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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agattgcaggacttgtgatttgtgttgttatttgataggtgtattgtttttgtaaaaaaagggttttaaatactgaattttttcaattgatgatatgcagGGGATTGCTTTAGCTGTTGGAGACTGGTACTTCGACCGATCTGGCATTAAAGCCATCGACTGCCCCTACCCTTGTGACAAGACCTGCCACAATCTAGTAT

Basic information

species Vitis vinifera
transcript Vv14s0060g00230.t01
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0060g00230.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: LOC_Os01g21630.1 (Oryza sativa), 3'ss of exon 8
-----------------------------------------------------------agattgcagg-acttgtgatttgtgttgttatttgataggtgtattgtttttgtaaaaaaagggttttaaatactgaattttttcaattgatg-atatgcagGGGATTGCTTTAGCTGTTGGAGACTGGTACTTCGACCGATCTGGCATTAAAGCCATCGACTGCCCCTACCCTTGTGACAAGACCTGCCACAATCTAGTAT
| | ||||| || | || | | | | | || || | ||||| ||| | || | | || || || ||||||| ||||| ||||||| ||||||||||| | ||| ||| | || |||||||| ||||||||||| |||||||| || |||||||| | |||
gtactttccaccttgcttaattagtgtgtgtccatgtaattgttcagagctacaagagaaaactgcagacgttttcagtacttgcagacgaagaacctgaatgg-gattatgcataaaaaaatacttacttttcagtttcatgctgttcttggatgtgcagGGAATTGCAAAGTCTGTTGGTGACTGGTACTTTGGTCGAGCTGAGGTGAAGGCCATCGATTGCCCCTACCCCTGTGACAAAACATGCCACAACATCATAT

upper sequence: Vv14s0060g00230.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA20G22210.1 (Glycine max), 3'ss of exon 11
agattgcaggacttgtgatttgtgttgttatttgataggtgtattgtttttgtaaaaaaagggttttaaatactgaattttttcaat-tgatgatatgcagGGGATTGCTTTAGCTGTTGGAGACTGGTACTTCGACCGATCTGGCATTAAAGCCATCGACTGCCCCTACCCTTGTGACAAGACCTGCCACAATCTAGTAT
| | || | || || || || || || ||| || | | | || || | | | | || || |||||||| |||||| | ||||||||||||||||| ||||||||| | | |||| ||||| || || || ||||||||||| || || || ||| |||| || |
tgtctttgaactctgaagctagtatttgtaattttcttatgc-ttccctttaaaattttaagatcttcctgtctaagtctaaactatatgcatttatgcagGCAATTGCTCTTGCTGTTGGAGACTGGTATTTCGACCGAGCAGTTGTTAAGGCCATTGATTGTCCTTACCCTTGTGATAATACATGTCACCATCTTGTCT

upper sequence: Vv14s0060g00230.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA03G38650.1 (Glycine max), 3'ss of exon 11
--------agattgcaggacttgtgatttgtgttgttatttgataggtgtattgtttttgtaaaaaaagggttttaaatactgaattttttcaattgatgatatgcagGGGATTGCTTTAGCTGTTGGAGACTGGTACTTCGACCGATCTGGCATTAAAGCCATCGACTGCCCCTACCCTTGTGACAAGACCTGCCACAATCTAGTAT
| || || ||| || | |||||| || | | || | | | | | || | | |||| | || |||| ||||||||| |||||| | ||||||||||||||||| ||||| ||| | || |||| ||||| || || || ||||||||||| || || ||||| |||| | |
tgctagtaatatatcattgctt-tggtctgtgtttgtaagtcacctctgataaatctctttgatttaaagatgttaatgtttagat-------attgccaatatgcagGCAATTGCTCTGGCTGTTGGAGACTGGTATTTCGATCGAGCAGGTGTTAAGGCCATTGATTGTCCTTACCCTTGTGATAATACATGCCATCATCTGATTT

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|110415561|gb|EC981480.1|EC981480
EST:     AGAGGCAGGATACGTGGTTTGCTGATAATTCTCCCATTATTAAAAACAAG                         GGGATTGCTTTAGCTGTTGGAGACTGGTACTTCGACCGATCTGGCATTAAA
genomic: AGAGGCAGGATACGTGGTTTGCTGATAATTCTCCCATTATTAAAAACAAGgtatgcctta ... tgatatgcagGGGATTGCTTTAGCTGTTGGAGACTGGTACTTCGACCGATCTGGCATTAAA
EST: gi|110363756|gb|EC927367.1|EC927367
EST:     AGAGGCAGGATACGTGGTTTGCTGATAATTCTCCCATTATTAAAAACAAG                         GGGATTGCTTTAGCTGTTGGAGACTGGTACTTCGACCGATCTGGCATTAAA
genomic: AGAGGCAGGATACGTGGTTTGCTGATAATTCTCCCATTATTAAAAACAAGgtatgcctta ... tgatatgcagGGGATTGCTTTAGCTGTTGGAGACTGGTACTTCGACCGATCTGGCATTAAA
EST: gi|110426622|gb|EC993036.1|EC993036
EST:     GAGGCAGGATACGTGGTTTGCTGATAATTCTCCCATTATTAAAAACAAG                         GGGATTGCTTTAGCTGTTGGAGACTGGTACTTCGACCGATCTGGCATTAAA
genomic: GAGGCAGGATACGTGGTTTGCTGATAATTCTCCCATTATTAAAAACAAGgtatgcctta ... tgatatgcagGGGATTGCTTTAGCTGTTGGAGACTGGTACTTCGACCGATCTGGCATTAAA
EST: gi|110717734|gb|EE093851.1|EE093851
EST:     AGAGGCAGGATACGTGGTTTGCTGATAATTCTCCCATTATTAAAAACAAG                         GGGATTGCTTTAGCTGTTGGAGACTGGTACTTCGACCGATCTGGCATTAAA
genomic: AGAGGCAGGATACGTGGTTTGCTGATAATTCTCCCATTATTAAAAACAAGgtatgcctta ... tgatatgcagGGGATTGCTTTAGCTGTTGGAGACTGGTACTTCGACCGATCTGGCATTAAA
EST: gi|110419357|gb|EC985576.1|EC985576
EST:     AGAGGCAGGATACGTGGTTTGCTGATAATTCTCCCATTATTAAAAACAAG                         GGGATTGCTTTAGCTGTTGGAGACTGGTACTTCGACCGATCTGGCATTAAA
genomic: AGAGGCAGGATACGTGGTTTGCTGATAATTCTCCCATTATTAAAAACAAGgtatgcctta ... tgatatgcagGGGATTGCTTTAGCTGTTGGAGACTGGTACTTCGACCGATCTGGCATTAAA
EST: gi|32246991|gb|CD712810.1|CD712810
EST:     AGAGGCAGGATACGTGGTTTGCTGATAATTCTCCCATTATTAAAAACAAG                         GGGATTGCTTTAGCTGTTGGAGACTGGTACTTCGACCGATCTGGCATTAAA
genomic: AGAGGCAGGATACGTGGTTTGCTGATAATTCTCCCATTATTAAAAACAAGgtatgcctta ... tgatatgcagGGGATTGCTTTAGCTGTTGGAGACTGGTACTTCGACCGATCTGGCATTAAA
EST: gi|32246638|gb|CD712457.1|CD712457
EST:     AGAGGCAGGATACGTGGTTTGCTGATAATTCTCCCATTATTAAAAACAAG                         GGGATTGCTTTAGCTGTTGGAGACTGGTACTTCGACCGATCTGGCATTAAA
genomic: AGAGGCAGGATACGTGGTTTGCTGATAATTCTCCCATTATTAAAAACAAGgtatgcctta ... tgatatgcagGGGATTGCTTTAGCTGTTGGAGACTGGTACTTCGACCGATCTGGCATTAAA
EST: gi|110363559|gb|EC927156.1|EC927156
EST:     AGAGGCAGGATACGTGGTTTGCTGATAATTCTCCCATTATTAAAAACAAG                         GGGATTGCTTTAGCTGTTGGAGACTGGTACTTCGACCGATCTGGCATTAAA
genomic: AGAGGCAGGATACGTGGTTTGCTGATAATTCTCCCATTATTAAAAACAAGgtatgcctta ... tgatatgcagGGGATTGCTTTAGCTGTTGGAGACTGGTACTTCGACCGATCTGGCATTAAA
EST: gi|110373299|gb|EC937521.1|EC937521
EST:     AGAGGCAGGATACGTGGTTTGCTGATAATTCTCCCATTATTAAAAACAAG                         GGGATTGCTTTAGCTGTTGGAGACTGGTACTTCGACCGATCTGGCATTAAA
genomic: AGAGGCAGGATACGTGGTTTGCTGATAATTCTCCCATTATTAAAAACAAGgtatgcctta ... tgatatgcagGGGATTGCTTTAGCTGTTGGAGACTGGTACTTCGACCGATCTGGCATTAAA
EST: gi|110397107|gb|EC962828.1|EC962828
EST:     AGAGGCAGGATACGTGGTTTGCTGATAATTCTCCCATTATTAAAAACAAG                         GGGATTGCTTTAGCTGTTGGAGACTGGTACTTCGACCGATCTGGCATTAAA
genomic: AGAGGCAGGATACGTGGTTTGCTGATAATTCTCCCATTATTAAAAACAAGgtatgcctta ... tgatatgcagGGGATTGCTTTAGCTGTTGGAGACTGGTACTTCGACCGATCTGGCATTAAA
EST: gi|110422538|gb|EC988864.1|EC988864
EST:     AGAGGCAGGATACGTGGTTTGCTGATAATTCTCCCATTATTAAAAACAAG                         GGGATTGCTTTAGCTGTTGGAGACTGGTACTTCGACCGATCTGGCATTAAA
genomic: AGAGGCAGGATACGTGGTTTGCTGATAATTCTCCCATTATTAAAAACAAGgtatgcctta ... tgatatgcagGGGATTGCTTTAGCTGTTGGAGACTGGTACTTCGACCGATCTGGCATTAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttttgtaaaaaaagggttttaaatactgaattttttcaattgatgatatgcagGGGATTGCTTTAGCTGTTGGAGACTGGTACTTCGACCGATCTGGCATTAAAGCCATCGACTGCCCCTACCCTTGTGACAAGACCTGCCACAATCTAGTAT
                                       aattgat  putative branch site (score: 4)
 ttttaaatactgaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agattgcaggacttgtgatttgtgttgttatttgataggtgtattgtttttgtaaaaaaagggttttaaatactgaattttttcaattgatgatatgcagGGGATTGCTTTAGCTGTTGGAGACTGGTACTTCGACCGATCTGGCATTAAAGCCATCGACTGCCCCTACCCTTGTGACAAGACCTGCCACAATCTAGTAT

- - tgcagga
- - - - - - - - - - - - - - - - - - - - - - - - - - -aaaaaaa