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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttacgtggcgtggtgttgatggagagaagaaagatcgtgggaatctgtttttacattttggcatgtttctaattttagttttatttatttattttcgcagGGACTAGGAATAACAGTGTTTGGCATGGCCTACATGTTTGTCCACGACGGCCTTGTCCACCGTCGATTCCCTGTCGGACCCATCGCCAACGTCCCTTATC

Basic information

species Vitis vinifera
transcript Vv02s0025g00240.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv02s0025g00240.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os04g48880.1 (Oryza sativa), 3'ss of exon 3
ttacgtggcgtggtgttgatggagagaagaaagatc---gtgggaatctgtttttacattttggcatgtttctaat----tttagttt--tatttatttattt-tcgcagGGACTAGGAATAACAGTGTTTGGCATGGCCTACATGTTTGTCCACGACGGCCTTGTCCACCGTCGATTCCCTGTCGGACCCATCGCCAACGTCCCTTATC
 || |    | |   |  | ||||     || | ||    |||    | |     || | |  |     | | | |    | |    |   |  | |   ||| |  ||||| || || || ||  |||| ||||||||||||||||| |||||||||||||| |||||||| || ||||| ||||| |||||||| || || || ||  
gtaagcccagcgccctgcagggagcacgtaacgctctctctggtcggccgggcccacctgtcagagccatccaattgggatctgacctgccacgtgtccgtttcttacagGGCCTCGGGATTACGCTGTTCGGCATGGCCTACATGTTCGTCCACGACGGCCTGGTCCACCGCCGCTTCCCCGTCGGCCCCATCGCGAATGTGCCCTACT

upper sequence: Vv02s0025g00240.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os03g03370.2 (Oryza sativa), 3'ss of exon 3
ttacgtggcgtggtgttgatggagagaagaaagatcgtgggaatctgtttttacattttggcatgtttctaattttagt-tttatttatttattt-tcgcagGGACTAGGAATAACAGTGTTTGGCATGGCCTACATGTTTGTCCACGACGGCCTTGTCCACCGTCGATTCCCTGTCGGACCCATCGCCAACGTCCCTTATC
   |||  | |  |||| |    ||     ||| | |      | || | |     | |||        | ||   |||  | |  | |   ||   |||||||||| || || ||  |||| || ||||| |||||||| |||||||||||||| |||||||| || ||||| || || |||||||||||||| || ||  
-agcgtttctttttgttcaatttgattgccaaggttgaatttttgtgatctggggctctgg-gcagagatgatccaagtgctgacgtgtccgttcgccgcagGGACTCGGGATCACGCTGTTCGGGATGGCGTACATGTTCGTCCACGACGGCCTGGTCCACCGCCGCTTCCCGGTGGGGCCCATCGCCAACGTGCCCTACT

upper sequence: Vv02s0025g00240.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os10g38940.1 (Oryza sativa), 3'ss of exon 2
ttacgtggcgtggtgttgatggagagaagaaagatcgtgggaatctgtttttacattt------tggcatgtttctaattttagttttatttatttattttcg-cagGGACTAGGAATAACAGTGTTTGGCATGGCCTACATGTTTGTCCACGACGGCCTTGTCCACCGTCGATTCCCTGTCGGACCCATCGCCAACGTCCCTTATC
    ||  ||| |||    | | | |   |    |  || |  |||  |||  | | |      || | |||  |    ||     | |  |         |  ||||| || || || ||  |||| || ||||| |||||||| |||||||||||||| |||||||| || ||||| || || |||||||  ||||| || ||  
----gtcacgtcgtg---gtcgggggcgtatccgttttgaggctcttctttatcgtctgatgggtgacgtgtcacgtggttggcgctgacgtggccgcgcgcaacagGGGCTTGGGATTACGCTGTTCGGGATGGCGTACATGTTCGTCCACGACGGCCTGGTCCACCGGCGCTTCCCCGTGGGGCCCATCGAGAACGTGCCCTACT

upper sequence: Vv02s0025g00240.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G164318_T01 (Zea mays), 3'ss of exon 3
-------------------------------------------ttacgtggcgtggtgttgatggagagaagaaagatcgtgggaatctgtttttacattttggcatgtttctaattttagtttta---tttatttattttc-----gcagGGACTAGGAATAACAGTGTTTGGCATGGCCTACATGTTTGTCCACGACGGCCTTGTCCACCGTCGATTCCCTGTCGGACCCATCGCCAACGTCCCTTATC
                                           |||  |||   | ||         ||  |     | || || |   ||   |    |  | || || ||  | | |  | | |   |  |  | | |||      ||||| || || || ||  |||| ||||||||||||||||| |||||||||||||| |||||||| || || || ||||| |||||||||||||| || ||  
gtaagctagccacgtacagtatctcggtgtgttgtgtgtctggttagttggttggctggctggacccagctgttgcctggtaggcagg-gtggctggcgtcagccacgtatccgactgtgatctcaccctccacgtgtcttcctcccacagGGCCTCGGGATTACGCTGTTCGGCATGGCCTACATGTTCGTCCACGACGGCCTGGTCCACCGCCGCTTTCCGGTCGGCCCCATCGCCAACGTGCCCTACT

upper sequence: Vv02s0025g00240.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G152135_T06 (Zea mays), 3'ss of exon 3
------------------------------ttacgtggcgtggt--gttgat-ggagagaagaaagatc-------gtgggaatctgtttttacattttggc----atgtttctaattttagtttta---tttatttattttcg-----cagGGACTAGGAATAACAGTGTTTGGCATGGCCTACATGTTTGTCCACGACGGCCTTGTCCACCGTCGATTCCCTGTCGGACCCATCGCCAACGTCCCTTATC
                               |   | |  | ||  |||| | ||   || ||   | |       | ||   |   |   | | | |  ||      |  ||  | | |  | | |   |  |  | | |||      ||||| || || || ||  |||| ||||||||||||||||| |||||||||||||| |||||||| || || || ||||| ||||||||| |||| || ||  
gtaagctagctagctagccacggactgtgcctggttagtttagttagttggttggtcggatgacccacctctctcagcggtggtgcctgcctgcctgtcagccacgggggatccgactgtgatctcaccctccacgtgtcttcatgtcacagGGCCTGGGGATTACGCTGTTCGGCATGGCCTACATGTTCGTCCACGACGGCCTGGTCCACCGCCGCTTTCCGGTCGGCCCCATCGCCGACGTGCCCTACT

upper sequence: Vv02s0025g00240.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G382534_T01 (Zea mays), 3'ss of exon 3
ttacgtggcgtggtgttgatggagagaagaaagatcgtgggaatctgtttttacattttggcatgtttctaattttagttttatttatttattttcgcagGGACTAGGAATAACAGTGTTTGGCATGGCCTACATGTTTGTCCACGACGGCCTTGTCCACCGTCGATTCCCTGTCGGACCCATCGCCAACGTCCCTTATC
    |||  ||     ||  |  ||  |   |     || | |   | |     |  |||||  |||  |   |   ||               |||||||| || || || ||  | || || |||||||||||||| || ||||||||||| |||||||| || ||||| ||||| |||||||  ||||| || ||  
----gtga-gtctctctgccgacgacgatccactctttgtgcacacgct-----agcttggccggttcttctctgacgtgcctcgcggcgtcgctcgcagGGGCTGGGGATCACGCTCTTCGGGATGGCCTACATGTTCGTGCACGACGGCCTCGTCCACCGCCGTTTCCCCGTCGGCCCCATCGAGAACGTGCCCTACT

upper sequence: Vv02s0025g00240.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G090051_T02 (Zea mays), 3'ss of exon 2
ttacgtggcgtggtgttgatggagagaagaaagatcgtgggaatctgttt--ttacattttggcatgtttctaattttagttttatttatttattttcgcagGGACTAGGAATAACAGTGTTTGGCATGGCCTACATGTTTGTCCACGACGGCCTTGTCCACCGTCGATTCCCTGTCGGACCCATCGCCAACGTCCCTTATC
 |||  ||  |     || ||  | |   || |  ||||       |      |    | ||   ||  | |   | | |      |   |    | ||||||| || || || ||  |||| || |||||||||||||| || ||||||||||| |||||||| || ||||| ||||| |||||||  ||||| || ||  
gtacacggtcttcctctggtgtggtggccaaggcacgtgcacgctcggccggctctgctctgctctgact-tggctctggccggcgtcgctcgcat-cgcagGGGCTGGGGATCACGTTGTTCGGGATGGCCTACATGTTCGTGCACGACGGCCTCGTCCACCGCCGCTTCCCCGTCGGGCCCATCGAGAACGTGCCCTACT

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|26258277|gb|CA809340.1|CA809340
EST:     CCTATGGCCTCTTCAACAAAGGCCTCGTCCCAGGTCTCTGTTTCGGAGCT                         GGACTAGGAATAACAGTGTTTGGCATGGCCTACATGTTTGTCCACGACGGC
genomic: CCTATGGCCTCTTCAACAAAGGCCTCGTCCCAGGTCTCTGTTTCGGAGCTgtgagtccct ... attttcgcagGGACTAGGAATAACAGTGTTTGGCATGGCCTACATGTTTGTCCACGACGGC
EST: gi|26257470|gb|CA808533.1|CA808533
EST:     CCTATGGCCTCTTCAACAAAGGCCTCGTCCCAGGTCTCTGTTTCGGAGCT                         GGACTAGGAATAACAGTGTTTGGCAT
genomic: CCTATGGCCTCTTCAACAAAGGCCTCGTCCCAGGTCTCTGTTTCGGAGCTgtgagtccct ... attttcgcagGGACTAGGAATAACAGTGTTTGGCAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtttttacattttggcatgtttctaattttagttttatttatttattttcgcagGGACTAGGAATAACAGTGTTTGGCATGGCCTACATGTTTGTCCACGACGGCCTTGTCCACCGTCGATTCCCTGTCGGACCCATCGCCAACGTCCCTTATC
                     ttctaat  putative branch site (score: 2)
                                          tttattttc  putative PPT
                 atgtttctaattttag  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttacgtggcgtggtgttgatggagagaagaaagatcgtgggaatctgtttttacattttggcatgtttctaattttagttttatttatttattttcgcagGGACTAGGAATAACAGTGTTTGGCATGGCCTACATGTTTGTCCACGACGGCCTTGTCCACCGTCGATTCCCTGTCGGACCCATCGCCAACGTCCCTTATC

- - - - - -ggtgttg
- - - - - - - - - - - - -gaagaaa
- - - - - - - - - - - - - - - - - tcgtggg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcatgtt