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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattggattgattacattggcattggtaacatttatctctcttgcttgtacattttcattgaattttgatggttttcctatgtttgtcttatagGGTCGGATGAAGGAATATATGCTTGGGTTGTTGCAAATCATGCACTTGGCAGTCTTGGAGGTGATCCTCGGGAAACAACTGGGATTATTGAGCTTGGTGG

Basic information

species Vitis vinifera
transcript Vv01s0026g02490.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv01s0026g02490.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA02G11980.1 (Glycine max), 3'ss of exon 1
------gtattggattgattacattggcattggtaacatttatctctcttgc--ttgtacattttcattgaattttgatggttttcctatgtttgtcttatagGGTCGGATGAAGGAATATATGCTTGGGTTGTTGCAAATCATGCACTTGGCAGTCTTGGAGGTGATCCTCGGGAAACAACTGGGATTATTGAGCTTGGTGG
        ||    || |||        ||| |||  | || |        |  |  |    |||  ||   || | ||| | ||  | || ||||   | ||| || ||||||||||| ||||||||||||||||| ||| |||||||||||| ||||||||||||||||  |||||| |||||||||||||| ||||||||
ttttttccatctctttaattttgcaataatttgtagtaatttttagaacaaccataatgtcattttgttagcttcttatgctattattgtggttgt---aaagGTTCTGATGAAGGAATGTATGCTTGGGTTGTTGCTAATTATGCACTTGGCACTCTTGGAGGTGATCCTTTGGAAACTACTGGGATTATTGAACTTGGTGG

upper sequence: Vv01s0026g02490.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA01G05750.1 (Glycine max), 3'ss of exon 1
-gtattggattgattacattggcattggtaacatttatctctcttgcttgtacattttcattgaatt--ttgatggttttcctatgtttgt---cttatagGGTCGGATGAAGGAATATATGCTTGGGTTGTTGCAAATCATGCACTTGGCAGTCTTGGAGGTGATCCTCGGGAAACAACTGGGATTATTGAGCTTGGTGG
  | ||| | | |||  | |    |  ||||  ||||   |           |||  |  ||   ||  ||| |  || | ||||  ||||     || ||| || ||||||||| | ||||||||||||||||| ||| ||||||||| || ||||||||||||||||  ||||||||||||||||||||| ||||||||
aattttgcaataattgtacttttgt-agtaatttttagaacaaccataatggcatggttgttagcttctttgcttcttatgctattattgtggttgtaaagGTTCTGATGAAGGAGTGTATGCTTGGGTTGTTGCTAATTATGCACTTGACACTCTTGGAGGTGATCCTTTGGAAACAACTGGGATTATTGAACTTGGTGG

upper sequence: Vv01s0026g02490.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT1G14250.1 (Arabidopsis thaliana), 3'ss of exon 2
gtattggattgattacattggcattggt--aacatttatctctct-tgcttgtacattttcattgaattttgatggtt-ttcctatgtttgtcttat--agGGTCGGATGAAGGAATATATGCTTGGGTTGTTGCAAATCATGCACTTGGCAGTCTTGGAGGTGATCCTCGGGAAACAACTGGGATTATTGAGCTTGGTGG
 | |    ||| || | ||    || ||  |    |  |   | |   | | | ||||  || |      || |  ||  |     |    | ||||  |||  | |||||||| || ||||||||||||||||| ||||| ||||||||    ||||| ||||||||   | ||||||| |||||| |||| ||||||||
-tttcattttgttttcttttagcttagttgagtgatagtaaatgtgcacatatccattggcaattggaagtgctaattactggggggaaaattttattcagGAACTGATGAAGGTATCTATGCTTGGGTTGTTGCCAATCACGCACTTGGTTCGCTTGGTGGTGATCCATTGAAAACAACGGGGATTGTTGAACTTGGTGG

upper sequence: Vv01s0026g02490.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT1G14230.1 (Arabidopsis thaliana), 3'ss of exon 1
------gtattggattgattacattggcattggtaacatttat---ctctcttgcttgtacattttcattgaattttgatggttttcctatgtttgtcttatagGGTCGGATGAAGGAATATATGCTTGGGTTGTTGCAAATCATGCACTTGGCAGTCTTGGAGGTGATCCTCGGGAAACAACTGGGATTATTGAGCTTGGTGG
       |||    | | |||  |  |   | |||| ||  ||    ||  |||  | |   |  |  |  ||||   |    | |   |   || ||    ||| || ||||||||  ||||||||||||||||||| |||||||| || ||    ||||||||||| |||    ||||||| || ||| |||| || |||||
tttttgttatatagtagcttagttgagtgctagtaaaataaatgagatccattggctattgttggtgttataattactagaaatcttggaaaattttc----agGATCTGATGAAGGTGTATATGCTTGGGTTGTTGCTAATCATGCGCTCGGTTCGCTTGGAGGTGAACCTTTAAAAACAACGGGAATTGTTGAACTCGGTGG

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|71860764|gb|DT009819.1|DT009819
EST:     TCGGGTATCAGGTTTTCAATTTCGGGACAGTTGGGCTTCTGTTATTACTG                         GGTCAGATGAAGGAATATATGCTTGGGTTGTTGCAAATCATGCACTTGGCA
genomic: TCGGGTATCAAGTTTTCAATTTCGGGACAGTTGGGCTTCTGTTATTACTGgtattggatt ... tgtcttatagGGTCGGATGAAGGAATATATGCTTGGGTTGTTGCAAATCATGCACTTGGCA
EST: gi|351013112|gb|FQ424817.1|FQ424817
EST:     TCGGGTATCAGGTTTTCAATTTCGGGACAGTTGGGCTTCTGTTATTACTG                         GGTCAGATGAAGGAATATATGCTTGGGTTGTTGCAAATCATGCACTTGGCA
genomic: TCGGGTATCAAGTTTTCAATTTCGGGACAGTTGGGCTTCTGTTATTACTGgtattggatt ... tgtcttatagGGTCGGATGAAGGAATATATGCTTGGGTTGTTGCAAATCATGCACTTGGCA
EST: gi|351055089|gb|FQ440428.1|FQ440428
EST:     TCGGGTATCAGGTTTTCAATTTCGGGACAGTTGGGCTTCTGTTATTACTG                         GGTCAGATGAAGGAA
genomic: TCGGGTATCAAGTTTTCAATTTCGGGACAGTTGGGCTTCTGTTATTACTGgtattggatt ... tgtcttatagGGTCGGATGAAGGAA
EST: gi|110356657|gb|EC919644.1|EC919644
EST:     TCGGGTATCAGGTTTTCAATTTCGGGACAGTTGGGCTTCTGTTATTACTG                         GGTCAGATGAAGGAATATATGCTTGGGTTGTTGCAAATCATGCACTTGGCA
genomic: TCGGGTATCAAGTTTTCAATTTCGGGACAGTTGGGCTTCTGTTATTACTGgtattggatt ... tgtcttatagGGTCGGATGAAGGAATATATGCTTGGGTTGTTGCAAATCATGCACTTGGCA
EST: gi|161718808|gb|FC066355.1|FC066355
EST:     TCGGGTATCAGGTTTTCAATTTCGGGACAGTTGGGCTTCTGTTATTACTG                         GGTCAGATGAAGGAATATATGCTTGGGTTGTTGCAAATCATGCACTTGGCA
genomic: TCGGGTATCAAGTTTTCAATTTCGGGACAGTTGGGCTTCTGTTATTACTGgtattggatt ... tgtcttatagGGTCGGATGAAGGAATATATGCTTGGGTTGTTGCAAATCATGCACTTGGCA
EST: gi|349830014|gb|FQ420274.1|FQ420274
EST:     TCGGATATCAGGTTTTCAATTTCGGGACAGTTGGGCTTCTGTTATTACTG                         GGTCAGATGAAGGAATATTTGCTTGG
genomic: TCGGGTATCAAGTTTTCAATTTCGGGACAGTTGGGCTTCTGTTATTACTGgtattggatt ... tgtcttatagGGTCGGATGAAGGAATATATGCTTGG
EST: gi|110712210|gb|EE089571.1|EE089571
EST:     CGGGTATCAAGTTTTCAATTTCAGGGA-AGTTGGGCTTCTGTTATTACTG                         GGGCGGATGAAGGAA-ATATGCTTGGGTTGTTGCAAATCATGCACTTGGCA
genomic: CGGGTATCAAGTTTTCAATTTC-GGGACAGTTGGGCTTCTGTTATTACTGgtattggatt ... tgtcttatagGGTCGGATGAAGGAATATATGCTTGGGTTGTTGCAAATCATGCACTTGGCA
EST: gi|351029320|gb|FQ436714.1|FQ436714
EST:     TCGGATATCAGGTTTTCCATTTCGGGACAGTTGGGCTTCTGTTATTACTG                         GGTCAGATGAAAGAATATATGCTTGGGTTGTTGCAAATCAAGCACTT
genomic: TCGGGTATCAAGTTTTCAATTTCGGGACAGTTGGGCTTCTGTTATTACTGgtattggatt ... tgtcttatagGGTCGGATGAAGGAATATATGCTTGGGTTGTTGCAAATCATGCACTT
EST: gi|161712811|gb|FC062334.1|FC062334
EST:     TCGGGTATCAGGTTTTCAATTTCGGGACAGTTGGGCTTCTGTTATTACTG                         GGTCAGATGAAGGAATATATGCTTGGGTTGTTGCAAATCATGCACTTGGCA
genomic: TCGGGTATCAAGTTTTCAATTTCGGGACAGTTGGGCTTCTGTTATTACTGgtattggatt ... tgtcttatagGGTCGGATGAAGGAATATATGCTTGGGTTGTTGCAAATCATGCACTTGGCA
EST: gi|110359018|gb|EC919806.1|EC919806
EST:     TCGGGTATCAGGTTTTCAATTTCGGGACAGTTGGGCTTCTGTTATTACTG                         GGTCAGATGAAGGAATATATGCTTGGGTTGTTGCAAATCATGCACTTGGCA
genomic: TCGGGTATCAAGTTTTCAATTTCGGGACAGTTGGGCTTCTGTTATTACTGgtattggatt ... tgtcttatagGGTCGGATGAAGGAATATATGCTTGGGTTGTTGCAAATCATGCACTTGGCA
EST: gi|351016897|gb|FQ424324.1|FQ424324
EST:     TCGGGTATCAGGTTTTCAATTTCGGGACAGTTGGGCTTCTGTTATTACTG                         GGTCAGATGAAGGAATATATGCTTGGGTTGTTGCAAATCATGCACTTGGCA
genomic: TCGGGTATCAAGTTTTCAATTTCGGGACAGTTGGGCTTCTGTTATTACTGgtattggatt ... tgtcttatagGGTCGGATGAAGGAATATATGCTTGGGTTGTTGCAAATCATGCACTTGGCA
EST: gi|110357251|gb|EC920660.1|EC920660
EST:     TCGGGTATCAGGTTTTCAATTTCGGGACAGTTGGGCTTCTGTTATTACTG                         GGTCAGATGAAGGAATATATGCTTGGGTTGTTGCAAATCATGCACTTGGCA
genomic: TCGGGTATCAAGTTTTCAATTTCGGGACAGTTGGGCTTCTGTTATTACTGgtattggatt ... tgtcttatagGGTCGGATGAAGGAATATATGCTTGGGTTGTTGCAAATCATGCACTTGGCA
EST: gi|161717559|gb|FC066257.1|FC066257
EST:     TCGGGTATCAGGTTTTCAATTTCGGGACAGTTGGGCTTCTGTTATTACTG                         GGTCAGATGAAGGAATATATGCTTGGGTTGTTGCAA-TCATGCACTTGGCA
genomic: TCGGGTATCAAGTTTTCAATTTCGGGACAGTTGGGCTTCTGTTATTACTGgtattggatt ... tgtcttatagGGTCGGATGAAGGAATATATGCTTGGGTTGTTGCAAATCATGCACTTGGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttgcttgtacattttcattgaattttgatggttttcctatgtttgtcttatagGGTCGGATGAAGGAATATATGCTTGGGTTGTTGCAAATCATGCACTTGGCAGTCTTGGAGGTGATCCTCGGGAAACAACTGGGATTATTGAGCTTGGTGG
                        ttttgat  putative branch site (score: 4)
                                           tttgtctt  putative PPT
            attttcattgaatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattggattgattacattggcattggtaacatttatctctcttgcttgtacattttcattgaattttgatggttttcctatgtttgtcttatagGGTCGGATGAAGGAATATATGCTTGGGTTGTTGCAAATCATGCACTTGGCAGTCTTGGAGGTGATCCTCGGGAAACAACTGGGATTATTGAGCTTGGTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG