Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacatttgtccttaccttagtgtctctaccctgtataaatttgggctgcattaatgttctaaatttgggctccattaatgttctaaatttgtcgctgcattgtaacagGCTTCCGAAGAAATGGAGTTACTGTACTAAGTGCTCTTCTGCCCGTTCCTGTAGCACTTGTGGTGGCAGTGGGAAGTTGAGTTCATAGTTTTGTTGTTAT

Basic information

species Vitis vinifera
transcript Vv06s0061g00330.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0061g00330.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA11G20080.1 (Glycine max), 3'ss of exon 3
gtacatttgtccttaccttagtgtctctaccctgtataaatttgggctgcattaatgttctaaatttgggctccattaatgttctaaatttgtcgc--tgcattgtaacagGCTTCCGAAGAAATGGAGTTACTGTACTAAGTGCTCTTCTGCCCGTTCCTGTAGCACTTGTGGTGGCAGTGGGAAGTTGAGTTCATAGTTTTGTTGTTAT-
       ||     |   | ||||        | ||||   ||||    ||    | || |   |||    | |  || | ||    |||   |||  |   ||||| ||| ||||| ||||||||||| || || || |||||||||||||  || ||||||   || |||||||||||||| ||| | ||||  |||||| |   |||  
-------tgattggatgatggtgtaaaactattttatactgttggttcacagcc-tattttctctttaattttc--tagt-ttagccattcaacgcaattacttgtaccagACTTCCAAAGAAATGGAGCTATTGCACAAAGTGCTCTTCTGGTCGATCCTGTTCAACCTGTGGTGGCAGTGGAAAGCTAAGTTACTAGTTTAGC-ATTACA

upper sequence: Vv06s0061g00330.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA12G08390.1 (Glycine max), 3'ss of exon 3
gtacatttgtccttaccttagtgtctctaccctgtataaatttgggctgcattaatgttctaaatttgggctccattaatgttctaaatttgtcgctgcattgtaacagGCTTCCGAAGAAATGGAGTTACTGTACTAAGTGCTCTTCTGCCCGTTCCTGTAGCACTTGTGGTGGCAGTGGGAAGTTGAGTTCATAGTTTTGTTGTTAT-
    |||      |    ||   |   |   |  | |   |         |||     | ||| |||    |   |||    |  || |   |  ||    |||| ||||||||| ||||| ||||| || || || |||||||||||||  || ||||||   || |||||||||||||| ||| | ||||  |||||| |   |||  
--tgattgaatgatgatgtaaaattgttttacactgtcggtgcacaacctattttctctttaattttttagt---ttagccattcaactcaattact----tgtaccagGCTTCCAAAGAAGTGGAGCTATTGCACAAAGTGCTCTTCTGGTCGATCCTGTTCAACCTGTGGTGGCAGTGGAAAGCTAAGTTACTAGTTTAGC-ATTACG
















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|30328665|gb|CD011927.1|CD011927
EST:     GAGAAGGCAAGATTGACTGCAAAGAATATGGCTACTCGATACACTGCAGG                         GCTTCCGAAGAAATGGAGTTACTGTACTAAGTGCTCTTCTGCCCGTTCCTG
genomic: GAGAAGGCAAGATTGACTGCAAAGAATATGGCTACTCGATACACTGCAGGgtacatttgt ... attgtaacagGCTTCCGAAGAAATGGAGTTACTGTACTAAGTGCTCTTCTGCCCGTTCCTG
EST: gi|352780899|gb|FQ466212.1|FQ466212
EST:     GAGAAGGCAAGATTGACTGCAAAGAATATGGCTACTCGATACACTGCAGG                         GCTTCCGAAGAAAGGGAGTTACTGTACTAAGTGCTCTTCTGCCCGTTCCTG
genomic: GAGAAGGCAAGATTGACTGCAAAGAATATGGCTACTCGATACACTGCAGGgtacatttgt ... attgtaacagGCTTCCGAAGAAATGGAGTTACTGTACTAAGTGCTCTTCTGCCCGTTCCTG
EST: gi|32249964|gb|CD715783.1|CD715783
EST:     GAGAAGGCAAGATTGACTGCAAAGAATATGGCTACTCGATACACTGCAGG                         GCTTCCGAAGAAATGGAGTTACTGTACTAAGTGCTCTTCTGCCCGTTCCTG
genomic: GAGAAGGCAAGATTGACTGCAAAGAATATGGCTACTCGATACACTGCAGGgtacatttgt ... attgtaacagGCTTCCGAAGAAATGGAGTTACTGTACTAAGTGCTCTTCTGCCCGTTCCTG
EST: gi|110426261|gb|EC992663.1|EC992663
EST:     GAGAAGGCAAGATTGACTGCAAAGAATATGGCTACTCGATACACTGCAGG                         GCTTCCGAAGAAATGGAGTTACTGTACTAAGTGCTCTTCTGCCCGTTCCTG
genomic: GAGAAGGCAAGATTGACTGCAAAGAATATGGCTACTCGATACACTGCAGGgtacatttgt ... attgtaacagGCTTCCGAAGAAATGGAGTTACTGTACTAAGTGCTCTTCTGCCCGTTCCTG
EST: gi|30328349|gb|CD011611.1|CD011611
EST:     GAGAAGGCAAGATTGACTGCAAAGAATATGGCTACTCGATACACTGCAGG                         GCTTCCGAAGAAATGGAGTTACTGTACTAAGTGCTCTTCTGCCCGTTCCTG
genomic: GAGAAGGCAAGATTGACTGCAAAGAATATGGCTACTCGATACACTGCAGGgtacatttgt ... attgtaacagGCTTCCGAAGAAATGGAGTTACTGTACTAAGTGCTCTTCTGCCCGTTCCTG
EST: gi|352776778|gb|FQ472665.1|FQ472665
EST:     GAGAAGGCAAGATTGACTGCAAAGAATATGGCTACTCGATACACTGCAGG                         GCTTCCGAAGAAATGGAGTTACTGTACTAAGTGCTCTTCTGCCCGTTCCTG
genomic: GAGAAGGCAAGATTGACTGCAAAGAATATGGCTACTCGATACACTGCAGGgtacatttgt ... attgtaacagGCTTCCGAAGAAATGGAGTTACTGTACTAAGTGCTCTTCTGCCCGTTCCTG
EST: gi|27578380|gb|CB001075.1|CB001075
EST:     GAGAAGGCAAGATTGACTGCAAAGAATATGGCTACTCGATACACTGCAGG                         GCTTCCGAAGAAATGGAGTTACTGTACTAAGTGCTCTTCTGCCCGTTCCTG
genomic: GAGAAGGCAAGATTGACTGCAAAGAATATGGCTACTCGATACACTGCAGGgtacatttgt ... attgtaacagGCTTCCGAAGAAATGGAGTTACTGTACTAAGTGCTCTTCTGCCCGTTCCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgttctaaatttgggctccattaatgttctaaatttgtcgctgcattgtaacagGCTTCCGAAGAAATGGAGTTACTGTACTAAGTGCTCTTCTGCCCGTTCCTGTAGCACTTGTGGTGGCAGTGGGAAGTTGAGTTCATAGTTTTGTTGTTAT
                           ttctaaa  putative branch site (score: 2)
                    attaatgttctaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacatttgtccttaccttagtgtctctaccctgtataaatttgggctgcattaatgttctaaatttgggctccattaatgttctaaatttgtcgctgcattgtaacagGCTTCCGAAGAAATGGAGTTACTGTACTAAGTGCTCTTCTGCCCGTTCCTGTAGCACTTGTGGTGGCAGTGGGAAGTTGAGTTCATAGTTTTGTTGTTAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG