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

...taatgcatttataattgtatactgtgatttctttaatatttgtagttatacttcatgtcttttattttctttatgatttttcctctctttcatttgtcagCCCTCGCTGCTGAAGTTTCTGTAGTTCCTCCATCACGATTAATGGCTCTCATTGGTCAGGCTCTGAAGTGGCAGCAACATCAAG

Basic information

species Vitis vinifera
transcript Vv17s0000g08930.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv17s0000g08930.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os01g21940.1 (Oryza sativa), 3'ss of exon 3
----------------------taatgcatttataattgtatactgtgatttctt-taatatttgtagttatac--ttcatgtcttttattttctttatgatttttcctct--ctttcatttgtcagCCCTCGCTGCTGAAGTTTCTGTAGTTCCTCCATCACGATTAATGGCTCTCATTGGTCAGGCTCTGAAGTGGCAGCAACATCAAG
                      |  | | ||  |||  |  |    | | | | | |||||   |   |    |  ||| | | | | ||  |  | ||  || | |||||  | | |   | |||||  | ||| |||||||||| |||||||| || || || |||||||| || |||||||||||| |||| ||||| || || ||||
gtgagcttgctgatcatttttcttcttccttactaaaaggttctcttaactccatataatacaggagctggagctattcttatttctaatcctaataatagttgtccctctgccatgccaatttcagCTATTGCTTCTGAAGTTTCAGTAGTTCCACCTTCTCGGTTAATGGCACTGATTGGTCAGGCTTTGAAATGGCAACAGCACCAAG

upper sequence: Vv17s0000g08930.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA05G30430.2 (Glycine max), 3'ss of exon 4
taatgcatttataattgtatactgtgatttctttaatatttgtagtt-atacttcatgtcttttattttctttatgatttttcctctctttcatttgtcagCCCTCGCTGCTGAAGTTTCTGTAGTTCCTCCATCACGATTAATGGCTCTCATTGGTCAGGCTCTGAAGTGGCAGCAACATCAAG
   | | | |   ||||  ||  |  |       |   |||||  || ||  || || |      ||| ||||| ||  ||  || || ||   || |||||  | || || |||||| ||||||| || ||||| ||||| |||||| | |||||||||||| ||||||||||||| |||||||
gttttcttcttccattgc-tagggatacagacaaacagtttgttattgatcttttattttggggttttactttaagaacttctctttcattgcattttcagCTATTGCAGCAGAAGTTACTGTAGTGCCACCATCCCGATTGATGGCTTTAATTGGTCAGGCTTTGAAGTGGCAGCAGCATCAAG

upper sequence: Vv17s0000g08930.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA08G13560.1 (Glycine max), 3'ss of exon 4
-------------------------------------------------------------------------------------taat--gcatttataattgtatactgtgatttct-----ttaatatttgtagtt-atacttcatgtctttta-------ttttctttatgatttttcctctctttcatttgtcagCCCTCGCTGCTGAAGTTTCTGTAGTTCCTCCATCACGATTAATGGCTCTCATTGGTCAGGCTCTGAAGTGGCAGCAACATCAAG
                                                                                     | ||  | | | | | || | | ||   ||| ||     |  | |  |  ||||  |  || || | ||||        ||| ||||| ||  ||  || || ||   || ||||| || || || |||||| ||||||| || ||||| ||||| |||||| | |||||||||||| | ||||||||||| |||||||
gtttctgtcttttacttttgtattagttactatctagttttgatactaattttttgttttttaattgtaatgaacaactgtttcttgattggaaatgaaagttttcttcttccattgctagggatccagacatacagtttgttattgatctatttttggggggttttactttaagaacttctctttcattgcattttcagCTCTTGCAGCAGAAGTTACTGTAGTGCCACCATCCCGATTGATGGCTTTAATTGGTCAGGCTTTAAAGTGGCAGCAGCATCAAG

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|71857684|gb|DT006739.1|DT006739
EST:     GCTTATCAAGATTCAACAAAAGAGAAACGTCGTGCTCAAATTGCCCAAG                         CCCTTGCTGCTGAAGTTTCTGTAGTTCCTCCATCACGATTAATGGCTCTCA
genomic: GCTTATCAAGATTCAACAAAAGAGAAACGTCGTGCTCAAATTGCCCAAGgttttcccct ... catttgtcagCCCTCGCTGCTGAAGTTTCTGTAGTTCCTCCATCACGATTAATGGCTCTCA
EST: gi|71863353|gb|DT012408.1|DT012408
EST:     GCTTATCAAGATTCAACAAAAGAGAAACGTCGTGCTCAAATTGCCCAAG                         CCCTTGCTGCTGAAGTTTCTGTAGTTCCTCCATCACGATTAAAGGCTCTCA
genomic: GCTTATCAAGATTCAACAAAAGAGAAACGTCGTGCTCAAATTGCCCAAGgttttcccct ... catttgtcagCCCTCGCTGCTGAAGTTTCTGTAGTTCCTCCATCACGATTAATGGCTCTCA
EST: gi|71859941|gb|DT008996.1|DT008996
EST:     GCTTATCAAGATTCAACAAAAGAGAAACGTCGTGCTCAAATTGCCCAAG                         CCCTTGCTGCTGAAGTTTCTGTAGTTCCTCCATCACGATTAATGGCTCTCA
genomic: GCTTATCAAGATTCAACAAAAGAGAAACGTCGTGCTCAAATTGCCCAAGgttttcccct ... catttgtcagCCCTCGCTGCTGAAGTTTCTGTAGTTCCTCCATCACGATTAATGGCTCTCA
EST: gi|33403436|gb|CF209063.1|CF209063
EST:     GCTTATCAAGATTCAACAAAAGAGAAACGTCGTGCTCAAATTGCCCAAG                         CCCTTGCTGCTGAAGTTTCTGTAGTTCCTCCATCACGATTAATGGCTCTCA
genomic: GCTTATCAAGATTCAACAAAAGAGAAACGTCGTGCTCAAATTGCCCAAGgttttcccct ... catttgtcagCCCTCGCTGCTGAAGTTTCTGTAGTTCCTCCATCACGATTAATGGCTCTCA
EST: gi|71862424|gb|DT011479.1|DT011479
EST:     GCTTATCAAGATTCAACAAAAGAGAAACGTCGTGCTCAAATTGCCCAAG                         CCCTTGCTGCTGAAGTTTCTGTAGTTCCTCCATCACGATTAATGGCTCTCA
genomic: GCTTATCAAGATTCAACAAAAGAGAAACGTCGTGCTCAAATTGCCCAAGgttttcccct ... catttgtcagCCCTCGCTGCTGAAGTTTCTGTAGTTCCTCCATCACGATTAATGGCTCTCA
EST: gi|71863915|gb|DT012970.1|DT012970
EST:     GCTTATCAAGATTCAACAAAAGAGAAACGTCGTGCTCAAATTGCCCAAG                         CCCTTGCTGCTGAAGTTTCTGTAGTTCCTCCATCACGATTAATGGCTCTCA
genomic: GCTTATCAAGATTCAACAAAAGAGAAACGTCGTGCTCAAATTGCCCAAGgttttcccct ... catttgtcagCCCTCGCTGCTGAAGTTTCTGTAGTTCCTCCATCACGATTAATGGCTCTCA
EST: gi|30129597|gb|CB914936.1|CB914936
EST:     GCTTATCAAGATTCAACAAAAGAGAAACGTCGTGCTCAAATTGCCCAAG                         CCCTTGCTGCTGAAGTTTCTGTAGTTCCTCCATCACGATTAATGGCTCTCA
genomic: GCTTATCAAGATTCAACAAAAGAGAAACGTCGTGCTCAAATTGCCCAAGgttttcccct ... catttgtcagCCCTCGCTGCTGAAGTTTCTGTAGTTCCTCCATCACGATTAATGGCTCTCA
EST: gi|71861729|gb|DT010784.1|DT010784
EST:     GCTTATCAAGATTCAACAAAAGAGAAACGTCGTGCTCAAATTGCCCAAG                         CCCTTGCTGCTGAAGTTTCTGTAGTTCCTCCATCACGATTAATGGCTCTCA
genomic: GCTTATCAAGATTCAACAAAAGAGAAACGTCGTGCTCAAATTGCCCAAGgttttcccct ... catttgtcagCCCTCGCTGCTGAAGTTTCTGTAGTTCCTCCATCACGATTAATGGCTCTCA
EST: gi|71862537|gb|DT011592.1|DT011592
EST:     GCTTATCAAGATTCAACAAAAGAGAAACGTCGTGCTCAAATTGCCCAAG                         CCCTTGCTGCTGAAGTTTCTGTAGTTCCTCCATCACGATTAATGGCTCTCA
genomic: GCTTATCAAGATTCAACAAAAGAGAAACGTCGTGCTCAAATTGCCCAAGgttttcccct ... catttgtcagCCCTCGCTGCTGAAGTTTCTGTAGTTCCTCCATCACGATTAATGGCTCTCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttatacttcatgtcttttattttctttatgatttttcctctctttcatttgtcagCCCTCGCTGCTGAAGTTTCTGTAGTTCCTCCATCACGATTAATGGCTCTCATTGGTCAGGCTCTGAAGTGGCAGCAACATCAAG
            tcttttattttcttta  CT-rich tract
         atgtcttttattttct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taatgcatttataattgtatactgtgatttctttaatatttgtagttatacttcatgtcttttattttctttatgatttttcctctctttcatttgtcagCCCTCGCTGCTGAAGTTTCTGTAGTTCCTCCATCACGATTAATGGCTCTCATTGGTCAGGCTCTGAAGTGGCAGCAACATCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
-aatgcat