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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttctattaacacctataaattcagaatgacaacctaaatatttagattcaccacaattagacaaatttctggtatgagttctcttcttttgtgctgatagGTTGCTCGTGGTGACAACAGTGGTGGAGAATCCATTCCCATGCTGTTGAGAGTTCCTCGTTTCTTTGATCCTTGGGGTGGTTATGATATGATTGGCTTTG

Basic information

species Vitis vinifera
transcript Vv05s0062g01250.t01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0062g01250.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: LOC_Os11g24540.2 (Oryza sativa), 3'ss of exon 10
ttctattaacacctataaattcagaatgac--aacctaaatatttagattcaccacaattagacaaatttctggtatgagttct--cttcttttgtgctg-atagGTTGCTCGTGGTGACAACAGTGGTGGAGAATCCATTCCCATGCTGTTGAGAGTTCCTCGTTTCTTTGATCCTTGGGGTGGTTATGATATGATTGGCTTTG---
     || | |  | ||  |||||   ||     |||  |   |     |     | ||||   |   || | || | || | |   |   |   | ||| | |||||||||||||||| |||  ||| | || |   ||||| ||||| || ||| | ||||||||||||||||| |||||||| ||||| ||||| |||||||   
-----ttgatatgtgtatcttcagttagatctgtcctgtaagatataccttttatctattatgaagtgttatagtgttagatatgattctatccatactgcacagGTTGCTCGTGGTGATAACTCTGGGGAAGCA---ATTCCGATGCTCTTAAGAATACCTCGTTTCTTTGATCCATGGGGTGGCTATGACATGATAGGCTTTGGTG

upper sequence: Vv05s0062g01250.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GRMZM2G082330_T01 (Zea mays), 3'ss of exon 10
ttctattaacacctataaattcagaatgacaacctaaatatttagattcaccacaattagacaaatttctggtatgagttctcttcttttgtgctga--------tagGTTGCTCGTGGTGACAACAGTGGTGGAGAATCCATTCCCATGCTGTTGAGAGTTCCTCGTTTCTTTGATCCTTGGGGTGGTTATGATATGATTGGCTTTG---
       |  || |||| |   |   |||| | | ||  ||||   ||  |  | |       | |      |||   | || |  |  ||   ||          |||||||||||||||| |||| |||    ||||| ||||| |||||  | ||  | || || ||||||||||| |||||||||||||||||||| |||||||   
-------attacatatacagggaacttgaccagccaa-catttgctttaccttctacccattgagtcctgattattcttgctgtattcatgctttggaaattactcagGTTGCTCGTGGTGATAACACTGG---GGAATCAATTCCTATGCTCCTAAGGATACCCCGCTTCTTTGATCCATGGGGTGGTTATGATATGATAGGCTTTGGTG

upper sequence: Vv05s0062g01250.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA08G47600.2 (Glycine max), 3'ss of exon 9
---------------ttctattaacacctataaattcagaatgacaacctaaatatttagattcaccacaattagacaaatttctggtatgagttctcttcttttgtgctgatagGTTGCTCGTGGTGACAACAGTGGTGGAGAATCCATTCCCATGCTGTTGAGAGTTCCTCGTTTCTTTGATCCTTGGGGTGGTTATGATATGATTGGCTTTG
               |||||| ||  |   |  ||| | || ||  |    |  |||  | ||    | | ||     |   |||   ||| | | |||| ||          |||||||||| ||||||||   |||||||||| | ||||| ||||| |||||| |||||||| | |||||||| ||||| |||||||| |||||||| ||||
aatggattctgtgttttctat-aatgctgctttattaaaaaggaaga---gagaattctggttt-ttatagttttttcatactcttacatgggctttcttttt----------agGTTGCTCGAGGTGACAAGGCTGGTGGAGAAGCAATTCCTATGCTTTTGAGATTTCCTCGTCTTTTTGATCCCTGGGGAGGTTATGACATGATTGGATTTG

upper sequence: Vv05s0062g01250.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA10G44490.1 (Glycine max), 3'ss of exon 10
--ttctattaacacctataaattcagaatga-----caacctaaatatttagattcaccacaattagacaaatttctggtatgagttctcttcttttgtgctgatagGTTGCTCGTGGTGACAACAGTGGTGGAGAATCCATTCCCATGCTGTTGAGAGTTCCTCGTTTCTTTGATCCTTGGGGTGGTTATGATATGATTGGCTTTG
  | |||| || |  || | || |    |       ||  || | |  | ||||| |  ||| | | |     | |||   | |    | | ||||        ||||||||||||||||||||    ||||| ||| | ||||| ||||| |||||| |||||||| | | ||||||||||||||| |||||||||||||| ||||
cttgctataaatatttagatatacgtttttctttttcattctcactcctgagatttattacactgaaaaggtgtcctgaagttatgagtttcctttc-------tagGTTGCTCGTGGTGACAAGGCCGGTGGTGAAGCAATTCCTATGCTTTTGAGATTTCCTCGTCTTTCTGATCCTTGGGGTGGCTATGATATGATTGGATTTG

upper sequence: Vv05s0062g01250.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA20G39260.1 (Glycine max), 3'ss of exon 9
ttctattaacacctataaa------ttcagaatgacaacctaaatatttagattcaccacaattagacaaatttctggtatgagttctcttcttttgtgctgatagGTTGCTCGTGGTGACAACAGTGGTGGAGAATCCATTCCCATGCTGTTGAGAGTTCCTCGTTTCTTTGATCCTTGGGGTGGTTATGATATGATTGGCTTTG
| |||| || |  || | |      ||  |  |  ||  || | |  | || || |  | | | | |     | |||   | |    | | ||||| |      |||||||||||||||||||    ||||| ||| | ||||| ||||| |||||| |||||||| | | ||||||||||||||| |||||||||||||| ||||
tgctataaatatttagatatacgttttttgtttttcattctcactcctgagttttattatactgaaaaggtctcctgtagttatgagtttccttttct------agGTTGCTCGTGGTGACAAGGCCGGTGGTGAAGCAATTCCTATGCTTTTGAGATTTCCTCGTCTTTCTGATCCTTGGGGTGGCTATGATATGATTGGATTTG

upper sequence: Vv05s0062g01250.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA18G53880.1 (Glycine max), 3'ss of exon 9
-----------ttctattaacacctataaattcagaatgacaacctaaatatttagattcaccacaattagacaaatttctggtatgagttctcttcttttgtgctgatagGTTGCTCGTGGTGACAACAGTGGTGGAGAATCCATTCCCATGCTGTTGAGAGTTCCTCGTTTCTTTGATCCTTGGGGTGGTTATGATATGATTGGCTTTG
            | | ||||||  | |   |    ||    ||   | | |||  | ||    | | ||     |   |||   ||| | | |||| ||          |||||||||| ||||||||   |||||| ||| | ||||| ||||| |||||| |||||||| | |||||||| ||||| |||||||| |||||||| ||||
tctaatggattctgtgttaacatgtgtctttattaaaaaggaagagaga-attctggttttttatagttttgtgatactcttacatgggctttcttttt----------agGTTGCTCGAGGTGACAAGGCTGGTGGGGAAGCAATTCCTATGCTTTTGAGATTTCCTCGTCTTTTTGATCCCTGGGGAGGTTATGACATGATTGGATTTG

upper sequence: Vv05s0062g01250.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: AT2G43070.1 (Arabidopsis thaliana), 3'ss of exon 10
ttctattaacacctata--aattcagaatgacaacctaaatattta--gattcaccacaattagacaaat---ttctggtatgagttctcttcttttgtgctgatagGTTGCTCGTGGTGACAACAGTGGTGGAGAATCCATTCCCATGCTGTTGAGAGTTCCTCGTTTCTTTGATCCTTGGGGTGGTTATGATATGATTGGCTTTG
 || || |      |||  | |  |   ||| ||   |   ||| |  |   ||    |  |   | | |   ||||  | |||     | |  |||||      ||||||| |  || |||| |||   ||| || |||||||| |||||  | ||  ||||||| |||||||||||||||||||||||||| |||||||| ||||
-tcaataactttgaatagtagtcgattgtgataattgagtaattgaagggcccagagaagctcagccagtatattcttatttgaaactcccttctttgt------agGTTGCCCAAGGAGACAGCAGCACTGGGGAGTCCATTCCGATGCTACTAAGGATTCCTCGGTTCTTTGATCCTTGGGGTGGTTATGACATGATTGGTTTTG

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|110688633|gb|EE067409.1|EE067409
EST:     TCTGGGTCTTCATATCACCAGTAATATTCAAAGACAGTGTTATGATAGCA                         GTTGCTCGTGGTGACAACAGTGGTGGAGAATCCATTCCCATGCTGTTGAGA
genomic: TCTGGGTCTTCATATCACCAGTAATATTCAAAGACAGTGTTATGATAGCAgtaagtcttt ... gtgctgatagGTTGCTCGTGGTGACAACAGTGGTGGAGAATCCATTCCCATGCTGTTGAGA
EST: gi|110731688|gb|EE106318.1|EE106318
EST:     TCTGGGTCTTCATATCACCAGTAATATTCAAAGACAGTGTTATGATAGCA                         GTTGCTCGTGGTGACAACAGTGGTGGAGAATCCATTCCCATGCTGTTGAGA
genomic: TCTGGGTCTTCATATCACCAGTAATATTCAAAGACAGTGTTATGATAGCAgtaagtcttt ... gtgctgatagGTTGCTCGTGGTGACAACAGTGGTGGAGAATCCATTCCCATGCTGTTGAGA
EST: gi|110687402|gb|EE064779.1|EE064779
EST:     TCTGGGTCTTCATATCACCAGTAATATTCAAAGACAGTGTTATGATAGCA                         GTTGCTCGTGGTGACAACAGTGGTGGAGAATCCATTCCCATGCTGTTGAGA
genomic: TCTGGGTCTTCATATCACCAGTAATATTCAAAGACAGTGTTATGATAGCAgtaagtcttt ... gtgctgatagGTTGCTCGTGGTGACAACAGTGGTGGAGAATCCATTCCCATGCTGTTGAGA
EST: gi|110395316|gb|EC960974.1|EC960974
EST:     TCTGGGTCTTCATATCACCAGTAATATTCAAAGACAGTGTTATGATAGCA                         GTTGCTCGTGGTGACAACAGTGGTGGAGAATCCATTCCCATGCTGTTGAGA
genomic: TCTGGGTCTTCATATCACCAGTAATATTCAAAGACAGTGTTATGATAGCAgtaagtcttt ... gtgctgatagGTTGCTCGTGGTGACAACAGTGGTGGAGAATCCATTCCCATGCTGTTGAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attcaccacaattagacaaatttctggtatgagttctcttcttttgtgctgatagGTTGCTCGTGGTGACAACAGTGGTGGAGAATCCATTCCCATGCTGTTGAGAGTTCCTCGTTTCTTTGATCCTTGGGGTGGTTATGATATGATTGGCTTTG
                                 ttctcttcttttgtgc  CT-rich tract
         aattagacaaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttctattaacacctataaattcagaatgacaacctaaatatttagattcaccacaattagacaaatttctggtatgagttctcttcttttgtgctgatagGTTGCTCGTGGTGACAACAGTGGTGGAGAATCCATTCCCATGCTGTTGAGAGTTCCTCGTTTCTTTGATCCTTGGGGTGGTTATGATATGATTGGCTTTG

- - - - acaccta
- - - - - - - - - - -cagaatg
- - - - - - - - - - - - - - - aacctaa
- - - - - - - - - - - - - - - - - - - - - - - - caccaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - agacaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tttctgg