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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcagcataatcaacatgccctggaaaagataaaagaaaaatgaaaaatatcaaccaaatatctagaaaaaaatattgaaatggtttatggtataacgcagGAATTCAGTTCTTCATGGGATATCAAAGCCACTCCAACCTTTTTCTTCCTCAGAGATGGGCAACAGGTAGACAAGCTTGTGGGGGCGAACAAACCTGAGC

Basic information

species Vitis vinifera
transcript Vv08s0040g00020.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0040g00020.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os05g07690.1 (Oryza sativa), 3'ss of exon 4
-------gcagcataatcaacatgccctggaaaagataaaagaaaaatgaaaaatatcaaccaaatatctagaaaaaaatattgaaatggtttatggtataacgcagGAATTCAGTTCTTCATGGGATATCAAAGCCACTCCAACCTTTTTCTTCCTCAGAGATGGGCAACAGGTAGACAAGCTTGTGGGGGCGAACAAACCTGAGC
        ||  | | | | | |  |    |  | ||  |      | |    || |        | |   ||   ||      || |   || |  | |   |||||| ||||| || ||||||||||||   || || || |||||||||||| | | | | | | | ||||| |||||||||||||| || |||||||||||||
agtcctgacattagagt-agcttctcacttagcatatctataggtcagggtgcatgttgtaatgttcttccgatttaac-----aactctcttgtattctc-tgcagGATTTCAGCTCATCATGGGATATCCGCGCAACGCCGACCTTTTTCTTCATAAAAAACGAGAAGCAGGTCGACAAGCTTGTGGGCGCCAACAAACCTGAGC
















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|32244946|gb|CD710765.1|CD710765
EST:     AGGCACACCCTTCTCTGATGTTTCTAACTGTTGATGTTGATGAACTAAGT                         GAATTCAGTTCTTCATGGGATATCAAAGCCACTCCAACCTTTTTCTTCCTC
genomic: AGGCACACCCTTCTCTGATGTTTCTAACTGTTGATGTTGATGAACTAAGTgtaagtaata ... tataacgcagGAATTCAGTTCTTCATGGGATATCAAAGCCACTCCAACCTTTTTCTTCCTC
EST: gi|110374147|gb|EC938715.1|EC938715
EST:     AGGCACACCCTTCCCTGATGTTTCTAACTGTTGATGTTGATGAACTAAGT                         GAATTCAGTTCTTCATGGGATATCAAAGCCACTCCAACCTTTTTCTTCCTC
genomic: AGGCACACCCTTCTCTGATGTTTCTAACTGTTGATGTTGATGAACTAAGTgtaagtaata ... tataacgcagGAATTCAGTTCTTCATGGGATATCAAAGCCACTCCAACCTTTTTCTTCCTC
EST: gi|34547173|gb|CF515405.1|CF515405
EST:     AGGCACACCCTTCCCTGATGTTTCTAACTGTTGATGTTGATGAACTAAGT                         GAATTCAGTTCTTCATGGGATATCAAAGCCACTCCAACCTTTTTCTTCCTC
genomic: AGGCACACCCTTCTCTGATGTTTCTAACTGTTGATGTTGATGAACTAAGTgtaagtaata ... tataacgcagGAATTCAGTTCTTCATGGGATATCAAAGCCACTCCAACCTTTTTCTTCCTC
EST: gi|27581758|gb|CB004453.1|CB004453
EST:     AGGCACACCCTTCTCTGATGTTTCTAACTGTTGATGTTGATGAACTAAGT                         GAATTCAGTTCTTCATGGGATATCAAAGCCACTCCAACCTTTTTCTTCCTC
genomic: AGGCACACCCTTCTCTGATGTTTCTAACTGTTGATGTTGATGAACTAAGTgtaagtaata ... tataacgcagGAATTCAGTTCTTCATGGGATATCAAAGCCACTCCAACCTTTTTCTTCCTC
EST: gi|110726854|gb|EE103001.1|EE103001
EST:     AGGCACACCCTTCTCTGATGTTTCTAACTGTTGATGTTGATGAACTAAGT                         GAATTCAGTTCTTCATGGGATATCAAAGCCACTCCAACCTTTTTCTTCCTC
genomic: AGGCACACCCTTCTCTGATGTTTCTAACTGTTGATGTTGATGAACTAAGTgtaagtaata ... tataacgcagGAATTCAGTTCTTCATGGGATATCAAAGCCACTCCAACCTTTTTCTTCCTC
EST: gi|32245165|gb|CD710984.1|CD710984
EST:     AGGCACACCCTTCTCTGATGTTTCTAACTGTTGATGTTGATGAACTAAGT                         GAATTCAGTTCTTCATGGGATATCAAAGCCACTCCAACCTTTTTCTTCCTC
genomic: AGGCACACCCTTCTCTGATGTTTCTAACTGTTGATGTTGATGAACTAAGTgtaagtaata ... tataacgcagGAATTCAGTTCTTCATGGGATATCAAAGCCACTCCAACCTTTTTCTTCCTC
EST: gi|34547261|gb|CF515493.1|CF515493
EST:     AGGCACACCCTTCCCTGATGTTTCTAACTGTTGATGTTGATGAACTAAGT                         GAATTCAGTTCTTCATGGGATATCAAAGCCACTCCAACCTTTTTCTTCCTC
genomic: AGGCACACCCTTCTCTGATGTTTCTAACTGTTGATGTTGATGAACTAAGTgtaagtaata ... tataacgcagGAATTCAGTTCTTCATGGGATATCAAAGCCACTCCAACCTTTTTCTTCCTC
EST: gi|32245155|gb|CD710974.1|CD710974
EST:     AGGCACACCCTTCTCTGATGTTTCTAACTGTTGATGTTGATGAACTAAGT                         GAATTCAGTTCTTCATGGGATATCAAAGCCACTCCAACCTTTTTCTTCCTC
genomic: AGGCACACCCTTCTCTGATGTTTCTAACTGTTGATGTTGATGAACTAAGTgtaagtaata ... tataacgcagGAATTCAGTTCTTCATGGGATATCAAAGCCACTCCAACCTTTTTCTTCCTC
EST: gi|32250353|gb|CD716172.1|CD716172
EST:     AGGCACACCCTTCTCTGATGTTTCTAACTGTTGATGTTGATGAACTAAGT                         GAATTCAGTTCTTCATGGGATATCAAAGCCACTCCAACCTTTTTCTTCCTC
genomic: AGGCACACCCTTCTCTGATGTTTCTAACTGTTGATGTTGATGAACTAAGTgtaagtaata ... tataacgcagGAATTCAGTTCTTCATGGGATATCAAAGCCACTCCAACCTTTTTCTTCCTC
EST: gi|161715399|gb|FC064896.1|FC064896
EST:     AGGCACACCCTTCCCTGATGTTTCTAACTGTTGATGTTGATGAACTAAGT                         GAATTCAGTTCTTCATGGGATATCAAAGCCACTCCAACCTTTTTCTTCCTC
genomic: AGGCACACCCTTCTCTGATGTTTCTAACTGTTGATGTTGATGAACTAAGTgtaagtaata ... tataacgcagGAATTCAGTTCTTCATGGGATATCAAAGCCACTCCAACCTTTTTCTTCCTC
EST: gi|110368898|gb|EC933032.1|EC933032
EST:     AGGCACACCCTTCTCTGATGTTTCTAACTGTTGATGTTGATGAACTAAGT                         GAATTCAGTTCTTCATGGGATATCAAAGCCACTCCAACCTTTTTCTTCCTC
genomic: AGGCACACCCTTCTCTGATGTTTCTAACTGTTGATGTTGATGAACTAAGTgtaagtaata ... tataacgcagGAATTCAGTTCTTCATGGGATATCAAAGCCACTCCAACCTTTTTCTTCCTC
EST: gi|110701721|gb|EE079613.1|EE079613
EST:     AGGCACACCCTTCTCTGATGTTTCTAACTGTTGATGTTGATGAACTAAGT                         GAATTCAGTTCTTCATGGGATATCAAAGCCACTCCAACCTTTTTCTTCCTC
genomic: AGGCACACCCTTCTCTGATGTTTCTAACTGTTGATGTTGATGAACTAAGTgtaagtaata ... tataacgcagGAATTCAGTTCTTCATGGGATATCAAAGCCACTCCAACCTTTTTCTTCCTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatatcaaccaaatatctagaaaaaaatattgaaatggtttatggtataacgcagGAATTCAGTTCTTCATGGGATATCAAAGCCACTCCAACCTTTTTCTTCCTCAGAGATGGGCAACAGGTAGACAAGCTTGTGGGGGCGAACAAACCTGAGC
                                            gtataac  putative branch site (score: 3)
          aaatatctagaaaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcagcataatcaacatgccctggaaaagataaaagaaaaatgaaaaatatcaaccaaatatctagaaaaaaatattgaaatggtttatggtataacgcagGAATTCAGTTCTTCATGGGATATCAAAGCCACTCCAACCTTTTTCTTCCTCAGAGATGGGCAACAGGTAGACAAGCTTGTGGGGGCGAACAAACCTGAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - -catgccc
- - - - - - - - - - -ggaaaag
- - - - - - - - - - - - - - - - aagaaaa
- - - - - - - - - - - - - - - - - - - - - aaaaata
- - - - - - - - - - - - - - - - - - - - - - - - -tcaacca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaaaaa