Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattgcagtttttgtttctccccctccccccaacccccatgtgctaaaatggaactgatggttttttgaacaaagaatcctcagtctttgtggagtagaacatatcaattgtatgttatagtgctaaagtggggtttataattgtatttgcagCTCAATAGTCCTGATCTATTTGATATGTATTCTGCTGGCATTGTACTGATGCAAATGGCAGTACCAAGTTTGAGGTCTACAGCGGGCTTAAAGAATTTCA

Basic information

species Vitis vinifera
transcript Vv08s0058g01450.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0058g01450.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA18G44800.1 (Glycine max), 3'ss of exon 3
gtattgcagtttttgtttctccccctccccccaacccccatgtgctaaaatggaactgatggttttttgaacaaagaatcctca----gtctttgtggagtagaacatatcaattgtatgttatagtgctaaagtggggtttataattgtattt-gcagCTCAATAGTCCTGATCTATTTGATATGTATTCTGCTGGCATTGTACTGATGCAAATGGCAGTACCAAGTTTGAGGTCTACAGCGGGCTTAAAGAATTTCA
                                                       |||      | |  |  ||  |||| |||    ||| || ||    || ||| |    || ||   | || |||   |      |   |  |||| ||| |||| | || ||||||||||| ||||||||||||||||| || ||||||||  ||||||||||| ||||||  || |||||| |||| |  || ||||||||| 
-------------------------------------------------------ctggcatcgtat--agtaattaatcttcatggagtcattttgtttaagtacacacagtttttaatgtgta-tgcattatcctcttccctgtttgttttttgcaGTTAAACAGTCCTGATCTGTTTGATATGTATTCTGCCGGGATTGTACTCCTGCAAATGGCAATACCAACCTTAAGGTCTCCAGCTGCTTTGAAGAATTTC-

upper sequence: Vv08s0058g01450.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA16G34620.1 (Glycine max), 3'ss of exon 3
gtattgcagtttttgtttctccccctccccccaacccccatgtgctaaaatggaactgatggttttttgaacaaagaatcctcagtctttgtggagtagaacatatcaattgtatgttatagtgctaaagtggggtt-tataattgtatttgcagCTCAATAGTCCTGATCTATTTGATATGTATTCTGCTGGCATTGTACTGATGCAAATGGCAGTACCAAGTTTGAGGTCTACAGCGGGCTTAAAGAATTTCA
                                                     ||        |   ||||  ||  || ||| |  ||  |  |     || |||   |||      | ||||||||||||| ||| | | ||| |  |||||| | || || |||||| | |||||||||||||| ||||| ||||||||  ||||||||||| ||||||| || |||||| | || |  || ||||||||||
----------------------------------------------------taatcacatactgactgaattaactattctccggtttgttccacatatacctatt--ttgctcagga-agtgctaaagtggagttatgtgattattgttgcagTTAAACAGCCCTGATTTGTTTGATATGTATTCAGCTGGGATTGTACTCCTGCAAATGGCAATACCAAGCTTAAGGTCTCCTGCTGCTTTGAAGAATTTCA
















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|351022402|gb|FQ445177.1|FQ445177
EST:     NNNNNNNTCCAGAGCCGATTGCTGCCTTTCTTTCTCCAATTTTATGGCAG                         CTCAATAGTCCTGATCTATTTGATATGTATTCTGCTGGCATTGTACTGATG
genomic: CCCCCCCTCCAGAGCCGATTGCTGCCTTTCTTTCTCCAATTTTATGGCAGgtattgcagt ... gtatttgcagCTCAATAGTCCTGATCTATTTGATATGTATTCTGCTGGCATTGTACTGATG
EST: gi|352768164|gb|FQ467303.1|FQ467303
EST:     NNNNNNNTCCAGAGCCGATTGCTGCCTTTCTTTCTCCAATTTTATGGCAG                         CTCAATAGTCCTGATCTATTTGATATGTATTCTGCTGGCATTGTACTGATG
genomic: CCCCCCCTCCAGAGCCGATTGCTGCCTTTCTTTCTCCAATTTTATGGCAGgtattgcagt ... gtatttgcagCTCAATAGTCCTGATCTATTTGATATGTATTCTGCTGGCATTGTACTGATG
EST: gi|352776905|gb|FQ474212.1|FQ474212
EST:     NNNNNNNTCCAGAGCCGATTGCTGCCTTTCTTTCTCCAATTTTATGGCAG                         CTCAATAGTCCTGATCTATTTGATATGTATTCTGCTGGCATTGTACTGATG
genomic: CCCCCCCTCCAGAGCCGATTGCTGCCTTTCTTTCTCCAATTTTATGGCAGgtattgcagt ... gtatttgcagCTCAATAGTCCTGATCTATTTGATATGTATTCTGCTGGCATTGTACTGATG
EST: gi|351033956|gb|FQ463011.1|FQ463011
EST:     NNNNNNNTCCAGAGCCGATTGCTGCCTTTCTTTCTCCAATTTTATGGCAG                         CTCAATAGTCCTGATCTATTTGATATGTATTCTGCTGGCATTGTACTGATG
genomic: CCCCCCCTCCAGAGCCGATTGCTGCCTTTCTTTCTCCAATTTTATGGCAGgtattgcagt ... gtatttgcagCTCAATAGTCCTGATCTATTTGATATGTATTCTGCTGGCATTGTACTGATG
EST: gi|110698906|gb|EE076940.1|EE076940
EST:     NNNNNNNTCCAGAGCCGATTGCTGCCTTTCTTTCTCCAATTTTATGGCAG                         CTCAATAGTCCTGATCTATTTGATATGTATTCTGCTGGCATTGTACTGATG
genomic: CCCCCCCTCCAGAGCCGATTGCTGCCTTTCTTTCTCCAATTTTATGGCAGgtattgcagt ... gtatttgcagCTCAATAGTCCTGATCTATTTGATATGTATTCTGCTGGCATTGTACTGATG
EST: gi|351057171|gb|FQ450878.1|FQ450878
EST:     NNNNNNNTCCAGAGCCGATTGCTGCCTTTCTTTCTCCAATTTTATGGCAG                         CTCAATAGTCCTGATCTATTTGATATGTATTCTGCTGGCATTGTACTGATG
genomic: CCCCCCCTCCAGAGCCGATTGCTGCCTTTCTTTCTCCAATTTTATGGCAGgtattgcagt ... gtatttgcagCTCAATAGTCCTGATCTATTTGATATGTATTCTGCTGGCATTGTACTGATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aacatatcaattgtatgttatagtgctaaagtggggtttataattgtatttgcagCTCAATAGTCCTGATCTATTTGATATGTATTCTGCTGGCATTGTACTGATGCAAATGGCAGTACCAAGTTTGAGGTCTACAGCGGGCTTAAAGAATTTCA
                       tgctaaa  putative branch site (score: 2)
                                    tttataattgtattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattgcagtttttgtttctccccctccccccaacccccatgtgctaaaatggaactgatggttttttgaacaaagaatcctcagtctttgtggagtagaacatatcaattgtatgttatagtgctaaagtggggtttataattgtatttgcagCTCAATAGTCCTGATCTATTTGATATGTATTCTGCTGGCATTGTACTGATGCAAATGGCAGTACCAAGTTTGAGGTCTACAGCGGGCTTAAAGAATTTCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA