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'   		9  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTCTTCTTAGCTTTATTGAAGGACCTCCATTTACCTTGCAGAGGCTTTGTGAGgtgactacaaactttgttctctttttttggggccactacgccttgggttgtcctagcattactcttcaggacaatggcatttatctcacagttgattctt...

Basic information

species Vitis vinifera
transcript Vv16s0039g02270.t01
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv16s0039g02270.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: GLYMA11G09810.1 (Glycine max), 5'ss of exon 6
TTCTTCTTAGCTTTATTGAAGGACCTCCATTTACCTTGCAGAGGCTTTGTGAGgtgactacaaactttgttctctttttttggggccactacgccttgggttgtcctagcattactctt--caggacaatggcatttatctcacagttgattctt--------------------------
  ||   | | || |||||||| |||||||| || ||||| |||||||||||||| | |      |||  | | | |  |  |    | ||      ||  | |     ||| |   ||  || |  |||  | |  || | |   |  ||| ||                          
CACTCACTTGTTTCATTGAAGGCCCTCCATTCACGTTGCAAAGGCTTTGTGAGgtaaatctg---tttcctttgtctgctgtgcattattatattccgg--tattaatacatcaagtttaacatgctaatatcgtaaatttgaatatctattgttaatttgtctgatattacattgaacag

upper sequence: Vv16s0039g02270.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: GLYMA12G02130.3 (Glycine max), 5'ss of exon 5
TTCTTCTTAGCTTTATTGAAGGACCTCCATTTACCTTGCAGAGGCTTTGTGAGgtga--ctacaaactttgttctct-----------ttttttggggccactacgccttgggttgtcctagcattactcttcagg-acaatggcatttatctcacagt-tgattctt----------
  ||   | | || |||||||| || |||||||| ||||| |||||||||||||| |  ||     ||||||   ||           | ||   |   || |||      | ||  | |   |  | | |  |     |||  |  || |  |   || ||||| |           
AACTCACTTGTTTCATTGAAGGCCCCCCATTTACGTTGCAAAGGCTTTGTGAGgtaaatctgttttctttgtctgctgtgcattattatattccagcatcaataccatcaagtttaacatgctaacattgtaaatttgtaatatctattgttgctttgtctgattttacattgaacag
















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|161721212|gb|FC070718.1|FC070718
EST:     TTCATAGCTTTATTGAAGGACCTCCATTTACCTTGCAGAGGCTTTGTGAG                         ATCCTATTGGATGCACAAAGCATTTATCCGTATCTTTCAAAGCTTGCTCTA
genomic: TTCTTAGCTTTATTGAAGGACCTCCATTTACCTTGCAGAGGCTTTGTGAGgtgactacaa ... tatcatgcagATCATATTGGATGCACAAAGCATTTATCCGTATCTTTCAAAGCTTGCTCTA
EST: gi|110719175|gb|EE096848.1|EE096848
EST:     TTCTTAGCTTTATTGAAGGACCTCCATTTACCTTGCAGAGGCTTTGTGAG                         ATCATATTGGATGCACAAAGCATTTATCCGTATCTTTCAAAGCTTGCTCTA
genomic: TTCTTAGCTTTATTGAAGGACCTCCATTTACCTTGCAGAGGCTTTGTGAGgtgactacaa ... tatcatgcagATCATATTGGATGCACAAAGCATTTATCCGTATCTTTCAAAGCTTGCTCTA
EST: gi|27584835|gb|CB007530.1|CB007530
EST:     TTCTTAGCTTTATTGAAGGACCTCCATTTACCTTGCAGAGGCTTTGTGAG                         ATCATATTGGATGCACAAAGCATTTATCCGTATCTTTCAAAGCTTGCTCTA
genomic: TTCTTAGCTTTATTGAAGGACCTCCATTTACCTTGCAGAGGCTTTGTGAGgtgactacaa ... tatcatgcagATCATATTGGATGCACAAAGCATTTATCCGTATCTTTCAAAGCTTGCTCTA
EST: gi|30125898|gb|CB911237.1|CB911237
EST:     TTCTTAGCTTTATTGAAGGACCTCCATTTACCTTGCAGAGGCTTTGTGAG                         ATCATATTGGATGCACAAAGCATTTATCCGTATCTTTCAAAGCTTGCTCTA
genomic: TTCTTAGCTTTATTGAAGGACCTCCATTTACCTTGCAGAGGCTTTGTGAGgtgactacaa ... tatcatgcagATCATATTGGATGCACAAAGCATTTATCCGTATCTTTCAAAGCTTGCTCTA
EST: gi|110686390|gb|EE063974.1|EE063974
EST:     TTCTTAGCTTTATTGAAGGACCTCCATTTACCTTGCAGAGGCTTTGTGAG                         ATCATATTGGATGCACAAAGCATTTATCCGTATCTTTCAAAGCTTGCTCTA
genomic: TTCTTAGCTTTATTGAAGGACCTCCATTTACCTTGCAGAGGCTTTGTGAGgtgactacaa ... tatcatgcagATCATATTGGATGCACAAAGCATTTATCCGTATCTTTCAAAGCTTGCTCTA
EST: gi|110698756|gb|EE076614.1|EE076614
EST:     TTCTTAGCTTTATTGAAGGACCTCCATTTACCTTGCAGAGGCTTTGTGAG                         ATCATATTGGATGCACAAAGCATTTATCCGTATCTTTCAAAGCTTGCTCTA
genomic: TTCTTAGCTTTATTGAAGGACCTCCATTTACCTTGCAGAGGCTTTGTGAGgtgactacaa ... tatcatgcagATCATATTGGATGCACAAAGCATTTATCCGTATCTTTCAAAGCTTGCTCTA
EST: gi|161718060|gb|FC067589.1|FC067589
EST:     TTCATAGCTTTATTGAAGGACCTCCATTTACCTTGCAGAGGCTTTGTGAG                         ATCCTATTGGATGCACAAAGCATTTATCCGTATCTT
genomic: TTCTTAGCTTTATTGAAGGACCTCCATTTACCTTGCAGAGGCTTTGTGAGgtgactacaa ... tatcatgcagATCATATTGGATGCACAAAGCATTTATCCGTATCTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTCTTCTTAGCTTTATTGAAGGACCTCCATTTACCTTGCAGAGGCTTTGTGAGgtgactacaaactttgttctctttttttggggccactacgccttgggttgtcctagcattactcttcaggacaatggcatttatctcacagttgattctt

- - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aggacaa