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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attgttttttgttccttaatttgtccaatgatctttaatatgaaatttatgccaagatgttttttaatccaactttttttttttttggacatttttgcagAGGCGCACGGGCAGCTGTGTGGGAGAATTTTAAAGACAATCCACTTTTTGACATCTCAACAGAGCACCCAATGACTTATTATGAGGACATGCAACGGGCT

Basic information

species Vitis vinifera
transcript Vv17s0000g00120.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv17s0000g00120.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os01g70190.1 (Oryza sativa), 3'ss of exon 3
-attgttttttgttccttaatttgtccaatgatctttaatatgaaatttatgccaagatgttttttaatccaactttttttttttttggacatttt----tgcagAGGCGCACGGGCAGCTGTGTGGGAGAATTTTAAAGACAATCCACTTTTTGACATCTCAACAGAGCACCCAATGACTTATTATGAGGACATGCAACGGGCT
    |      |  | |  | |    | ||| |   | ||| | | | |     | ||  | || ||| ||||   | ||  |       | || |    |||||||| || || ||| | ||||||||||| || ||  ||||||| |||||||||||||| ||||| ||||||   || || || ||||||||||| ||  | 
gtgagcaccaagaacatgcaatcactcgatgcttcctcataagcattgt---tgatgaattattgtaacccaaaagtcttgatgaacctgctttatgcaatgcagAGGTGCCCGTGCATCGGTGTGGGAGAACTTCAAGAACAATCCTCTTTTTGACATCTCCACAGACCACCCACCAACCTACTACGAGGACATGCAGCGTTCC

upper sequence: Vv17s0000g00120.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA05G33420.1 (Glycine max), 3'ss of exon 3
attgttttttgttccttaatttgtccaatgat-ctttaatatgaaa-----tttatgccaa-----gatgttttttaatccaactttttttttttttggacatttttgcagAGGCGCACGGGCAGCTGTGTGGGAGAATTTTAAAGACAATCCACTTTTTGACATCTCAACAGAGCACCCAATGACTTATTATGAGGACATGCAACGGGCT
         ||    ||  |   | ||||||| |||| |||  |||      ||    |||      ||  |  || ||  ||||     | ||||    || | ||||||||||||| | ||||| ||||||||||| ||||| |||||||  || ||||||||||| || ||||| ||||  ||||| || |||||||||||| | || 
--------atgaagtttggtgcatgcaatgatgctttcataacaaaacacacttggatcaacaaataatcctggttgatgaaactgaccgtgtttt---gcaatcttgcagAGGCGCAAGAGCAGCAGTGTGGGAGAACTTTAAGGACAATCTGCTGTTTGACATCTCCACTGAGCATCCAACCACTTACTACGAGGACATGCAAAGAGCC

upper sequence: Vv17s0000g00120.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA06G17140.1 (Glycine max), 3'ss of exon 3
---attgttttttgttccttaatttgtccaatgatctttaatatgaaatttatgccaagatgttttttaatccaactttttttttttttggacatttttgcagAGGCGCACGGGCAGCTGTGTGGGAGAATTTTAAAGACAATCCACTTTTTGACATCTCAACAGAGCACCCAATGACTTATTATGAGGACATGCAACGGGCT
   ||    ||| ||||| |   |||     |       || | |||    |    | |||  |      || ||||   | |  ||||| |   | || |||||| ||  | ||||| ||||||||||| ||||| ||||||||||| |||||||| || |||||||| ||||  || || || |||||||||||||| |||
tgcatgaagtttggttccatgtcttgatgctttcataccaaaacgaataacaataaatgatcctgaaagctcaaactgactgtacttttgta---tcttacagAGGTGCCAGAGCAGCAGTGTGGGAGAACTTTAAGGACAATCCACTGTTTGACATTTCCACAGAGCATCCAACAACATACTACGAGGACATGCAACGAGCT

upper sequence: Vv17s0000g00120.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA04G37920.1 (Glycine max), 3'ss of exon 3
attgttttttgttccttaa--tttgtccaatgatctttaatat-gaaatttatgccaag--atgttttttaa--tccaactttttttttttttggacatttttgcagAGGCGCACGGGCAGCTGTGTGGGAGAATTTTAAAGACAATCCACTTTTTGACATCTCAACAGAGCACCCAATGACTTATTATGAGGACATGCAACGGGCT
     |     | | | ||  || || | |||   |   |||   |||   ||| |||   ||| |  | ||    |||  |   | |  |||||    | ||  ||||| ||  | ||||| ||||||||||| ||||| ||||||||||| |||||||| || || ||||| ||||  || ||||| ||||| |||||||| || 
-----taagcatgcatgaagtttggttccatgtcttgatataccaaaacaaatgacaaaaaatgatcctgaaagctcaaactgactgtactttggta--tcttatagAGGTGCCAGAGCAGCAGTGTGGGAGAACTTTAAGGACAATCCACTGTTTGACATTTCCACTGAGCATCCAACAACATATTACGAGGATATGCAACGAGCA

upper sequence: Vv17s0000g00120.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT5G61840.1 (Arabidopsis thaliana), 3'ss of exon 3
-------------------------------------------------------------------------attgtttttt--gttccttaatttgtccaatgatctttaatatgaaatttatgccaagatgttttttaatccaactttttttttttt------tggacatttttg---------------cagAGGCGCACGGGCAGCTGTGTGGGAGAATTTTAAAGACAATCCACTTTTTGACATCTCAACAGAGCACCCAATGACTTATTATGAGGACATGCAACGGGCT
                                                                         |||| ||| |  |||    | ||||  ||   | ||  || | | ||  | |  ||   |||||||  | |||    || || || |      ||   || ||||               ||| || ||| | |||||||| ||||| || || ||||||||||| || |||||||||||||||||||||||||  || |||||||||||||||||  | || 
gtaatttttttcttatgaaagttcttagctattgttcataataaatttcataaatctcctaaaacagttcataattgctttatcggtttggaattttggacataaaactcaaaaaaggaaaatttatcagactgtttttagagccatggattgttcttataatcagtgatgatgtttgtttgtcaaactggcacagGGGTGCAAGAGCAGCTGTATGGGAAAACTTCAAAGACAATCCGCTGTTTGACATCTCAACAGAGCACCCAACAACATATTATGAGGACATGCAGAGAGCA

upper sequence: Vv17s0000g00120.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: PP1S7_455V6.1 (Physcomitrella patens), 3'ss of exon 4
-attgttttttgttccttaatttgtccaatg-atctttaatatgaaatttatgccaagatgttttttaatccaactttttttttttttggaca--tttttgcagAGGCGCACGGGCAGCTGTGTGGGAGAATTTTAAAGACAATCCACTTTTTGACATCTCAACAGAGCACCCAATGACTTATTATGAGGACATGCAACGGGCT
   ||     |  |  ||| ||  ||   ||  | |||| | |     ||   |   |   ||| |||  |  |||   || ||  |||||    | |||||||||||||| | |||||| | ||||| ||||| ||||| || ||| | || |||||||| |||||||| |||   ||||| ||||| ||||||||||| || 
gcatgcaagctagttttta-ttcatcttttgtgtatttattcttttgcttcctcttgg---tttgttagacatactgagttcttcattggatgattctttgcagAGGCGCAAGAGCAGCTATCTGGGAAAATTTCAAAGATAACCCATTGTTCGACATCTCGACAGAGCATCCAGCAACTTACTATGAAGACATGCAACGCGCA

upper sequence: Vv17s0000g00120.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: EFJ05285 (Selaginella moellendorffii), 3'ss of exon 3
attgttttttgttccttaatttgtccaatgatctttaatatgaaatttatgccaagatgttttttaatccaactttttttttttttggacatttttgcagAGGCGCACGGGCAGCTGTGTGGGAGAATTTTAAAGACAATCCACTTTTTGACATCTCAACAGAGCACCCAATGACTTATTATGAGGACATGCAACGGGCT
               | || || ||  |  |      |||  |||  | ||     |    | ||| |||    |    |||| |       |  ||||| || || || || ||||| ||||||||||| || || ||||| || ||||||||||| || |||||||| || || || |||||||||||||| || |||
--------------gtaaagttctctcaatac-----atagaaaagctttgtttgaaaagatcttattccgttctgacattttct-----gctcatgcagGGGTGCTCGTGCTGCTGTTTGGGAGAATTTCAAGGATAATCCTCTCTTTGACATCTCTACCGAGCACCCGATTACGTACTATGAGGACATGCAGCGAGCT

upper sequence: Vv17s0000g00120.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: EFJ25836 (Selaginella moellendorffii), 3'ss of exon 3
attgttttttgttccttaatttgtccaatgatctttaatatgaaatttatgccaagatgttttttaatccaactttttttttttttggacatttttgcagAGGCGCACGGGCAGCTGTGTGGGAGAATTTTAAAGACAATCCACTTTTTGACATCTCAACAGAGCACCCAATGACTTATTATGAGGACATGCAACGGGCT
               | || || ||  |  |  |   | |  |  ||| |   || |  | ||   || |   | |    |||  ||     |  ||||| || || || || ||||| ||||||||||| || || ||||| || ||||||||||| || |||||||| || || || || ||||||||||| || |||
--------------gtaaagttctctcaatacat---agaaaagctttgtttgaaaagatctt---attcggttctgacatttgctg----ctcatgcagGGGTGCTCGTGCTGCTGTTTGGGAGAATTTCAAGGATAATCCTCTCTTTGACATCTCTACCGAGCACCCGATTACGTACTACGAGGACATGCAGCGAGCT

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|351023339|gb|FQ432722.1|FQ432722
EST:     GGATTGTTCTATGATGTAGGAAATGACCCAGAAGGTGGTTATTATGCAAG                         AGGCGCACGGGCAGCTGTGTGGGAGAATTTTAAAGACAATCCACTTTTTGA
genomic: GGATTGTTCTATGATGTAGGAAATGACCCAGAAGGTGGTTATTATGCAAGgtattcctca ... atttttgcagAGGCGCACGGGCAGCTGTGTGGGAGAATTTTAAAGACAATCCACTTTTTGA
EST: gi|110718481|gb|EE095362.1|EE095362
EST:     GGATTGTTCTATGATGTAGGAAATGACCCAGAAGGTGGTTATTATGCAAG                         AGGTGCACGGGCAGCTGTGTGGGAGAATTTTAAAGACAATCCACTTTTTGA
genomic: GGATTGTTCTATGATGTAGGAAATGACCCAGAAGGTGGTTATTATGCAAGgtattcctca ... atttttgcagAGGCGCACGGGCAGCTGTGTGGGAGAATTTTAAAGACAATCCACTTTTTGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttatgccaagatgttttttaatccaactttttttttttttggacatttttgcagAGGCGCACGGGCAGCTGTGTGGGAGAATTTTAAAGACAATCCACTTTTTGACATCTCAACAGAGCACCCAATGACTTATTATGAGGACATGCAACGGGCT
                ttttaat  putative branch site (score: 3)
                                            cattttt  putative PPT
           atgttttttaatccaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attgttttttgttccttaatttgtccaatgatctttaatatgaaatttatgccaagatgttttttaatccaactttttttttttttggacatttttgcagAGGCGCACGGGCAGCTGTGTGGGAGAATTTTAAAGACAATCCACTTTTTGACATCTCAACAGAGCACCCAATGACTTATTATGAGGACATGCAACGGGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - ccaatga
- - - - - - - - - - - - - - - - - - aatatgaa
- - - - - - - - - - - - - - - - - - - - - - - -tatgcca