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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ataatggcatgtattgtgcatcttctcttgtatcaacatctctctctctctctctctctctctctctctctctccaaccttttactttatacatatacagGCTTTCTATTGAAGAAAAGTGAAAAAACTAATGGATGGAGCAGGCGATGGTTTGTTTTAAATGAAAAGACTGGCAAG

Basic information

species Vitis vinifera
transcript Vv18s0089g00350.t01
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0089g00350.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: LOC_Os06g13820.1 (Oryza sativa), 3'ss of exon 14
ataatggcatgtattgtgcatcttctcttgtatcaacatctct-ctctctctctctctc------tctctctctctctctccaaccttttactttatacatata----cagGCTTTCTATTGAAGAAAAGTGAAAAAACTAATGGATGGAGCAGGCGATGGTTTGTTTTAAATGAAAAGACTGGCAAG
              | || | | | |  || |   | |  | |  | | ||||  | |       |   |     | |    |  | || | ||| ||||| |     |||| |  || ||||||||||||| |||||| ||||||||||| ||| | ||||||||  | ||||| || |  || |||
-----------ccctttgaaccatttggtgaaatgaaacatttgttttgtctcattgtaaaaaagtacatgcaaatataaatattcgttaattttgtacatttttcttcagGTTACCTTTTGAAGAAAAGTGCAAAAACAAATGGATGGAGTAGGAGGTGGTTTGTCCTCAATGAGAAAAGCGGAAAG

upper sequence: Vv18s0089g00350.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: LOC_Os02g50550.1 (Oryza sativa), 3'ss of exon 14
-------------------------------------------------------------------------ataatggcatgtattgtgcatcttctcttgtatcaacat----------ctctctctctctctctctctctctctctctctctccaaccttttactttatacatatacagGCTTTCTATTGAAGAAAAGTGAAAAAACTAATGGATGGAGCAGGCGATGGTTTGTTTTAAATGAAAAGACTGGCAAG
                                                                          || ||  || | |  |   |  |  |  ||| |  ||            |   ||| | ||    | |  || | |  |     |     || |||  |   ||  ||||||  || ||||||||||||| ||||| ||||| ||||||||   ||||||||||  ||||||| |||| ||| |||
gtataatgatgcgctgatgcaccataggttatcattcctgtagtttttttttatttactctggctcttcacagctagtgtaatctttcatttgtagttacaagtaactgcagatggttttggttaattctgtatcctggtttggcttttttgcatataagatgatttcttcttttctactcagGCTACCTTTTGAAGAAAAGTGCAAAAAATAATGAATGGAGCAAAAGATGGTTTGTCCTAAATGAGAAGAGTGGAAAG

upper sequence: Vv18s0089g00350.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: GLYMA09G00430.2 (Glycine max), 3'ss of exon 14
ataatggcatgtattgtgcatcttctcttgtatcaacatctctctctctctctctctctctctctctctctctccaacc-ttttactttatacatatacagGCTTTCTATTGAAGAAAAGTGAAAAAACTAATGGATGGAGCAGGCGATGGTTTGTTTTAAATGAAAAGACTGGCAAG
    |    |  | |       ||     ||  |||  |  |    | | | | ||    |   |      ||  |||   ||| ||||||   | | |||| ||| |||| |||||||||| |||||||||||| ||||||||||||||||||||  ||||||||||||| || |||
gagctatgcttaaatacatgaatttggaagttacaatgtgccaaagtatatatttcaaaattattaataaactaaaactacttttctttat-tgttttcagGATTTTTATTAAAGAAAAGTGCAAAAACTAATGGTTGGAGCAGGCGATGGTTTGTGCTAAATGAAAAGACAGGAAAG

upper sequence: Vv18s0089g00350.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: GLYMA12G37100.1 (Glycine max), 3'ss of exon 14
---------ataatggcatgtattgtgcatcttctcttgtatcaacatctctctctctctctctctctctctctctctctctccaaccttttactttatacatatacagGCTTTCTATTGAAGAAAAGTGAAAAAACTAATGGATGGAGCAGGCGATGGTTTGTTTTAAATGAAAAGACTGGCAAG
          |||  ||||| ||| || |  || |  |||  |||  | | | | ||    |   |      ||    ||     || |||  ||||||   | | |||| ||| | || |||||||||| |||||||||||| ||||||||||||||||||||  ||||||| ||||| || |||
agctaatgcttaaatgcatgaatt-tggaagttgtaatgtgccaaagtatatatttcaaaattattaataaactaaaact-----actttt--ctttat-tgtttgcagGATTTTTGTTAAAGAAAAGTGCAAAAACTAATGGTTGGAGCAGGCGATGGTTTGTGCTAAATGAGAAGACAGGAAAG

upper sequence: Vv18s0089g00350.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: AT1G10290.1 (Arabidopsis thaliana), 3'ss of exon 14
---ataatggcatgtattgtgcatcttctcttgtatcaacatctctctctctctctctctctctctctctctctctccaaccttttactttatacatatacagGCTTTCTATTGAAGAAAAGTGAAAAAACTAATGGATGGAGCAGGCGATGGTTTGTTTTAAATGAAAAGACTGGCAAG
   || ||  | |    | |   |||||| |   |   | | ||  ||        ||  ||  |    |   |  | ||   || ||| | | ||| ||  || |   || |||||||||||| |||||| ||||| ||||| ||||||||||||||| | ||||| || ||||| |||
tgcatgatttcttcatgtctttttcttctttatcacttaaaactaacttgacaaaactaacttccaaggtagataacaaatactt-actcttttcattta--gGGTACTTAATGAAGAAAAGTGCAAAAACAAATGGGTGGAGTAGGCGATGGTTTGTTCTGAATGAGAAAACTGGAAAG

upper sequence: Vv18s0089g00350.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: AT1G59610.1 (Arabidopsis thaliana), 3'ss of exon 14
ataatggcatgtattgtgcatcttctcttgtatcaacatctctctctctctctctctctctctctctctctctccaacc----ttttactttatacatatacagGCTTTCTATTGAAGAAAAGTGAAAAAACTAATGGATGGAGCAGGCGATGGTTTGTTTTAAATGAAAAGACTGGCAAG
    | || |  |    || |    |    | |  |  | |   | | |        |   ||  |    ||| ||||     ||||| | | |   | | |||| |   || |||||||||||| ||| || ||||| ||||| ||||||||||||||| | |||||||| ||||| |||
-ctttagctttgacctagcgtaggataagtttttgaggttttagtttgttataaaaaccaactgccaaggtcttcaacagaaattttattctgt---tgtgcagGGTACTTAATGAAGAAAAGTGCAAAGACAAATGGGTGGAGTAGGCGATGGTTTGTTCTGAATGAAAAAACTGGAAAG

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|161719802|gb|FC065762.1|FC065762
EST:     AGAGGGCTCAGCTTTGAAGATAGCTGGTCCTGGTGGTGAGATCACAGCAG                         GCTTTCTATTGAAGAAAAGTGAAAAAACTAATGGATGGAGCAGGCGATGGT
genomic: AGAGGGCTCAGCTTTGAAGATAGCTGGTCCTGGTGGTGAGATCACAGCAGgtatgcttct ... acatatacagGCTTTCTATTGAAGAAAAGTGAAAAAACTAATGGATGGAGCAGGCGATGGT
EST: gi|32270986|gb|CD720145.1|CD720145
EST:     AGAGGGCTCAGCTTTGAAGATAGCTGGTCCTGGTGGTGAGATCACAGCAG                         GCTTTCTATTGAAGAAAAGTGAAAAAACTAATGGATGGAGCAGGCGATGGT
genomic: AGAGGGCTCAGCTTTGAAGATAGCTGGTCCTGGTGGTGAGATCACAGCAGgtatgcttct ... acatatacagGCTTTCTATTGAAGAAAAGTGAAAAAACTAATGGATGGAGCAGGCGATGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctctctctctctctctctctctctctctccaaccttttactttatacatatacagGCTTTCTATTGAAGAAAAGTGAAAAAACTAATGGATGGAGCAGGCGATGGTTTGTTTTAAATGAAAAGACTGGCAAG
       tctctctctctctctc  CT-rich tract
                                  ttttactttatacata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ataatggcatgtattgtgcatcttctcttgtatcaacatctctctctctctctctctctctctctctctctctccaaccttttactttatacatatacagGCTTTCTATTGAAGAAAAGTGAAAAAACTAATGGATGGAGCAGGCGATGGTTTGTTTTAAATGAAAAGACTGGCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG
- - - gcatgta
- - - - - - - - - catcttc
- - - - - - - - - - - - - - - - -caacatc