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

...taagtatcggtttttgttttttgttttgttttcaatttctgaaaaagtacgaacttattgatattatctccttaatttttcccttttaactcaacatcagGCAAAGTGTGAAGCCGCATATTTTGTTGTGGTTCTACATCATCTAAGATCTGTAGTGATAGCTGTACGAGGAACTGAGACTCCCGAGGACCTCATAACTG

Basic information

species Vitis vinifera
transcript Vv05s0124g00200.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0124g00200.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA10G44440.1 (Glycine max), 3'ss of exon 5
taagtatcggtttttgttttttgttttgt---tttcaatttctgaaaaagtacgaacttattgatattatctccttaattt--ttcccttttaactcaacatcagGCAAAGTGTGAAGCCGCATATTTTGTTGTGGTTCTACATCATCTAAGATCTGTAGTGATAGCTGTACGAGGAACTGAGACTCCCGAGGACCTCATAACTG
      ||  ||| ||| |  |||| ||    ||||  ||| |  |  |    |   | ||| |||||   |  || ||    ||   |||||   | |   ||||  ||||||||||| ||||||||| |||||||||||||||| |||  ||||||||| || ||| ||||||||||||| || || |||||||| |||||||
-----ctcaatttatgtatgatgttatgcatatttctgtttttatattatactggcttaatttatatttaattattcataaagtttttttttatacccatgccagGTCAAGTGTGAAGCTGCATATTTTATTGTGGTTCTACATCAACTACAATCTGTAGTAATTGCTATACGAGGAACTGAAACCCCAGAGGACCTAATAACTG

upper sequence: Vv05s0124g00200.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA20G39210.1 (Glycine max), 3'ss of exon 6
taagtatcggtttttgttttttgttttg--ttttcaatttctgaaaaagtacgaacttattgatattatctccttaattt--ttcccttttaactcaacatcagGCAAAGTGTGAAGCCGCATATTTTGTTGTGGTTCTACATCATCTAAGATCTGTAGTGATAGCTGTACGAGGAACTGAGACTCCCGAGGACCTCATAACTG
      |   ||| ||| |  | |  ||  | |||  ||| |  |  |    |   | ||| |||||   |  || ||    |||  ||| |   | |   ||||  ||||||||||| ||||||||| |||||||||||||||| ||   |||||| || || ||| |||| |||||||| || || |||||||| |||||||
----acttaatttatgtatgatatcatgaatattctgtttttatattatactggcttaatttatatttaattatttataaagttctttttgatacccattccagGTCAAGTGTGAAGCTGCATATTTTATTGTGGTTCTACATCAACTTCAATCTGTGGTAATTGCTATACGTGGAACTGAAACCCCAGAGGACCTAATAACTG

upper sequence: Vv05s0124g00200.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT1G05790.2 (Arabidopsis thaliana), 3'ss of exon 7
------------taagtatcggtttttgttttttgttttgttttcaatttctgaaaaagtacgaacttattgatattatctccttaatttttcccttttaactcaacatcagGCAAAGTGTGAAGCCGCATATTTTGTTGTGGTTCTACATCATCTAAGATCTGTAGTGATAGCTGTACGAGGAACTGAGACTCCCGAGGACCTCATAACTG
             ||       |    ||| |||| | ||||||  |||| |  |  || |    |||  | ||  |||    |||||| |||  || |  |        |||  |||||| ||||  |||| |||||||| ||  ||||| |||| |||| ||| || || ||||| ||||||||||||||  | || |||||||||||||
tttagtagaaaacaaactgttatcgaagttgtttgatatgttttgcatttatccatcagaat---ctttctcat-ctattcgtttaattattctattgtggc--------agGAGAAGTGTAAAGCAACATACTTTGTTGTAGTCTTACATTATCTTAGATGTGTTGTAATTGCTGTTCGAGGAACTGAGACGGCTGAAGACCTCATAACTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtacgaacttattgatattatctccttaatttttcccttttaactcaacatcagGCAAAGTGTGAAGCCGCATATTTTGTTGTGGTTCTACATCATCTAAGATCTGTAGTGATAGCTGTACGAGGAACTGAGACTCCCGAGGACCTCATAACTG
                                      ttttaac  putative branch site (score: 2)
                              tttttcccttttaact  CT-rich tract
      aacttattgatattat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taagtatcggtttttgttttttgttttgttttcaatttctgaaaaagtacgaacttattgatattatctccttaatttttcccttttaactcaacatcagGCAAAGTGTGAAGCCGCATATTTTGTTGTGGTTCTACATCATCTAAGATCTGTAGTGATAGCTGTACGAGGAACTGAGACTCCCGAGGACCTCATAACTG

- - - - - - - - - - - - - - - - - - - -tgaaaaa