatctatttgtccgctcccacgtaaagagacatatttctgaacaccaactttatt-taaagcttatttatttattttttttggcagTCAATGTGCAGTCATTATCTGGATCCCCTGCCAACTTTCAAGCTTACACGGCATTATTAAAACCTCATGAGAGAATCATGGCACTTGATCTTCCTCATGG
|| | | | || | | ||||||| | | || |||| |||| |||| |||||||||||||||||||| || || || |||||||||| || || || || | ||||| || || ||||| ||||| |||||| | ||||| ||
----------------------------------------------gtacgttttatcagtggcgaaaggataaagctc--tgacttcttttctttg-cagTTAATGTGCAGTCATTATCTGGTTCTCCAGCAAACTTTCAAGTGTATACAGCTTTGCTTAAACCACACGAAAGAATTATGGCTCTTGATTTACCTCACGG

upper sequence: Vv18s0001g07960.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: EFJ32604 (Selaginella moellendorffii), 3'ss of exon 5
tttgtttaaatcatttatctatttgtccgctcccacgtaaagagacatatttctgaacaccaactttatt-taaagcttatttatttattttttttggcagTCAATGTGCAGTCATTATCTGGATCCCCTGCCAACTTTCAAGCTTACACGGCATTATTAAAACCTCATGAGAGAATCATGGCACTTGATCTTCCTCATGG
|| | | | || | | ||||||| | | || |||| |||| ||||||||||||||||||||||||| || || || |||||||||| || || || || | ||||| || || ||||| ||||| |||||| | ||||| ||
----------------------------------------------gtacgttttatcagtggcgaaaggataaagctc--tgacttcttttctttg-cagTCAATGTGCAGTCATTATCTGGTTCTCCAGCAAACTTTCAAGTGTATACAGCTTTGCTTAAACCACACGAAAGAATTATGGCTCTTGATTTACCTCACGG

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|352776821|gb|FQ472708.1|FQ472708
EST:     TCAGAAGCGTGCATTAGAAGCTTTCCAGTTGGACCCTGCAAAATGGGGAG                         TCAATGTGCAGTCATTATCTGGATCCCCTGCCAACTTTCAAGCTTACACGG
genomic: TCAGAAGCGTGCATTAGAAGCTTTCCAGTTGGACCCTGCAAAATGGGGAGgtaaacgaac ... tttttggcagTCAATGTGCAGTCATTATCTGGATCCCCTGCCAACTTTCAAGCTTACACGG
EST: gi|352795184|gb|FQ477294.1|FQ477294
EST:     TCAGAAGCGTGCATTAGAAGCTTTCCAGTTGGACCCTGCAAAATGGGGAG                         TCAATGTGCAGTCATTATCTGGATCCCCTGCCAACTTTCAAGCTTACACTG
genomic: TCAGAAGCGTGCATTAGAAGCTTTCCAGTTGGACCCTGCAAAATGGGGAGgtaaacgaac ... tttttggcagTCAATGTGCAGTCATTATCTGGATCCCCTGCCAACTTTCAAGCTTACACGG
EST: gi|71862434|gb|DT011489.1|DT011489
EST:     TCAGAAGCGTGCATTAGAAGCTTTCCAGTTGGACCCTGCAAAATGGGGAG                         TCAATGTGCAGTCATTATCTGGATCCCCTGCCAACTTTCAAGCTTACACTG
genomic: TCAGAAGCGTGCATTAGAAGCTTTCCAGTTGGACCCTGCAAAATGGGGAGgtaaacgaac ... tttttggcagTCAATGTGCAGTCATTATCTGGATCCCCTGCCAACTTTCAAGCTTACACGG
EST: gi|71855735|gb|DT004790.1|DT004790
EST:     TCAGAAGCGTGCATTAGAAGCTTTCCAGTTGGACCCTGCAAAATGGGGAG                         TCAATGTGCAGTCATTATCTGGATCCCCTGCCAACTTTCAAGCTTACACTG
genomic: TCAGAAGCGTGCATTAGAAGCTTTCCAGTTGGACCCTGCAAAATGGGGAGgtaaacgaac ... tttttggcagTCAATGTGCAGTCATTATCTGGATCCCCTGCCAACTTTCAAGCTTACACGG
EST: gi|71854985|gb|DT004040.1|DT004040
EST:     TCAGAAGCGTGCATTAGAAGCTTTCCAGTTGGACCCTGCAAAATGGGGAG                         TCAATGTGCAGTCATTATCTGGATCCCCTGCCAACTTT
genomic: TCAGAAGCGTGCATTAGAAGCTTTCCAGTTGGACCCTGCAAAATGGGGAGgtaaacgaac ... tttttggcagTCAATGTGCAGTCATTATCTGGATCCCCTGCCAACTTT
EST: gi|71858517|gb|DT007572.1|DT007572
EST:     TCAGAAGCGTGCATTAGAAGCTTTCCAGTTGGACCCTGCAAAATGGGGAG                         TCAATGTGCAGTCATTATCTGGATCCCCTGCCAACTTTTCAAGCTTTACAC
genomic: TCAGAAGCGTGCATTAGAAGCTTTCCAGTTGGACCCTGCAAAATGGGGAGgtaaacgaac ... tttttggcagTCAATGTGCAGTCATTATCTGGATCCCCTGCCAACTTT-CAAGCTT-ACAC
EST: gi|71857493|gb|DT006548.1|DT006548
EST:     TCAGAAGCGTGCATTAGAAGCTTTCCAGTTGGACCCTGCAAAATGGGGAG                         TCAATGTGCAGTCATTATCTGGATCCCCTGCCAACTTTCAAGCTTACACTG
genomic: TCAGAAGCGTGCATTAGAAGCTTTCCAGTTGGACCCTGCAAAATGGGGAGgtaaacgaac ... tttttggcagTCAATGTGCAGTCATTATCTGGATCCCCTGCCAACTTTCAAGCTTACACGG
EST: gi|71858780|gb|DT007835.1|DT007835
EST:     TCAGAAGCGTGCATTAGAAGCTTTCCAGTTGGACCCTGCAAAATGGGGAG                         TCAATGTGCAGTCATTATCTGGATCCCCTGCCAACTTTCAAGCTTACAC
genomic: TCAGAAGCGTGCATTAGAAGCTTTCCAGTTGGACCCTGCAAAATGGGGAGgtaaacgaac ... tttttggcagTCAATGTGCAGTCATTATCTGGATCCCCTGCCAACTTTCAAGCTTACAC
EST: gi|71854655|gb|DT003710.1|DT003710
EST:     TCAGAAGCGTGCATTAGAAGCTTTCCAGTTGGACCCTGCAAAATGGGGAG                         TCAATGTGCAGTCATTATCTGGATCCCCTGCCAACTTTCAAGCTTACA
genomic: TCAGAAGCGTGCATTAGAAGCTTTCCAGTTGGACCCTGCAAAATGGGGAGgtaaacgaac ... tttttggcagTCAATGTGCAGTCATTATCTGGATCCCCTGCCAACTTTCAAGCTTACA
EST: gi|161708846|gb|FC059632.1|FC059632
EST:     TCAGAAGCGTGCATTAGAAGCTTTCCAGTTGGACCCTGCAAAATGGGGAG                         TCAATGTGCAGTCATTATCTGGATCCCCTGCCAACTTTCAAGCTTACACTG
genomic: TCAGAAGCGTGCATTAGAAGCTTTCCAGTTGGACCCTGCAAAATGGGGAGgtaaacgaac ... tttttggcagTCAATGTGCAGTCATTATCTGGATCCCCTGCCAACTTTCAAGCTTACACGG
EST: gi|352781776|gb|FQ469074.1|FQ469074
EST:     TCAGAAGCGTGCATTAGAAGCTTTCCAGTTGGACCCTGCAAAATGGGGAG                         TCAATGTGCAGTCATTATCTGGATCCCCTGCCAACTTTCAAGCTTACACGG
genomic: TCAGAAGCGTGCATTAGAAGCTTTCCAGTTGGACCCTGCAAAATGGGGAGgtaaacgaac ... tttttggcagTCAATGTGCAGTCATTATCTGGATCCCCTGCCAACTTTCAAGCTTACACGG
EST: gi|110359383|gb|EC920779.1|EC920779
EST:     TCAGAAGCGTGCATTAGAAGCTTTCCAGTTGGACCCTGCAAAATGGGGAG                         TCAATGTGCAGTCATTATCTGGATCCCCTGCCAACTTTCAAGCTTACACTG
genomic: TCAGAAGCGTGCATTAGAAGCTTTCCAGTTGGACCCTGCAAAATGGGGAGgtaaacgaac ... tttttggcagTCAATGTGCAGTCATTATCTGGATCCCCTGCCAACTTTCAAGCTTACACGG
EST: gi|71858467|gb|DT007522.1|DT007522
EST:     TCAGAAGCGTGCATTAGAAGCTTTCCAGTTGGACCCTGCAAAATGGGGAG                         TCAATGTGCAGTCATTATCTGGATCCCCTGCCAACTTTCAAGCTTACACTG
genomic: TCAGAAGCGTGCATTAGAAGCTTTCCAGTTGGACCCTGCAAAATGGGGAGgtaaacgaac ... tttttggcagTCAATGTGCAGTCATTATCTGGATCCCCTGCCAACTTTCAAGCTTACACGG
EST: gi|294966030|gb|GW837397.1|GW837397
EST:     TCAGAAGCGTGCATTAGAAGCTTTCCAGTTGGACCCTGCAAAATGGGGAG                         TCAATGTGCAGTCATTATCTGGATCCCCTGCCAACTTTCAAGCTTACACTG
genomic: TCAGAAGCGTGCATTAGAAGCTTTCCAGTTGGACCCTGCAAAATGGGGAGgtaaacgaac ... tttttggcagTCAATGTGCAGTCATTATCTGGATCCCCTGCCAACTTTCAAGCTTACACGG
EST: gi|71855977|gb|DT005032.1|DT005032
EST:     TCAGAAGCGTGCATTAGAAGCTTTCCAGTTGGACCCTGCAAAATGGGGAG                         TCAATGTGCAGTCATTATCTGGATCCCCTGCCAACTTTCCAGCTTACACTG
genomic: TCAGAAGCGTGCATTAGAAGCTTTCCAGTTGGACCCTGCAAAATGGGGAGgtaaacgaac ... tttttggcagTCAATGTGCAGTCATTATCTGGATCCCCTGCCAACTTTCAAGCTTACACGG
EST: gi|71857388|gb|DT006443.1|DT006443
EST:     TCAGAAGCGTGCATTAGAAGCTTTCCAGTTGGACCCTGCAAAATGGGGAG                         TCAATGTGCAGTCATTATCTGGATCCCCTGCCAACTTTCAAGCTTACACTG
genomic: TCAGAAGCGTGCATTAGAAGCTTTCCAGTTGGACCCTGCAAAATGGGGAGgtaaacgaac ... tttttggcagTCAATGTGCAGTCATTATCTGGATCCCCTGCCAACTTTCAAGCTTACACGG
EST: gi|352764283|gb|FQ471263.1|FQ471263
EST:     TCAGAAGCGTGCATTAGAAGCTTTCCAGTTGGACCCTGCAAAATGGGGAG                         TCAATGTGCAGTCATTATCTGGATCCCCTGCCAACTTTCAAGCTTACACGG
genomic: TCAGAAGCGTGCATTAGAAGCTTTCCAGTTGGACCCTGCAAAATGGGGAGgtaaacgaac ... tttttggcagTCAATGTGCAGTCATTATCTGGATCCCCTGCCAACTTTCAAGCTTACACGG
EST: gi|352768688|gb|FQ467900.1|FQ467900
EST:     TCAGAAGCGTGCATTAGAAGCTTTCCAGTTGGACCCTGCAAAATGGGGAG                         TCAATGTGCAGTCATTATCTGGATCCCCTGCCAACTTTCAAGCTTACACGG
genomic: TCAGAAGCGTGCATTAGAAGCTTTCCAGTTGGACCCTGCAAAATGGGGAGgtaaacgaac ... tttttggcagTCAATGTGCAGTCATTATCTGGATCCCCTGCCAACTTTCAAGCTTACACGG
EST: gi|71858984|gb|DT008039.1|DT008039
EST:     TCAGAAGCGTGCATTAGAAGCTTTCCAGTTGGACCCTGCAAAATGGGGAG                         TCAATGTGCAGTCATTATCTGGATCCCCTGCCAACTTTCAAGCTTACACTG
genomic: TCAGAAGCGTGCATTAGAAGCTTTCCAGTTGGACCCTGCAAAATGGGGAGgtaaacgaac ... tttttggcagTCAATGTGCAGTCATTATCTGGATCCCCTGCCAACTTTCAAGCTTACACGG
EST: gi|71859287|gb|DT008342.1|DT008342
EST:     TCAGAAGCGTGCATTAGAAGCTTTCCAGTTGGACCCTGCAAAATGGGGAG                         TCAATGTGCAGTCATTATCTGGATCCCCTGCCAACTTTCAAGCTTACACTG
genomic: TCAGAAGCGTGCATTAGAAGCTTTCCAGTTGGACCCTGCAAAATGGGGAGgtaaacgaac ... tttttggcagTCAATGTGCAGTCATTATCTGGATCCCCTGCCAACTTTCAAGCTTACACGG
EST: gi|161713667|gb|FC062807.1|FC062807
EST:     TCAGAAGCGTGCATTAGAAGCTTTCCAGTTGGACCCTGCAAAATGGGGAG                         TCAATGTGCAGTCATTATCTGGATCCCCTGCCAACTTTCAAGCTTACACTG
genomic: TCAGAAGCGTGCATTAGAAGCTTTCCAGTTGGACCCTGCAAAATGGGGAGgtaaacgaac ... tttttggcagTCAATGTGCAGTCATTATCTGGATCCCCTGCCAACTTTCAAGCTTACACGG
EST: gi|352765325|gb|FQ466022.1|FQ466022
EST:     TCAGAAGCGTGCATTAGAAGCTTTCCAGTTGGACCCTGCAAAATGGGGAG                         TCAATGTGCAGTCATTATCTGGATCCCCTGCCAACTTTCAAGCTTACCCGG
genomic: TCAGAAGCGTGCATTAGAAGCTTTCCAGTTGGACCCTGCAAAATGGGGAGgtaaacgaac ... tttttggcagTCAATGTGCAGTCATTATCTGGATCCCCTGCCAACTTTCAAGCTTACACGG
EST: gi|71856061|gb|DT005116.1|DT005116
EST:     TCAGAAGCGTGCATTAGAAGCTTTCCAGTTGGACCCTGCAAAATGGGGAG                         TCAATGTGCAGTCATTATCTGGATCCCCTGCCAACTTTCAAGCTTACACTG
genomic: TCAGAAGCGTGCATTAGAAGCTTTCCAGTTGGACCCTGCAAAATGGGGAGgtaaacgaac ... tttttggcagTCAATGTGCAGTCATTATCTGGATCCCCTGCCAACTTTCAAGCTTACACGG
EST: gi|71857262|gb|DT006317.1|DT006317
EST:     TCAGAAGCGTGCATTAGAAGCTTTCCAGTTGGACCCTGCAAAATGGGGAG                         TCAATGTGCAGTCATTATCTGGATCCCCTGCCAACTTTCAAGCTTACACTG
genomic: TCAGAAGCGTGCATTAGAAGCTTTCCAGTTGGACCCTGCAAAATGGGGAGgtaaacgaac ... tttttggcagTCAATGTGCAGTCATTATCTGGATCCCCTGCCAACTTTCAAGCTTACACGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catatttctgaacaccaactttatttaaagcttatttatttattttttttggcagTCAATGTGCAGTCATTATCTGGATCCCCTGCCAACTTTCAAGCTTACACGGCATTATTAAAACCTCATGAGAGAATCATGGCACTTGATCTTCCTCATGG
                                  tttatttatttttttt  CT-rich tract
 accaactttatttaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttgtttaaatcatttatctatttgtccgctcccacgtaaagagacatatttctgaacaccaactttatttaaagcttatttatttattttttttggcagTCAATGTGCAGTCATTATCTGGATCCCCTGCCAACTTTCAAGCTTACACGGCATTATTAAAACCTCATGAGAGAATCATGGCACTTGATCTTCCTCATGG

- - - -aaatcat
- - - - - - - - - - - - - -cgctccc
- - - - - - - - - - - - - - - - - - - aaagaga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - acaccaa