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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aatattgtcatcatttatccaactttacattcatttttgcatctgatgtcaatgtaataattattttatggtattgcctttgtttccttaatttgttcagGATCCTTATTTCAGAATGACACGGGATGTTGCTCCTCGGATAGGATATCACAAGCCCGCATTGATTGAATCATTATTCTTCCCTGCCCTTCAG

Basic information

species Vitis vinifera
transcript Vv12s0028g03370.t01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv12s0028g03370.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os12g35570.3 (Oryza sativa), 3'ss of exon 5
aatattgtcatcatttatccaact-ttacattcatttttgcatctgatgtcaatgtaataattattttatggtattgcctttgtttccttaatttgttc----agGATCCTTATTTCAGAATGACACGGGATGTTGCTCCTCGGATAGGATATCACAAGCCCGCATTGATTGAATCATTATTCTTCCCTGCCCTTCAG
  | |  | |   ||||   | || ||  |    ||  ||  |||| | |  | ||   | ||  |   |||  |||  || | |   |  ||||||||    |||||||||||||||| ||||| ||||| ||||||||  | || || || || || ||  |||| ||||||||   ||| |||||||| ||||||
--tttctttaat-tttaggtagctattgtagatgttcatgt-tctgttatgcaagtttgagttgctcattggatttgagtt-gctcattggatttgttcttccagGATCCTTATTTCAGGATGACCCGGGACGTTGCTCCAAGAATTGGTTACCAGAAACCATCATTAATTGAATCGAGATTTTTCCCTGCTCTTCAG

upper sequence: Vv12s0028g03370.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA13G11390.1 (Glycine max), 3'ss of exon 5
aatattgtcatcatttatccaactttacattcatttttgcatctgatgtcaatgtaataattattttatggtattgcc--tttgtttccttaatttgttcagGATCCTTATTTCAGAATGACACGGGATGTTGCTCCTCGGATAGGATATCACAAGCCCGCATTGATTGAATCATTATTCTTCCCTGCCCTTCAG
| ||||    || | |        ||||||    | | | ||   ||| ||     ||  ||| ||| |   |||     ||| | |   | || | |||||||||| ||||| ||||||||||| ||||||||||||   || || |  |||||||| || ||||||||||||||||||||||| ||  | |||
agtattcat-tcttattcttggtattacatgtgatataggatac-atggcaggcacatttttaatttttttaattaatagtttatctttatgatatattcagGATCCATATTTTAGAATGACACGTGATGTTGCTCCTAAAATGGGTTTCCACAAGCCAGCCTTGATTGAATCATTATTCTTCCCAGCATTACAG

upper sequence: Vv12s0028g03370.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA03G25740.1 (Glycine max), 3'ss of exon 5
---aatattgtcatcatt-tatccaactttacattcatttttgcatctgatgtcaatgtaataattattttatggtattgcctttgtttccttaatttgttcagGATCCTTATTTCAGAATGACACGGGATGTTGCTCCTCGGATAGGATATCACAAGCCCGCATTGATTGAATCATTATTCTTCCCTGCCCTTCAG
    |     ||||  || |        || |||    | | | |||  ||||  || ||| ||  | || | |  || |  ||| ||||  | || | |||||||||| ||||| ||||||||||| ||||||||||||   || || |  |||||||| || ||||||||||||||||||||||| ||  | |||
atgcaagcattcattgttattcttggtattgcatgtgatataggatcc-atgtgcatttaaaaaaaaattaa-gtaatagtttttctttc--tgatatattcagGATCCATATTTTAGAATGACACGTGATGTTGCTCCTAAAATGGGTTTCCACAAGCCAGCCTTGATTGAATCATTATTCTTCCCAGCATTACAG

upper sequence: Vv12s0028g03370.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: AT3G04600.2 (Arabidopsis thaliana), 3'ss of exon 7
------------------------------------------------------------------------------------aatattgtcatcatttatccaactttacattcatttttgcatctgatgtcaatgta--ataattat-tttatggt--attgcctttgtttccttaatttgttcagGATCCTTATTTCAGAATGACACGGGATGTTGCTCCTCGGATAGGATATCACAAGCCCGCATTGATTGAATCATTATTCTTCCCTGCCCTTCAG----
                                                                                    | |     |||    ||      |  | | ||| |||    | || | || |||||  | | || | |||||     ||     ||  ||  |   |||||||||||||||||||| |||||||| || ||||| || || ||| |||| |||  |||||||||  ||||||| |||  ||| || |||||  | |||    
gtgtgctgttttcttactttttatattaacctgtttgcctttttaaaagattaataacttcccattggtataaaaatgtctgtgactgcgagcatgtgatacttccatccataatcagtttcttttatgttttccatgtatcacatttgtatttataaccaatctttctttctttttggttttgttcagGATCCTTATTTTAGAATGACTCGTGATGTCGCACCCCGGTTAGGCTATAGCAAGCCCGCCCTGATTGAGTCAACATTTTTTCCTGCGTTGCAGGCAA

upper sequence: Vv12s0028g03370.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: AT3G04600.3 (Arabidopsis thaliana), 3'ss of exon 7
------------------------------------------------------------------------------------aatattgtcatcatttatccaactttacattcatttttgcatctgatgtcaatgta--ataattat-tttatggt--attgcctttgtttccttaatttgttcagGATCCTTATTTCAGAATGACACGGGATGTTGCTCCTCGGATAGGATATCACAAGCCCGCATTGATTGAATCATTATTCTTCCCTGCCCTTCAG
                                                                                    | |     |||    ||      |  | | ||| |||    | || | || |||||  | | || | |||||     ||     ||  ||  |   |||||||||||||||||||| |||||||| || ||||| || || ||| |||| |||  |||||||||  ||||||| |||  ||| || |||||  | |||
gtgtgctgttttcttactttttatattaacctgtttgcctttttaaaagattaataacttcccattggtataaaaatgtctgtgactgcgagcatgtgatacttccatccataatcagtttcttttatgttttccatgtatcacatttgtatttataaccaatctttctttctttttggttttgttcagGATCCTTATTTTAGAATGACTCGTGATGTCGCACCCCGGTTAGGCTATAGCAAGCCCGCCCTGATTGAGTCAACATTTTTTCCTGCGTTGCAG

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|27581897|gb|CB004592.1|CB004592
EST:     TCTCTGGAAAAGATGATCTTCGTTGCTTGATTCCATGTGCTATTGATCAG                         GATCCTTATTTCAGAATGACACGGGATGTTGCTCCTCGGATAGGATATCAC
genomic: TCTCTGGAAAAGATGATCTTCGTTGCTTGATTCCGTGTGCTATTGATCAGgttgagtctt ... atttgttcagGATCCTTATTTCAGAATGACACGGGATGTTGCTCCTCGGATAGGATATCAC
EST: gi|27582130|gb|CB004825.1|CB004825
EST:     GGAAAAGATGATCTTCGTTGCTTGATTCCATGTGCTATTGATCAG                         GATCCTTATTTCAGAATGACACGGGATGTTGCTCCTCGGATAGGATATCAC
genomic: GGAAAAGATGATCTTCGTTGCTTGATTCCGTGTGCTATTGATCAGgttgagtctt ... atttgttcagGATCCTTATTTCAGAATGACACGGGATGTTGCTCCTCGGATAGGATATCAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgtcaatgtaataattattttatggtattgcctttgtttccttaatttgttcagGATCCTTATTTCAGAATGACACGGGATGTTGCTCCTCGGATAGGATATCACAAGCCCGCATTGATTGAATCATTATTCTTCCCTGCCCTTCAG
                                        ccttaat  putative branch site (score: 4)
                                              tttgttc  CT-rich tract
     aatgtaataattattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aatattgtcatcatttatccaactttacattcatttttgcatctgatgtcaatgtaataattattttatggtattgcctttgtttccttaatttgttcagGATCCTTATTTCAGAATGACACGGGATGTTGCTCCTCGGATAGGATATCACAAGCCCGCATTGATTGAATCATTATTCTTCCCTGCCCTTCAG

- - - gtcatca
- - - - - - - - -tccaact
- - - - - - - - - - - - - -cattcat
- - - - - - - - - - - - - - - - - - - gcatctg
- - - - - - - - - - - - - - - - - - - - - - - - -caatgta