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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaaaaacttggttcttgaaaatatacaattatatccttttgtcatatggagcctatggattgttgaggctaagcaatgttttcttgtttgaattgaacagATATACCCACCAATCAATGTCCTCCCATCACTGTCTCGTTTAATGAAG

Basic information

species Vitis vinifera
transcript Vv03s0038g02760.t01
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv03s0038g02760.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA20G24070.2 (Glycine max), 3'ss of exon 12
aaaaaacttggttcttgaaaatatacaatta-tatccttttgtcatatggagcctatgg-attgttgaggctaagcaatgttttcttgtttgaattgaacagATATACCCACCAATCAATGTCCTCCCATCACTGTCTCGTTTAATGAAG
       |   | |||||| |  | || ||| | |   ||    || | ||    ||      |   |  |||| || | |  |  | ||| || ||  |||||||||||||||||||| |||||||||||||| ||||| || ||||||
-ggtggttaattgcttgaatagttgcatttactgttgattaactatgtagatttaatattgaggccaaaactaaacattctaattattttt-aactgggcagATATACCCACCAATCAACGTCCTCCCATCACTATCTCGGTTGATGAAG

upper sequence: Vv03s0038g02760.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA09G38110.1 (Glycine max), 3'ss of exon 11
aaaaaacttggttcttgaaaatatacaattatatccttttgtcatatggagcctatggattgtt-----gaggctaagcaatgttttcttgtttgaattgaacagATATACCCACCAATCAATGTCCTCCCATCACTGTCTCGTTTAATGAAG
       |   ||   | |  |||  ||||| | ||  ||  || || |  | || | | | ||     ||  |||| || |   ||| | ||| | | |  |||||||| ||||||||||||||||| |||||| |||||||||| ||||||
-tcttgatgtatttaagtaggtatcaaattaaagccactttgcaaattg--cttacgaaatattagactgaaactaaacattcaattccttttttattgg--cagATATATCCACCAATCAATGTCCTTCCATCATTGTCTCGTTTGATGAAG

upper sequence: Vv03s0038g02760.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA10G42940.2 (Glycine max), 3'ss of exon 11
--aaaaaacttggttcttgaaaatatacaattatatccttttgtcatatggagcctatgg-attgttgaggctaagcaatgttttcttgtttgaattgaacagATATACCCACCAATCAATGTCCTCCCATCACTGTCTCGTTTAATGAAG
   |  |  | | || ||| | || |    | ||     ||    || ||||    ||      |   |  |||| || | |  |  | ||| || ||| ||||||||||||||||||||||||||||| ||||| ||||| || ||||||
gtcaccatttagattgttggagatttttgttgat--tgattaactatgtggatttaatattgaggccaaacctaaacattctaattcttttt-aactgagcagATATACCCACCAATCAATGTCCTCCCGTCACTATCTCGGTTGATGAAG

upper sequence: Vv03s0038g02760.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA18G48280.1 (Glycine max), 3'ss of exon 11
aaaaaacttggttcttgaaaatatacaatta--tatccttttgtcatatggagcctatggattgttgaggctaagc--aatgttt--tcttgtttgaattgaacagATATACCCACCAATCAATGTCCTCCCATCACTGTCTCGTTTAATGAAG-
      ||  ||||||||   |||  || ||  ||||   ||          || || | | | ||      || |  ||  ||   |    |||  ||||| |||||||| || |||||||||||||| |||||| |||||||||| |||||| 
-----gctctgttcttgatg-tatttaagtaggtatcaaattaaagccacttgcttacgaaatattagactgaaacttaacattcaattccttttttattga-cagaTATATCCTCCAATCAATGTCCTTCCATCATTGTCTCGTTTGATGAAGG

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|110375541|gb|EC940537.1|EC940537
EST:     ATATCACTGAGGGTCAGATTTACATTGACAGACAGCTCCACAATCGACAG                         ATATACCCACCAATCAATGTCCTGCCATCACTGTCTCGTTTAATGAAG
genomic: ATATCACTGAGGGCCAGATTTACATTGACAGACAGCTCCACAATCGACAGgtaaggttat ... aattgaacagATATACCCACCAATCAATGTCCTCCCATCACTGTCTCGTTTAATGAAG
EST: gi|110362645|gb|EC926192.1|EC926192
EST:     ATATCACTGAGGGTCAGATTTACATTGACAGACAGCTCCACAATCGACAG                         ATATACCCACCAATCAATGTCCTGCCATCACTGTCTCGTTTAATGAAG
genomic: ATATCACTGAGGGCCAGATTTACATTGACAGACAGCTCCACAATCGACAGgtaaggttat ... aattgaacagATATACCCACCAATCAATGTCCTCCCATCACTGTCTCGTTTAATGAAG
EST: gi|110357509|gb|EC921103.1|EC921103
EST:     ATATCACTGAGGGTCAGATTTACATTGACAGACAGCTCCACAATCGACAG                         ATATACCCACCAATCAATGTCCTGCCATCACTGTCTCGTTTAATGAAG
genomic: ATATCACTGAGGGCCAGATTTACATTGACAGACAGCTCCACAATCGACAGgtaaggttat ... aattgaacagATATACCCACCAATCAATGTCCTCCCATCACTGTCTCGTTTAATGAAG
EST: gi|110720101|gb|EE095728.1|EE095728
EST:     ATATCACTGAGGGCCAGATTTACATTGACAGACAGCTCCACAATCGACAG                         ATATACCCACCAATCAATGTCCTCCCATCACTGTCTCGTTTAATGAAG
genomic: ATATCACTGAGGGCCAGATTTACATTGACAGACAGCTCCACAATCGACAGgtaaggttat ... aattgaacagATATACCCACCAATCAATGTCCTCCCATCACTGTCTCGTTTAATGAAG
EST: gi|110719306|gb|EE097131.1|EE097131
EST:     ATATCACTGAGGGCCAGATTTACATTGACAGACAGCTCCACAATCGACAG                         ATATACCCACCAATCAATGTCCTCCCATCACTGTCTCGTTTAATGAAG
genomic: ATATCACTGAGGGCCAGATTTACATTGACAGACAGCTCCACAATCGACAGgtaaggttat ... aattgaacagATATACCCACCAATCAATGTCCTCCCATCACTGTCTCGTTTAATGAAG
EST: gi|22013013|gb|BQ798047.1|BQ798047
EST:     ATCACTGAGGGCCAGATTTACATTGACAGACAGCTCCACAATCGACAG                         ATATACCCACCAATCAATGTCCTCCCATCACTGTCTCGTTTAATGAAG
genomic: ATCACTGAGGGCCAGATTTACATTGACAGACAGCTCCACAATCGACAGgtaaggttat ... aattgaacagATATACCCACCAATCAATGTCCTCCCATCACTGTCTCGTTTAATGAAG
EST: gi|110712807|gb|EE088186.1|EE088186
EST:     ATATCACTGAGGGCCAGATTTACATTGACAGACAGCTCCACAATCGACAG                         ATATACCCACCAATCAATGTCCTCCCATCACTGTCTCGTTTAATGAAG
genomic: ATATCACTGAGGGCCAGATTTACATTGACAGACAGCTCCACAATCGACAGgtaaggttat ... aattgaacagATATACCCACCAATCAATGTCCTCCCATCACTGTCTCGTTTAATGAAG
EST: gi|30251466|gb|CB969199.1|CB969199
EST:     ATATCACTGAGGGTCAGATTTACATTGACAGACAGCTCCACAATCGACAG                         ATATACCCACCAATCAATGTCCTGCCATCACTGTCTCGTTTAATGAAG
genomic: ATATCACTGAGGGCCAGATTTACATTGACAGACAGCTCCACAATCGACAGgtaaggttat ... aattgaacagATATACCCACCAATCAATGTCCTCCCATCACTGTCTCGTTTAATGAAG
EST: gi|110690712|gb|EE068109.1|EE068109
EST:     ATATCACTGAGGGTCAGATTTACATTGACAGACAGCTCCACAATCGACAG                         ATATACCCACCAATCAATGTCCTCCCATCACTGTCTCGTTTAATGAAG
genomic: ATATCACTGAGGGCCAGATTTACATTGACAGACAGCTCCACAATCGACAGgtaaggttat ... aattgaacagATATACCCACCAATCAATGTCCTCCCATCACTGTCTCGTTTAATGAAG
EST: gi|33402634|gb|CF208261.1|CF208261
EST:     ATATCACTGAGGGTCAGATTTACATTGACAGACAGCTCCACAATCGACAG                         ATATACCCACCAATCAATGTCCTCCCATCACTGTCTCGTTTAATGAAG
genomic: ATATCACTGAGGGCCAGATTTACATTGACAGACAGCTCCACAATCGACAGgtaaggttat ... aattgaacagATATACCCACCAATCAATGTCCTCCCATCACTGTCTCGTTTAATGAAG
EST: gi|110723346|gb|EE100552.1|EE100552
EST:     ATATCACTGAGGGCCAGATTTACATTGACAGACAGCTCCACAATCGACAG                         ATATACCCACCAATCAATGTCCTCCCATCACTGTCTCGTTTAATGAAG
genomic: ATATCACTGAGGGCCAGATTTACATTGACAGACAGCTCCACAATCGACAGgtaaggttat ... aattgaacagATATACCCACCAATCAATGTCCTCCCATCACTGTCTCGTTTAATGAAG
EST: gi|34542515|gb|CF510747.1|CF510747
EST:     ATATCACTGAGGGTCAGATTTACATTGACAGACAGCTCCACAATCGACAG                         ATATACCCACCAATCAATGTCCTGCCATCACTGTCTCGTTTAATGAAG
genomic: ATATCACTGAGGGCCAGATTTACATTGACAGACAGCTCCACAATCGACAGgtaaggttat ... aattgaacagATATACCCACCAATCAATGTCCTCCCATCACTGTCTCGTTTAATGAAG
EST: gi|349813104|gb|FQ411344.1|FQ411344
EST:     ATATCACTGAGGGCCAGATTTACATTGACAGACAGCTCCACAATCGACAG                         ATATACCCACCAATCAATGTCCTCCCATCACTGTCTCGTTTAATGAAG
genomic: ATATCACTGAGGGCCAGATTTACATTGACAGACAGCTCCACAATCGACAGgtaaggttat ... aattgaacagATATACCCACCAATCAATGTCCTCCCATCACTGTCTCGTTTAATGAAG
EST: gi|110414446|gb|EC980278.1|EC980278
EST:     ATATCACTGAGGGTCAGATTTACATTGACAGACAGCTCCACAATCGACAG                         ATATACCCACCAATCAATGTCCTGCCATCACTGTCTCGTTTAATGAAG
genomic: ATATCACTGAGGGCCAGATTTACATTGACAGACAGCTCCACAATCGACAGgtaaggttat ... aattgaacagATATACCCACCAATCAATGTCCTCCCATCACTGTCTCGTTTAATGAAG
EST: gi|156737783|gb|EV241904.1|EV241904
EST:     ATATCACTGAGGGCCAGATTTACATTGACAGACAGCTCCACAATCGACAG                         ATATACCCACCAATCAATGTCCTCCCATCACTGTCTCGTTTAATGAAG
genomic: ATATCACTGAGGGCCAGATTTACATTGACAGACAGCTCCACAATCGACAGgtaaggttat ... aattgaacagATATACCCACCAATCAATGTCCTCCCATCACTGTCTCGTTTAATGAAG
EST: gi|110376681|gb|EC941748.1|EC941748
EST:     ATATCACTGAGGGTCAGATTTACATTGACAGACAGCTCCACAATCGACAG                         ATATACCCACCAATCAATGTCCTGCCATCACTGTCTCGTTTAATGAAG
genomic: ATATCACTGAGGGCCAGATTTACATTGACAGACAGCTCCACAATCGACAGgtaaggttat ... aattgaacagATATACCCACCAATCAATGTCCTCCCATCACTGTCTCGTTTAATGAAG
EST: gi|110705729|gb|EE082911.1|EE082911
EST:     ATATCACTGAGGGCCAGATTTACATTGACAGACAGCTCCACAATCGACAG                         ATATACCCACCAATCAATGTCCTCCCATCACTGTCTCGTTTAATGAAG
genomic: ATATCACTGAGGGCCAGATTTACATTGACAGACAGCTCCACAATCGACAGgtaaggttat ... aattgaacagATATACCCACCAATCAATGTCCTCCCATCACTGTCTCGTTTAATGAAG
EST: gi|110364580|gb|EC927938.1|EC927938
EST:     CTGAGGGTCAGATTTACATTGACAGACAGCTCCACAATCGACAG                         ATATACCCACCAATCAATGTCCTCCCATCACTGTCTCGTTTAATGAAG
genomic: CTGAGGGCCAGATTTACATTGACAGACAGCTCCACAATCGACAGgtaaggttat ... aattgaacagATATACCCACCAATCAATGTCCTCCCATCACTGTCTCGTTTAATGAAG
EST: gi|30320892|gb|CD004154.1|CD004154
EST:     TATCACTGAGGGCCAGATTTACA-TGNACAGACAGCTCCACAATCGACAG                         ATATACCCACCAATCAATGTCCTCCCATCACTGTCTCGTTTAATGAAG
genomic: TATCACTGAGGGCCAGATTTACATTG-ACAGACAGCTCCACAATCGACAGgtaaggttat ... aattgaacagATATACCCACCAATCAATGTCCTCCCATCACTGTCTCGTTTAATGAAG
EST: gi|34542425|gb|CF510657.1|CF510657
EST:     ATATCACTGAGGGTCAGATTTACATTGACAGACAGCTCCACAATCGACAG                         ATATACCCACCAATCAATGTCCTGCCATCACTGTCTCGTTTAATGAAG
genomic: ATATCACTGAGGGCCAGATTTACATTGACAGACAGCTCCACAATCGACAGgtaaggttat ... aattgaacagATATACCCACCAATCAATGTCCTCCCATCACTGTCTCGTTTAATGAAG
EST: gi|30251540|gb|CB969273.1|CB969273
EST:     AGATTTACATTGACAGACAGCNT-CACAATCGACAG                         ATATACCCACCAATCAATGTCCTGCCATCACTGTCTCGTTTAATGAAG
genomic: AGATTTACATTGACAGACAGC-TCCACAATCGACAGgtaaggttat ... aattgaacagATATACCCACCAATCAATGTCCTCCCATCACTGTCTCGTTTAATGAAG
EST: gi|110687127|gb|EE064266.1|EE064266
EST:     ATATCACTGAGGGTCAGATTTACATTGACAGACAGCTCCACAATCGACAG                         ATATACCCACCAATCAATGTCCTGCCATCACTGTCTCGTTTAATGAAG
genomic: ATATCACTGAGGGCCAGATTTACATTGACAGACAGCTCCACAATCGACAGgtaaggttat ... aattgaacagATATACCCACCAATCAATGTCCTCCCATCACTGTCTCGTTTAATGAAG
EST: gi|27755418|gb|CB036173.1|CB036173
EST:     ATATCACTGAGGGCCAGATTTACATTGACAGACAGCTCCACAATCGACAG                         ATATACCCACCAATCAATGTCCTCCCATCACTGTCTCGTTTAATGAAG
genomic: ATATCACTGAGGGCCAGATTTACATTGACAGACAGCTCCACAATCGACAGgtaaggttat ... aattgaacagATATACCCACCAATCAATGTCCTCCCATCACTGTCTCGTTTAATGAAG
EST: gi|110424996|gb|EC991371.1|EC991371
EST:     ATATCACTGAGGGCCAGATTTACATTGACAGACAGCTCCACAATCGACAG                         ATATACCCACCAATCAATGTCCTCCCATCACTGTCTCGTTTTATGAAG
genomic: ATATCACTGAGGGCCAGATTTACATTGACAGACAGCTCCACAATCGACAGgtaaggttat ... aattgaacagATATACCCACCAATCAATGTCCTCCCATCACTGTCTCGTTTAATGAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atggagcctatggattgttgaggctaagcaatgttttcttgtttgaattgaacagATATACCCACCAATCAATGTCCTCCCATCACTGTCTCGTTTAATGAAG
                             aatgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaaaaacttggttcttgaaaatatacaattatatccttttgtcatatggagcctatggattgttgaggctaagcaatgttttcttgtttgaattgaacagATATACCCACCAATCAATGTCCTCCCATCACTGTCTCGTTTAATGAAG

aaaaaac
- - - - - - - - gaaaata
- - - - - - - - - - - - - - - - - ccttttg
- - - - - - - - - - - - - - - - - - - - - - - tggagcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - -tggattg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctaagca