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

...ggttacttttgaaacctggctttttgttttccagctctactgatatactggggaaattgctaaccttatacattcttgtatttttgttctcaaaatacagCTCTGAATGAAGCACTAAAGAAGGAAGTAGAGAGGCTTAAGATTGCTACTGGAGAAATAATGACCTCCTCAGATGCATACAATTTGGGAATGCACCATGT

Basic information

species Vitis vinifera
transcript Vv13s0067g02900.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv13s0067g02900.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os03g21800.2 (Oryza sativa), 3'ss of exon 3
---ggttacttttgaaacctggctttttgttttccagctctactgatatactggggaaattgctaaccttatacattcttgtatttttgttctcaaaatacagCTCTGAATGAAGCACTAAAGAAGGAAGTAGAGAGGCTTAAGATTGCTACTGGAGAAATAATGACCTCCTCAGATGCATACAATTTGGGAATGCACCATGT
     |||  || || |  | |   |      |  ||    | |   | |||| |    |  ||     |     |      |  | || | | |   | ||||||||||||| ||||||||| ||||| | |||||||||||| | |||||||| || || |  |  |||   ||  |||| |   ||||| |||| |||||
tgtaattatattggatatgtagaagtgatagctggagtatgaattgca-actgtgagcgtacct--ttctggttctaacaaaaagtgtgatataatttttcagCTCTGAATGATGCACTAAAGCAGGAACTGGAGAGGCTTAAGCTCGCTACTGGTGAGATGACAAATTCCAATGAGACATATAGCATGGGACTGCAACATGT

upper sequence: Vv13s0067g02900.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os07g48180.1 (Oryza sativa), 3'ss of exon 3
---ggttacttttgaaacctggctttttgttttccagctctactgatatactggggaaattgctaaccttatacattcttgtatttttgttctcaaaatacagCTCTGAATGAAGCACTAAAGAAGGAAGTAGAGAGGCTTAAGATTGCTACTGGAGAAATAATGACCTCCTCAGATGCATACAATTTGGGAATGCACCATGT
     | || |||  |||    ||| |     ||     |     ||| | | ||  |  || |    ||     |  | | | |    |  |       ||||||| || || ||||| ||| ||||||| |||||||||||||||||||| || || ||    |  ||    ||||| || |||   |||||||| || ||
agtattgacattttgaac--aacttgtgaacatctgaaacacagcatagattaggatacgtgttgtttttcctgctaatagaaataccatatt-gtttcgcagCTCTCAACGATGCACTGAAGCAGGAAGTGGAGAGGCTTAAGATTGCTACGGGTGAGATGGCAAAGTCAAATGATGCGTATAATACAGGAATGCAGCAGGT

upper sequence: Vv13s0067g02900.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G151295_T02 (Zea mays), 3'ss of exon 3
--ggttacttttgaaacctggctttttgttttccagctctactgatatactggggaaattgctaaccttatacattcttgtatttttgttctcaaaatacagCTCTGAATGAAGCACTAAAGAAGGAAGTAGAGAGGCTTAAGATTGCTACTGGAGAAATAATGACCTCCTCAGATGCATACAATTTGGGAATGCACCATGT
    |||| ||| |               |      ||  |   ||||          ||  |   ||| |||||||| | ||  |       |   | ||||||||||||| ||||||||| ||||  | |||||||||||| ||| |||||| || || |  |  |||   ||  |||| ||  || || | || ||| |
ctaattacattttacttacacagaacaaataaatgactggaac-atatgacaatttctttattctacttgtacattct-gaataatctcatgtatcttgcagCTCTGAATGATGCACTAAAGCAGGAGCTGGAGAGGCTTAAGCTTGTTACTGGTGAGATGACCAATTCCAGTGAGACATATAACATGAGATTTCAGCATAT

upper sequence: Vv13s0067g02900.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA04G40010.1 (Glycine max), 3'ss of exon 3
----ggttacttt-tgaaacctggctttttgttttccagctctactgatatactggggaaattgctaaccttatacattcttgtatttttgttctcaaaatacagCTCTGAATGAAGCACTAAAGAAGGAAGTAGAGAGGCTTAAGATTGCTACTGGAGAAATAATGACCTCCTCAGATGCATACAATTTGGGAATGCA-CCATGT--
       |  ||| | |||| |    |  | | ||     | |||  |   | |      | | | | |||  |    |||   |   || |     | |||||||||| ||||||||||| ||||| ||||| ||  |||| |||||||| ||||| || ||| | |         ||||  |   |||||||||||| |||  |  
gtgtttctgttttgttaaacttcagctaatatattgttatt-tac-aactcatttccatgacttcaaccctcctg---tctcaaaaaattataaaatatatacagCTCTAAATGAAGCACTGAAGAAAGAAGTTGATGGGCTCAAGATTGCAACTGGCGAGATAGTAATGCAT---AATGCCCATGGTTTGGGAATGCATCCACTTAC

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|351047307|gb|FQ454918.1|FQ454918
EST:     GCTTAAGCTTAGGTTACAAGCTATGGAACAACAAGCTCAACTACGCGATG                         CTCTGAATGAAGCACTAAAGAAGGAA
genomic: GCTTAAGCTTAGGTTACAAGCTATGGAACAACAAGCTCAACTACGTGATGgtatgttcaa ... caaaatacagCTCTGAATGAAGCACTAAAGAAGGAA
EST: gi|110390594|gb|EC955513.1|EC955513
EST:     GCTTAAGCTTAGGTTACAAGCTATGGAACAACAAGCTCAACTACGTGATG                         CTCTGAATGAAGCACTAAAGAAGGAAGTAGAGAGGCTTAAGATTGCTACTG
genomic: GCTTAAGCTTAGGTTACAAGCTATGGAACAACAAGCTCAACTACGTGATGgtatgttcaa ... caaaatacagCTCTGAATGAAGCACTAAAGAAGGAAGTAGAGAGGCTTAAGATTGCTACTG
EST: gi|351031577|gb|FQ459834.1|FQ459834
EST:     GCTTAAGCTTAGGTTACAAGCTATGGAACAACAAGCTCAACTACGTGATG                         CTCTGAATGAAGCACTAAAGAAGGAAGTAGAGAGGCTTAA
genomic: GCTTAAGCTTAGGTTACAAGCTATGGAACAACAAGCTCAACTACGTGATGgtatgttcaa ... caaaatacagCTCTGAATGAAGCACTAAAGAAGGAAGTAGAGAGGCTTAA
EST: gi|349826371|gb|FQ417868.1|FQ417868
EST:     GCTTAAGCTTAGGTTACAAGCTATGGAACAACAAGCTCAACTACGTGATG                         CTCTGAATGAAGCACTAAAGAAGGAAGTAGAGAGGCTTAAGATTGCTACTG
genomic: GCTTAAGCTTAGGTTACAAGCTATGGAACAACAAGCTCAACTACGTGATGgtatgttcaa ... caaaatacagCTCTGAATGAAGCACTAAAGAAGGAAGTAGAGAGGCTTAAGATTGCTACTG
EST: gi|110388249|gb|EC952981.1|EC952981
EST:     GCTTAAGCTTAGGTTACAAGCTATGGAACAACAAGCTCAACTACGTGATG                         CTCTGAATGAAGCACTAAAGAAGGAAGTAGAGAGGCTTAAGATTGCTACTG
genomic: GCTTAAGCTTAGGTTACAAGCTATGGAACAACAAGCTCAACTACGTGATGgtatgttcaa ... caaaatacagCTCTGAATGAAGCACTAAAGAAGGAAGTAGAGAGGCTTAAGATTGCTACTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tactggggaaattgctaaccttatacattcttgtatttttgttctcaaaatacagCTCTGAATGAAGCACTAAAGAAGGAAGTAGAGAGGCTTAAGATTGCTACTGGAGAAATAATGACCTCCTCAGATGCATACAATTTGGGAATGCACCATGT
            tgctaac  putative branch site (score: 1)
                                   tttttgttctc  putative PPT
                          attcttgtattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggttacttttgaaacctggctttttgttttccagctctactgatatactggggaaattgctaaccttatacattcttgtatttttgttctcaaaatacagCTCTGAATGAAGCACTAAAGAAGGAAGTAGAGAGGCTTAAGATTGCTACTGGAGAAATAATGACCTCCTCAGATGCATACAATTTGGGAATGCACCATGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - -tgaaacc
- - - - - - - - tggcttt
- - - - - - - - - - - - - - ttccagc
- - - - - - - - - - - - - - - - - - ctactga
- - - - - - - - - - - - - - - - - - - - - - atactgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - gctaacc