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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtgatctatagtgtgataaattatgtcttcttatctccaatgctatctgctgagtgaacacatgctcattactggtttctttctataatagttgtcctagttttttctttctcatcatataaaactttggttatagGAAGAGGACTTCCAACTGTCCAAGATTTCGGTTGTGGACTTTTCCTGTTCTTGTGGATGGACCTTTTGGAGTGGTCTCTGCTGCTGAGTTCATCGGGATA

Basic information

species Vitis vinifera
transcript Vv12s0035g02150.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv12s0035g02150.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G068557_T01 (Zea mays), 3'ss of exon 2
gtatgtgatctatagtgtgataaattatgtcttcttatctccaatgctatctgctgagtgaacacatgctcattactggtttctttctataatagttgtcctagttttttctttctcatcatataaaactttggttatagGAAGAGGACTTCCAACTGTCCAAGATTTCGGTTGTGGACTTTTCCTGTTCTTGTGGATGGACCTTTTGGAGTGGTCTCTGCTGCTGAGTTCATCGGGATA
                                    | ||   ||  | | | |  ||  |   | |||||    ||| || |  |  ||      | | ||||| ||    |   | |        ||||  |    ||||| ||||       ||  |  || ||  || | |||||||| ||||||||||| || || || |||||||| |||||||| | |||||||||||| || 
----------------------------agagcagaaccttgcataatttttacatag--atttcctgctc----ctgcttccggttcatgtacactattctagtattcatctctactttt------acttgcgcgccagGAAAAGGAAGCTGCGCTCACTGAGTTTCAGGCTCTGGACTTTCCCTGTTCTTGTAGACGGCCCCTTTGGAGTTGTCTCTGCAGTTGAGTTCATCGGAATT

upper sequence: Vv12s0035g02150.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT5G49740.1 (Arabidopsis thaliana), 3'ss of exon 2
gtatgtgatctatagtgtgataaattatgtcttcttatctccaatgctatctgctgagtgaacacatgctcattactggtttctttctataat-agttgtcctagttttttctttctcatcatataaaactttggttatagGAAGAGGACTTCCAACTGTCCAAGATTTCGGTTGTGGACTTTTCCTGTTCTTGTGGATGGACCTTTTGGAGTGGTCTCTGCTGCTGAGTTCATCGGGATA
              ||  |     ||  |  ||||| |  | | |     ||  ||| |       || |  |     ||| ||| | ||||| |    |  || |  | | | | |  |    | |    |||  |  ||||||| ||   | || |  || || ||| || | ||||| ||||||||||||||||||||||| |||||||| || ||||| ||||||||  | || || 
--------------gtacgtacggttgagatttcttttaactatt-----ctattgatt-------tgattgt-----gttgcttacaataattaagcatattaataatatatgtgtgtttccgtga----ttg--tgaagGAAGAAGATAACGAAATTCCCGAGGTTTAGGCTATGGACATTTCCTGTTCTTGTGGATGGACCATTTGGAGTTGTTTCTGCAGCTGAGTTTCTTGGAATT

upper sequence: Vv12s0035g02150.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT5G49730.1 (Arabidopsis thaliana), 3'ss of exon 2
gtatgtgatctatagtgtgataaattatgtcttcttatctccaatgctatctgctgagtgaacacatgctcattactggtttctttctataatagttgtcctagttttttctttctcatcatataaaactttggttat--agGAAGAGGACTTCCAACTGTCCAAGATTTCGGTTGTGGACTTTTCCTGTTCTTGTGGATGGACCTTTTGGAGTGGTCTCTGCTGCTGAGTTCATCGGGATA
                                                      |  ||| |   ||   |   | ||  ||||||   |  ||    |  | ||| || | |     |  | |   |   || || |  ||||||| ||  || || |  || || ||| || | ||||| || |||||||||||||||||||| |||||||| || ||||| ||||||||  | || || 
-----------------------------------------------------gtacgtgtaataatatccccaattgcattcttttggttgtatcaatttttgttcttgcataaatgt-gtgtgtcatgatgattgtgaagGAAGAAGATATCGAAATTCCCGAGGTTTAGGCTATGGACATTCCCTGTTCTTGTGGATGGACCATTTGGAGTTGTTTCTGCAGCTGAGTTTCTTGGAATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctataatagttgtcctagttttttctttctcatcatataaaactttggttatagGAAGAGGACTTCCAACTGTCCAAGATTTCGGTTGTGGACTTTTCCTGTTCTTGTGGATGGACCTTTTGGAGTGGTCTCTGCTGCTGAGTTCATCGGGATA
                                atcatataaaacttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtgatctatagtgtgataaattatgtcttcttatctccaatgctatctgctgagtgaacacatgctcattactggtttctttctataatagttgtcctagttttttctttctcatcatataaaactttggttatagGAAGAGGACTTCCAACTGTCCAAGATTTCGGTTGTGGACTTTTCCTGTTCTTGTGGATGGACCTTTTGGAGTGGTCTCTGCTGCTGAGTTCATCGGGATA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT