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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACGGCCTCAAGGTGGACAAGATATATTGTCCCTAATGGGTCAGATGATGAAGCCCAGGAAAACAGAAATCACTGATAAGTTACGACAGGAAATTAACAAGgtatcattttctggatgggagatattaacctatattttttcatttcttttgaactctaaatctgtagttatacaaacaggttaattggggaacaatcttt...

Basic information

species Vitis vinifera
transcript Vv06s0004g02910.t01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0004g02910.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: LOC_Os07g08170.1 (Oryza sativa), 5'ss of exon 6
ACGGCCTCAAGGTGGACAAGATATATTGTCCCTAATGGGTCAGATGATGAAGCCCAGGAAAACAGAAATCACTGATAAGTTACGACAGGAAATTAACAAGgtatc---attttctggatgggag-atattaacctatattttttcatttcttttgaactctaaatctgtagttatacaaacaggttaattggggaacaatcttt------
 |  || ||||| || |||||||| |||||||| ||||| ||||||||||||||  ||||||| ||||||||||| ||| ||||||| ||||| || |||||||    |||| |    | | || |      | | ||    |  |   | ||| |     |  || | | |   | |      ||||       ||  | | |      
TCAACCACAAGGAGGCCAAGATATTTTGTCCCTTATGGGACAGATGATGAAGCCACGGAAAACTGAAATCACTGAGAAGCTACGACAAGAAATCAATAAGgtattcaaatttcccatgtagcagcactgctgcttttaaaagtggaccacatttaataaacatgtcaggattggcatatgatctttaacatctatactgtatgttgctag

upper sequence: Vv06s0004g02910.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GRMZM2G032267_T02 (Zea mays), 5'ss of exon 6
ACGGCCTCAAGGTGGACAAGATATATTGTCCCTAATGGGTCAGATGATGAAGCCCAGGAAAACAGAAATCACTGATAAGTTACGACAGGAAATTAACAAGgtatcattttctggatgggagatattaacctatattttttcatttcttttgaactctaaatctgtagttatacaaacaggttaattggggaacaatcttt------------
 | ||| |||||||| |||||||| |||||||| ||||| ||||||||||||||  |||| || |||||||| || ||| |||| || ||||| || ||||| |   ||| |   |       | |    |   |||| |      | |  || | ||    | || | ||  ||  |  || |   |     ||  |||            
CCAGCCACAAGGTGGCCAAGATATTTTGTCCCTTATGGGCCAGATGATGAAGCCACGGAAGACTGAAATCACCGAAAAGCTACGCCAAGAAATCAATAAGgttttgattttttttttcagctaactttttttagttttataggcagtatcaaatttta----tataatcatgtaagaatcttcacctgattttaaattttacatggtgaaag

upper sequence: Vv06s0004g02910.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GRMZM2G018697_T03 (Zea mays), 5'ss of exon 7
ACGGCCTCAAGGTGGACAAGATATATTGTCCCTAATGGGTCAGATGATGAAGCCCAGGAAAACAGAAATCACTGATAAGTTACGACAGGAAATTAACAAGgtatcattttctggatgggagatattaacctatattttttcatttcttttg-aactctaaatctg--tagttatacaaacaggtt-aattggggaacaatcttt-----------
 | ||| |||||||| |||||||| |||||||| ||||| ||||||||||| ||  | || || |||||||| || ||  |||| || |||||||| ||||| |  || | |           | ||  | || ||||||  ||||||  | |     |||| ||  ||   ||| ||  |  || |  |||     ||| ||            
TCAGCCACAAGGTGGCCAAGATATTTTGTCCCTTATGGGCCAGATGATGAAACCACGAAAGACTGAAATCACCGAAAAACTACGCCAAGAAATTAATAAGgttttcttctttttg--------acta--ccattttttttagtttcttaggcagtatcaaatttggataaccatataagaattttcagctggtttttaattttatatgatgacag

upper sequence: Vv06s0004g02910.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA08G21830.1 (Glycine max), 5'ss of exon 6
ACGGCCTCAAGGTGGACAAGATATATTGTCCCTAATGGGTCAGATGATGAAGCCCAGGAAAACAGAAATCACTGATAAGTTACGACAGGAAATTAACAAGgtatcattttctggatgggagatattaacctatattttttcatttcttttgaactctaaa--tctgtagttatacaaacaggttaattggg-gaacaatcttt
||| |||||||| |||||||||||  |||| || ||||||||||||||||||||||||||||||||||||||||| |||||  | || || |||||||||||||   |||    |     ||||  |   | || ||| | |||| |    ||   |||   ||   |  |   |       |||       |  ||||   |
ACGACCTCAAGGGGGACAAGATATTCTGTCTCTGATGGGTCAGATGATGAAGCCCAGGAAAACAGAAATCACTGACAAGTTGAGGCAAGAGATTAACAAGgtat---tttaataacttttgatacaagtttgtagtttcttatttatgggaaaaattaagggtcgaaaagtgagcttttgtcttagcaatttgttcaattgct

upper sequence: Vv06s0004g02910.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA07G02170.1 (Glycine max), 5'ss of exon 6
ACGGCCTCAAGGTGGACAAGATATATTGTCCCTAATGGGTCAGATGATGAAGCCCAGGAAAACAGAAATCACTGATAAGTTACGACAGGAAATTAACAAGgtatcattttctggatgggagatattaacctatattttttcatttcttttgaactct-----aaatctgtagttatacaaacaggttaattggggaacaatcttt
||| |||||||| |||||||||||  |||| || |||||||||||||||||||| ||||||||||| |||||||| |||||  | || ||||||||||||||||   ||||   |     ||||  |   | || |||  ||| | |  | |  | |     ||||     ||   | |||   | |  ||    | |||| | |
ACGACCTCAAGGGGGACAAGATATTCTGTCTCTTATGGGTCAGATGATGAAGCCTAGGAAAACAGAGATCACTGACAAGTTGAGGCAAGAAATTAACAAGgtat---tttcataacttttgatacaagtttgtagttt--catctttaattagttatggggaaaattaagggtctaaaaaatgagcttttttcttagcaatttct

upper sequence: Vv06s0004g02910.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: PP1S4_73V6.1 (Physcomitrella patens), 5'ss of exon 7
ACGGCCTCAAGGTGGACAAGATATATTGTCCCTAATGGGTCAGATGATGAAGCCCAGGAAAACAGAAATCACTGATAAGTTACGACAGGAAATTAACAAGgtatcattttctgg------atgggagatattaacctatattttttcat----ttcttttg-aactctaaatctgtagtta-----tacaaacaggttaattggggaacaatcttt-----------------------------
 || |||||||| || ||||||||||||||| | ||||| ||||||||||| ||  | || || ||||| |||||||| |||||||| || ||||||||||||   |||  ||          |    |||  ||    |   |   |     |  | ||| |||  || ||   || | |     ||       || |   ||| ||| |  ||                              
TCGCCCTCAAGGAGGCCAAGATATATTGTCCATGATGGGCCAGATGATGAAACCTCGTAAGACTGAAATTACTGATAAATTACGACAAGAGATTAACAAGgtaatttttcttgacgctgtgctgtgagtatggacaagaaacctcgtacaaagtcgtgttgtaacattatattattaatcaagaggtaatgctgagtcagaagggcaacgagtttgagatggtttctcgttcatttgtggtgcag

upper sequence: Vv06s0004g02910.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: EFJ33466 (Selaginella moellendorffii), 5'ss of exon 6
ACGGCCTCAAGGTGGACAAGATATATTGTCCCTAATGGGTCAGATGATGAAGCCCAGGAAAACAGAAATCACTGATAAGTTACGACAGGAAATTAACAAGgtatcattttctggatgggagatattaacctatattttttcatttcttttgaactctaaatctgtagttatacaaacaggttaattggggaacaatcttt
 || ||||||||||||||||||||  | ||| | ||||| |||||||||||||| |  || || || |||||||||||| | || |||||||| ||||||||       |       || | |  | | || |  | ||||     ||||  | |     |||  ||   ||      |  |  ||| || |        
GCGTCCTCAAGGTGGACAAGATATTCTTTCCATGATGGGACAGATGATGAAGCCGAAAAAGACTGAGATCACTGATAAGCTGCGGCAGGAAATCAACAAGgt-------tagcagccggcgttcgtcagctctcctgtttcgaggattttctatt----gtctaaaggattatgtgtggcatgtttgtggcag-------

upper sequence: Vv06s0004g02910.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: EFJ27201 (Selaginella moellendorffii), 5'ss of exon 6
ACGGCCTCAAGGTGGACAAGATATATTGTCCCTAATGGGTCAGATGATGAAGCCCAGGAAAACAGAAATCACTGATAAGTTACGACAGGAAATTAACAAGgtatcattttctggatgggagatattaacctatattttttcatttcttttgaactctaaatctgtagttatacaaacaggttaattggggaacaatcttt
 || ||||||||||||||||||||  | ||| | ||||| |||||||||||||| |  || || || |||||||||||  |||| || ||||| ||||||||       | |   |  |   |  |    |     |||||  || | | ||    ||  | ||   |  |     |||                     
GCGTCCTCAAGGTGGACAAGATATTCTTTCCATGATGGGACAGATGATGAAGCCGAAAAAGACTGAGATCACTGATAAACTACGGCAAGAAATCAACAAGgttagccggtgttcgtcagctctcctgttttgaggattttctattgtctagaggattatgtgtgggatctttgtggcag---------------------

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|27586915|gb|CB009610.1|CB009610
EST:     GGAAAACAGAAATCACTGATAAGTTACGACAGGAAATTAACAAG                         GTTGTTAACCGTTACATCGATGAAGGTGTGGCAGAGCTTGTTCCTGGGGTC
genomic: GGAAAACAGAAATCACTGATAAGTTACGACAGGAAATTAACAAGgtatcatttt ... tgaatgacagGTTGTTAACCGTTACATCGATGAAGGTGTGGCAGAGCTTGTTCCTGGGGTC
EST: gi|71885171|gb|DT034226.1|DT034226
EST:     AGCCCAGGAAAACAGAAATCACTGATAAGTTACGACAGGAAATTAACAAG                         GTTGTTAACCGTTACATCGATGAAGGTGTGGCAGAGCTTGTTCCTGGGGTC
genomic: AGCCCAGGAAAACAGAAATCACTGATAAGTTACGACAGGAAATTAACAAGgtatcatttt ... tgaatgacagGTTGTTAACCGTTACATCGATGAAGGTGTGGCAGAGCTTGTTCCTGGGGTC
EST: gi|110689388|gb|EE065570.1|EE065570
EST:     AGCCCAGGAAAACAGAAATCACTGATAAGTTACGACAGGAAATTAACAAG                         GTTGTTAACCGTTACATCGATGAAGGTGTGGCAGAGCTTGTTCCTGGGGTC
genomic: AGCCCAGGAAAACAGAAATCACTGATAAGTTACGACAGGAAATTAACAAGgtatcatttt ... tgaatgacagGTTGTTAACCGTTACATCGATGAAGGTGTGGCAGAGCTTGTTCCTGGGGTC
EST: gi|71863654|gb|DT012709.1|DT012709
EST:     AGCCCAGGAAAACAGAAATCACTGATAAGTTACGACAGGAAATTAACAAG                         GTTGTTAACCGTTACATCGATGAAGGTGTGGCAGAGCTTGTTCCTGGGGTC
genomic: AGCCCAGGAAAACAGAAATCACTGATAAGTTACGACAGGAAATTAACAAGgtatcatttt ... tgaatgacagGTTGTTAACCGTTACATCGATGAAGGTGTGGCAGAGCTTGTTCCTGGGGTC
EST: gi|71865178|gb|DT014233.1|DT014233
EST:     AGCCCAGGAAAACAGAAATCACTGATAAGTTACGACAGGAAATTAACAAG                         GTTGTTAACCGTTACATCGATGAAGGTGTGGCAGAGCTTGTTCCTGGGGTC
genomic: AGCCCAGGAAAACAGAAATCACTGATAAGTTACGACAGGAAATTAACAAGgtatcatttt ... tgaatgacagGTTGTTAACCGTTACATCGATGAAGGTGTGGCAGAGCTTGTTCCTGGGGTC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACGGCCTCAAGGTGGACAAGATATATTGTCCCTAATGGGTCAGATGATGAAGCCCAGGAAAACAGAAATCACTGATAAGTTACGACAGGAAATTAACAAGgtatcattttctggatgggagatattaacctatattttttcatttcttttgaactctaaatctgtagttatacaaacaggttaattggggaacaatcttt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -atacaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggaacaa