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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgataaatagggcttctcatgttttatgtcattctcctgcatgtgtgtcatggacttcgtatgagacctcacatggttaattacacaatatcacttgtagGATCTGTGCTGGGTGCAACTGCGAGATTGGTCATGGAAGATATTTGAGTTGCATGGGTGCTGTTTGGCATCCAGAATGTTTTCGTTGCCGTGCTTGTGGG

Basic information

species Vitis vinifera
transcript Vv04s0023g01030.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0023g01030.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os06g08400.1 (Oryza sativa), 3'ss of exon 4
tgataaatagggcttctcatgttttatgtcattctcctgcatgtg-tgtcatggacttcgtatgagacctcacatggttaat-tacacaatatcacttgtagGATCTGTGCTGGGTGCAACTGCGAGATTGGTCATGGAAGATATTTGAGTTGCATGGGTGCTGTTTGGCATCCAGAATGTTTTCGTTGCCGTGCTTGTGGG
   |  |  |    |      |  ||  |  |   |  | ||| | ||    |   | | | |       |   |  ||||| || ||  |         ||||  ||||| || ||  || | ||||||||||||||  | |   | ||||||||||| |||||||||||||||||||||||||| || | |||||||   
--ctgcactgatacttggggatggtaattggtaagcgagaatgggatgctgcgagttgcttttactcttactgtttcttaatatatacgcttatttcctcagGACTTGTGCCGGATGTCACAGTGAGATTGGTCATGGGCGTTTCCTTAGTTGCATGGGAGCTGTTTGGCATCCAGAATGTTTTCGCTGTCATGCTTGTAAT

upper sequence: Vv04s0023g01030.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G017845_T04 (Zea mays), 3'ss of exon 4
-tgataaataggg-cttctcatgttttatgtcattctcctgcatgtgtgtcatggacttcgtatgagacctcacatggttaattacacaa---tatcacttgtagGATCTGTGCTGGGTGCAACTGCGAGATTGGTCATGGAAGATATTTGAGTTGCATGGGTGCTGTTTGGCATCCAGAATGTTTTCGTTGCCGTGCTTGTGGG
 | ||    | |  |    || | |   || |||      | |  | |    | ||| |  | |        |  |  |||  || || |   | |    || ||    || || || ||  || | ||||||||||| ||  | | | | ||||||||||| |||||||||||||| |||||||||||||||| ||| ||| | 
gtaatgctcaagaacacaccaggatgattggcatg-----gaagatatcattttgaccttttttctcttactatttttttatataaactaacttcttttctgcagAGCATGCGCAGGATGTCACAGAGAGATTGGTCACGGGCGTTTTCTCAGTTGCATGGGAGCTGTTTGGCATCCGGAATGTTTTCGTTGCCATGCATGTAGT

upper sequence: Vv04s0023g01030.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA16G25750.1 (Glycine max), 3'ss of exon 4
----tgataaatagggcttctcatgttttatgtcattctcctgcatgtgtgtcatggacttcgtatgagacctcacatggttaattacacaatatcacttgtagGATCTGTGCTGGGTGCAACTGCGAGATTGGTCATGGAAGATATTTGAGTTGCATGGGTGCTGTTTGGCATCCAGAATGTTTTCGTTGCCGTGCTTGTGGG
     |||| |      || | ||||||  | |   |    | | ||  | | |   |      | ||| |   |  |||||  ||    ||| |  |||| || ||||||||||| ||||| | ||||||||| |||||||||| ||||||||||||||| | |  ||||||||||||||||||| |||||| ||||||    
atcaagatagaagacatttataatgtttccttttcataaatt-cttgaattttacttataaaaca-gaggctaaaactggttc-ttgggaaatgt-gcttgcagAATCTGTGCTGGCTGCAATTCCGAGATTGGCCATGGAAGATTTTTGAGTTGCATGGGAGGTTATTGGCATCCAGAATGTTTTTGTTGCCATGCTTGCAAA

upper sequence: Vv04s0023g01030.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA02G06720.2 (Glycine max), 3'ss of exon 4
---tgataaatagggcttctcatgttttatgtcattctcctgcatgtgtgtcatggacttcgtatgagacctcacatggttaattacacaatatcacttgtagGATCTGTGCTGGGTGCAACTGCGAGATTGGTCATGGAAGATATTTGAGTTGCATGGGTGCTGTTTGGCATCCAGAATGTTTTCGTTGCCGTGCTTGTGGG
    |||| |       | | ||||||| | |   |    | | ||  | | |   |        |||     || |||||  || || ||| |  |||| || |||||| |||| || ||    |||||||| |||||||||| ||||||||||||||| | |  ||||||||||||||| ||| |||||| ||||||    
tcaagatagaagatatctataatgttttcttttcataaatt-cttgaattttacttataaaaacagaggttaaacctggttc-ttgcaaaatgt-gcttgcagAATCTGTTCTGGCTGTAATGCTGAGATTGGCCATGGAAGATTTTTGAGTTGCATGGGAGGTTATTGGCATCCAGAATGCTTTTGTTGCCATGCTTGCAAA

upper sequence: Vv04s0023g01030.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA12G19010.1 (Glycine max), 3'ss of exon 3
---tgataaatagggcttctcatgttttatgtcattctcctgcatgtgtgtcatggacttcgtatgagacctcacatggttaattacacaatatcacttgtagGATCTGTGCTGGGTGCAACTGCGAGATTGGTCATGGAAGATATTTGAGTTGCATGGGTGCTGTTTGGCATCCAGAATGTTTTCGTTGCCGTGCTTGTGGG
    |||| |       | | ||||||| | |   |    | | ||  | | |   |        |||     || |||||  || || ||| |  |||| || ||||||||||| || ||    |||||| | |||||||||| ||||||||||||||| | |  ||||||||| ||||| ||| |||||| ||||||    
tcaagatagaagacatctataatgttttcttttcataaatt-cttgaattttacttataaaaacagaggttaaacctggttc-ttgcaaaatgtt-cttgcagAATCTGTGCTGGCTGTAATGCTGAGATTAGCCATGGAAGATTTTTGAGTTGCATGGGAGGTTATTGGCATCCGGAATGCTTTTGTTGCCATGCTTGCAAA

upper sequence: Vv04s0023g01030.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA01G38640.1 (Glycine max), 3'ss of exon 3
tgataaatagggcttctcatgttt-tatgtca--ttctcctgcatgtgtgtca-tggacttcgtatgagacctcacatggttaattacacaatatcacttgtagGATCTGTGCTGGGTGCAACTGCGAGATTGGTCATGGAAGATATTTGAGTTGCATGGGTGCTGTTTGGCATCCAGAATGTTTTCGTTGCCGTGCTTGTGGG
   ||| |      | | |  ||| | | |||   | || || || | | | | |    |    |  |    | |     ||   |  | ||| |  | || || ||||||||||| |||||    |||||||| || ||||||| ||| ||||||||||| | ||| |||||||||||||| ||  | |||| ||| |||   
---taattgacatctttgaaatttatttttcaaggtttcatgaatctttattaattttttaaaaacaaagatttaaccttttttctgtaaaatct-gcctgcagAATCTGTGCTGGATGCAAGACTGAGATTGGCCAAGGAAGATTTTTAAGTTGCATGGGAGGTGTCTGGCATCCAGAATGCTTCTGCTGCCATGCATGTCAT

upper sequence: Vv04s0023g01030.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA11G06650.2 (Glycine max), 3'ss of exon 1
tgataaatagggcttctcatgttt-tatgtcat--tctcctgcatgtgtgtcatggacttcgtatgagacctcacatggttaattacacaatatcacttgtagGATCTGTGCTGGGTGCAACTGCGAGATTGGTCATGGAAGATATTTGAGTTGCATGGGTGCTGTTTGGCATCCAGAATGTTTTCGTTGCCGTGCTTGTGGG
  ||||        | | |  ||| | | |||   | || || || | | | |   | |    |  |    | |     ||   |  | ||| |  | || || ||||||||||| |||||    |||||||| || ||||||| ||| ||||||||||| | ||| |||||||||||||| ||  | |||| ||| ||    
--ataatcgacatctttgaaatttatttttcaaggtttcatgaatctttattaattattagaaacaaagatttaaccttttttctgtaaaatct-gcctgcagAATCTGTGCTGGATGCAAGACTGAGATTGGCCAAGGAAGATTTTTAAGTTGCATGGGAGGTGTCTGGCATCCAGAATGCTTCTGCTGCCATGCATGCCAT

upper sequence: Vv04s0023g01030.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT4G36860.1 (Arabidopsis thaliana), 3'ss of exon 4
------------------tgataaatagggcttctcatgttttatgtcattctc----ctgcat-gtg-tgtcatggact-tcgtatgagacctcacatggttaattacacaatatcacttgt--------agGATCTGTGCTGGGTGCAACTGCGAGATTGGTCATGGAAGATATTTGAGTTGCATGGGTGCTGTTTGGCATCCAGAATGTTTTCGTTGCCGTGCTTGTGGG
                     |||       |||| |  ||||  | || | ||    ||  || ||| | | ||| |   ||  || ||  |  |    || ||||        |   || |        ||||| ||||  || ||| |    ||||| || |||||||| | | |||||||||||||||  ||||||||||| ||||||||  |||||  ||| ||||  
gtaaatggttcaaaaatacattaatgtccatttcttagattttcagacactatcatctctagatagtgatatgatgcatgatcacattagctccaatg-agtcaattttgtttctttgtttattttcttggagGATATGTGTCGGTTGCCAAGCTGAGATAGGACATGGAAGGTTTCTGAGTTGCATGGGTGGCGTTTGGCATCCTGAATGTTTCTGTTGCAATGCATGTGAT

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|110720145|gb|EE095821.1|EE095821
EST:     GCTGGAAATATATTTCAACCTTTTCCATCATTCTTTTCACCTGGTTATAG                         GATCTGTGCTGGGTGCAACTGCGAGATTGGTCATGGAAGATATTTGAGTTG
genomic: GCTGGAAATATATTTCAACCTTTTCCATCATTCTTTTCACCTGGTTATAGgtacatgctg ... tcacttgtagGATCTGTGCTGGGTGCAACTGCGAGATTGGTCATGGAAGATATTTGAGTTG
EST: gi|46917880|gb|CN547209.1|CN547209
EST:     GCTGGAAATATATTTCAACCTTTTCCATCATTCTTTTCACCTGGTTATAG                         GATCTGTGCTGGGTGCAACTGCGAGATTGGTCATGGAAGATATTTGAGTTG
genomic: GCTGGAAATATATTTCAACCTTTTCCATCATTCTTTTCACCTGGTTATAGgtacatgctg ... tcacttgtagGATCTGTGCTGGGTGCAACTGCGAGATTGGTCATGGAAGATATTTGAGTTG
EST: gi|46917879|gb|CN547208.1|CN547208
EST:     GCTGGAAATATATTTCAACCTTTTCCATCATTCTTTTCACCTGGTTATAG                         GATCTGTGCTGGGTGCAACTGCGAGATTGGTCATGGAAGATATTTGAGTTG
genomic: GCTGGAAATATATTTCAACCTTTTCCATCATTCTTTTCACCTGGTTATAGgtacatgctg ... tcacttgtagGATCTGTGCTGGGTGCAACTGCGAGATTGGTCATGGAAGATATTTGAGTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtcatggacttcgtatgagacctcacatggttaattacacaatatcacttgtagGATCTGTGCTGGGTGCAACTGCGAGATTGGTCATGGAAGATATTTGAGTTGCATGGGTGCTGTTTGGCATCCAGAATGTTTTCGTTGCCGTGCTTGTGGG
                               ttaattacacaatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgataaatagggcttctcatgttttatgtcattctcctgcatgtgtgtcatggacttcgtatgagacctcacatggttaattacacaatatcacttgtagGATCTGTGCTGGGTGCAACTGCGAGATTGGTCATGGAAGATATTTGAGTTGCATGGGTGCTGTTTGGCATCCAGAATGTTTTCGTTGCCGTGCTTGTGGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - aaatagg
- - - - - - - -ctcatgt
- - - - - - - - - - - - - -gtcattc
- - - - - - - - - - - - - - - - - tcctgca
- - - - - - - - - - - - - - - - - - - - -tgtgtgt
- - - - - - - - - - - - - - - - - - - - - - - - catggac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cctcaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cacaata