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'   		9  
 5'  3'   		10  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgattagtgaaactcatataaagtattttctgtaaacaacccatattttcaagcatttgaggtctcccaaggaggagtccttgattcattggaaacactaactctgttttgaattgaaaataggatgtgattcaagatatggaacaaattttttctaacacattgttatgtgggtttctgtaattggatcagGTAATCAACAACCTGAATGCAATGGAGAAAGGGTTGATTTGTTGGTGAGGCTTGGGTTGTTGAAGCTAGTAAGCGGGATATCTGGTATAACACAGGAATC

Basic information

species Vitis vinifera
transcript Vv12s0034g02390.t01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv12s0034g02390.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: AT1G22930.1 (Arabidopsis thaliana), 3'ss of exon 9
gtttgattagtgaaactcatataaagtattttctgtaaacaacccatattttcaagcatttgaggtctcccaaggaggagtccttgattcattggaaacactaactctgttttgaattgaaaataggatgtgattcaagatatggaacaaattttttctaacacattgttatgtgggtttctgtaattggatcagGTAATCAACAACCTGAATGCAATGGAGAAAGGGTTGATTTGTTGGTGAGGCTTGGGTTGTTGAAGCTAGTAAGCGGGATATCTGGTATAACACAGGAATC---
                                                                                     | ||   | |  || || |       |||||  |||     ||  |   |     ||| ||  | |      |||| |  || | || ||  |||       ||| |||     ||||| | | |||||||| |||||||| |||||||||   ||||||||||||||||||||||| || |    | || ||||| ||||||  |||     
-------------------------------------------------------------------------------------gttttgcttgttaccctca-------ttgaa--gaagtctagaaataccttcttttatagattatagca---ctaaaatgttttcatttgctttt-------tggttcataagGTCAACTATCAGAATGCAAGGGAGAAAGAGTTGATTTGGCAGTGAGGCTTGGGTTGTTGAAGCTGGTGAATCAGGTAGCTGGTTTAACACCAGAAGTTCT
















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|71882773|gb|DT031828.1|DT031828
EST:     AACTAATGGAAGCCAAGTGACTTCGGTTCCTTCAGCTGCAACTAGTACAG                         GTAATCAAGAACCTGAATGCAATGGAGAAAGGGTTGATTTGTTGGTGAGGC
genomic: AACTAATGGAAGCCAAGTGACTTCGGTTCCTTCAGCTGCAACTAGTACAGgtttgattag ... attggatcagGTAATCAACAACCTGAATGCAATGGAGAAAGGGTTGATTTGTTGGTGAGGC
EST: gi|71882190|gb|DT031245.1|DT031245
EST:     GCCAAGTGACTTCGGTTCCTTCAGCTGCAACTAGTACAG                         GTAATCAAGAACCTGAATGCAATGGAGAAAGGGTTGATTTGTTGGTGAGGC
genomic: GCCAAGTGACTTCGGTTCCTTCAGCTGCAACTAGTACAGgtttgattag ... attggatcagGTAATCAACAACCTGAATGCAATGGAGAAAGGGTTGATTTGTTGGTGAGGC
EST: gi|71883765|gb|DT032820.1|DT032820
EST:     AACTAATGGAAGCCAAGTGACTTCGGTTCCTTCAGCTGCAACTAGTACAG                         GTAATCAAGAACCTGAATGCAATGGAGAAAGGGTTGATTTGTTGGTGAGGC
genomic: AACTAATGGAAGCCAAGTGACTTCGGTTCCTTCAGCTGCAACTAGTACAGgtttgattag ... attggatcagGTAATCAACAACCTGAATGCAATGGAGAAAGGGTTGATTTGTTGGTGAGGC
EST: gi|110693590|gb|EE069953.1|EE069953
EST:     AACTAATGGAAGCCAAGTGACTTCGGTTCCTTCAGCTGCAACTAGTACAG                         GTAATCAAGAACCTGAATGGCA-TGGAGAAAGGGTTGATTTGTTGG
genomic: AACTAATGGAAGCCAAGTGACTTCGGTTCCTTCAGCTGCAACTAGTACAGgtttgattag ... attggatcagGTAATCAACAACCTGAATG-CAATGGAGAAAGGGTTGATTTGTTGG
EST: gi|71884359|gb|DT033414.1|DT033414
EST:     AACTAATGGAAGCCAAGTGACTTCGGTTCCTTCAGCTGCAACTAGTACAG                         GTAATCAAGAACCTGAATGCAATGGAGAAAGGGTTGATTTGTTGGTGAGGC
genomic: AACTAATGGAAGCCAAGTGACTTCGGTTCCTTCAGCTGCAACTAGTACAGgtttgattag ... attggatcagGTAATCAACAACCTGAATGCAATGGAGAAAGGGTTGATTTGTTGGTGAGGC
EST: gi|71881157|gb|DT030212.1|DT030212
EST:     AACTAATGGAAGCCAAGTGACTTCGGTTCCTTCAGCTGCAACTAGTACAG                         GTAATCAAGAACCTGAATGCAATGGAGAAAGGGTTGATTTGTTGGTGAGGC
genomic: AACTAATGGAAGCCAAGTGACTTCGGTTCCTTCAGCTGCAACTAGTACAGgtttgattag ... attggatcagGTAATCAACAACCTGAATGCAATGGAGAAAGGGTTGATTTGTTGGTGAGGC
EST: gi|71890110|gb|DT039165.1|DT039165
EST:     GCCAAGTGACTTCGGTTCCTTCAGCTGCAACTAGTACAG                         GTAATCAAGAACCTGAATGCAATGGAGAAAGGGTTGATTTGTTGGTGAGGC
genomic: GCCAAGTGACTTCGGTTCCTTCAGCTGCAACTAGTACAGgtttgattag ... attggatcagGTAATCAACAACCTGAATGCAATGGAGAAAGGGTTGATTTGTTGGTGAGGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatggaacaaattttttctaacacattgttatgtgggtttctgtaattggatcagGTAATCAACAACCTGAATGCAATGGAGAAAGGGTTGATTTGTTGGTGAGGCTTGGGTTGTTGAAGCTAGTAAGCGGGATATCTGGTATAACACAGGAATC
               ttctaac  putative branch site (score: 1)
     aacaaattttttctaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgattagtgaaactcatataaagtattttctgtaaacaacccatattttcaagcatttgaggtctcccaaggaggagtccttgattcattggaaacactaactctgttttgaattgaaaataggatgtgattcaagatatggaacaaattttttctaacacattgttatgtgggtttctgtaattggatcagGTAATCAACAACCTGAATGCAATGGAGAAAGGGTTGATTTGTTGGTGAGGCTTGGGTTGTTGAAGCTAGTAAGCGGGATATCTGGTATAACACAGGAATC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC