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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gaaaaatgggtgtttatgtttatatatgtttttatgtatcttagtgtgtgatttctattataagttttgtttatgatgatgtgataacttggttttacagCAAAGTTATGGATGTCTTCATTAAGGCTGCAGAATACATGGAAATTCCAGTCCGTAGGACTGACAATGAGCCCCTTCAGAAACTGTTCATGTTAGTAAGG

Basic information

species Vitis vinifera
transcript Vv16s0050g01460.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv16s0050g01460.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os04g24180.1 (Oryza sativa), 3'ss of exon 6
-----gaaaaatgggtgtttatgtttatatatgtttttatgtatcttagtgtgtgatttctattataagttttgtttatgatgatgtgataacttggttttacagCAAAGTTATGGATGTCTTCATTAAGGCTGCAGAATACATGGAAATTCCAGTCCGTAGGACTGACAATGAGCCCCTTCAGAAACTGTTCATGTTAGTAAGG
           || |  |   |  |  |||  ||| | |  |||   | ||  |  ||| |   |||  | |  |   ||    | |  |  ||   | || ||||||||| |||||||||||||||||||||||||| || ||||| || ||||||||  | | |||| |||| ||| | |||||| | ||  |    || |||
ccaaattgtcctgagcatcctttctgttatcagttct-agatatgaaaatgcctcgtttttgacata--tctgatccgtggaactat--tggctgtatgttgcagCAAAGTCATGGATGTCTTCATTAAGGCTGCAGAGTATATGGAGATGCCAGTCCGGCGCAGTGACGATGAACCCTTGCAGAAATTATTTGTAGCTGTTAGG

upper sequence: Vv16s0050g01460.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G167868_T01 (Zea mays), 3'ss of exon 5
----gaaaaatgggtgt-ttatgtttatatatgtttttatgtatcttagtgtgtgatttctattataagttttgtttatgatgatgtgataacttggttttacagCAAAGTTATGGATGTCTTCATTAAGGCTGCAGAATACATGGAAATTCCAGTCCGTAGGACTGACAATGAGCCCCTTCAGAAACTGTTCATGTTAGTAAGG
    |  |||    | | ||  || |  || |  ||    |  |   |     || ||  | ||       |||  |      ||| | |   |   | | ||||||||||||||||||||||||| |||||||||||||| ||||| || ||||| ||  | | |||  |||| |||||||| ||| ||||  |    || || 
ttccgggaaacttctatattgggtcttaatttacttgctagccttcaaaatcatgtttcattttcc----cttgcctg-atccatgggttgtttccatgtcacagCAAAGTTATGGATGTCTTCATCAAGGCTGCAGAATATATGGAGATGCCAGTTCGACGCAGTGATGATGAACCCCTTCAAAAATTGTTTGTAGCTGTTAGA

upper sequence: Vv16s0050g01460.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G007871_T02 (Zea mays), 3'ss of exon 5
--gaaaaatgggtgtttatgtttatatatgtttttatgtatcttagtgtgtgatttctattataagttttgtttatgatgatgtgataacttggttttacagCAAAGTTATGGATGTCTTCATTAAGGCTGCAGAATACATGGAAATTCCAGTCCGTAGGACTGACAATGAGCCCCTTCAGAAACTGTTCATGTTAGTAAGG
  |      ||    || | ||| |   ||||  | |   |  |||  |  ||  ||   | |     |||| |  |   ||| | |   |   | | ||||||||||||| ||||||||||| |||||||||||||| ||||| || ||||| ||  | | |||  |||| ||||| || ||| ||||  |    || || 
tagcttccaggaaacttctatttttg-gtgttaatttacttgctagctttcgaaatcatgtttttcccttgtgtgagcc-atgagttgtttccatgtcacagCAAAGTTATAGATGTCTTCATCAAGGCTGCAGAATATATGGAGATGCCAGTTCGACGCAGTGATGATGAACCCCTGCAAAAATTGTTTGTAGCTGTTAGA

upper sequence: Vv16s0050g01460.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA15G20400.1 (Glycine max), 3'ss of exon 6
gaaaaatgggtgtttatgtttatatatgtttttatgtatcttagtgtgtgatttctattataagtttt----gtttatgatgatgtgataacttggttttacagCAAAGTTATGGATGTCTTCATTAAGGCTGCAGAATACATGGAAATTCCAGTCCGTAGGACTGACAATGAGCCCCTTCAGAAACTGTTCATGTTAGTAAGG
     |    |      |      | |     |   ||   |||  | |  ||| || | |||  |||    |||||      |||||  | |  ||  ||||||||||| |||||||||||||| |||||||| ||||| |||||||||||||| |||||||||||  |||| || |||||||| || || ||||| ||||||
---tgagttatccccccgcccccctctcccaattcatacaatagc-tatcttttatactttaaactttcaaagtttaattatttgtgaatattatgtggtacagCAAAGTCATGGATGTCTTCATCAAGGCTGCTGAATATATGGAAATTCCAGTTCGTAGGACTGATGATGAACCTCTTCAGAAGCTTTTTATGTTGGTAAGG

upper sequence: Vv16s0050g01460.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA09G08830.1 (Glycine max), 3'ss of exon 6
----gaaaaatgggtgtttatgtttatatatgtttttatgtatcttagtgtgtgatttctat-tataagttttgtttatgatgatgtgataacttggttttacagCAAAGTTATGGATGTCTTCATTAAGGCTGCAGAATACATGGAAATTCCAGTCCGTAGGACTGACAATGAGCCCCTTCAGAAACTGTTCATGTTAGTAAGG
    ||||| || ||  |     ||  |  || |   ||   | |   | | |  |||  || | |||  |||  ||||     |||||  | |  ||| ||||||||||| |||||||||||||| |||||||| ||||| |||||||||||||||||||| |||||  | || || ||||| || || || ||||| ||||||
gattgaaaattgagttatcccccttccaattgatacaataggtatcttt-tatactttaaatgtttaaagtttaattatt----tgtgaatattatgttgtacagCAAAGTAATGGATGTCTTCATCAAGGCTGCTGAATATATGGAAATTCCAGTCCGTAGAACTGATGACGAACCTCTTCAAAAGCTTTTTATGTTGGTAAGG

upper sequence: Vv16s0050g01460.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT1G79940.3 (Arabidopsis thaliana), 3'ss of exon 6
gaaaaatgggtgtttatgtttatatatgtttttatgtatct--tagtgtgtgat-------ttctattataagttttgtttatga--tgatgtgataacttggttttacagCAAAGTTATGGATGTCTTCATTAAGGCTGCAGAATACATGGAAATTCCAGTCCGTAGGACTGACAATGAGCCCCTTCAGAAACTGTTCATGTTAGTAAGG
     ||      | ||    |||||  ||    ||   ||  | |||  |||         | | || |   || | | |||||  || | | | |  ||  || | ||||||||||||||| || ||||  ||||| || || |||||||| |||||||| ||||| |||||  |||| || || ||||| || || ||||  || |||
---gtatattcactcatacccatatacattcaagtgatgctattggtgcatgacaaatgggctgtgttttcgtttgtttgtatgacatgttttaaaatttttattgtccagCAAAGTTATGGAAGTTTTCACCAAGGCAGCTGAGTACATGGAGATTCCAGTTCGTAGAACTGATGATGAACCTCTGCAGAAGCTCTTTATGTCTGTTAGG

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|351014635|gb|FQ437637.1|FQ437637
EST:     CAAACTCTGTCTATTTACTATTACTTCATGAAACCTTCTTTGGCCCCAAG                         CAAAGTTATGGATGTCTTCATTAAGGCTGCAGAATACATGGAAATTCCAGT
genomic: CAAACTCTGTCTACTTACTATTACTTCATGAAACCTTCTTTGGCCCCAAGgtattatgtt ... ggttttacagCAAAGTTATGGATGTCTTCATTAAGGCTGCAGAATACATGGAAATTCCAGT
EST: gi|351040685|gb|FQ438229.1|FQ438229
EST:     CAAACTCTGTCTATTTACTATTACTTCATGAAACCTTCTTTGGCCCCAAG                         CAAAGTTATGGATGTCTTCATTAAGGCTGCAGAATACATGGAAATTCCAGT
genomic: CAAACTCTGTCTACTTACTATTACTTCATGAAACCTTCTTTGGCCCCAAGgtattatgtt ... ggttttacagCAAAGTTATGGATGTCTTCATTAAGGCTGCAGAATACATGGAAATTCCAGT
EST: gi|29782441|gb|CB347748.2|CB347748
EST:     AACTCTGTCTACTTACNGA-TCCTTCATG-AACCTTTC-TTGGCCCCAAG                         CAAAGTTATGGATGTCTTCATTAAGGCTGCAGAATACATGGAAATTCCAGT
genomic: AACTCTGTCTACTTAC-TATTACTTCATGAAACC-TTCTTTGGCCCCAAGgtattatgtt ... ggttttacagCAAAGTTATGGATGTCTTCATTAAGGCTGCAGAATACATGGAAATTCCAGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgtgatttctattataagttttgtttatgatgatgtgataacttggttttacagCAAAGTTATGGATGTCTTCATTAAGGCTGCAGAATACATGGAAATTCCAGTCCGTAGGACTGACAATGAGCCCCTTCAGAAACTGTTCATGTTAGTAAGG
                                    tgataac  putative branch site (score: 2)
     atttctattataagtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gaaaaatgggtgtttatgtttatatatgtttttatgtatcttagtgtgtgatttctattataagttttgtttatgatgatgtgataacttggttttacagCAAAGTTATGGATGTCTTCATTAAGGCTGCAGAATACATGGAAATTCCAGTCCGTAGGACTGACAATGAGCCCCTTCAGAAACTGTTCATGTTAGTAAGG

gaaaaat
- - - -gggtgtt
- - - - - - - - - - - - - - - - - - - - - -gtgtgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgatgtg