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'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttttatccatacttgttccttttcaattacaatagtcatgatgcaattctttttctgatttctccttttttgcttggtttattatccttttatttaaagCTTACAGACCTCAAAAAGCAGCCTGTTACTTTGAAATGGAAGGATAACAGTTGCACCACAGTAGAAATTTCTGGTCTTGATATTGGATGGGGCCAG

Basic information

species Vitis vinifera
transcript Vv00s0250g00020.t01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv00s0250g00020.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: AT3G52180.1 (Arabidopsis thaliana), 3'ss of exon 9
------------------------cttttatccatacttgttccttttcaattacaatagt---catga-tgca-attctttttctgatttctccttttttgcttggt-ttattatccttttat---ttaaagCTTACAGACCTCAAAAAGCAGCCTGTTACTTTGAAATGGAAGGATAACAGTTGCACCACAGTAGAAATTTCTGGTCTTGATATTGGATGGGGCCAG
                         |  |  | ||  |||       ||| || || |  |   ||||| |||  |    ||  ||| || ||    |  || ||  | ||        | |||   | |||||||||||  ||||| | | || |||||||| ||| |  ||| |||||  | | | ||| ||||||||||||||| ||||| ||||||||||| |||
gtgagtcagcgttcaactttcacaatgcttcctatgtttgaaaaacctcagttccattgattagcatgagtgcgcaacagttacctggttccttgactcctgattattgtttccgggtgtatatggataaaagCTTACAGGACTCAAGAGGAAGACTGTTACTCTGACACTGAAAGATAAGGGGTTCTCCAGAGTAGAAATTTCTGGCCTTGACATTGGATGGGGACAG

upper sequence: Vv00s0250g00020.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: AT3G52180.2 (Arabidopsis thaliana), 3'ss of exon 9
------------------------cttttatccatacttgttccttttcaattacaatagt---catga-tgca-attctttttctgatttctccttttttgcttggt-ttattatccttttat---ttaaagCTTACAGACCTCAAAAAGCAGCCTGTTACTTTGAAATGGAAGGATAACAGTTGCACCACAGTAGAAATTTCTGGTCTTGATATTGGATGGGGCCAG----
                         |  |  | ||  |||       ||| || || |  |   ||||| |||  |    ||  ||| || ||    |  || ||  | ||        | |||   | |||||||||||  ||||| | | || |||||||| ||| |  ||| |||||  | | | ||| ||||||||||||||| ||||| ||||||||||| |||    
gtgagtcagcgttcaactttcacaatgcttcctatgtttgaaaaacctcagttccattgattagcatgagtgcgcaacagttacctggttccttgactcctgattattgtttccgggtgtatatggataaaagCTTACAGGACTCAAGAGGAAGACTGTTACTCTGACACTGAAAGATAAGGGGTTCTCCAGAGTAGAAATTTCTGGCCTTGACATTGGATGGGGACAGGTAA
















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|30329318|gb|CD012580.1|CD012580
EST:     CCAAAGCTGGATGCTATCAAAAGTGCTACTGCTGATATA                         CTTACAGACCTCAAAAAGCAGCCTGTTACTNTGAAATGGAAGGATAACAGT
genomic: CCAAAGCTGGATGCTATCAAAAGTGCTACTGCTGATATAgtgggtgatt ... ttatttaaagCTTACAGACCTCAAAAAGCAGCCTGTTACTTTGAAATGGAAGGATAACAGT
EST: gi|37188932|gb|CF608281.1|CF608281
EST:     GCTCGAGCTTCCCAAAGCTGGATGCTATCAAAAGTGCTACTGCTGATATA                         CTTACAGACCTCAAAAAGCAGCCTGTTACTTTGAAATGGAAGGATAACAGT
genomic: GCTCGAGCTTCCCAAAGCTGGATGCTATCAAAAGTGCTACTGCTGATATAgtgggtgatt ... ttatttaaagCTTACAGACCTCAAAAAGCAGCCTGTTACTTTGAAATGGAAGGATAACAGT
EST: gi|30252735|gb|CB970286.1|CB970286
EST:     GCTCGAGCTTCCCAAAGCTGGATGCTATCAAAAGTGCTACTGCTGATATA                         CTTACAGACCTCAAAAAGCAGCCTGTTACTTTGAAATGGAAGGATAACAGT
genomic: GCTCGAGCTTCCCAAAGCTGGATGCTATCAAAAGTGCTACTGCTGATATAgtgggtgatt ... ttatttaaagCTTACAGACCTCAAAAAGCAGCCTGTTACTTTGAAATGGAAGGATAACAGT
EST: gi|110366419|gb|EC930325.1|EC930325
EST:     GCTCGAGCTTCCCAAAGCTGGATGCTATCAAAAGTGCTACTGCTGATATA                         CTTACAGACCTCAAAAAGCAGCCTGTTACTTTGAAATGGAAGGATAACAGT
genomic: GCTCGAGCTTCCCAAAGCTGGATGCTATCAAAAGTGCTACTGCTGATATAgtgggtgatt ... ttatttaaagCTTACAGACCTCAAAAAGCAGCCTGTTACTTTGAAATGGAAGGATAACAGT
EST: gi|110390476|gb|EC955386.1|EC955386
EST:     GCTCGAGCTTCCCAAAGCTGGATGCTATCAAAAGTGCTACTGCTGATATA                         CTTACAGACCTCAAAAAGCAGCCTGTTACTTTGAAATGGAAGGATAACAGT
genomic: GCTCGAGCTTCCCAAAGCTGGATGCTATCAAAAGTGCTACTGCTGATATAgtgggtgatt ... ttatttaaagCTTACAGACCTCAAAAAGCAGCCTGTTACTTTGAAATGGAAGGATAACAGT
EST: gi|27582920|gb|CB005615.1|CB005615
EST:     GCTCGAGCTTCCCAAAGCTGGATGCTATCAAAAGTGCTACTGCTGATATA                         CTTACAGACCTCAAAAAGCAGCCTGTTACTTTGAAATGGAAGGATAACAGT
genomic: GCTCGAGCTTCCCAAAGCTGGATGCTATCAAAAGTGCTACTGCTGATATAgtgggtgatt ... ttatttaaagCTTACAGACCTCAAAAAGCAGCCTGTTACTTTGAAATGGAAGGATAACAGT
EST: gi|110723499|gb|EE100881.1|EE100881
EST:     GCTCGAGCTTCCCAAAGCTGGATGCTATCAAAAGTGCTACTGCTGATATA                         CTTACAGACCTC
genomic: GCTCGAGCTTCCCAAAGCTGGATGCTATCAAAAGTGCTACTGCTGATATAgtgggtgatt ... ttatttaaagCTTACAGACCTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aattctttttctgatttctccttttttgcttggtttattatccttttatttaaagCTTACAGACCTCAAAAAGCAGCCTGTTACTTTGAAATGGAAGGATAACAGTTGCACCACAGTAGAAATTTCTGGTCTTGATATTGGATGGGGCCAG
        ttctgat  putative branch site (score: 3)
                                 tttattatcctttt  putative PPT
                                 tttattatccttttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cttttatccatacttgttccttttcaattacaatagtcatgatgcaattctttttctgatttctccttttttgcttggtttattatccttttatttaaagCTTACAGACCTCAAAAAGCAGCCTGTTACTTTGAAATGGAAGGATAACAGTTGCACCACAGTAGAAATTTCTGGTCTTGATATTGGATGGGGCCAG

- - - -ccatact
- - - - - - - - - - - - - - - - - - - - gatgcaa