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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctgttgttctgtgaagcttatagattattatgctgattgctttaaggttattatctctgcaattcattggctcatcaactgtttcttcattttgttacagGCCATACTGGAGATGTTATTTCCCAAATACTCAAGCAATAATTTATGTTGTTGACTCAAGTGACACTGATAGAATTGTAATAGCCAAGGATGAATTTCAT

Basic information

species Vitis vinifera
transcript Vv04s0008g07360.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0008g07360.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os08g15040.2 (Oryza sativa), 3'ss of exon 4
--ctgttgttctgtgaagcttatagattattatgctgattgctttaaggttattatctctgcaattcattggctcatcaactgtttcttcattttgttacagGCCATACTGGAGATGTTATTTCCCAAATACTCAAGCAATAATTTATGTTGTTGACTCAAGTGACACTGATAGAATTGTAATAGCCAAGGATGAATTTCAT
   ||||   |   ||  ||  |||||||||   ||   | | ||      | ||    ||  |    |     |  ||      | ||||  || |||  |||||||||||||||| || || |||||||| || || || ||||||||||| || |||||||| || |||||  ||||||  || || || || ||||||
ctttgttaggcatggattctcttagattatttgacttccttccttttaaagactaggcatgacacgtttctctacgccattaacatattcaccttttta--gGCCATACTGGAGATGCTACTTTCCAAATACCCAGGCTATCATTTATGTTGTCGATTCAAGTGATACAGATAGGCTTGTAACGGCAAAAGAAGAGTTTCAT

upper sequence: Vv04s0008g07360.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT2G24765.1 (Arabidopsis thaliana), 3'ss of exon 4
---------------------------------------------ctgt-tgttctgtgaagcttatagattattatgctgattgctttaaggttattatctctgcaattcattggctcatcaactgtttcttcattttgttacagGCCATACTGGAGATGTTATTTCCCAAATACTCAAGCAATAATTTATGTTGTTGACTCAAGTGACACTGATAGAATTGTAATAGCCAAGGATGAATTTCAT
                                              ||  | | ||||||||   ||  |  |      || |  | | ||| ||||  | | |    ||       |  || | || |     ||||| | |||||||||||||| |||| |||||||| ||||| |||||| | || |||||||||||||| ||||| || |||||||| |   | || || || || ||||||
gtagcttaatgacctcgtttctcatttctagatatgatgaacatattgcatctactgtgaagga-atgaagaacagaaatgctc-catcaagattatactgtttttgttttgcccaattttctaatggt-----atttt-tgacagGCCATACTGGCGATGCTATTTCCCGAATACACAAGCAGTGATCTATGTTGTTGACTCGAGTGATACAGATAGAATCGGGGTGGCGAAAGAGGAGTTTCAT
















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|30137308|gb|CB922646.1|CB922646
EST:     ATCTGGGTGGACAGACAAGTATCAG                         GCCATACTGGAGATGTTATTTCCCAAATACTCAAGCAATAATTTATGTTGT
genomic: ATCTGGGTGGACAGACAAGTATCAGgtaactttct ... tttgttacagGCCATACTGGAGATGTTATTTCCCAAATACTCAAGCAATAATTTATGTTGT
EST: gi|33406636|gb|CF212263.1|CF212263
EST:     ATCTGGGTGGACAGACAAGTATCAG                         GCCATACTGGAGATGTTATTTCCCAAATACTCAAGCAATAATTTATGTTGT
genomic: ATCTGGGTGGACAGACAAGTATCAGgtaactttct ... tttgttacagGCCATACTGGAGATGTTATTTCCCAAATACTCAAGCAATAATTTATGTTGT
EST: gi|30126854|gb|CB912193.1|CB912193
EST:     ATCTGGGTGGACAGACAAGTATCAG                         GCCATACTGGAGATGTTATTTCCCANATACTCAAGCAATAATTTATGTTGT
genomic: ATCTGGGTGGACAGACAAGTATCAGgtaactttct ... tttgttacagGCCATACTGGAGATGTTATTTCCCAAATACTCAAGCAATAATTTATGTTGT
EST: gi|33408309|gb|CF213936.1|CF213936
EST:     ATCTGGGTGGACAGACAAGTATCAG                         GCCATACTGGAGATGTTATTTCCCAAATACTCAAGCAATAATTTATGTTGT
genomic: ATCTGGGTGGACAGACAAGTATCAGgtaactttct ... tttgttacagGCCATACTGGAGATGTTATTTCCCAAATACTCAAGCAATAATTTATGTTGT
EST: gi|33408221|gb|CF213848.1|CF213848
EST:     ATCTGGGTGGACAGACAAGTATCAG                         GCCATACTGGAGATGTTATTTCCCAAATACTCAAGCAATAATTTATGTTGT
genomic: ATCTGGGTGGACAGACAAGTATCAGgtaactttct ... tttgttacagGCCATACTGGAGATGTTATTTCCCAAATACTCAAGCAATAATTTATGTTGT
EST: gi|110406223|gb|EC971789.1|EC971789
EST:     ATCTGGGTGGACAGACAAGTATCAG                         GCCATACTGGAGATGTTATTTCCCAAATACTCAAGCAATAATTTATGTTGT
genomic: ATCTGGGTGGACAGACAAGTATCAGgtaactttct ... tttgttacagGCCATACTGGAGATGTTATTTCCCAAATACTCAAGCAATAATTTATGTTGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggttattatctctgcaattcattggctcatcaactgtttcttcattttgttacagGCCATACTGGAGATGTTATTTCCCAAATACTCAAGCAATAATTTATGTTGTTGACTCAAGTGACACTGATAGAATTGTAATAGCCAAGGATGAATTTCAT
                                 ctgtttcttcatttt  CT-rich tract
                                           attttgtta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctgttgttctgtgaagcttatagattattatgctgattgctttaaggttattatctctgcaattcattggctcatcaactgtttcttcattttgttacagGCCATACTGGAGATGTTATTTCCCAAATACTCAAGCAATAATTTATGTTGTTGACTCAAGTGACACTGATAGAATTGTAATAGCCAAGGATGAATTTCAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
ctgttgt
- - - - - -tgaagct
- - - - - - - - - - - - - - - - -tgattgc
- - - - - - - - - - - - - - - - - - - - - - - - - - -tctctgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctcatca