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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgttaacgagtgaatgtattacttcatgttccactaaactgttcattttactcgtcattctttaattatttttacatttatcttgtcatttctttctctaattataagattataacacttcactttttggaacagGTTAACCCACATACCCACCAGCTAAAGCTATGTGATTTTGGAAGTGCAAAAGTTTTG

Basic information

species Vitis vinifera
transcript Vv07s0005g02100.t01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv07s0005g02100.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: PP1S306_62V6.1 (Physcomitrella patens), 3'ss of exon 4
-----------------------gtatgttaacgagtgaatgtattacttcatgtt--ccactaaactgttcatttt----actcgtcattctttaattatttttacatttat-cttgtcatttctttctctaat-tataaga------------ttataacac-ttcactttt---tggaacagGTTAACCCACATACCCACCAGCTAAAGCTATGTGATTTTGGAAGTGCAAAAGTTTTG
                         ||||   | |||   |  |  ||   ||| |  |   | ||    || | ||     |||| |||   |  |   |  ||||    ||  |||  ||   |  |   ||  || | ||            |  |||||   |    |||   ||| |||||| || || ||||| |||||||| || || ||||||||||||||||| |||||  ||
gtacgtgtgtccgacgaatcttgtcatgtgttcaagtatcttgaaaacacgatgctgactgtttaagcactcgtatttgttgctcggcatgggtggaagctggttactgagatgtttggtatgagtcacgggaaagtacaggagttgccgtggtgtcgtaacaaacttgtgtttgcatggcacagGTGAATCCTCATACGCACCAGCTGAAACTGTGTGATTTTGGAAGTGCGAAAGTGCTG

upper sequence: Vv07s0005g02100.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: PP1S52_55V6.1 (Physcomitrella patens), 3'ss of exon 5
-----------------------gtatgttaacgag--tgaatgtattac--ttcatgttccactaaactgtt--cattttactcgtcattctttaattatttttacatttatcttgtcatttctttctctaattataagattataacacttcactttt-tggaacagGTTAACCCACATACCCACCAGCTAAAGCTATGTGATTTTGGAAGTGCAAAAGTTTTG
                       |||||| ||   |   || |  |  ||  || | |  | ||     || |   |||    | |      ||| ||| | |   |||  |    ||  |     | |  || | |     |  |    ||   || | |||  ||||| || || || || || |||||||||||||| || ||||||||||| |||||||||
gtaatattgtgttgtgagtattagtatgtaaatatggtcgactcgagcacagtttaagaccgacagttgtggtattattgaggtggatgaggtttgattgtatgagcatcgagga-gttgtcaaggtgtggaagtgtggtgatgaagaggttggtttgtgtggtgcagGTGAATCCCCACACGCATCAGCTAAAGCTATGCGACTTTGGAAGTGCGAAAGTTTTG

upper sequence: Vv07s0005g02100.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: EFJ04915 (Selaginella moellendorffii), 3'ss of exon 5
gtatgttaacgagtgaatgtattacttcatgttccactaaactgttcattttactcgtcattctttaattatttttacatttatcttgtcatttctttctctaattataagattataacacttcactttttggaacagGTTAACCCACATACCCACCAGCTAAAGCTATGTGATTTTGGAAGTGCAAAAGTTTTG
                                                                                 ||    ||| ||    |    | | ||  |    ||   |||   || |  | ||||||||| || ||||| |||||||| ||||||||||||||||| || || |||||  ||
--------------------------------------------------------------------------------gtaggaggtccttgtccttaggattgatttgtacttactgcttttgttgtaagtacagGTTAATCCCCATACACACCAGCTGAAGCTATGTGATTTTGGCAGCGCCAAAGTGCTG

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|33405137|gb|CF210764.1|CF210764
EST:     ATGGTGGTATTGGAGTATGCCACAGGGATATAAAACCTCAAAATTTATTG                         GCTAACCCACATACCCACCAGCTAAAGCTATGTGATTTTGGAAGTGCAAAA
genomic: ATGGTGGTATTGGAGTATGCCACAGGGATATAAAACCTCAAAATTTATTGgtatgttaac ... tttggaacagGTTAACCCACATACCCACCAGCTAAAGCTATGTGATTTTGGAAGTGCAAAA
EST: gi|30125127|gb|CB910466.1|CB910466
EST:     ATGGTGGTATTGGAGTATGCCACAGGTATATAAAACCTCAAAATTTATTG                         GTTAACCCACATACCCACCAGCTAAAGCTATGTGATTTTGGAAGTGCAAAA
genomic: ATGGTGGTATTGGAGTATGCCACAGGGATATAAAACCTCAAAATTTATTGgtatgttaac ... tttggaacagGTTAACCCACATACCCACCAGCTAAAGCTATGTGATTTTGGAAGTGCAAAA
EST: gi|161712353|gb|FC061927.1|FC061927
EST:     ATGGTGGTATTGGAGTATGCCACAGGGATATAAAACCTCAAAATTTATTG                         GTTAACCCACATACCCACCAGCTAAAGCTATGTGATTTTGGAAGTGCAAAA
genomic: ATGGTGGTATTGGAGTATGCCACAGGGATATAAAACCTCAAAATTTATTGgtatgttaac ... tttggaacagGTTAACCCACATACCCACCAGCTAAAGCTATGTGATTTTGGAAGTGCAAAA
EST: gi|30133168|gb|CB918507.1|CB918507
EST:     ATGGTGGTATTGGAGTATGCCACAGGTATATAAAACCTCAAAATTTATTG                         GTTAACCCACATACCCACCAGCTAAAGCTATGTGATTTTGGAAGTGCAAAA
genomic: ATGGTGGTATTGGAGTATGCCACAGGGATATAAAACCTCAAAATTTATTGgtatgttaac ... tttggaacagGTTAACCCACATACCCACCAGCTAAAGCTATGTGATTTTGGAAGTGCAAAA
EST: gi|110710881|gb|EE087442.1|EE087442
EST:     ATGGTGGTATTGGAGTATGCCACAGGGATATAAAACCTCAAAATTTATTG                         GTTAACCCACATACCCACCAGCTAAAGCTATGTGATTTTGGAAGTGCAAAA
genomic: ATGGTGGTATTGGAGTATGCCACAGGGATATAAAACCTCAAAATTTATTGgtatgttaac ... tttggaacagGTTAACCCACATACCCACCAGCTAAAGCTATGTGATTTTGGAAGTGCAAAA
EST: gi|71875370|gb|DT024425.1|DT024425
EST:     ATGGTGGTATTGGAGTATGCCACAGGGATATAAAACCTCAAAATTTATTG                         GTTAACCCACATACCCACCAGCTAAAGCTATGTGATTTTGGAAGTGCAAAA
genomic: ATGGTGGTATTGGAGTATGCCACAGGGATATAAAACCTCAAAATTTATTGgtatgttaac ... tttggaacagGTTAACCCACATACCCACCAGCTAAAGCTATGTGATTTTGGAAGTGCAAAA
EST: gi|110700287|gb|EE078155.1|EE078155
EST:     ATTGGAGTATGTCACAGGGATATAAAACCTCAAAATTTATTG                         GTTAACCCACATACCCACCAGCTAAAGCTATGTGATTTTGGAAGTGCAAAA
genomic: ATTGGAGTATGCCACAGGGATATAAAACCTCAAAATTTATTGgtatgttaac ... tttggaacagGTTAACCCACATACCCACCAGCTAAAGCTATGTGATTTTGGAAGTGCAAAA
EST: gi|30252766|gb|CB970317.1|CB970317
EST:     ATGGTGGTATTGGAGTATGCCTCAGGGATATAAAACCTCAAAATTTATTG                         GTTAACCCACATACCCACCAGCTAAAGCTATGTGATTTTGGAAGTGCAAAA
genomic: ATGGTGGTATTGGAGTATGCCACAGGGATATAAAACCTCAAAATTTATTGgtatgttaac ... tttggaacagGTTAACCCACATACCCACCAGCTAAAGCTATGTGATTTTGGAAGTGCAAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttgtcatttctttctctaattataagattataacacttcactttttggaacagGTTAACCCACATACCCACCAGCTAAAGCTATGTGATTTTGGAAGTGCAAAAGTTTTG
                             ttataac  putative branch site (score: 2)
                                     cttcacttttt  CT-rich tract
       atttctttctctaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgttaacgagtgaatgtattacttcatgttccactaaactgttcattttactcgtcattctttaattatttttacatttatcttgtcatttctttctctaattataagattataacacttcactttttggaacagGTTAACCCACATACCCACCAGCTAAAGCTATGTGATTTTGGAAGTGCAAAAGTTTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG