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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctggaggtctttgtttgaacactctaatttcaaataacttatctatctgtacttttatttatttatttgttatctcactgttatcagttatgtttttcagGACATATACTCTATCAAATTACCAGGAAATCCTAAACTTGGTGAAGGAAAACCTGAAAATCAAAACCATGCAGTTATATTTACTCGTGGAAATGCAATTC

Basic information

species Vitis vinifera
transcript Vv06s0004g01200.t01
intron # 32
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0004g01200.t01 (Vitis vinifera), 3'ss of exon 32
lower sequence: GLYMA20G38860.1 (Glycine max), 3'ss of exon 37
--ctggaggtctttgtttgaacactctaatttcaaataacttatctatctgtacttttatttatttatttgttatctcactgttatcagttatgttttt----cagGACATATACTCTATCAAATTACCAGGAAATCCTAAACTTGGTGAAGGAAAACCTGAAAATCAAAACCATGCAGTTATATTTACTCGTGGAAATGCAATTC
   ||   |  ||||||  |      ||  ||   |||| ||   ||  | | ||||  |||| ||  ||| || ||| || |  | |  | | || ||    ||||| ||||||||  | |||||||| |||||||| ||| | || ||||| || || || |||||||| |||||| |||||||||| |||||||||||| | |
ttttgctagcttttgtt--attgaattagattgccataa-ttgcttaggt-tgctttcttttactt--ttgctacctccctttattgaagttttttgttgtcgcagGAGATATACTCAGTAAAATTACCTGGAAATCCCAAATTGGGAGAAGGGAAGCCCGAGAATCAAAATCATGCAATTATATTTACGCGTGGAAATGCAGTCC

upper sequence: Vv06s0004g01200.t01 (Vitis vinifera), 3'ss of exon 32
lower sequence: GLYMA10G44150.2 (Glycine max), 3'ss of exon 35
ctggaggtctttgtttgaacactctaatttcaaataacttatctatctgtacttttatttattt-----atttgttatctcactgtta--tcagttatgtttttcagGACATATACTCTATCAAATTACCAGGAAATCCTAAACTTGGTGAAGGAAAACCTGAAAATCAAAACCATGCAGTTATATTTACTCGTGGAAATGCAATTC
       |  ||| ||        |  ||| |  |  | || || ||| |    |||  ||  |     |||||| |   || |  ||  |   || | | |  ||||| ||||||||  | || || || |||||||| ||| | |||||||| || || || |||||||| |||||| || ||||||| |||||||||||| | |
-------taattgcttaggttgctttcttttacttttcctacctctctattgaattagatagctttgatatttgtcactccatttgtaagttttttttatctcacagGAGATATACTCGGTGAAGTTGCCTGGAAATCCCAAATTGGGTGAAGGGAAGCCCGAGAATCAAAATCATGCAATTGTATTTACGCGTGGAAATGCAGTCC

upper sequence: Vv06s0004g01200.t01 (Vitis vinifera), 3'ss of exon 32
lower sequence: AT3G07160.1 (Arabidopsis thaliana), 3'ss of exon 34
--------------------------------------------------------------------------------------------------ctggaggtctttgtttgaacactctaatttcaaataacttatctatctg-tacttttatttatttatttgttatctcactgttatcagttatgtttttcagGACATATACTCTATCAAATTACCAGGAAATCCTAAACTTGGTGAAGGAAAACCTGAAAATCAAAACCATGCAGTTATATTTACTCGTGGAAATGCAATTC
                                                                                                      | |   |   | |||   |    || |       ||  || | || | ||| |||||  |||| ||  ||  |    || |   |||| || | ||||| || ||||| || || || || ||  | || |||||||| ||||| |||||||| ||||||||||| ||  || | |||||||| |||||||| || |
gtaaactgttattatctgtgaacccagacgtaaactagtgttcttgtttcactaatgtttgaaacacttgatcatactttaattgatcgataaactgtgcttacgctgtaaatggaattttgcgtttcctcccccttttcctctttggtccttctattttgttatatggaatgaccactttgttctttat-ttatgcagGAAATTTACTCCATAAAGTTGCCTGGGGACCCGAAACTTGGCGAAGGCAAACCTGAGAATCAAAACCACGCCATTGTGTTTACTCGCGGAAATGCTATCC

upper sequence: Vv06s0004g01200.t01 (Vitis vinifera), 3'ss of exon 32
lower sequence: PP1S145_49V6.1 (Physcomitrella patens), 3'ss of exon 33
-ctggaggtc-tttgtttgaacactctaatttcaaataacttatctatctgtacttttatttatttatttgttatctcactgttatcagttatgtttttcagGACATATACTCTATCAAATTACCAGGAAATCCTAAACTTGGTGAAGGAAAACCTGAAAATCAAAACCATGCAGTTATATTTACTCGTGGAAATGCAATTC
  | ||  || |||  || |  |   |    |||  |   |  | |   | |||    ||| |  |       |||     | |||    |  |     ||||| || |||||||| ||||| || ||| |    |   | || || || || ||||||||||||||||||||  |||| |||||||||||  | ||  |||
atttgatttcatttaattaagtaacttttcatcatgttgttcctgttattttacaaggattgaaatccccaaaatcctcacggtatggaattggac--gcagGAAATTTACTCTATAAAATTGCCCGGAGAAGTAATTTTAGGGGAGGGCAAGCCTGAAAATCAAAACCATGCGATTATTTTTACTCGTGGGGAAGCCCTTC

upper sequence: Vv06s0004g01200.t01 (Vitis vinifera), 3'ss of exon 32
lower sequence: PP1S13_132V6.1 (Physcomitrella patens), 3'ss of exon 34
ctggaggtctttgtttgaacactctaatttcaaataacttatctatctgtacttttatttatttatttgttatctcactgttatcagttatgtttttcagGACATATACTCTATCAAATTACCAGGAAATCCTAAACTTGGTGAAGGAAAACCTGAAAATCAAAACCATGCAGTTATATTTACTCGTGGAAATGCAATTC
  |     | |  | ||    |    |       | || |    || || | |     |   | |  |   |  |     | ||  ||||   | | ||||| || ||||| || ||||| || ||| |   ||  || || || || || |||||||| |||||||||||| || |||||||||||||| | || ||||
aagttaagcctcatctgccagcagagacccaccgtgacgtcgaaatgtgcaataggtataggtcaactccgaaattctgttgatttgttactatctgcagGAAATCTACTCCATAAAATTGCCTGGAGAAGTTATTCTGGGAGAGGGCAAGCCTGAAAACCAAAACCATGCAATTGTATTTACTCGTGGAGAGGCCATTC

upper sequence: Vv06s0004g01200.t01 (Vitis vinifera), 3'ss of exon 32
lower sequence: PP1S160_88V6.1 (Physcomitrella patens), 3'ss of exon 35
ctggaggtctttgtttgaacactctaatttcaaataacttatctatctgtacttttatttatttatttgttatctcactgttatcagttatgtt--tttcagGACATATACTCTATCAAATTACCAGGAAATCCTAAACTTGGTGAAGGAAAACCTGAAAATCAAAACCATGCAGTTATATTTACTCGTGGAAATGCAATTC
| |   || |||  |   | |  ||||| |     | |||   |         |  ||    | |  |||| |||||  ||  |   | || ||  |  |||  |||||||||  ||||  | || ||      |||||| || ||||||||||| ||||||||||| |||||  | ||||||| ||||||  ||||| |||
cagccagtattttatctgagatcctaatgttcggaatctttaatgatgaggtatacataacctgaagtgtt-tctcaaagt-gtgcataatcttggtcgcagATCATATACTCAGTCAAGCTCCCTGGGCCGTTTAAACTCGGAGAAGGAAAACCAGAAAATCAAAATCATGCTATCATATTTAGTCGTGGGGATGCAGTTC

upper sequence: Vv06s0004g01200.t01 (Vitis vinifera), 3'ss of exon 32
lower sequence: EFJ07568 (Selaginella moellendorffii), 3'ss of exon 34
ctggaggtctttgtttgaacactctaatttcaaataacttatctatctgtacttttatttatttatttgttatctcactgttatc-agttatgtttttcagGACATATACTCTATCAAATTACCAGGAAATCCTAAACTTGGTGAAGGAAAACCTGAAAATCAAAACCATGCAGTTATATTTACTCGTGGAAATGCAATTC
                                                         |    |   |     |   ||| | ||| | | | ||  | ||||| || ||| ||||||||||||| |||||||| |||||||| ||||| || |||||||||||||| |||||  |||| ||||| |||||| ||||||| |
--------------------------------------------------------gtacgctcgctatgcgttcaactttaatctaatcaggtactacagGATATCTACACTATCAAATTACCGGGAAATCCAAAACTTGGAGAAGGCAAGCCTGAAAATCAAAATCATGCGATTATTTTTACCCGTGGAGATGCAATAC

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|30252507|gb|CB970058.1|CB970058
EST:     CAGAGTTCTATTCTAAACTTGTGAAAGCTGATATCAATGGGAAAGATCAG                         GAAATATACTCTATCAAATTGCCAGGAAATCCTAAACTTGGTGAAGGAAAA
genomic: CAGAGTTCTATTCTAAACTTGTGAAAGCTGATATCAATGGGAAAGATCAGgttcatgcat ... tgtttttcagGACATATACTCTATCAAATTACCAGGAAATCCTAAACTTGGTGAAGGAAAA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctgtacttttatttatttatttgttatctcactgttatcagttatgtttttcagGACATATACTCTATCAAATTACCAGGAAATCCTAAACTTGGTGAAGGAAAACCTGAAAATCAAAACCATGCAGTTATATTTACTCGTGGAAATGCAATTC
                          atctcac  putative branch site (score: 3)
                                             tgtttttc  putative PPT
     acttttatttatttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctggaggtctttgtttgaacactctaatttcaaataacttatctatctgtacttttatttatttatttgttatctcactgttatcagttatgtttttcagGACATATACTCTATCAAATTACCAGGAAATCCTAAACTTGGTGAAGGAAAACCTGAAAATCAAAACCATGCAGTTATATTTACTCGTGGAAATGCAATTC

- - - - - - - - - -cactcta
- - - - - - - - - - - - - - - caaataa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctcactg