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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttcaaaacattatggtttactgtaaagtgctcattcacaaaccaattttgtttttgtttttgtcattcagctgtcactaattacatgaattgtctacagTGTGCAACTGCAAACCCTGATGGCCTTAAGAGAGCTCTTGTAATTGGAGGAGGAATAGCTAACTTTACTGATGTTGCTGCTACTTTTAATGGCATAATTC

Basic information

species Vitis vinifera
transcript Vv01s0127g00260.t01
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv01s0127g00260.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA02G04120.2 (Glycine max), 3'ss of exon 10
---------------------------------------------------------------------------------------tttcaaaacattatggttta--ctgtaaagtgctcattcacaaaccaattttgtttttgtttttgtcattcagctgtcactaattacatgaattgtctacagTGTGCAACTGCAAACCCTGATGGCCTTAAGAGAGCTCTTGTAATTGGAGGAGGAATAGCTAACTTTACTGATGTTGCTGCTACTTTTAATGGCATAATTC
                                                                                        | | ||   |     | ||     ||   |   ||| |  |         || |    ||  | |  |  | || | | |||   | |   || | | ||||||||||||||||||||||||||||  |||||||||||||| || |||||||| ||||| |||||||||||||||||||| || |||| ||| |||||||
gtaattaacctatatctctgcgttgcttttggtctaaatatcaatttagagatttagcattcatgcttacatgatcagaatgtccttgtccgaattgtcccaatatagctcttatgatatgcatgctaactttgcacctgataccattggtattttgtatctatta-taacctccttttttctttccagTGTGCAACTGCAAACCCTGATGGCCAGAAGAGAGCTCTTGTGATAGGAGGAGGCATAGCCAACTTTACTGATGTTGCTGCCACATTTAGTGGTATAATTC

upper sequence: Vv01s0127g00260.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA01G03530.1 (Glycine max), 3'ss of exon 10
---------------------------------------------------------------------------------------tttcaaaacattatggttta--ctgtaaagtgctcattcacaaaccaattttgtttttgtttttgtcattcagctgtcactaattacatgaattgtctacagTGTGCAACTGCAAACCCTGATGGCCTTAAGAGAGCTCTTGTAATTGGAGGAGGAATAGCTAACTTTACTGATGTTGCTGCTACTTTTAATGGCATAATTC
                                                                                        |   ||   |     | ||     ||   |   ||| |  |         || |    ||  | |  |  |  | | | |||   | |   || | | ||||||||||||||||||||||||| ||  |||||||||||||| || |||||||| ||||| |||||||||||||||||||| || |||| ||| |||||||
gtaattaacctatatctctgctttgtttttggtcttaatatcaatttagagatttagcattcatgcttacatgatcagactgtccttgtctgaagtgtccaaatatagctcttatgatatgcatgctaaccttgcacctgataccattggtattttgtatgtatta-taacctccttttttctttccagTGTGCAACTGCAAACCCTGATGACCAGAAGAGAGCTCTTGTGATAGGAGGAGGCATAGCCAACTTTACTGATGTTGCTGCCACATTTAGTGGTATAATTC

upper sequence: Vv01s0127g00260.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA08G17010.1 (Glycine max), 3'ss of exon 10
------------------------------------------------------------------tttcaaaacattatggtttac--tgtaaagtgctcattca-caaaccaattttgtttttgtttttgtcattcagctgtcactaattac-atgaa----ttgtctacagTGTGCAACTGCAAACCCTGATGGCCTTAAGAGAGCTCTTGTAATTGGAGGAGGAATAGCTAACTTTACTGATGTTGCTGCTACTTTTAATGGCATAATTC
                                                                    |||     || | |||||   |||       |   | | ||||   ||  |  |||||      | ||  ||   |   | ||  | ||||     |  | | |||||||||||| |||| ||||||||||  ||| |||| ||||| || || || |||||||||||||||||||||||||||||||| || | |||||||||||
gtaatcgattcttatctcaaacatcattgttggcatatttatggataaactatttttgctttatgcgatcagccatttctcgtttagagtgtgtgaaaatagcttatcaaatgcatgctacttttgaaac-atgatatagtgattctttatctctatgacaatctcttttgcagTGTGCAACTTCAAATCCTGATGGCCAAAAGCGAGCCCTTGTGATAGGTGGGGGAATAGCTAACTTTACTGATGTTGCTGCTACGTTCAGTGGCATAATTC

upper sequence: Vv01s0127g00260.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA15G42140.2 (Glycine max), 3'ss of exon 9
tttcaaaacattatggtttactgtaaagtgctcat----tcacaaaccaattttgtttttgtttttgtcattcagctgtcactaattacatgaattgtctacagTGTGCAACTGCAAACCCTGATGGCCTTAAGAGAGCTCTTGTAATTGGAGGAGGAATAGCTAACTTTACTGATGTTGCTGCTACTTTTAATGGCATAATTC
    || |   || |  |   || |||  ||| ||    |  ||  | | |||      || | | || ||||     || ||| | |||  |  | | | |||||||||||| |||| ||||||||||  ||| |||| |||||  | || ||||||||||||||||||||||||||||||||||| || |  ||||||||||
-ccaaacattctaagagtgtgtgaaaatagcttatgaaattgcatgctactttgaaacatgatatagtgattctttaatctcta-tgaca--atctctttgcagTGTGCAACTTCAAATCCTGATGGCCAAAAGCGAGCCCTTGTGGTAGGTGGAGGAATAGCTAACTTTACTGATGTTGCTGCTACATTCAGCGGCATAATTC

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|110363218|gb|EC926793.1|EC926793
EST:     GAGCACCAAATGAAGAGGAAGTATTGCAGTATGCTAGAGTTGTAATTGAT                         TGTGCAACTGCAAACCCTGATGGCCTTAAGAGAGCTCTTGTAATTGGAGGA
genomic: GAGCACCAAATGAAGAGGAAGTATTGCAGTATGCTAGAGTTGTAATTGATgtaaggactc ... ttgtctacagTGTGCAACTGCAAACCCTGATGGCCTTAAGAGAGCTCTTGTAATTGGAGGA
EST: gi|71882514|gb|DT031569.1|DT031569
EST:     GAGCACCAAATGAAGAGGAAGTATTGCAGTATGCTAGAGTTGTAATTGAT                         TGTGCAACTGCAAACCCTGATGGCCTTAAGAGAGCTCTTGTAATTGGAGGA
genomic: GAGCACCAAATGAAGAGGAAGTATTGCAGTATGCTAGAGTTGTAATTGATgtaaggactc ... ttgtctacagTGTGCAACTGCAAACCCTGATGGCCTTAAGAGAGCTCTTGTAATTGGAGGA
EST: gi|111125104|gb|EE253722.1|EE253722
EST:     GAGCACCAAATGAAGAGGAAGTGTTGCAGTATGCTAGAGTTGTAATTGAT                         TGTGCAACTGCAAACCCTGATGGCCTTAAGAGAGCTCTTGTAATTGGAGGA
genomic: GAGCACCAAATGAAGAGGAAGTATTGCAGTATGCTAGAGTTGTAATTGATgtaaggactc ... ttgtctacagTGTGCAACTGCAAACCCTGATGGCCTTAAGAGAGCTCTTGTAATTGGAGGA
EST: gi|32247604|gb|CD713423.1|CD713423
EST:     GAGCACCAAATGAAGAGGAAGTATTGCAGTATGCTAGAGTTGTAATTGAT                         TGTGCAACTGCAAACCCTGATGGCCTTAAGAGAGCTCTTGTAATTGGAGGA
genomic: GAGCACCAAATGAAGAGGAAGTATTGCAGTATGCTAGAGTTGTAATTGATgtaaggactc ... ttgtctacagTGTGCAACTGCAAACCCTGATGGCCTTAAGAGAGCTCTTGTAATTGGAGGA
EST: gi|351054175|gb|FQ450257.1|FQ450257
EST:     GAGCACCAAATGAAGAGGAAGTATTGCAGTATGCTAGAGTTGTAATTGAT                         TGTGCAACTGCAAACCCTGATGGCCTTAAGAGAGCTCTTGTAATTGGAGGA
genomic: GAGCACCAAATGAAGAGGAAGTATTGCAGTATGCTAGAGTTGTAATTGATgtaaggactc ... ttgtctacagTGTGCAACTGCAAACCCTGATGGCCTTAAGAGAGCTCTTGTAATTGGAGGA
EST: gi|71888760|gb|DT037815.1|DT037815
EST:     GAGCACCAAATGAAGAGGAAGTATTGCAGTATGCTAGAGTTGTAATTGAT                         TGTGCAACTGCAAACCCTGATGGCCTTAAGAGAGCTCTTGTAATTGGAGGA
genomic: GAGCACCAAATGAAGAGGAAGTATTGCAGTATGCTAGAGTTGTAATTGATgtaaggactc ... ttgtctacagTGTGCAACTGCAAACCCTGATGGCCTTAAGAGAGCTCTTGTAATTGGAGGA
EST: gi|30325227|gb|CD008489.1|CD008489
EST:     GAGCACCAAATGAAGAGGAAGTATTGCAGTATGCTAGAGTTGTAATTGAT                         TGTGCAACTGCAAACCCTGATGGCCTTAAGAGAGCTCTTGTAATTGGAGGA
genomic: GAGCACCAAATGAAGAGGAAGTATTGCAGTATGCTAGAGTTGTAATTGATgtaaggactc ... ttgtctacagTGTGCAACTGCAAACCCTGATGGCCTTAAGAGAGCTCTTGTAATTGGAGGA
EST: gi|110698225|gb|EE075525.1|EE075525
EST:     GAGCACCAAATGAAGAGGAAGTATTGCAGTATGCTAGAGTTGTAATTGAT                         TGTGCAACTGCAAACCCTGATGGCCTTAAGAGAGCTCTTGTAATTGGAGGA
genomic: GAGCACCAAATGAAGAGGAAGTATTGCAGTATGCTAGAGTTGTAATTGATgtaaggactc ... ttgtctacagTGTGCAACTGCAAACCCTGATGGCCTTAAGAGAGCTCTTGTAATTGGAGGA
EST: gi|349820930|gb|FQ408638.1|FQ408638
EST:     GAGCACCAAATGAAGAGGAAGTATTGCAGTATGCTAGAGTTGTAATTGAT                         TGTGCAACTGCAAACCCTGATGGCCTTAAGAGAGCTCTTGTAATTGGAGGA
genomic: GAGCACCAAATGAAGAGGAAGTATTGCAGTATGCTAGAGTTGTAATTGATgtaaggactc ... ttgtctacagTGTGCAACTGCAAACCCTGATGGCCTTAAGAGAGCTCTTGTAATTGGAGGA
EST: gi|110702653|gb|EE078810.1|EE078810
EST:     GAGCACCAAATGAAGAGGAAGTATTGCAGTATGCTAGAGTTGTAATTGAT                         TGTGCAACTGCAAACCCTGATGGCCTTAAGAGAGCTCTTGTAATTGGAGGA
