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

...tttgaaaagtagaattgtttattggattcgtgaatctgtgtttcctgatttgttcttcccagtaaaaatgcttaggcctctcttgtgatgcttcttgcagACCATCAGTTACATGGCAGAGCGCATTGTAGGCACTGGATCGTTTGGAATTGTTTTTCAG

Basic information

species Vitis vinifera
transcript Vv12s0028g01810.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv12s0028g01810.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G472625_T02 (Zea mays), 3'ss of exon 2
tttgaaaagtagaattgtttattggattcgtgaat-ctgtgtttcctgatttgttcttcccagtaaaaatgcttaggcctctcttgtgatgcttcttgcagACCATCAGTTACATGGCAGAGCGCATTGTAGGCACTGGATCGTTTGGAATTGTTTTTCAG
 | |||        |  |   |||   |   |  | |   ||||  |    | ||| |  |   |      | |  |    |||| ||    |  |||||||||||||||||||||||||| ||  | || || || || || ||||| || || || |||
-tcgaattccttcctgctcagttgctctgacgcctgcctagtttgttaccctcttcgtgtcctcagttgctcatttgttcttcttctggccttaattgcagACCATCAGTTACATGGCAGAACGTGTCGTGGGTACGGGCTCATTTGGGATCGTCTTCCAG

upper sequence: Vv12s0028g01810.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA12G15470.2 (Glycine max), 3'ss of exon 2
tttgaaaagtaga-attgtttattggattcgtgaatctgtgtttcctgatttgttcttcccagtaaaaatgctta----ggcctctcttgtgatgcttcttgcagACCATCAGTTACATGGCAGAGCGCATTGTAGGCACTGGATCGTTTGGAATTGTTTTTCAG
 |  |  | || | ||| | | | |  | |   ||    |        |||| ||||||  |   ||  |  ||     |    ||    |||| |  | ||||||||||||||||||||||||| ||  |||| ||||||||||| |||||| |||||||||||
atgcattaatatatattatctttggagtccaaaaaaaaataa-----aatttattcttcgtaaataacttatttgttatgattacttccatgataccacctgcagACCATCAGTTACATGGCAGAACGTGTTGTTGGCACTGGATCATTTGGAGTTGTTTTTCAG

upper sequence: Vv12s0028g01810.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA06G42840.1 (Glycine max), 3'ss of exon 2
tttgaaaagtagaattgtttattggattcgtga----atctgtgtttcctgatttgttcttcccagtaaaaatgctta----ggcctctcttgtgatgcttcttgcagACCATCAGTTACATGGCAGAGCGCATTGTAGGCACTGGATCGTTTGGAATTGTTTTTCAG
        ||  |||   || |   ||| ||||     |||| ||||| | |||||||||||  |   ||  |  ||     |    ||    |||| |  | ||||||||||||||||||||||||| ||  |||| ||||||||||| |||||| ||||||| |||
-------ggttcaataactt-taaaattggtgatattgtctgagtttcattatttgttcttcgtaaataacttatttgttatgattccttccctgataccacctgcagACCATCAGTTACATGGCAGAACGTGTTGTTGGCACTGGATCATTTGGAGTTGTTTTCCAG

upper sequence: Vv12s0028g01810.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA12G33950.1 (Glycine max), 3'ss of exon 2
--tttgaaaagtagaattgtttatt--ggattcgtgaatctgtgtttcctgatttgttcttcccagtaaaaatgcttaggcctctcttgtgatgcttcttgcagACCATCAGTTACATGGCAGAGCGCATTGTAGGCACTGGATCGTTTGGAATTGTTTTTCAG
  ||||||   || |||||  |  |   ||||  |||   ||   | |  |  ||    || |   ||    | | ||    | |  | | |||| ||||||||||||||||||||||||| || ||  |||| ||||||||||| ||||| |||||||| |||
attttgaa---taaaattgactgcttaagattgatgatgatggcatccacgggtttcaatttcttttattctt-cataaatttgtgctctaatgcctcttgcagACCATCAGTTACATGGCCGAACGTGTTGTTGGCACTGGATCATTTGGCATTGTTTTCCAG

upper sequence: Vv12s0028g01810.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA13G36570.1 (Glycine max), 3'ss of exon 1
-----tttgaa-aagtagaattgtttattggattcgtga----atctgtgtttcctgatttgttcttcccagtaaaaatgcttaggcctctcttgtgatgcttcttgcagACCATCAGTTACATGGCAGAGCGCATTGTAGGCACTGGATCGTTTGGAATTGTTTTTCAG
     |||||| ||    || || ||    ||||  |||    |||   |  |    |||| ||||   |   | ||||         | |  |   ||||  |||||||||||||||||||||||| || ||  |||| ||||||||||| || ||||||||||| |||
agaattttgaataaaattaaatgcttg--agattgatgataacatccacgggtttcaatttcttctattcttcataaat--------ttgtgctcgaatgccacttgcagACCATCAGTTACATGGCTGAACGTGTTGTTGGCACTGGATCATTCGGAATTGTTTTCCAG

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|71860504|gb|DT009559.1|DT009559
EST:     GTCATATAATTTCCACCACCATTGGAGGCAAAAATGGAGAGCCTAAACAG                         ACCATCAGTTACATGGCAGAGCGCATTGTAGGCACTGGATCGTTTGGAATT
genomic: GTCATATAATTTCCACCACCATTGGAGGCAAAAATGGAGAGCCTAAACAGgtgagagttg ... cttcttgcagACCATCAGTTACATGGCAGAGCGCATTGTAGGCACTGGATCGTTTGGAATT
EST: gi|71857679|gb|DT006734.1|DT006734
EST:     GTCATATAATTTCCACCACCATTGGAGGCAAAAATGGAGAGCCTAAACAG                         ACCATCAGTTACATGGCAGAGCGCATTGTAGGCACTGGATCGTTTGGAATT
genomic: GTCATATAATTTCCACCACCATTGGAGGCAAAAATGGAGAGCCTAAACAGgtgagagttg ... cttcttgcagACCATCAGTTACATGGCAGAGCGCATTGTAGGCACTGGATCGTTTGGAATT
EST: gi|110725002|gb|EE101323.1|EE101323
EST:     GTCATATAATTTCCACCACCATTGGAGGCAAAAATGGAGAGCCTAAACAG                         ACCATCAGTTACATGGCAGAGCGCATTGTAGGCACTGGATCGTTTGGAATT
genomic: GTCATATAATTTCCACCACCATTGGAGGCAAAAATGGAGAGCCTAAACAGgtgagagttg ... cttcttgcagACCATCAGTTACATGGCAGAGCGCATTGTAGGCACTGGATCGTTTGGAATT
EST: gi|349830587|gb|FQ416885.1|FQ416885
EST:     GTCATATAATTTCCACCACCATTGGAGGCAAAAATGGAGAGCCTAAACAG                         ACCATCAGTTACATGGCAGAGCGCATTGTAGGCACTGGATCGTTTGGAATT
genomic: GTCATATAATTTCCACCACCATTGGAGGCAAAAATGGAGAGCCTAAACAGgtgagagttg ... cttcttgcagACCATCAGTTACATGGCAGAGCGCATTGTAGGCACTGGATCGTTTGGAATT
EST: gi|351023941|gb|FQ423364.1|FQ423364
EST:     GTCATATAATTTCCACCACCATTGGAGGCAAAAATGGAGAGCCTAAACAG                         ACCATCAGTTACATGGCAGAGCGCATTGTAGGCACTGGATCGTTTGGAATT
genomic: GTCATATAATTTCCACCACCATTGGAGGCAAAAATGGAGAGCCTAAACAGgtgagagttg ... cttcttgcagACCATCAGTTACATGGCAGAGCGCATTGTAGGCACTGGATCGTTTGGAATT
EST: gi|71862284|gb|DT011339.1|DT011339
EST:     GTCATATAATTTCCACCACCATTGGAGGCAAAAATGGAGAGCCTAAACAG                         ACCATCAGTTACATGGCAGAGCGCATTGTAGGCACTGGATCGTTTGGAATT
genomic: GTCATATAATTTCCACCACCATTGGAGGCAAAAATGGAGAGCCTAAACAGgtgagagttg ... cttcttgcagACCATCAGTTACATGGCAGAGCGCATTGTAGGCACTGGATCGTTTGGAATT
EST: gi|71859164|gb|DT008219.1|DT008219
EST:     GTCATATAATTTCCACCACCATTGGAGGCAAAAATGGAGAGCCTAAACAG                         ACCATCAGTTACATGGCAGAGCGCATTGTAGGCACTGGATCGTTTGGAATT
genomic: GTCATATAATTTCCACCACCATTGGAGGCAAAAATGGAGAGCCTAAACAGgtgagagttg ... cttcttgcagACCATCAGTTACATGGCAGAGCGCATTGTAGGCACTGGATCGTTTGGAATT
EST: gi|33402557|gb|CF208184.1|CF208184
EST:     GTCATATAATTTCCACCACCATTGGAGGCAAAAATGGAGAGCCTAAACAG                         ACCATCAGATACATGGCAGAGCGCATTGTAGGCACTGGATCGTTTGGAATT
genomic: GTCATATAATTTCCACCACCATTGGAGGCAAAAATGGAGAGCCTAAACAGgtgagagttg ... cttcttgcagACCATCAGTTACATGGCAGAGCGCATTGTAGGCACTGGATCGTTTGGAATT
EST: gi|351020144|gb|FQ445751.1|FQ445751
EST:     GTCATATAATTTCCACCACCATTGGAGGCAAAAATGGAGAGCCTAAACAG                         ACCATCAGTTACATGGCAGAGCGCATTGTAGGCACTGGATCGTTTGGAATT
genomic: GTCATATAATTTCCACCACCATTGGAGGCAAAAATGGAGAGCCTAAACAGgtgagagttg ... cttcttgcagACCATCAGTTACATGGCAGAGCGCATTGTAGGCACTGGATCGTTTGGAATT
EST: gi|351040389|gb|FQ434522.1|FQ434522
EST:     GTCATATAATTTCCACCACCATTGGAGGCAAAAATGGAGAGCCTAAACAG                         ACCATCAGTTACATGGCAGAGCGCATTGTAGGCACTGGATCGTTTGGAATT
genomic: GTCATATAATTTCCACCACCATTGGAGGCAAAAATGGAGAGCCTAAACAGgtgagagttg ... cttcttgcagACCATCAGTTACATGGCAGAGCGCATTGTAGGCACTGGATCGTTTGGAATT
EST: gi|352765011|gb|FQ473659.1|FQ473659
EST:     GTCATATAATTTCCACCACCATTGGAGGCAAAAATGGAGAGCCTAAACAG                         ACCATCAGTTACATGGCAGAGCGCATTGTAGGCACTGGATCGTTTGGAATT
genomic: GTCATATAATTTCCACCACCATTGGAGGCAAAAATGGAGAGCCTAAACAGgtgagagttg ... cttcttgcagACCATCAGTTACATGGCAGAGCGCATTGTAGGCACTGGATCGTTTGGAA-T
EST: gi|71863774|gb|DT012829.1|DT012829
EST:     GTCATATAATTTCCACCACCATTGGAGGCAAAAATGGAGAGCCTAAACAG                         ACCATCAGTTACATGGCAGAGCGCATTGTAGGCACTGGATCGTTTGGAATT
genomic: GTCATATAATTTCCACCACCATTGGAGGCAAAAATGGAGAGCCTAAACAGgtgagagttg ... cttcttgcagACCATCAGTTACATGGCAGAGCGCATTGTAGGCACTGGATCGTTTGGAATT
EST: gi|110719282|gb|EE097083.1|EE097083
EST:     GTCATATAATTTCCACCACCATTGGAGGCAAAAATGGAGAGCCTAAACAG                         ACCATCAGTTACATGGCAGAGCGCATTGTAGGCACTGGATCGTTTGGAATT
genomic: GTCATATAATTTCCACCACCATTGGAGGCAAAAATGGAGAGCCTAAACAGgtgagagttg ... cttcttgcagACCATCAGTTACATGGCAGAGCGCATTGTAGGCACTGGATCGTTTGGAATT
EST: gi|351025140|gb|FQ433557.1|FQ433557
EST:     GTCATATAATTTCCACCACCATTGGAGGCAAAAATGGAGAGCCTAAACAG                         ACCATCAGTTACATGGCAGAGCGCATTGTAGGCACTGGATCGTTTGGAATT
genomic: GTCATATAATTTCCACCACCATTGGAGGCAAAAATGGAGAGCCTAAACAGgtgagagttg ... cttcttgcagACCATCAGTTACATGGCAGAGCGCATTGTAGGCACTGGATCGTTTGGAATT
EST: gi|71860474|gb|DT009529.1|DT009529
EST:     GTCATATAATTTCCACCACCATTGGAGGCAAAAATGGAGAGCCTAAACAG                         ACCATCAGTTACATGGCAGAGCGCATTGTAGGCACTGGATCGTTTGGAATT
genomic: GTCATATAATTTCCACCACCATTGGAGGCAAAAATGGAGAGCCTAAACAGgtgagagttg ... cttcttgcagACCATCAGTTACATGGCAGAGCGCATTGTAGGCACTGGATCGTTTGGAATT
EST: gi|71860811|gb|DT009866.1|DT009866
EST:     GTCATATAATTTCCACCACCATTGGAGGCAAAAATGGAGAGCCTAAACAG                         ACCATCAGTTACATGGCAGAGCGCATTGTAGGCACTGGATCGTTTGGAATT
genomic: GTCATATAATTTCCACCACCATTGGAGGCAAAAATGGAGAGCCTAAACAGgtgagagttg ... cttcttgcagACCATCAGTTACATGGCAGAGCGCATTGTAGGCACTGGATCGTTTGGAATT
EST: gi|351036312|gb|FQ458687.1|FQ458687
EST:     GTCATATAATTTCCACCACCATTGGAGGCAAAAATGGAGAGCCTAAACAG                         ACCATCAGTTACATGGCAGAGCGCATTGTAGGCACTGGATCGTTTGGAATT
genomic: GTCATATAATTTCCACCACCATTGGAGGCAAAAATGGAGAGCCTAAACAGgtgagagttg ... cttcttgcagACCATCAGTTACATGGCAGAGCGCATTGTAGGCACTGGATCGTTTGGAATT
EST: gi|71854956|gb|DT004011.1|DT004011
EST:     GTCATATAATTTCCACCACCATTGGAGGCAAAAATGGAGAGCCTAAACAG                         ACCATCAGTTACATGGCAGAGCGCATTGTAGGCACTGGATCGTTTGGAATT
genomic: GTCATATAATTTCCACCACCATTGGAGGCAAAAATGGAGAGCCTAAACAGgtgagagttg ... cttcttgcagACCATCAGTTACATGGCAGAGCGCATTGTAGGCACTGGATCGTTTGGAATT
EST: gi|71861673|gb|DT010728.1|DT010728
EST:     GTCATATAATTTCCACCACCATTGGAGGCAAAAATGGAGAGCCTAAACAG                         ACCATCAGTTACATGGCAGAGCGCATTGTAGGCACTGGATCGTTTGGAATT
genomic: GTCATATAATTTCCACCACCATTGGAGGCAAAAATGGAGAGCCTAAACAGgtgagagttg ... cttcttgcagACCATCAGTTACATGGCAGAGCGCATTGTAGGCACTGGATCGTTTGGAATT
EST: gi|110718800|gb|EE096049.1|EE096049
EST:     GTCATATAATTTCCACCACCATTGGAGGCAAAAATGGAGAGCCTAAACAG                         ACCATCAGTTACATGGCAGAGCGCATTGTAGGCACTGGATCGTTTGGAATT
genomic: GTCATATAATTTCCACCACCATTGGAGGCAAAAATGGAGAGCCTAAACAGgtgagagttg ... cttcttgcagACCATCAGTTACATGGCAGAGCGCATTGTAGGCACTGGATCGTTTGGAATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgatttgttcttcccagtaaaaatgcttaggcctctcttgtgatgcttcttgcagACCATCAGTTACATGGCAGAGCGCATTGTAGGCACTGGATCGTTTGGAATTGTTTTTCAG
 tcctgat  putative branch site (score: 3)
                                           tgcttctt  putative PPT
               agtaaaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttgaaaagtagaattgtttattggattcgtgaatctgtgtttcctgatttgttcttcccagtaaaaatgcttaggcctctcttgtgatgcttcttgcagACCATCAGTTACATGGCAGAGCGCATTGTAGGCACTGGATCGTTTGGAATTGTTTTTCAG

- - aaaagta
- - - - - - - - - - - - - - - - - - - - -ttcctga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgcttag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cctctct