Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acatcaaaaaatgaaaaactaaagataaaacaaaacgatggaaaggcaaaattaaaacaaaacatctatttatattctttattggttccttgtattgcagGATTGTGAGAGAAGAGCCATAGCTAAGTTGTTCCGTCACAGGTCTGAGGAGAAGCGAAATATTCTTCAAGCAGCAGCAGAGTGAAAAAAGTGTTATATTG

Basic information

species Vitis vinifera
transcript Vv18s0072g01020.t01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0072g01020.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: AT1G34550.1 (Arabidopsis thaliana), 3'ss of exon 7
acatcaaaaaatgaaaaactaaagataaaacaaaacgatggaaaggcaaaattaaaacaaaacatctatttatattctttattggttccttgt----attgcagGATTGTGAGAGAAGAGCCATAGCTAAGTTGTTCCGTCACAGGTCTGAGGAGAAGCGAAATATTCTTCAAGCAGCAGCAGAGTGAAAAAAGTGTTATATTG--
  || ||  |     | | | | |    |  |     | |   |   | ||  | |     |  | |  |||| || | | ||| |||||  |    ||| ||||| ||||||||||||   || || ||||||||||||||||| || || |||||||||||  || | |||||||||  | | | || ||     ||| |||  
-tatgaattaggttcatatttaggtctgagtag--ttacgagtatcgagaaccagatttctaagtttccttatgttttgt-ttgtttcctcatctggatttcagGACTGTGAGAGAAGAAAAATTGCAAAGTTGTTCCGTCACAGATCAGACGAGAAGCGAAACCTTATACAAGCAGCAATACAATAAACAA--CTCTATGTTGTA
















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|30320401|gb|CD003663.1|CD003663
EST:     AGTTGAGAAGGGTTAATCCAGGCAAACCATTTCATCTTAATATGTTCAAG                         GATTGTGAGAGAAGAGCCATAGCTAAGTTGTTCCGTCACAGGTCCGAGGAG
genomic: AGTTGAGAAGGGTTAATCCAGGCAAACCATTTCATCTTAATATGTTCAAGgtgaagaatt ... tgtattgcagGATTGTGAGAGAAGAGCCATAGCTAAGTTGTTCCGTCACAGGTCTGAGGAG
EST: gi|26262106|gb|CA813169.1|CA813169
EST:     AGTTGAGAAGGGTTAATCCAGGCAAACCATTTCATCTTAATATGTTCAAG                         GATTGTGAGAGAAGAGCCATAGCTAAGTTGTTCCGTCACAGGTCTGAGGAG
genomic: AGTTGAGAAGGGTTAATCCAGGCAAACCATTTCATCTTAATATGTTCAAGgtgaagaatt ... tgtattgcagGATTGTGAGAGAAGAGCCATAGCTAAGTTGTTCCGTCACAGGTCTGAGGAG
EST: gi|32248777|gb|CD714596.1|CD714596
EST:     AGTTGAGAAGGGTTAATCCAGGCAAACCATTTCATCTTAATATGTTCAAG                         GATTGTGAGAGAAGAGCCATAGCTAAGTTGTTCCGTCACAGGTCCGAGGAG
genomic: AGTTGAGAAGGGTTAATCCAGGCAAACCATTTCATCTTAATATGTTCAAGgtgaagaatt ... tgtattgcagGATTGTGAGAGAAGAGCCATAGCTAAGTTGTTCCGTCACAGGTCTGAGGAG
EST: gi|18458392|gb|BM436670.1|BM436670
EST:     AGTTGAGAAGGGTTAATCCAGGCAAACCATTTCATCTTAATATGTTCAAG                         GATTGTGAGAGAAGAGCCATAGCTAAGTTGTTCCGTCACAGGTCCGAGGAG
genomic: AGTTGAGAAGGGTTAATCCAGGCAAACCATTTCATCTTAATATGTTCAAGgtgaagaatt ... tgtattgcagGATTGTGAGAGAAGAGCCATAGCTAAGTTGTTCCGTCACAGGTCTGAGGAG
EST: gi|30321011|gb|CD004273.1|CD004273
EST:     AGTTGAGAAGGGTTAATCCAGGCAAACCATTTCATCTTAATATGTTCAAG                         GATTGTGAGAGAAGAGCCATAGCTAAGTTGTTCCGTCACAGGTCCGAGGAG
genomic: AGTTGAGAAGGGTTAATCCAGGCAAACCATTTCATCTTAATATGTTCAAGgtgaagaatt ... tgtattgcagGATTGTGAGAGAAGAGCCATAGCTAAGTTGTTCCGTCACAGGTCTGAGGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcaaaattaaaacaaaacatctatttatattctttattggttccttgtattgcagGATTGTGAGAGAAGAGCCATAGCTAAGTTGTTCCGTCACAGGTCTGAGGAGAAGCGAAATATTCTTCAAGCAGCAGCAGAGTGAAAAAAGTGTTATATTG
                                        ttccttgt  CT-rich tract
     attaaaacaaaacatc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acatcaaaaaatgaaaaactaaagataaaacaaaacgatggaaaggcaaaattaaaacaaaacatctatttatattctttattggttccttgtattgcagGATTGTGAGAGAAGAGCCATAGCTAAGTTGTTCCGTCACAGGTCTGAGGAGAAGCGAAATATTCTTCAAGCAGCAGCAGAGTGAAAAAAGTGTTATATTG

- - -aaaaaat
- - - - - - - -aaactaa
- - - - - - - - - - - - - -aaacaaa
- - - - - - - - - - - - - - - - - - gatggaaa
- - - - - - - - - - - - - - - - - - - - - - ggcaaaa