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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtttttttaccttctctttcttattttgtttcttttttgggcttgggatcatcagcttccaggtttataagattttcactcaagggtgttatgctggcagGTTGCCACATTTATTGTTCAAAAAATTCTGTTGGATGATGTGGGCTTGGATTATATTTGTACTACGGCAGAGCGATTTTTTGCAGTAGGTCGAGTTTTGG

Basic information

species Vitis vinifera
transcript Vv19s0090g00930.t01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv19s0090g00930.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: LOC_Os03g57130.1 (Oryza sativa), 3'ss of exon 6
gtttttttaccttctctttcttattttgtttcttttttgggcttgggatcatcagcttccaggtttataagattttcactcaagggtgttatgctggcagGTTGCCACATTTATTGTTCAAAAAATTCTGTTGGATGATGTGGGCTTGGATTATATTTGTACTACGGCAGAGCGATTTTTTGCAGTAGGTCGAGTTTTGG
|  |  | |    ||  | | |  |     |    | | |   ||   |     | ||    | ||      |  | |  |||      |||  | |||||||||||| |||||||||||||| |||||| | |||||||| ||  |    || || ||| |||| || || || || ||||| ||||   | ||| |  
gaataatgatgcacttgtacctggtagcaataggctgtagtactgtattagatggatttggtgcttcatttttgctaatccaatcaacgtatttttgcagGTTGCCACCTTTATTGTTCAAAAGATTCTGCTTGATGATGTTGGGCTTCGCTACATATGTGCTACTGCTGAACGTTTCTTTGCCGTAGCCAGTGTTCTAT

upper sequence: Vv19s0090g00930.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA08G43220.1 (Glycine max), 3'ss of exon 6
gtttttttaccttctct--ttcttattttgtttcttttttgggcttgggatcatcagcttccaggtttataagattttcactcaagggtgttatgctggcagGTTGCCACATTTATTGTTCAAAAAATTCTGTTGGATGATGTGGGCTTGGATTATATTTGTACTACGGCAGAGCGATTTTTTGCAGTAGGTCGAGTTTTGG
  |  || | ||| |    || | | | | |||  | | ||  | |      || |   |  |       | | || ||     |  |   |||     |||||||| ||||||||||||||||||||||||||||| |||||||||||||| |||||||||||||| || ||||| ||||| ||||||||||||||| |||
--tgcttgatctttttaaattgtcactgtcttttatatatgtacataaataaataatagtatattggagcatggttgtctaatgaaagctctatcaccccagGTTGCAACATTTATTGTTCAAAAAATTCTGTTGGACGATGTGGGCTTGGACTATATTTGTACTACAGCGGAGCGCTTTTTCGCAGTAGGTCGAGTTCTGG

upper sequence: Vv19s0090g00930.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA18G10400.1 (Glycine max), 3'ss of exon 6
gtttttttaccttctctttcttattttgtttcttttttgggcttgggatcatcagcttccaggtttataagattttcactcaagggtgttatgctggcagGTTGCCACATTTATTGTTCAAAAAATTCTGTTGGATGATGTGGGCTTGGATTATATTTGTACTACGGCAGAGCGATTTTTTGCAGTAGGTCGAGTTTTGG
 | ||||||  ||  |  | || |||  |    | | |   | |      || |   |  |       | | || ||     |  |   ||      |||||||| ||||||||||||||||||||||||||||| |||||||||||||| || ||||||||||| || ||||| |||||||| |||||||||||| |||
atctttttaaattgccactgttgtttgatcatctatatttacataaataaataatagtatattggagcatggttgtctaatgaaagctctaccaccccagGTTGCAACATTTATTGTTCAAAAAATTCTGTTGGACGATGTGGGCTTGGACTACATTTGTACTACAGCGGAGCGCTTTTTTGCGGTAGGTCGAGTTCTGG

upper sequence: Vv19s0090g00930.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA02G46250.1 (Glycine max), 3'ss of exon 6
-gttt-ttttaccttctctttcttattttgtttcttttttgggcttgggatcatcagcttccaggtttataagattttcactcaagggtgttatgctggcagGTTGCCACATTTATTGTTCAAAAAATTCTGTTGGATGATGTGGGCTTGGATTATATTTGTACTACGGCAGAGCGATTTTTTGCAGTAGGTCGAGTTTTGG
 |||| ||||| |  || | |  |  |    || | |      |     ||  | |      |  ||      | | | |   |||  |    |  |  |||||||| || ||||| |||||||||||||||||||| ||  |||| ||| | |||||||| ||||| |||||||| |||| ||||||||||||||||||||
tgtttgttttagccactatctgctgatcctcttttatacctatcaaataattgtaaaaggaaaaattgtgtgtaatctaatggaag--ttccgtcatttcagGTTGCAACCTTTATAGTTCAAAAAATTCTGTTGGACGAAATGGGTTTGAAATATATTTGCACTACAGCAGAGCGCTTTTATGCAGTAGGTCGAGTTTTGG

upper sequence: Vv19s0090g00930.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA14G02480.1 (Glycine max), 3'ss of exon 6
-gtttttttaccttctctttcttattttgtttcttttttgggcttgggatcatcagcttccaggtttataagattttcactcaagggtgttatgctggcagGTTGCCACATTTATTGTTCAAAAAATTCTGTTGGATGATGTGGGCTTGGATTATATTTGTACTACGGCAGAGCGATTTTTTGCAGTAGGTCGAGTTTTGG
 |||| |||     | || || |  |    || | |      |     ||  | |      |  ||| |  |   |  | |  | | |         ||||||||| || ||||| |||||||||||||||||||| ||  | || ||| | |||||||||||||| |||||||| |||| |||||||| || ||||||||
tgtttgttt-ttgccactctcgtgatcctcttttatgccaatcaaataattgtaaaagggaaaatttgtgtgtaatctaatggaagttccaccaactgcagGTTGCAACCTTTATAGTTCAAAAAATTCTGTTGGACGAAATTGGTTTGAAATATATTTGTACTACAGCAGAGCGCTTTTATGCAGTAGCTCAAGTTTTGG

upper sequence: Vv19s0090g00930.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: AT3G20800.1 (Arabidopsis thaliana), 3'ss of exon 6
gtttttttaccttctctttcttattttgtttcttttttgggcttgggatcatc---agcttccaggtttataagattttcactcaagggtgttatgctggcagGTTGCCACATTTATTGTTCAAAAAATTCTGTTGGATGATGTGGGCTTGGATTATATTTGTACTACGGCAGAGCGATTTTTTGCAGTAGGTCGAGTTTTGG
 |   |  | |   |  | |     |    |  | | |    |     ||||    ||  | ||      |  | ||     | ||     |  |  || ||||| || ||||||||||||||||| || |||||||||||||||||  ||||||| || || || || |||||||| ||||||||||| |||||||| ||||
-tccatagaaccagttctgcgccaatgaaatggtgtctacattgaaactcattgaaagtgtgcaacccctt--gcttacgtattaacataatgttaatgacagGTGGCAACATTTATTGTTCAAAAGATACTGTTGGATGATGTGGGGATGGATTACATCTGCACAACAGCAGAGCGGTTTTTTGCAGTTGGTCGAGTGTTGG

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|110384705|gb|EC949163.1|EC949163
EST:     TTCCGCTGTGCCTACGCACCATGGAGATGGGGAGTGAATTGTCAAAAACA                         GTTGCCACATTTATTGTTCAAAAAATTCTGTTGGATGATGTGGGCTTGGAT
genomic: TTCCGCTGTGCCTACGCACCATGGAGATGGGGAGTGAATTGTCAAAAACAgtaagtgccc ... atgctggcagGTTGCCACATTTATTGTTCAAAAAATTCTGTTGGATGATGTGGGCTTGGAT
EST: gi|33405642|gb|CF211269.1|CF211269
EST:     CATGGAGATGGGGAGTGAATTGTCAAAAACA                         GTTGCCACATTTATTGTTCAAAAAATTCTGTTGGATGATGTGGGCTTGGAT
genomic: CATGGAGATGGGGAGTGAATTGTCAAAAACAgtaagtgccc ... atgctggcagGTTGCCACATTTATTGTTCAAAAAATTCTGTTGGATGATGTGGGCTTGGAT
EST: gi|110391951|gb|EC957020.1|EC957020
EST:     TTCCGCTGTGCCTACGCACCATGGAGATGGGGAGTGAATTGTCAAAAACA                         GTTGCCACATTTATTGTTCAAAAAATTCTGTTGGATGATCTGGGCTTGGAT
genomic: TTCCGCTGTGCCTACGCACCATGGAGATGGGGAGTGAATTGTCAAAAACAgtaagtgccc ... atgctggcagGTTGCCACATTTATTGTTCAAAAAATTCTGTTGGATGATGTGGGCTTGGAT
EST: gi|110730135|gb|EE106867.1|EE106867
EST:     TTCCGCTGTGCCTACGCACCATGGAGATGGGGAGTGAATTGTCAAAAACA                         GTTGCCACATTTATTGTTCAAAAAATTCTGTTGGATGATGTGGGCTTGGAT
genomic: TTCCGCTGTGCCTACGCACCATGGAGATGGGGAGTGAATTGTCAAAAACAgtaagtgccc ... atgctggcagGTTGCCACATTTATTGTTCAAAAAATTCTGTTGGATGATGTGGGCTTGGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggatcatcagcttccaggtttataagattttcactcaagggtgttatgctggcagGTTGCCACATTTATTGTTCAAAAAATTCTGTTGGATGATGTGGGCTTGGATTATATTTGTACTACGGCAGAGCGATTTTTTGCAGTAGGTCGAGTTTTGG
                  tttataagattttca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttttttaccttctctttcttattttgtttcttttttgggcttgggatcatcagcttccaggtttataagattttcactcaagggtgttatgctggcagGTTGCCACATTTATTGTTCAAAAAATTCTGTTGGATGATGTGGGCTTGGATTATATTTGTACTACGGCAGAGCGATTTTTTGCAGTAGGTCGAGTTTTGG

- - - - -ccttctc
- - - - - - - - - - - - - - - - - - - gggcttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - gcttcca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gggtgtt