genomic: GAGCACCAAATGAAGAGGAAGTATTGCAGTATGCTAGAGTTGTAATTGATgtaaggactc ... ttgtctacagTGTGCAACTGCAAACCCTGATGGCCTTAAGAGAGCTCTTGTAATTGGAGGA
EST: gi|32271862|gb|CD721021.1|CD721021
EST:     GAGCACCAAATGAAGAGGAAGTATTGCAGTATGCTAGAGTTGTAATTGAT                         TGTGCAACTGCAAACCCTGATGGCCTTAAGAGAGCTCTTGTAATTGGAGGA
genomic: GAGCACCAAATGAAGAGGAAGTATTGCAGTATGCTAGAGTTGTAATTGATgtaaggactc ... ttgtctacagTGTGCAACTGCAAACCCTGATGGCCTTAAGAGAGCTCTTGTAATTGGAGGA
EST: gi|351035742|gb|FQ463587.1|FQ463587
EST:     GAGCACCAAATGAAGAGGAAGTATTGCAGTATGCTAGAGTTGTAATTGAT                         TGTGCAACTGCAAACCCTGATGGCCTTAAGAGAGCTCTTGTAATTGGAGGA
genomic: GAGCACCAAATGAAGAGGAAGTATTGCAGTATGCTAGAGTTGTAATTGATgtaaggactc ... ttgtctacagTGTGCAACTGCAAACCCTGATGGCCTTAAGAGAGCTCTTGTAATTGGAGGA
EST: gi|32271741|gb|CD720900.1|CD720900
EST:     GAGCACCAAATGAAGAGGAAGTATTGCAGTATGCTAGAGTTGTAATTGAT                         TGTGCAACTGCAAACCCTGATGGCCTTAAGAGAGCTCTTGTAATTGGAGGA
genomic: GAGCACCAAATGAAGAGGAAGTATTGCAGTATGCTAGAGTTGTAATTGATgtaaggactc ... ttgtctacagTGTGCAACTGCAAACCCTGATGGCCTTAAGAGAGCTCTTGTAATTGGAGGA
EST: gi|349822202|gb|FQ412466.1|FQ412466
EST:     GAGCACCAAATGAAGAGGAAGTATTGCAGTATGCTAGAGTTGTAATTGAT                         TGTGCAACTGCAAACCCTGATGGCCTTAAGAGAGCTCTTGTAATTGGAGGA
genomic: GAGCACCAAATGAAGAGGAAGTATTGCAGTATGCTAGAGTTGTAATTGATgtaaggactc ... ttgtctacagTGTGCAACTGCAAACCCTGATGGCCTTAAGAGAGCTCTTGTAATTGGAGGA
EST: gi|110416323|gb|EC982295.1|EC982295
EST:     GAGCACCAAATGAAGAGGAAGTATTGCAGTATGCTAGAGTTGTAATTGAT                         TGTGCAACTGCAAACCCTGATGGCCTTAAGAGAGCTCTTGTAATTGGAGGA
genomic: GAGCACCAAATGAAGAGGAAGTATTGCAGTATGCTAGAGTTGTAATTGATgtaaggactc ... ttgtctacagTGTGCAACTGCAAACCCTGATGGCCTTAAGAGAGCTCTTGTAATTGGAGGA
EST: gi|111125102|gb|EE253720.1|EE253720
EST:     GAGCACCAAATGAAGAGGAAGTGTTGCAGTATGCTAGAGTTGTAATTGAT                         TGTGCAACTGCAAACCCTGATGGCCTTAAGAGAGCTCTTGTAATTGGAGGA
genomic: GAGCACCAAATGAAGAGGAAGTATTGCAGTATGCTAGAGTTGTAATTGATgtaaggactc ... ttgtctacagTGTGCAACTGCAAACCCTGATGGCCTTAAGAGAGCTCTTGTAATTGGAGGA
EST: gi|110422467|gb|EC988792.1|EC988792
EST:     GAGCACCAAATGAAGAGGAAGTATTGCAGTATGCTAGAGTTGTAATTGAT                         TGTGCAACTGCAAACCCTGATGGCCTTAAGAGAGCTCTTGTAATTGGAGGA
genomic: GAGCACCAAATGAAGAGGAAGTATTGCAGTATGCTAGAGTTGTAATTGATgtaaggactc ... ttgtctacagTGTGCAACTGCAAACCCTGATGGCCTTAAGAGAGCTCTTGTAATTGGAGGA
EST: gi|32272154|gb|CD721313.1|CD721313
EST:     GAGCACCAAATGAAGAGGAAGTATTGCAGTATGCTAGAGTTGTAATTGAT                         TGTGCAACTGCAAACCCTGATGGCCTTAAGAGAGCTCTTGTAATTGGAGGA
genomic: GAGCACCAAATGAAGAGGAAGTATTGCAGTATGCTAGAGTTGTAATTGATgtaaggactc ... ttgtctacagTGTGCAACTGCAAACCCTGATGGCCTTAAGAGAGCTCTTGTAATTGGAGGA
EST: gi|71882170|gb|DT031225.1|DT031225
EST:     GAGCACCAAATGAAGAGGAAGTATTGCAGTATGCTAGAGTTGTAATTGAT                         TGTGCAACTGCAAACCCTGATGGCCTTAAGAGAGCTCTTGTAATTGGAGGA
genomic: GAGCACCAAATGAAGAGGAAGTATTGCAGTATGCTAGAGTTGTAATTGATgtaaggactc ... ttgtctacagTGTGCAACTGCAAACCCTGATGGCCTTAAGAGAGCTCTTGTAATTGGAGGA
EST: gi|161718453|gb|FC065040.1|FC065040
EST:     GAGCA--AA-TGAAGAGGAAGTATTGCAGTATGCTAGAGTTGTAATTGAT                         TGTGCAACTGCAAACCCTGATGGCCTTAAGAGAGCTCTTTGTA-TTGGAGG
genomic: GAGCACCAAATGAAGAGGAAGTATTGCAGTATGCTAGAGTTGTAATTGATgtaaggactc ... ttgtctacagTGTGCAACTGCAAACCCTGATGGCCTTAAGAGAGCTCTT-GTAATTGGAGG
EST: gi|46910213|gb|CN545588.1|CN545588
EST:     CAAATGAAGAGGAAGTATTGCAGTATGCTAGAGTTGTAATTGAT                         TGTGCAACTGCAAACCCTGATGGCCTTAAGAGAGCTCTTGTAATTGGAGGA
genomic: CAAATGAAGAGGAAGTATTGCAGTATGCTAGAGTTGTAATTGATgtaaggactc ... ttgtctacagTGTGCAACTGCAAACCCTGATGGCCTTAAGAGAGCTCTTGTAATTGGAGGA
EST: gi|351044803|gb|FQ449057.1|FQ449057
EST:     GAGCACCAAATGAAGAGGAAGTATTGCAGTATGCTAGAGTTGTAATTGAT                         TGTGCAACTGCAAACCCTGATGGCCTTAAGAGAGCTCTTGTAATTGGAGGA
genomic: GAGCACCAAATGAAGAGGAAGTATTGCAGTATGCTAGAGTTGTAATTGATgtaaggactc ... ttgtctacagTGTGCAACTGCAAACCCTGATGGCCTTAAGAGAGCTCTTGTAATTGGAGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attttgtttttgtttttgtcattcagctgtcactaattacatgaattgtctacagTGTGCAACTGCAAACCCTGATGGCCTTAAGAGAGCTCTTGTAATTGGAGGAGGAATAGCTAACTTTACTGATGTTGCTGCTACTTTTAATGGCATAATTC
                              cactaat  putative branch site (score: 2)
                                 taattacatgaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttcaaaacattatggtttactgtaaagtgctcattcacaaaccaattttgtttttgtttttgtcattcagctgtcactaattacatgaattgtctacagTGTGCAACTGCAAACCCTGATGGCCTTAAGAGAGCTCTTGTAATTGGAGGAGGAATAGCTAACTTTACTGATGTTGCTGCTACTTTTAATGGCATAATTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - aaaacat
- - - - - - - - - - - - - - - ctcattc
- - - - - - - - - - - - - - - - - - - caaacca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cattcag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgtcac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -acatgaa