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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttcacatatttatctatcttgggagatcattgtaacatttctacttgtatatttctttctaatttttgtgttacttatcatctattttttccctttatagGTGCGAAGCATTTCCAACATACCCTAGAACTTATGATATGGTGCATGCTGCTGGACTTCTATCTCTTGAAACTAGTCAGCAGCGCAGGTGCACCATGCTC

Basic information

species Vitis vinifera
transcript Vv18s0001g05800.t01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0001g05800.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: LOC_Os02g51860.1 (Oryza sativa), 3'ss of exon 6
-------ttcacatatttatctatcttgggagatcattgtaacatttctacttgtatatttctttctaatttttgtgttacttatcatctattttttccctttatagGTGCGAAGCATTTCCAACATACCCTAGAACTTATGATATGGTGCATGCTGCTGGACTTCTATCTCTTGAAACTAGTCAGCAGCGCAGGTGCACCATGCTC
           ||| | ||   | |||   ||||  |||||    || |  |  | |  |  |  |  |  || |    ||| || |   || |    | | | |||||| |||||||||||||| || || ||||| ||||||||||| ||||||| |||  ||||||| ||||| |     ||  |||  || ||  | |  || 
aatgcaacatgcatgtgtaagaacctttttagat--ttgtag---ttatgttgatctgctgatcacataccttcgatcgactgataaa--atgtgaaacgtgtttagGTGTGAAGCATTTCCAACTTATCCAAGAACATATGATATGGTCCATGCTGATGGCTTTCTATCACTTGAGAAGCACCAAAAGCATAGATGTTCTACTCTT

upper sequence: Vv18s0001g05800.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GRMZM2G140893_T01 (Zea mays), 3'ss of exon 6
-ttcacatatttatctatcttgggagatcattgtaacatttctacttgtatatttctttctaatttttgtgttacttatcatctattttttccctttatagGTGCGAAGCATTTCCAACATACCCTAGAACTTATGATATGGTGCATGCTGCTGGACTTCTATCTCTTGAAACTAGTCAGCAGCGCAGGTGCACCATGCTC
 || |   ||  ||| |  |    |  | || |  |  ||||  | | |  || | |   | ||  |   ||||  |      |   |   |   |  |||||| || |||||| |||| ||||| ||||| ||||||||||||||||||| |||  ||||||| ||||| |  |  ||  |||  || ||  | |  || 
attgatgcata-atcaaagtatcaatttgatagacaactttcggcatatcaatctttggatcatcctccagttaaatgatcgatggatggacatgtgttagGTGTGACGCATTTGCAACTTACCCAAGAACATATGATATGGTGCATGCTGATGGCTTTCTATCACTTGAGAAGACCCACAAGCATAGATGTTCTACTCTT

upper sequence: Vv18s0001g05800.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GRMZM2G000764_T01 (Zea mays), 3'ss of exon 7
ttcacatatttatctatcttgggagatca-ttgtaacatttctacttgtatatttctttctaatttttgtgttacttatcatctattttttccctttatagGTGCGAAGCATTTCCAACATACCCTAGAACTTATGATATGGTGCATGCTGCTGGACTTCTATCTCTTGAAACTAGTCAGCAGCGCAGGTGCACCATGCTC
 | |   |  |||| || | |  |||  | || |  ||| |  |  | |  | ||    | ||  ||    | | | ||      ||       | |  ||||| || ||||||||||| ||||| ||||| |||||||||||||| |||| |||  ||||||| ||| | |  |  ||  |||  || ||  | |  || 
ataagtgaagtatcaat-tcgacagacaacttattgcatattgatctttggagtttggaccaaccttcagttaaataatggatggttggacatgtgttcagGTGTGATGCATTTCCAACTTACCCAAGAACATATGATATGGTGCACGCTGATGGTTTTCTATCACTTCAGAAGAACCACAAGCATAGATGTTCTACTCTT

upper sequence: Vv18s0001g05800.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GRMZM5G824698_T01 (Zea mays), 3'ss of exon 4
ttcacatatttatctatct-tgggagatcattgtaacatttctacttgtatatttctttctaatttttgtgttacttatcatctattttttccctttatagGTGCGAAGCATTTCCAACATACCCTAGAACTTATGATATGGTGCATGCTGCTGGACTTCTATCTCTTGAAACTAGTCAGCAGCGCAGGTGCACCATGCTC
     | ||| ||  ||   ||  | |||| | | | |       ||    || ||  ||| |   ||  ||||  |      |   |   |   |  |||||| || |||||| | || ||||| ||||| ||||||||||||||||||| |||  ||||||| ||||| |  |  ||  |||  || ||  | |  || 
-atggagattgatgcataagtgaaatatcaatttgatagacaactttcggcatatcaatctcaaccttcagttaaatgatcgatggatggacatgtgttagGTGTGACGCATTTGCGACTTACCCAAGAACATATGATATGGTGCATGCTGATGGCTTTCTATCACTTGAGAAGACCCACAAGCATAGATGTTCTACTCTT

upper sequence: Vv18s0001g05800.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA14G35070.1 (Glycine max), 3'ss of exon 6
ttcacatatttatctatcttgggagatcat-tgtaacatttctacttgtatatttctttctaatttttgtgttacttatcatctattttttccc----tttatagGTGCGAAGCATTTCCAACATACCCTAGAACTTATGATATGGTGCATGCTGCTGGACTTCTATCTCTTGAAACTAGTCAGCAGCGCAGGTGCACCATGCTC---
  | |||| |  |  ||      ||||  | || |  ||   |  |||     | ||   ||   | |   || ||||  |  |||  |||        || ||||||||| || |||||||| ||||||||||| |||||  |||||||||| || |||||||| || |||||||||    || ||| ||| ||| |||| ||    
ggctcatagtcgttgat-----aagattttgtgaagaatagtttgttgataggtcctacatagaatatagtttccttaaaaattatgatttttggtggcttctagGTGCGAGGCTTTTCCAACGTACCCTAGAACCTATGACTTGGTGCATGCAGCAGGACTTCTGTCCCTTGAAACTG---AGAAGCACAGATGCTCCATACTTGAC

upper sequence: Vv18s0001g05800.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA13G01750.1 (Glycine max), 3'ss of exon 7
ttcacatatttatctatcttgggagatcat-tgtaacatttctacttgtatatttctttctaatttttgtgttacttatcatctat----tttttccctttatagGTGCGAAGCATTTCCAACATACCCTAGAACTTATGATATGGTGCATGCTGCTGGACTTCTATCTCTTGAAACTAGTCAGCAGCGCAGGTGCACCATGCTC---
 ||| |||||  |  ||      ||||  | || |  ||   || |||     | ||    |  || |   || |||| ||  |||    |||      || |||||| || || |||||||| ||||| ||||| |||||  ||||||||||||| ||||||||||| |||||||||    |||||| ||| ||| |||||||    
ctcatatattctttgat-----aagattttgtgaagaatagttagttgctaggtcctacgcagattatagtttccttaacaaatatgacttttggtggcttctagGTGTGAGGCTTTTCCAACGTACCCCAGAACCTATGACTTGGTGCATGCTGCAGGACTTCTATCCCTTGAAACTG---AGCAGCACAGATGCTCCATGCTTGAC

upper sequence: Vv18s0001g05800.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA06G10760.1 (Glycine max), 3'ss of exon 7
----ttcacatatttatctatcttgggagatcattgtaacatttctacttgtatatttctttctaatttttgtgttacttatcatctatttttt--ccctttatagGTGCGAAGCATTTCCAACATACCCTAGAACTTATGATATGGTGCATGCTGCTGGACTTCTATCTCTTGAAACTAGTCAGCAGCGCAGGTGCACCATGCTC
    ||||  | | | |  || |   || | | |   ||||| |  | || |  ||||| || |      |    || ||| ||| ||| | ||    | || |||||| || || || ||||| || |||||||| |||||  |||||||||| ||||||||| |||| ||||||  |  |||||||||||| || |||||||| 
cttgttcaattttgttttaatttcttgataccttccaaacatatagaattattgatttccttatg-----taaaata-ttagcatttatgtcttgataccttctagGTGTGAGGCCTTCCCAACGTATCCTAGAACCTATGACTTGGTGCATGCAGCTGGACTTTTATCCCTTGAATTTGCTCAGCAGCGCAGATGTACCATGCTT

upper sequence: Vv18s0001g05800.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA04G10920.1 (Glycine max), 3'ss of exon 6
ttcacatatttatctatcttgggagatcattgtaacatttctacttgtatatttctttcta--atttttgtgttacttatcatctattttttccc---tttatagGTGCGAAGCATTTCCAACATACCCTAGAACTTATGATATGGTGCATGCTGCTGGACTTCTATCTCTTGAAACTAGTCAGCAGCGCAGGTGCACCATGCTC
        ||     |   |    | | ||||| | ||| | | |||   |     | ||   | || |   || ||||  || |   |  ||     ||| |||||| || || || ||||| ||||||||||| |||||  |||| ||||| || |||||| |||| ||||||  |  |||||||||||| || |||||||| 
-----gccttgtgaaaaggtcactgttaattgttagattacgatttggggaacaactgctgccacttataaatttcttacaattttgatcatctgtggtttctagGTGTGAGGCCTTCCCAACGTACCCTAGAACCTATGACTTGGTCCATGCAGCAGGACTTTTATCCCTTGAATTTGCTCAGCAGCGCAGCTGTACCATGCTT

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|34546818|gb|CF515050.1|CF515050
EST:     TACCTTCCCTTGATCCTGGATAGAGGATTTGTTGGCGTATTGCATGACTG                         GTGCGAAGCATTTCCAACATACCCTAGGACTTATGATATGGTGCATGCTGC
genomic: TACCTTCCCTTGATCCTGGATAGAGGATTTGTTGGCGTATTGCATGACTGgtaagttcta ... ccctttatagGTGCGAAGCATTTCCAACATACCCTAGAACTTATGATATGGTGCATGCTGC
EST: gi|26260243|gb|CA811306.1|CA811306
EST:     GATAGAGGATTTGTTGGCGTATTGCATGACTG                         GTGCGAAGCATTTCCAACATACCCTAGAACTTATGATATGGTGCATGCTGC
genomic: GATAGAGGATTTGTTGGCGTATTGCATGACTGgtaagttcta ... ccctttatagGTGCGAAGCATTTCCAACATACCCTAGAACTTATGATATGGTGCATGCTGC
EST: gi|71882003|gb|DT031058.1|DT031058
EST:     TACCTTCCCTTGATCCTGGATAGAGGATTTGTTGGCGTATTGCATGACTG                         GTGCGAAGCATTTCCAACATACCCTAGAACTTATGATATGGTGCATGCTGC
genomic: TACCTTCCCTTGATCCTGGATAGAGGATTTGTTGGCGTATTGCATGACTGgtaagttcta ... ccctttatagGTGCGAAGCATTTCCAACATACCCTAGAACTTATGATATGGTGCATGCTGC
EST: gi|110722969|gb|EE099743.1|EE099743
EST:     TACCTTCCCTTGATCCTGGATAGAGGATTTGTTGGCGTATTGCATGACTG                         GTGCGAAGCATTTCCAACATACCCTAGAACTTATGATATGGTGCATGCTGC
genomic: TACCTTCCCTTGATCCTGGATAGAGGATTTGTTGGCGTATTGCATGACTGgtaagttcta ... ccctttatagGTGCGAAGCATTTCCAACATACCCTAGAACTTATGATATGGTGCATGCTGC
EST: gi|294966233|gb|GW839456.1|GW839456
EST:     TACCTTCCCTTGATCCTGGATAGAGGATTTGTCGGCGTATTGCATGACTG                         GTGCGAAGCATTTCCAAAATACCCTAGAACTTATGATATGGTGCATGCTGC
genomic: TACCTTCCCTTGATCCTGGATAGAGGATTTGTTGGCGTATTGCATGACTGgtaagttcta ... ccctttatagGTGCGAAGCATTTCCAACATACCCTAGAACTTATGATATGGTGCATGCTGC
EST: gi|34546639|gb|CF514871.1|CF514871
EST:     TACCTTCCCTTGATCCTGGATAGAGGATTTGTTGGCGTATTGCATGACTG                         GTGCGAAGCATTTCCAACATACCCTAGGACTTATGATATGGTGCATGCTGC
genomic: TACCTTCCCTTGATCCTGGATAGAGGATTTGTTGGCGTATTGCATGACTGgtaagttcta ... ccctttatagGTGCGAAGCATTTCCAACATACCCTAGAACTTATGATATGGTGCATGCTGC
EST: gi|161719756|gb|FC068650.1|FC068650
EST:     TACCTTCCCTTGATCCTGGATAGAGGATTTGTTGGCGTATTGCATGACTG                         GTGCGAAGCATTTCCAACATACCCTAGAACTTATGATATGGTGCATGCTGC
genomic: TACCTTCCCTTGATCCTGGATAGAGGATTTGTTGGCGTATTGCATGACTGgtaagttcta ... ccctttatagGTGCGAAGCATTTCCAACATACCCTAGAACTTATGATATGGTGCATGCTGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtatatttctttctaatttttgtgttacttatcatctattttttccctttatagGTGCGAAGCATTTCCAACATACCCTAGAACTTATGATATGGTGCATGCTGCTGGACTTCTATCTCTTGAAACTAGTCAGCAGCGCAGGTGCACCATGCTC
           ttctaat  putative branch site (score: 2)
                            cttatcatctattttt  putative PPT
     atttctttctaatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttcacatatttatctatcttgggagatcattgtaacatttctacttgtatatttctttctaatttttgtgttacttatcatctattttttccctttatagGTGCGAAGCATTTCCAACATACCCTAGAACTTATGATATGGTGCATGCTGCTGGACTTCTATCTCTTGAAACTAGTCAGCAGCGCAGGTGCACCATGCTC

- - - - - - - - - - - - - - - - - - - - ctacttg