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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttcaccccccactgaacaaaaaaaagagattctagaaactttgttcatctttgttcagcatttttttttgggttctcatttctaagtgtcattcttcagGTTATAGATGCAGCAAATGAAGTAGTTTGTAGCATTGACAGGGATGAATTAGCAAAATATTTTTCACTCAAAAGTGATCCAGAAGATGAGGAGGCAGAG

Basic information

species Vitis vinifera
transcript Vv16s0050g00490.t01
intron # 30
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv16s0050g00490.t01 (Vitis vinifera), 3'ss of exon 30
lower sequence: GLYMA09G25250.1 (Glycine max), 3'ss of exon 30
---cttcaccccccactgaacaaaaaaaagagattctagaaactttgttcatctttgttcagcatttttttttgggttctcatttctaagtgtcattcttcagGTTATAGATGCAGCAAATGAAGTAGTTTGTAGCATTGACAGGGATGAATTAGCAAAATATTTTTCACTCAAAAGTGATCCAGAAGATGAGGAGGCAGAG
    || |  ||  || |    | |  || || || |   |     |||  |  | |||  |  |  |        |    || ||    | ||| | | |||||  | | |||||| ||||| ||  ||   || |||||||| || ||  ||||||||| |||| |||| |||| |||||||||||||||||| ||||||
tgttttgagtcctaacaggtttatatgaaaagtttatcctatagaagtttgtactggtttcgtgtcgtaa---aactatgaatatcatgatttcaatttgcagGTGGTTGGTGCAGCCAATGAGGTGATTAACAGTATTGACAGAGAAGAGCTAGCAAAATTTTTTGCACTAAAAAATGATCCAGAAGATGAGGAAGCAGAG

upper sequence: Vv16s0050g00490.t01 (Vitis vinifera), 3'ss of exon 30
lower sequence: GLYMA10G37900.1 (Glycine max), 3'ss of exon 30
cttcaccccccactgaacaaaaaaaagagattctagaaactttgttcatctttgttcagcatttttttttgggttctcattt-ctaagtgt-cattcttcagGTTATAGATGCAGCAAATGAAGTAGTTTGTAGCATTGACAGGGATGAATTAGCAAAATATTTTTCACTCAAAAGTGATCCAGAAGATGAGGAGGCAGAG
 |     |  || | |    | | |  | ||| |  ||  |||       | ||      ||         | ||||       || |  | || | | ||||| || |||||||||||||| ||  ||   || ||||| || || || || ||||||| |||| |||| |||| |||||||||||||||||| || |||
gtattgacgacatttagtgtagatataaaattgttcaa--tttagcagcgtgtgaatgatataaaaaggctgattctggggcattatgcatacactttgcagGTAATTGATGCAGCAAATGAGGTTATTGACAGTATTGATAGAGAAGAGTTGGCAAAATTTTTTGCACTAAAAAATGATCCAGAAGATGAGGAAGCCGAG
















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|349809590|gb|FQ414480.1|FQ414480
EST:     ATGCAAAGATAAAGATTCTTGGAAGCCTAAAACATGGCACTGATGAAGAGCGCTCAGAGTGGAGAAAGTTAGCTGCCTCTCTCAAG
genomic: ATGCAAAGATAAAGATTCTTGGAAGCCTAAAACATGGCACTGATGAAGAGCGCTCAGAGTGGAGAAAGTTAGCTGCCTCTCTCAAG
EST: gi|349817461|gb|FQ407251.1|FQ407251
EST:     ATGCAAAGATAAAGATTCTTGGAAGCCTAAAACATGGCACTGATGAAGAGCGCTCAGAGTGGAGAAAGTTAGCTGCCTCTCTCAAG
genomic: ATGCAAAGATAAAGATTCTTGGAAGCCTAAAACATGGCACTGATGAAGAGCGCTCAGAGTGGAGAAAGTTAGCTGCCTCTCTCAAG
EST: gi|351039026|gb|FQ457701.1|FQ457701
EST:     ATGCAAAGATAAAGATTCTTGGAAGCCTAAAACATGGCACTGATGAAGAGCGCTCAGAGTGGAGAAAGTTAGCTGCCTCTCTCAAG
genomic: ATGCAAAGATAAAGATTCTTGGAAGCCTAAAACATGGCACTGATGAAGAGCGCTCAGAGTGGAGAAAGTTAGCTGCCTCTCTCAAG
EST: gi|351056447|gb|FQ454308.1|FQ454308
EST:     ATGCAAAGATAAAGGTTCTTGGAAGCCTAAAACATGGCACTGATGAAGAGCGCTCAGAGTGGAGAAAGTTAGCTGCCTCTCTCAAG
genomic: ATGCAAAGATAAAGATTCTTGGAAGCCTAAAACATGGCACTGATGAAGAGCGCTCAGAGTGGAGAAAGTTAGCTGCCTCTCTCAAG
EST: gi|349811562|gb|FQ409558.1|FQ409558
EST:     ATGCAAAGATAAAGATTCTTGGAAGCCTAAAACATGGCACTGATGAAGAGCGCTCAGAGTGGAGAAAGTTAGCTGCCTCTCTCAAG
genomic: ATGCAAAGATAAAGATTCTTGGAAGCCTAAAACATGGCACTGATGAAGAGCGCTCAGAGTGGAGAAAGTTAGCTGCCTCTCTCAAG
EST: gi|351044162|gb|FQ452835.1|FQ452835
EST:     ATGCAAAGATAAAGATTCTTGGAAGCCTAAAACATGGCACTGATGAAGAGCGCTCAGAGTGGAGAAAGTTAGCTGCCTCTCTCAAG
genomic: ATGCAAAGATAAAGATTCTTGGAAGCCTAAAACATGGCACTGATGAAGAGCGCTCAGAGTGGAGAAAGTTAGCTGCCTCTCTCAAG
EST: gi|349811041|gb|FQ406029.1|FQ406029
EST:     ATGCAAAGATAAAGATTCTTGGAAGCCTAAAACATGGCACTGATGAAGAGCGCTCAGAGTGGAGAAAGTTAGCTGCCTCTCTCAAG
genomic: ATGCAAAGATAAAGATTCTTGGAAGCCTAAAACATGGCACTGATGAAGAGCGCTCAGAGTGGAGAAAGTTAGCTGCCTCTCTCAAG
EST: gi|349818352|gb|FQ409127.1|FQ409127
EST:     ATGCAAAGATAAAGATTCTTGGAAGCCTAAAACATGGCACTGATGAAGAGCGCTCAGAGTGGAGAAAGTTAGCTGCCTCTCTCAAG
genomic: ATGCAAAGATAAAGATTCTTGGAAGCCTAAAACATGGCACTGATGAAGAGCGCTCAGAGTGGAGAAAGTTAGCTGCCTCTCTCAAG
EST: gi|351042671|gb|FQ451086.1|FQ451086
EST:     ATGCAAAGATAAAGATTCTTGGAAGCCTAAAACATGGCACTGATGAAGAGCGCTCAGAGTGGAGAAAGTTAGCTGCCTCTCTCAAG
genomic: ATGCAAAGATAAAGATTCTTGGAAGCCTAAAACATGGCACTGATGAAGAGCGCTCAGAGTGGAGAAAGTTAGCTGCCTCTCTCAAG
EST: gi|349824505|gb|FQ413172.1|FQ413172
EST:     ATGCAAAGATAAAGATTCTTGGAAGCCTAAAACATGGCACTGATGAAGAGCGCTCAGAGTGGAGAAAGTTAGCTGCCTCTCTCAAG
genomic: ATGCAAAGATAAAGATTCTTGGAAGCCTAAAACATGGCACTGATGAAGAGCGCTCAGAGTGGAGAAAGTTAGCTGCCTCTCTCAAG
EST: gi|349824556|gb|FQ413223.1|FQ413223
EST:     ATGCAAAGATAAAGATTCTTGGAAGCCTAAAACATGGCACTGATGAAGAGCGCTCAGAGTGGAGAAAGTTAGCTGCCTCTCTCAAG
genomic: ATGCAAAGATAAAGATTCTTGGAAGCCTAAAACATGGCACTGATGAAGAGCGCTCAGAGTGGAGAAAGTTAGCTGCCTCTCTCAAG
EST: gi|349814862|gb|FQ410085.1|FQ410085
EST:     ATGCAAAGATAAAGATTCTTGGAAGCCTAAAACATGGCACTGATGAAGAGCGCTCAGAGTGGAGAAAGTTAGCTGCCTCTCTCAAG
genomic: ATGCAAAGATAAAGATTCTTGGAAGCCTAAAACATGGCACTGATGAAGAGCGCTCAGAGTGGAGAAAGTTAGCTGCCTCTCTCAAG
EST: gi|349813697|gb|FQ413931.1|FQ413931
EST:     ATGCAAAGATAAAGATTCTTGGAAGCCTAAAACATGGCACTGATGAAGAGCGCTCAGAGTGGAGAAAGTTAGCTGCCTCTCTCAAG
genomic: ATGCAAAGATAAAGATTCTTGGAAGCCTAAAACATGGCACTGATGAAGAGCGCTCAGAGTGGAGAAAGTTAGCTGCCTCTCTCAAG
EST: gi|351034908|gb|FQ458265.1|FQ458265
EST:     ATGCAAAGATAAAGATTCTTGGAAGCCTAAAACATGGCACTGATGAAGAGCGCTCAGAGTGGAGAAAGTTAGCTGCCTCTCTCAAG
genomic: ATGCAAAGATAAAGATTCTTGGAAGCCTAAAACATGGCACTGATGAAGAGCGCTCAGAGTGGAGAAAGTTAGCTGCCTCTCTCAAG
EST: gi|349811081|gb|FQ406069.1|FQ406069
EST:     ATGCAAAGATAAAGATTCTTGGAAGCCTAAAACATGGCACTGATGAAGAGCGCTCAGAGTGGAGAAAGTTAGCTGCCTCTCTCAAG
genomic: ATGCAAAGATAAAGATTCTTGGAAGCCTAAAACATGGCACTGATGAAGAGCGCTCAGAGTGGAGAAAGTTAGCTGCCTCTCTCAAG
EST: gi|351035476|gb|FQ463321.1|FQ463321
EST:     ATGCAAAGATAAAGATTCTTGGAAGCCTAAAACATGGCACTGATGAAGAGCGCTCAGAGTGGAGAAAGTTAGCTGCCTCTCTCAAG
genomic: ATGCAAAGATAAAGATTCTTGGAAGCCTAAAACATGGCACTGATGAAGAGCGCTCAGAGTGGAGAAAGTTAGCTGCCTCTCTCAAG
EST: gi|351045622|gb|FQ440807.1|FQ440807
EST:     ATGCAAAGATAAAGATTCTTGGAAGCCTAAAACATGGCACTGATGAAGAGCGCTCAGAGTGGAGAAAGTTAGCTGCCTCTCTCAAG
genomic: ATGCAAAGATAAAGATTCTTGGAAGCCTAAAACATGGCACTGATGAAGAGCGCTCAGAGTGGAGAAAGTTAGCTGCCTCTCTCAAG
EST: gi|349822506|gb|FQ412770.1|FQ412770
EST:     ATGCAAAGATAAAGATTCTTGGAAGCCTAAAACATGGCACTGATGAAGAGCGCTCAGAGTGGAGAAAGTTAGCTGCCTCTCTCAAG
genomic: ATGCAAAGATAAAGATTCTTGGAAGCCTAAAACATGGCACTGATGAAGAGCGCTCAGAGTGGAGAAAGTTAGCTGCCTCTCTCAAG
EST: gi|349810172|gb|FQ401618.1|FQ401618
EST:     ATGCAAAGATAAAGATTCTTGGAAGCCTAAAACATGGCACTGATGAAGAGCGCTCAGAGTGGAGAAAGTTAGCTGCCTCTCTCAAG
genomic: ATGCAAAGATAAAGATTCTTGGAAGCCTAAAACATGGCACTGATGAAGAGCGCTCAGAGTGGAGAAAGTTAGCTGCCTCTCTCAAG
EST: gi|351038517|gb|FQ464383.1|FQ464383
EST:     ATGCAAAGATAAAGATTCTTGGAAGCCTAAAACATGGCACTGATGAAGAGCGCTCAGAGTGGAGAAAGTTAGCTGCCTCTCTCAAG
genomic: ATGCAAAGATAAAGATTCTTGGAAGCCTAAAACATGGCACTGATGAAGAGCGCTCAGAGTGGAGAAAGTTAGCTGCCTCTCTCAAG
EST: gi|349814599|gb|FQ399239.1|FQ399239
EST:     ATGCAAAGATAAAGATTCTTGGAAGCCTAAAACATGGCACTGATGAAGAGCGCTCAGAGTGGAGAAAGTTAGCTGCCTCTCTCAAG
genomic: ATGCAAAGATAAAGATTCTTGGAAGCCTAAAACATGGCACTGATGAAGAGCGCTCAGAGTGGAGAAAGTTAGCTGCCTCTCTCAAG
EST: gi|349819862|gb|FQ404534.1|FQ404534
EST:     ATGCAAAGATAAAGATTCTTGGAAGCCTAAAACATGGCACTGATGAAGAGCGCTCAGAGTGGAGAAAGTTAGCTGCCTCTCTCAAG
genomic: ATGCAAAGATAAAGATTCTTGGAAGCCTAAAACATGGCACTGATGAAGAGCGCTCAGAGTGGAGAAAGTTAGCTGCCTCTCTCAAG
EST: gi|349807376|gb|FQ401368.1|FQ401368
EST:     ATGCAAAGATAAAGATTCTTGGAAGCCTAAAACATGGCACTGATGAAGAGCGCTCAGAGTGGAGAAAGTTAGCTGCCTCTCTCAAG
genomic: ATGCAAAGATAAAGATTCTTGGAAGCCTAAAACATGGCACTGATGAAGAGCGCTCAGAGTGGAGAAAGTTAGCTGCCTCTCTCAAG
EST: gi|349814881|gb|FQ410104.1|FQ410104
EST:     ATGCAAAGATAAAGATTCTTGGAAGCCTAAAACATGGCACTGATGAAGAGCGCTCAGAGTGGAGAAAGTTAGCTGCCTCTCTCAAG
genomic: ATGCAAAGATAAAGATTCTTGGAAGCCTAAAACATGGCACTGATGAAGAGCGCTCAGAGTGGAGAAAGTTAGCTGCCTCTCTCAAG
EST: gi|352795665|gb|FQ480253.1|FQ480253
EST:     ATGCAAAGATAAAGATTCTTGGAAGCCTAAAACATGGCACTGATGAAGAGCGCTCAGAGTGGAGAAAGTTAGCTGCCTCTCTCAAG
genomic: ATGCAAAGATAAAGATTCTTGGAAGCCTAAAACATGGCACTGATGAAGAGCGCTCAGAGTGGAGAAAGTTAGCTGCCTCTCTCAAG
EST: gi|349812607|gb|FQ407226.1|FQ407226
EST:     ATGCAAAGATAAAGATTCTTGGAAGCCTAAAACATGGCACTGATGAAGAGCGCTCAGAGTGGAGAAAGTTAGCTGCCTCTCTCAAG
genomic: ATGCAAAGATAAAGATTCTTGGAAGCCTAAAACATGGCACTGATGAAGAGCGCTCAGAGTGGAGAAAGTTAGCTGCCTCTCTCAAG
EST: gi|351056626|gb|FQ442454.1|FQ442454
EST:     ATGCAAAGATAAAGATTCTTGGAAGCCTAAAACATGGCACTGATGAAGAGCGCTCAGAGTGGAGAAAGTTAGCTGCCTCTCTCAAG
genomic: ATGCAAAGATAAAGATTCTTGGAAGCCTAAAACATGGCACTGATGAAGAGCGCTCAGAGTGGAGAAAGTTAGCTGCCTCTCTCAAG
EST: gi|349815086|gb|FQ410309.1|FQ410309
EST:     ATGCAAAGATAAAGATTCTTGGAAGCCTAAAACATGGCACTGATGAAGAGCGCTCAGAGTGGAGAAAGTTAGCTGCCTCTCTCAAG
genomic: ATGCAAAGATAAAGATTCTTGGAAGCCTAAAACATGGCACTGATGAAGAGCGCTCAGAGTGGAGAAAGTTAGCTGCCTCTCTCAAG
EST: gi|351047462|gb|FQ454954.1|FQ454954
EST:     ATGCAAAGATAAAGATTCTTGGAAGCCTAAAACATGGCACTGATGAAGAGCGCTCAGAGTGGAGAAAGTTAGCTGCCTCTCTCAAG
genomic: ATGCAAAGATAAAGATTCTTGGAAGCCTAAAACATGGCACTGATGAAGAGCGCTCAGAGTGGAGAAAGTTAGCTGCCTCTCTCAAG
EST: gi|351026108|gb|FQ428120.1|FQ428120
EST:     ATGCAAAGATAAAGATTCTTGGAAGCCTAAAACATGGCACTGATGAAGAGCGCTCAGAGTGGAGAAAGTTAGCTGCCTCTCTCAAG
genomic: ATGCAAAGATAAAGATTCTTGGAAGCCTAAAACATGGCACTGATGAAGAGCGCTCAGAGTGGAGAAAGTTAGCTGCCTCTCTCAAG
EST: gi|71875416|gb|DT024471.1|DT024471
EST:     ATGCAAAGATAAAGATTCTTGGAAGCCTAAAACATGGCACTGATGAAGAGCTCTCAGAGTGGAGAAAGTTAGCTGCCTCTCTCAAG
genomic: ATGCAAAGATAAAGATTCTTGGAAGCCTAAAACATGGCACTGATGAAGAGCGCTCAGAGTGGAGAAAGTTAGCTGCCTCTCTCAAG
EST: gi|351051717|gb|FQ449531.1|FQ449531
EST:     ATGCAAAGATAAAGATTCTTGGAAGCCTAAAACATGGCACTGATGAAGAGCGCTCAGAGTGGAGAAAGTTAGCTGCCTCTCTCAAG
genomic: ATGCAAAGATAAAGATTCTTGGAAGCCTAAAACATGGCACTGATGAAGAGCGCTCAGAGTGGAGAAAGTTAGCTGCCTCTCTCAAG
EST: gi|349816321|gb|FQ399431.1|FQ399431
EST:     ATGCAAAGATAAAGATTCTTGGAAGCCTAAAACATGGCACTGATGAAGAGCGCTCAGAGTGGAGAAAGTTAGCTGCCTCTCTCAAG
genomic: ATGCAAAGATAAAGATTCTTGGAAGCCTAAAACATGGCACTGATGAAGAGCGCTCAGAGTGGAGAAAGTTAGCTGCCTCTCTCAAG
EST: gi|351053468|gb|FQ459215.1|FQ459215
EST:     ATGCAAAGATAAAGATTCTTGGAAGCCTAAAACATGGCACTGATGAAGAGCGCTCAGAGTGGAGAAAGTTAGCTGCCTCTCTCAAG
genomic: ATGCAAAGATAAAGATTCTTGGAAGCCTAAAACATGGCACTGATGAAGAGCGCTCAGAGTGGAGAAAGTTAGCTGCCTCTCTCAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcatctttgttcagcatttttttttgggttctcatttctaagtgtcattcttcagGTTATAGATGCAGCAAATGAAGTAGTTTGTAGCATTGACAGGGATGAATTAGCAAAATATTTTTCACTCAAAAGTGATCCAGAAGATGAGGAGGCAGAG
                                            tcattcttc  CT-rich tract
               attttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cttcaccccccactgaacaaaaaaaagagattctagaaactttgttcatctttgttcagcatttttttttgggttctcatttctaagtgtcattcttcagGTTATAGATGCAGCAAATGAAGTAGTTTGTAGCATTGACAGGGATGAATTAGCAAAATATTTTTCACTCAAAAGTGATCCAGAAGATGAGGAGGCAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - -cccccca
- - - - - - - - - aaaaaaa
- - - - - - - - - - - - - - - - - agaaact