Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttctataaacaaataaagtttcttcacctttgcattttagcgttaggtaacaactaacaacacattctgaagtttattctatttttatgtcattttccagAATAGAGATAGATACAAAGCTTCCCATAGTTGGTGAGCAGAAGTGGAAGATATGGATTTGTTCCTTCAATGTACCAATGGCACCTGGGAAAACTCGTTCG

Basic information

species Vitis vinifera
transcript Vv06s0061g00790.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0061g00790.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G339563_T01 (Zea mays), 3'ss of exon 4
-----ttctataaacaaataaagtt-tcttcacctttgcattttagcgttaggtaacaactaa-caacacattctgaagtttattctatttttatgtca------ttttccagAATAGAGATAGATACAAAGCTTCCCATAGTTGGTGAGCAGAAGTGGAAGATATGGATTTGTTCCTTCAATGTACCAATGGCACCTGGGAAAACTCGTTCG
     ||  | |||   |    ||  ||||    | || | |  |   |||  || ||  ||| |||  || ||   |     ||||    || ||| |      || | ||||||||||||||| |||||| | |||||  |||| || ||||| |||   ||||||||||| || |||||  | |||||||| || ||||| |||||||| 
gtaagtttcagaaaagtacctggtcatctttgagtgtggagtg-attcttatttaccacttaagcaattcagtcgttatacggttctgaacttctgttaactggcttgtacagAATAGAGATAGACACAAAGTTACCCATTTTTGGCGACCAGAAATGGGTCATATGGATTTGCTCTTTCAACATTCCAATGGCCCCAGGGAAGACTCGTTCT

upper sequence: Vv06s0061g00790.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA11G19800.1 (Glycine max), 3'ss of exon 4
-----ttctataaacaaataaagtttcttcacctttgcattttagcgttaggtaacaactaacaacacattctgaagtttattctatttttatgtcattttccagAATAGAGATAGATACAAAGCTTCCCATAGTTGGTGAGCAGAAGTGGAAGATATGGATTTGTTCCTTCAATGTACCAATGGCACCTGGGAAAACTCGTTCG
        |  ||| || ||   || ||| | | | | ||  |   |||   |       |        | |||||| | |   || ||     |  | || ||| || ||||| ||||| || || ||  |||||||||| ||||| |||    ||||||| |||||||||||||| || ||||||||||| || ||||| || 
agatgcatttcaaataacta---ttactttatcctaggatgctgttgttttctttt--tcatttgttgctactgaagctcaaagtacttggcattgttattgcagGATTGAGATTGATACCAAACTCCCTGTAGTTGGTGACCAGAAATGGGTAGTATGGATATGTTCCTTCAATGTCCCCATGGCACCTGGTAAGACTCGCTCC
















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|30299354|gb|CB976148.1|CB976148
EST:     AACCCACGAATCAGTGCCAAATTTGTTGCACCTTGTTATTATATGAATAA                         AATAGAGATAGATACAAAGCTTCCCATAGTTGGTGAGCAGAAGTGGAAGAT
genomic: AACCCACGAATCAGTGCCAAATTTGTTGCACCTTGTTATTATATGAATAAgtaagttgac ... cattttccagAATAGAGATAGATACAAAGCTTCCCATAGTTGGTGAGCAGAAGTGGAAGAT
EST: gi|30322149|gb|CD005411.1|CD005411
EST:     CACGAATCAGTGCCAAATTTGTTGCACCTTGTTATTATATGAATAA                         AATAGAGATAGATACAAAGCTTCCCATAGTTGGTGAGCAGAAGTGGAAGAT
genomic: CACGAATCAGTGCCAAATTTGTTGCACCTTGTTATTATATGAATAAgtaagttgac ... cattttccagAATAGAGATAGATACAAAGCTTCCCATAGTTGGTGAGCAGAAGTGGAAGAT
EST: gi|110398498|gb|EC964901.1|EC964901
EST:     AACCCACGAATCAGTGCCAAATTTGTTGCACCTTGTTATTATATGAATAA                         AATAGAGATAGATACAAAGCTTCCCATAGTTGGTGAGCAGAAGTGGAAGAT
genomic: AACCCACGAATCAGTGCCAAATTTGTTGCACCTTGTTATTATATGAATAAgtaagttgac ... cattttccagAATAGAGATAGATACAAAGCTTCCCATAGTTGGTGAGCAGAAGTGGAAGAT
EST: gi|110359771|gb|EC921878.1|EC921878
EST:     CAGTGCCAAATTTGTTGCACCTTGTTATTATATGAATAA                         AATAGAGATAGATACAAAGCTTCCCATAGTTGGTGAGCAGAAGTGGAAGAT
genomic: CAGTGCCAAATTTGTTGCACCTTGTTATTATATGAATAAgtaagttgac ... cattttccagAATAGAGATAGATACAAAGCTTCCCATAGTTGGTGAGCAGAAGTGGAAGAT
EST: gi|22009482|gb|BQ794516.1|BQ794516
EST:     CTTG-TATTATATG-AT-A                         AATAGAGATAGAT-CCAAGCTTCCCATAG-TGGTGAGCAGAAGTGGAAGAT
genomic: CTTGTTATTATATGAATAAgtaagttgac ... cattttccagAATAGAGATAGATACAAAGCTTCCCATAGTTGGTGAGCAGAAGTGGAAGAT
EST: gi|46917618|gb|CN546947.1|CN546947
EST:     AACCCACGAATCAGTGCCAAATTTGTTGCACCTTGTTATTATATGAATAA                         AATAGAGATAGATACAAAGCTTCCCATAGTTGGTGAGCAGAAGTGGAAGAT
genomic: AACCCACGAATCAGTGCCAAATTTGTTGCACCTTGTTATTATATGAATAAgtaagttgac ... cattttccagAATAGAGATAGATACAAAGCTTCCCATAGTTGGTGAGCAGAAGTGGAAGAT
EST: gi|110393693|gb|EC959113.1|EC959113
EST:     CAGTGCCAAATTTGTTGCACCTTGTTATTATATGAATAA                         AATAGAGATAGATACAAAGCTTCCCATAGTTGGTGAGCAGAAGTGGAAGAT
genomic: CAGTGCCAAATTTGTTGCACCTTGTTATTATATGAATAAgtaagttgac ... cattttccagAATAGAGATAGATACAAAGCTTCCCATAGTTGGTGAGCAGAAGTGGAAGAT
EST: gi|30323198|gb|CD006460.1|CD006460
EST:     CACGAATCAGTGCCAAATTTGTTGCACCTTGTTATTATATGAATAA                         AATAGAGATAGATACAAAGCTTCCCATAGTTGGTGAGCAGAAGTGGAAGAT
genomic: CACGAATCAGTGCCAAATTTGTTGCACCTTGTTATTATATGAATAAgtaagttgac ... cattttccagAATAGAGATAGATACAAAGCTTCCCATAGTTGGTGAGCAGAAGTGGAAGAT
EST: gi|294964949|gb|GW838752.1|GW838752
EST:     AACCCACGAATCAGTGCCAAATTTGTTGCACCTTGTTATTATATGAATAA                         AATAGAGATAGATACAAAGCTTCCCATAGTTGGTGAGCAGAAGTGGAAGAT
genomic: AACCCACGAATCAGTGCCAAATTTGTTGCACCTTGTTATTATATGAATAAgtaagttgac ... cattttccagAATAGAGATAGATACAAAGCTTCCCATAGTTGGTGAGCAGAAGTGGAAGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggtaacaactaacaacacattctgaagtttattctatttttatgtcattttccagAATAGAGATAGATACAAAGCTTCCCATAGTTGGTGAGCAGAAGTGGAAGATATGGATTTGTTCCTTCAATGTACCAATGGCACCTGGGAAAACTCGTTCG
      aactaac  putative branch site (score: 1)
                                            tcattttcc  putative PPT
                        aagtttattctatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttctataaacaaataaagtttcttcacctttgcattttagcgttaggtaacaactaacaacacattctgaagtttattctatttttatgtcattttccagAATAGAGATAGATACAAAGCTTCCCATAGTTGGTGAGCAGAAGTGGAAGATATGGATTTGTTCCTTCAATGTACCAATGGCACCTGGGAAAACTCGTTCG

- - - - - aaataaa
- - - - - - - - - - -cttcacc
- - - - - - - - - - - - - - - - - - - - - - - gtaacaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -caacaca