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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttataaatcaatttataaattcctattgggttcttgtaaactggagaatttatgaattaggtttagaagtgattctaaatgggtgacgttttgagcagGGTCTTGTAGATTCCGACACGTTACCTCTTAATGTTTCACGAGAAATGCTTCAACAACACAGCAGTTTGAAAACAATTAAGAAGAAGCTTATCCGCAAGG

Basic information

species Vitis vinifera
transcript Vv18s0001g14500.t01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0001g14500.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: LOC_Os06g50300.1 (Oryza sativa), 3'ss of exon 10
gttataaatcaatttataaattcctattgggttcttgtaaactggagaatttatgaattaggtttagaagtgattctaaatgggtga--cgttttgagcagGGTCTTGTAGATTCCGACACGTTACCTCTTAATGTTTCACGAGAAATGCTTCAACAACACAGCAGTTTGAAAACAATTAAGAAGAAGCTTATCCGCAAGG
             |  || ||| |||||   |  |     ||  |  | |  ||  |||   ||  | ||     |||||    | |    || |  | ||||||| || || || ||||| || ||||| ||||| |||||||||||||| |||||||| |||||  |||| || || |||||||| || |||||||| |
------------gtactagattactatt---tcatgaacgacacggtattccattcattgacttatgcagc----ctaaacctataagctattatctgtagGGTCTCGTCGACTCGGACACATTGCCTCTCAATGTATCACGAGAAATGCTCCAACAACATAGCAGCCTGAAGACCATCAAGAAGAAACTAATCCGCAAAG

upper sequence: Vv18s0001g14500.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GRMZM2G399073_T02 (Zea mays), 3'ss of exon 12
gttataaatcaatttataaattcctattgggttcttgtaaactggagaatttatgaattaggtttagaagtgattctaaatgggtgacgttttgagcagGGTCTTGTAGATTCCGACACGTTACCTCTTAATGTTTCACGAGAAATGCTTCAACAACACAGCAGTTTGAAAACAATTAAGAAGAAGCTTATCCGCAAGG
          | | |||   | | |   | |    | || | |    |||||   |   |  | |   | | | ||| |    ||||  || |    ||||| |||| || || |||||  | || || ||||| |||||||||||||| |||||||| |||||| |||| || || ||||||||||| |||||||| |
--------gtactatattgctacttcaagagcaaatatacaatt---aatttgaaaggcatatgttatactaaatcttac--agtgatattctctctagGGTATTGTTGACTCAGACACACTGCCGCTGAATGTGTCACGAGAAATGCTCCAACAACATAGCAGTCTGAAGACTATCAAGAAGAAGCTGATCCGCAAAG

upper sequence: Vv18s0001g14500.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GRMZM2G141931_T02 (Zea mays), 3'ss of exon 10
gttataaatcaatttataaattcctattgggttcttgtaaactggagaatttatgaattaggtttagaagtgattctaaatgggtgacgttttgagcagGGTCTTGTAGATTCCGACACGTTACCTCTTAATGTTTCACGAGAAATGCTTCAACAACACAGCAGTTTGAAAACAATTAAGAAGAAGCTTATCCGCAAGG
||  |  || | | | | ||     |  | || ||  | || |  |    | |||   |||    ||     |   || |   |||   || |  | ||||| |||| || || |||||| | || || || || ||||||||||||||||||||||| |||||| | || || || ||||||||||| |||||||| |
gtactgtattactgtttcaaga---aacgcgtactattcaattcaat--ctgatgtcatag---caggctaaaccttaca---gtggttttatctgtagGGTATTGTTGACTCGGACACGCTGCCCCTGAACGTGTCACGAGAAATGCTTCAACAACATAGCAGTCTCAAGACCATCAAGAAGAAGCTGATCCGCAAAG

upper sequence: Vv18s0001g14500.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA14G40320.3 (Glycine max), 3'ss of exon 10
gttataaatcaatttataaattcctattg--ggttcttgtaaactg-gagaat--ttatgaattaggtttagaagtgattctaaatgggtgacgttttgagcagGGTCTTGTAGATTCCGACACGTTACCTCTTAATGTTTCACGAGAAATGCTTCAACAACACAGCAGTTTGAAAACAATTAAGAAGAAGCTTATCCGCAAGG
    ||       || |   ||  |||||  | |   | ||   |  ||| ||  | || | ||  | | | || || ||||       |||||||  || ||||||||||| ||||| ||||| || || |||||||| ||||||||||||||||||||||| || ||| |||| ||||| |||||||| |||||  | || |
---gtaggcattgttgtgctttgttattgcagataaatatattttatgaggatcataataatttttgctaacaaatgtttcttt-----tgacgttgggaacagGGTCTTGTTGATTCTGACACTTTGCCACTTAATGTATCACGAGAAATGCTTCAACAACATAGTAGTCTGAAGACAATCAAGAAGAAACTTATTAGGAAAG

upper sequence: Vv18s0001g14500.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA17G37820.1 (Glycine max), 3'ss of exon 10
gttataaatcaatttataaattcctattg-ggttcttgtaaactggagaatt-tatgaattaggtttagaagtgattctaaatgggtgacgttttgagcagGGTCTTGTAGATTCCGACACGTTACCTCTTAATGTTTCACGAGAAATGCTTCAACAACACAGCAGTTTGAAAACAATTAAGAAGAAGCTTATCCGCAAGG
| ||  |||    || |   ||  |||||  | |    || | |  |  ||  |  |||| |  |||   | | | | | | |   |||||||  || ||||||||||| ||||| ||||| || || |||||||| || |||||||||||||| ||||| || ||| | || ||||| |||||||| |||||  | ||  
ggtaggaattg--ttgtgctttgttattgcagataaaatatattttatgatgatcagaataatttttgctaataaatgttacttt-tgacgttgggaacaGGGTCTTGTTGATTCTGACACATTGCCACTTAATGTATCGCGAGAAATGCTTCAGCAACATAGTAGTCTAAAGACAATCAAGAAGAAACTTATTAGGAAA-

upper sequence: Vv18s0001g14500.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: AT4G24190.2 (Arabidopsis thaliana), 3'ss of exon 10
gttataaatcaatttataaattc-ctattgggttcttgtaaactggagaatttatgaattaggtttagaagtgattctaaatgggtgacgttttgagcagGGTCTTGTAGATTCCGACACGTTACCTCTTAATGTTTCACGAGAAATGCTTCAACAACACAGCAGTTTGAAAACAATTAAGAAGAAGCTTATCCGCAAGG
    ||||  | || | | |    |||  ||||||||  ||       ||||||||   ||            || |  || | | |  | |||  |||||||||||| || || ||||| || ||||| ||||| ||| ||||||||||||||||||||||||| || || ||||||||||||||||||||||| ||||
---gtaaactacttgaaagacaaactaaggggttctttcaataca---aatttatgggctaa-----------atccctaacgtgagttgctttt-gcagGGTCTTGTTGACTCTGACACATTGCCTCTAAATGTATCAAGAGAAATGCTTCAACAACACAGCAGCTTAAAGACAATTAAGAAGAAGCTTATCCGAAAGG

upper sequence: Vv18s0001g14500.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: PP1S126_38V6.1 (Physcomitrella patens), 3'ss of exon 10
--------------------------------------------------------------gttataaatcaatttataaattcctattgggttcttgtaaactggagaatttatgaattaggtttagaagtgattctaaatg--ggtgacgttttgagcagGGTCTTGTAGATTCCGACACGTTACCTCTTAATGTTTCACGAGAAATGCTTCAACAACACAGCAGTTTGAAAACAATTAAGAAGAAGCTTATCCGCAAGG
                                                                || |||||   ||  |   |  ||      |   |  ||  | ||  || ||  |     |||     | | | | | ||  | ||  || ||  ||||||  |||| || || |||||  | ||| | ||||| || ||||||||||| ||||| |||||||| || ||||| ||||||||||||||  |||||||||
gtgagcacgatgcagaatattcaaaatctcatagcacatagtgtagctcttagagtgcatctcctagaaatcccattccattgttttaactatcttcagcgaatcgtagtgttgatccaaagaatttttttctaagtttcactgacgatgttgtgttttgcagGGCATTGTGGACTCTGACACTCTCCCTTTGAATGTGTCTCGAGAAATGCTGCAACAGCACAGCAGCTTAAAAACCATTAAGAAGAAGCTCGTCCGCAAGG

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|294967276|gb|GW840151.1|GW840151
EST:     TTTCTGAAGAATTTGATGAGCTTTTGCCCAAGTATCTGAACCTTTTGAAG                         GGTCTTGTAGATTCCGACACGTTACCTCTTAATGTTTCACGAGAAATGCTT
genomic: TTTCTGAAGAATTTGATGAGCTTTTGCCCAAGTATCTGAACTTTTTGAAGgttataaatc ... ttttgagcagGGTCTTGTAGATTCCGACACGTTACCTCTTAATGTTTCACGAGAAATGCTT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gagaatttatgaattaggtttagaagtgattctaaatgggtgacgttttgagcagGGTCTTGTAGATTCCGACACGTTACCTCTTAATGTTTCACGAGAAATGCTTCAACAACACAGCAGTTTGAAAACAATTAAGAAGAAGCTTATCCGCAAGG
                             ttctaaa  putative branch site (score: 2)
     tttatgaatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttataaatcaatttataaattcctattgggttcttgtaaactggagaatttatgaattaggtttagaagtgattctaaatgggtgacgttttgagcagGGTCTTGTAGATTCCGACACGTTACCTCTTAATGTTTCACGAGAAATGCTTCAACAACACAGCAGTTTGAAAACAATTAAGAAGAAGCTTATCCGCAAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC