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'   		15  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CACTAGGTTAATACAAAGAGTTGCTCCAAAGAGTTATCAACAGGCTCTTGGTGAAGTTTATGTTACACAAAAATTTCTGGAGAATTTTTCTGGTGATCAGgtatatgatgataatttagcaaacaaaaccatttttctgtcagttgaaaaagaggacaaaaaaggaaaagaaagttccgtgaaattgcataattgatgtt...

Basic information

species Vitis vinifera
transcript Vv17s0000g05800.t01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv17s0000g05800.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA05G01290.1 (Glycine max), 5'ss of exon 5
CACTAGGTTAATACAAAGAGTTGCTCCAAAGAGTTATCAACAGGCTCTTGGTGAAGTTTATGTTACACAAAAATTTCTGGAGAATTTTTCTGGTGATCAGgtatatgatgataattta-gcaa--acaaaaccatttttctgtcagttgaaaaagaggacaaaaaaggaaaagaaagttccgtgaaattgcataattgatgtt
 || |||||||||||||||||| ||||||||||||| || |||||| |||| ||||| ||||| |||||||||||||| |||||||||| ||| |||||||||||| |  ||||   | |  |   | |||  | |    |  ||  | ||||| | | ||      | || ||| | |    |||     ||  || |  ||
TACGAGGTTAATACAAAGAGTTTCTCCAAAGAGTTACCAGCAGGCTTTTGGGGAAGTCTATGTGACACAAAAATTTCTAGAGAATTTTTGTGGAGATCAGgtatatcaaaataagacatgttagtgctaaataaatgaaattccaagt-aaaaatatgccattcgctgtaaggaatgatagaagaatcaaaat--ttcacatt

upper sequence: Vv17s0000g05800.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA17G10610.1 (Glycine max), 5'ss of exon 6
CACTAGGTTAATACAAAGAGTTGCTCCAAAGAGTTATCAACAGGCTCTTGGTGAAGTTTATGTTACACAAAAATTTCTGGAGAATTTTTCTGGTGATCAGgtatatgatgataattta-gcaa--acaaaaccatttttctgtcagttgaaaaagaggacaaaaaaggaaaagaaagttccgtgaaattgcataattgatgtt
 || |||||||||||||||||| ||||||||||||| || |||||| |||||||||| ||||| |||||||| ||||| |||||||||| ||| || ||||||||| |  ||||     |  |   | |||  | |    |  ||  | ||||| | | ||      | ||   ||     |  ||||  ||||||||    |
TACAAGGTTAATACAAAGAGTTTCTCCAAAGAGTTACCAGCAGGCTTTTGGTGAAGTCTATGTGACACAAAAGTTTCTAGAGAATTTTTGTGGAGACCAGgtatatcaaaataagacgcgttagtgctaaataaatgaaattccaagt-aaaaatatgccattctctgtaagagaataatagaaaaat--cataattgcccat

upper sequence: Vv17s0000g05800.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA05G01300.2 (Glycine max), 5'ss of exon 6
CACTAGGTTAATACAAAGAGTTGCTCCAAAGAGTTATCAACAGGCTCTTGGTGAAGTTTATGTTACACAAAAATTTCTGGAGAATTTTTCTGGTGATCAGgtatatgatgataattta-gcaa--acaaaaccatttttctgtcagttgaaaaagaggacaaaaaaggaaaagaaagttccgtgaaattgcataattgatgtt
 || | |||||||||||||||| ||||||||||||| || |||||| |||| ||||||||||| |||||||| ||||| ||||||||||  || |||||||||||| |  ||||  || |  |   | |||  | | |  |  ||  |  |||   |         | ||  ||  | |    |||  |  ||   | ||   
TACAAAGTTAATACAAAGAGTTTCTCCAAAGAGTTACCAGCAGGCTTTTGGGGAAGTTTATGTGACACAAAAGTTTCTAGAGAATTTTTGCGGGGATCAGgtatatcaaaataagatatgttagtgctaaataaatgtaatcccaagtacaaatatgccattctctgtaatggattgatggaagaatctaaattgctcat---

upper sequence: Vv17s0000g05800.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: PP1S41_177V6.1 (Physcomitrella patens), 5'ss of exon 7
CACTAGGTTAATACAAAGAGTTGCTCCAAAGAGTTATCAACAGGCTCTTGGTGAAGTTTATGTTACACAAAAATTTCTGGAGAATTTTTCTGGTGATCAGgtatatgatgataatttagcaaacaaaaccatttttctgtcagttgaaaaagaggacaaaa--aaggaaaagaaagttccgtgaaattgcataattgatgtt--
  |  |  | || ||  | ||||| |||||||| | |   |||||  | || || ||   |||||||||||||||||| ||||| ||||||||||||||||||||  || ||  ||| |||  ||   ||||      |  |||| | | ||  |        |    || |||  |||     | ||  ||  ||     |  
TGCCCGACTCATCCAGCGGGTTGCACCAAAGAGCTTTGCCCAGGCGGTAGGGGAGGTCACTGTTACACAAAAATTTCTCGAGAACTTTTCTGGTGATCAGgtata--attattcttttgcattcatggccatcaa--aggtagtttatagaggcgtttgctccactacaatgaagattctaaccacttttatttttttctctca

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|110718820|gb|EE096093.1|EE096093
EST:     GTGAAGTTTATGTTACGCAAAAATTTCTGGAGAATTTTTCTGGTGATCAG                         GTTCGTTTCCTGGCGAGGTCTTTTGCAGTGCCAGGAAATCATCTTGGGCAG
genomic: GTGAAGTTTATGTTACACAAAAATTTCTGGAGAATTTTTCTGGTGATCAGgtatatgatg ... tatctggcagGTTCGTTTCCTGGCGAGGTCTTTTGCAGTGCCAGGAAATCATCTTGGGCAG
EST: gi|161717382|gb|FC069212.1|FC069212
EST:     GTGAAGTTTATGTTACACAAAAATTTCTGGAGAATTTTTCTGGTGATCAG                         GTTCGTTTCCTGGCGAGGTCTTTTGCAGTGCCAGGAAATCATCTTGG
genomic: GTGAAGTTTATGTTACACAAAAATTTCTGGAGAATTTTTCTGGTGATCAGgtatatgatg ... tatctggcagGTTCGTTTCCTGGCGAGGTCTTTTGCAGTGCCAGGAAATCATCTTGG
EST: gi|71875127|gb|DT024182.1|DT024182
EST:     GTGAAGTTTATGTTACACAAAAATTTCTGGAGAATTTTTCTGGTGATCAG                         GTTCGTTTCCTGGCGAGGTCTTTTGCAGTGCCAGGAAATCATCTTGGGCAG
genomic: GTGAAGTTTATGTTACACAAAAATTTCTGGAGAATTTTTCTGGTGATCAGgtatatgatg ... tatctggcagGTTCGTTTCCTGGCGAGGTCTTTTGCAGTGCCAGGAAATCATCTTGGGCAG
EST: gi|161714309|gb|FC062610.1|FC062610
EST:     GTGAAGTTTATGTTACACAAAAATTTCTGGAGAATTTTTCTGGTGATCAG                         GTTCGTTTCCTGGCGAGGTCTTTTGCAGTGCCAGGAAATCATCT-GGGCAG
genomic: GTGAAGTTTATGTTACACAAAAATTTCTGGAGAATTTTTCTGGTGATCAGgtatatgatg ... tatctggcagGTTCGTTTCCTGGCGAGGTCTTTTGCAGTGCCAGGAAATCATCTTGGGCAG
EST: gi|37184316|gb|CF603670.1|CF603670
EST:     ATTTTTCTGGTGATCAG                         GTTCGTTTCCTGGCGAGGTCTTTTGCAGTGCCAGGAAATCATCTTGGGCAG
genomic: ATTTTTCTGGTGATCAGgtatatgatg ... tatctggcagGTTCGTTTCCTGGCGAGGTCTTTTGCAGTGCCAGGAAATCATCTTGGGCAG
EST: gi|110698054|gb|EE075624.1|EE075624
EST:     GTGAAGTTTATGTTACACAAAAATTTCTGGAGAATTTTTCTGGTGATCAG                         GTTCGTTTCCTGGCGAGGTCTTTTGCAGTGCCAGGAAATCATCTTGGGCAG
genomic: GTGAAGTTTATGTTACACAAAAATTTCTGGAGAATTTTTCTGGTGATCAGgtatatgatg ... tatctggcagGTTCGTTTCCTGGCGAGGTCTTTTGCAGTGCCAGGAAATCATCTTGGGCAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CACTAGGTTAATACAAAGAGTTGCTCCAAAGAGTTATCAACAGGCTCTTGGTGAAGTTTATGTTACACAAAAATTTCTGGAGAATTTTTCTGGTGATCAGgtatatgatgataatttagcaaacaaaaccatttttctgtcagttgaaaaagaggacaaaaaaggaaaagaaagttccgtgaaattgcataattgatgtt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gatgataa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaacaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaaaga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaaaag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaagaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtgaaat