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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacattctacttctttttattttttgttttttaacttttggtttgagcttaaaccatctggatttctcatctatgcaaaattttatgaatttttagGAAAAACAGAAGGGGAAGATTGGAATTCTCTTGGACACCGTCTGGTATGAACCTCTTACCAGATCGAAGGATGACCAGCAAGCAGCTCAGAGAGCCATAG

Basic information

species Vitis vinifera
transcript Vv14s0006g01790.t01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0006g01790.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G148176_T01 (Zea mays), 3'ss of exon 6
-------------------------------------------------------------gtacattctacttctttttattttttgttttttaacttttg-gtttgagcttaaaccatctggatttctcatctatgcaaaattttatgaatttttagGAAAAACAGAAGGGGAAGATTGGAATTCTCTTGGACACCGTCTGGTATGAACCTCTTACCAGATCGAAGGATGACCAGCAAGCAGCTCAGAGAGCCATAG
                                                             ||      | |  |  |  |  ||| |||   ||| |     ||  | | | |  |   | | |  |      ||| |    |    | ||     ||    | |||||||||||||||||||||||| ||||   ||| ||||| |||||| | | |      || |  ||||||   ||||| ||| ||||||  |
gtaaaaataaaatgcagacctgctaactatatatttcaagcctccgaacccagaaccagaagtgtgaattgca-cggtgcagatttagttcagtaattaaaatgtcagtgttcaggcatccagaaaatgatccgtattccttttccactaaacgaacagCTTCACCAGAAGGGGAAGATTGGAATTCTCCTGGATTTCGTGTGGTACGAACCTTTCAGCGACAGCAATGCGGACCAGGCTGCAGCACAGCGAGCCAGGG
















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|349821518|gb|FQ408077.1|FQ408077
EST:     TGCTTTTATCTCATGCGGCAGCCGCTCAGAGATACCGTGAGAAATATCAA                         GAAAAACAGAAGGGGAAGATTGGAATTCTCTTGGACACCGTCTGGTATGAA
genomic: TGCTTTTATCTCATGCGGCAGCCGCTCAGAGATACCGTGAGAAATATCAAgtacattcta ... gaatttttagGAAAAACAGAAGGGGAAGATTGGAATTCTCTTGGACACCGTCTGGTATGAA
EST: gi|351041108|gb|FQ444085.1|FQ444085
EST:     TGCTTTTATCTCATGCGGCAGCCGCTCAGAGATACCGTGAGAAATATCAA                         GAAAAACAGAAGGGGAAGATTGGAATTCTCTTGGACACCGTCTGGTATGAA
genomic: TGCTTTTATCTCATGCGGCAGCCGCTCAGAGATACCGTGAGAAATATCAAgtacattcta ... gaatttttagGAAAAACAGAAGGGGAAGATTGGAATTCTCTTGGACACCGTCTGGTATGAA
EST: gi|349833335|gb|FQ416713.1|FQ416713
EST:     TGCTTTTATCTCATGCGGCAGCCGCTCAGAGATACCGTGAGAAATATCAA                         GAAAAACAGAAGGGGAAGATTGGAATTCTCTTGGACACCGTCTGGTATGAA
genomic: TGCTTTTATCTCATGCGGCAGCCGCTCAGAGATACCGTGAGAAATATCAAgtacattcta ... gaatttttagGAAAAACAGAAGGGGAAGATTGGAATTCTCTTGGACACCGTCTGGTATGAA
EST: gi|71870097|gb|DT019152.1|DT019152
EST:     GCTTTTATCTCATGCGGCAGCCGCTCAGAGATACCGTGANGAA-TATCAA                         GAAAAACAGAAGGGGAAGA
genomic: GCTTTTATCTCATGCGGCAGCCGCTCAGAGATACCGTGA-GAAATATCAAgtacattcta ... gaatttttagGAAAAACAGAAGGGGAAGA
EST: gi|349820762|gb|FQ404136.1|FQ404136
EST:     TGCTTTTATCTCATGCGGCAGCCGCTCAGAGATACCGTGAGAAATATCAA                         GAAAAACAGAAGGGGAAGATTGGAATTCTCTTGGACACCGTCTGGTATGAA
genomic: TGCTTTTATCTCATGCGGCAGCCGCTCAGAGATACCGTGAGAAATATCAAgtacattcta ... gaatttttagGAAAAACAGAAGGGGAAGATTGGAATTCTCTTGGACACCGTCTGGTATGAA
EST: gi|349826342|gb|FQ417839.1|FQ417839
EST:     TGCTTTTATCTCATGCGGCAGCCGCTCAGAGATACCGTGAGAAATATCAA                         GAAAAACAGAAGGGGAAGATTGGAATTCTCTTGGACACCGTCTGGTATGAA
genomic: TGCTTTTATCTCATGCGGCAGCCGCTCAGAGATACCGTGAGAAATATCAAgtacattcta ... gaatttttagGAAAAACAGAAGGGGAAGATTGGAATTCTCTTGGACACCGTCTGGTATGAA
EST: gi|349826549|gb|FQ418640.1|FQ418640
EST:     TGCTTTTATCTCATGCGGCAGCCGCTCAGAGATACCGTGAGAAATATCAA                         GAAAAACAGAAGGGGAAGATTGGAATTCTCTTGGACACCGTCTGGTATGAA
genomic: TGCTTTTATCTCATGCGGCAGCCGCTCAGAGATACCGTGAGAAATATCAAgtacattcta ... gaatttttagGAAAAACAGAAGGGGAAGATTGGAATTCTCTTGGACACCGTCTGGTATGAA
EST: gi|349817382|gb|FQ405386.1|FQ405386
EST:     TGCTTTTATCTCATGCGGCAGCCGCTCAGAGATACCGTGAGAAATATCAA                         GAAAAACAGAAGGGGAAGATTGGAATTCTCTTGGACACCGTCTGGTATGAA
genomic: TGCTTTTATCTCATGCGGCAGCCGCTCAGAGATACCGTGAGAAATATCAAgtacattcta ... gaatttttagGAAAAACAGAAGGGGAAGATTGGAATTCTCTTGGACACCGTCTGGTATGAA
EST: gi|351055499|gb|FQ442295.1|FQ442295
EST:     TGCTTTTATCTCATGCGGCAGCCGCTCAGAGATACCGTGAGAAATATCAA                         GAAAAACAGAAGGGGAAGATTGGAATTCTCTTGGACACCGTCTGGTATGAA
genomic: TGCTTTTATCTCATGCGGCAGCCGCTCAGAGATACCGTGAGAAATATCAAgtacattcta ... gaatttttagGAAAAACAGAAGGGGAAGATTGGAATTCTCTTGGACACCGTCTGGTATGAA
EST: gi|349811362|gb|FQ407588.1|FQ407588
EST:     TGCTTTTATCTCATGCGGCAGCCGCTCAGAGATACCGTGAGAAATATCAA                         GAAAAACAGAAGGGGAAGATTGGAATTCTCTTGGACACCGTCTGGTATGAA
genomic: TGCTTTTATCTCATGCGGCAGCCGCTCAGAGATACCGTGAGAAATATCAAgtacattcta ... gaatttttagGAAAAACAGAAGGGGAAGATTGGAATTCTCTTGGACACCGTCTGGTATGAA
EST: gi|351047302|gb|FQ454913.1|FQ454913
EST:     TGCTTTTATCTCATGCGGCAGCCGCTCAGAGATACCGTGAGAAATATCAA                         GAAAAACAGAAGGGGAAGATTGGAATTCTCTTGGACACCGTCTGGTATGAA
genomic: TGCTTTTATCTCATGCGGCAGCCGCTCAGAGATACCGTGAGAAATATCAAgtacattcta ... gaatttttagGAAAAACAGAAGGGGAAGATTGGAATTCTCTTGGACACCGTCTGGTATGAA
EST: gi|351055347|gb|FQ441945.1|FQ441945
EST:     TGCTTTTATCTCATGCGGCAGCCGCTCAGAGATACCGTGAGAAATATCAA                         GAAAAACAGAAGGGGAAGATTGGAATTCTCTTGGACACCGTCTGGTATGAA
genomic: TGCTTTTATCTCATGCGGCAGCCGCTCAGAGATACCGTGAGAAATATCAAgtacattcta ... gaatttttagGAAAAACAGAAGGGGAAGATTGGAATTCTCTTGGACACCGTCTGGTATGAA
EST: gi|351019898|gb|FQ439715.1|FQ439715
EST:     TGCTTTTATCTCATGCGGCAGCCGCTCAGAGATACCGTGAGAAATATCAA                         GAAAAACAGAAGGGGAAGATTGGAATTCTCTTGGACACCGTCTGGTATGAA
genomic: TGCTTTTATCTCATGCGGCAGCCGCTCAGAGATACCGTGAGAAATATCAAgtacattcta ... gaatttttagGAAAAACAGAAGGGGAAGATTGGAATTCTCTTGGACACCGTCTGGTATGAA
EST: gi|349813416|gb|FQ413650.1|FQ413650
EST:     TGCTTTTATCTCATGCGGCAGCCGCTCAGAGATACCGTGAGAAATATCAA                         GAAAAACAGAAGGGGAAGATTGGAATTCCCTTGGACACCGTCTGGTATGAA
genomic: TGCTTTTATCTCATGCGGCAGCCGCTCAGAGATACCGTGAGAAATATCAAgtacattcta ... gaatttttagGAAAAACAGAAGGGGAAGATTGGAATTCTCTTGGACACCGTCTGGTATGAA
EST: gi|71866255|gb|DT015310.1|DT015310
EST:     TGCTTTTATCTCATGCGGCAGCCGCTCAGAGATACCGTGAGAAATATCAA                         GAAAAACAGAAGGGGAAGATTGGAATTCTCTTGGACACCGTCTGGTATGAA
genomic: TGCTTTTATCTCATGCGGCAGCCGCTCAGAGATACCGTGAGAAATATCAAgtacattcta ... gaatttttagGAAAAACAGAAGGGGAAGATTGGAATTCTCTTGGACACCGTCTGGTATGAA
EST: gi|351056118|gb|FQ453580.1|FQ453580
EST:     TGCTTTTATCTCATGCGGCAGCCGCTCAGAGATACCGTGAGAAATATCAA                         GAAAAACAGAAGGGGAAGATTGGAATTCTCTTGGACACCGTCTGGTATGAA
genomic: TGCTTTTATCTCATGCGGCAGCCGCTCAGAGATACCGTGAGAAATATCAAgtacattcta ... gaatttttagGAAAAACAGAAGGGGAAGATTGGAATTCTCTTGGACACCGTCTGGTATGAA
EST: gi|351016119|gb|FQ432074.1|FQ432074
EST:     TGCTTTTATCTCATGCGGCAGCCGCTCAGAGATACCGTGAGAAATATCAA                         GAAAAACAGAAGGGGAAGATTGGAATTCTCTTGGACACCGTCTGGTATGAA
genomic: TGCTTTTATCTCATGCGGCAGCCGCTCAGAGATACCGTGAGAAATATCAAgtacattcta ... gaatttttagGAAAAACAGAAGGGGAAGATTGGAATTCTCTTGGACACCGTCTGGTATGAA
EST: gi|351043324|gb|FQ451376.1|FQ451376
EST:     TGCTTTTATCTCATGCGGCAGCCGCTCAGAGATACCGTGAGAAATATCAA                         GAAAAACAGAAGGGGAAGATTGGAATTCTCTTGGACACCGTCTGGTATGAA
genomic: TGCTTTTATCTCATGCGGCAGCCGCTCAGAGATACCGTGAGAAATATCAAgtacattcta ... gaatttttagGAAAAACAGAAGGGGAAGATTGGAATTCTCTTGGACACCGTCTGGTATGAA
EST: gi|351029000|gb|FQ435001.1|FQ435001
EST:     TGCTTTTATCTCATGCGGCAGCCGCTCAGAGATACCGTGAGAAATATCAA                         GAAAAACAGAAGGGGAAGATTGGAATTCTCTTGGACACCGTCTGGTATGAA
genomic: TGCTTTTATCTCATGCGGCAGCCGCTCAGAGATACCGTGAGAAATATCAAgtacattcta ... gaatttttagGAAAAACAGAAGGGGAAGATTGGAATTCTCTTGGACACCGTCTGGTATGAA
EST: gi|351016022|gb|FQ431977.1|FQ431977
EST:     TGCTTTTATCTCATGCGGCAGCCGCTCAGAGATACCGTGAGAAATATCAA                         GAAAAACAGAAGGGGAAGATTGGAATTCTCTTGGACACCGTCTGGTATGAA
genomic: TGCTTTTATCTCATGCGGCAGCCGCTCAGAGATACCGTGAGAAATATCAAgtacattcta ... gaatttttagGAAAAACAGAAGGGGAAGATTGGAATTCTCTTGGACACCGTCTGGTATGAA
EST: gi|351032857|gb|FQ461746.1|FQ461746
EST:     TGCTTTTATCTCATGCGGCAGCCGCTCAGAGATACCGTGAGAAATATCAA                         GAAAAACAGAAGGGGAAGATTGGAATTCTCTTGGACACCGTCTGGTATGAA
genomic: TGCTTTTATCTCATGCGGCAGCCGCTCAGAGATACCGTGAGAAATATCAAgtacattcta ... gaatttttagGAAAAACAGAAGGGGAAGATTGGAATTCTCTTGGACACCGTCTGGTATGAA
EST: gi|110425826|gb|EC992219.1|EC992219
EST:     TGCTTTTATCTCATGCGGCAGCCGCTCAGAGATACCGTGAGAAATATCAA                         GAAAAACAGAAGGGGAAGATTGGAATTCTCTTGGACACCGTCTGGTATGAA
genomic: TGCTTTTATCTCATGCGGCAGCCGCTCAGAGATACCGTGAGAAATATCAAgtacattcta ... gaatttttagGAAAAACAGAAGGGGAAGATTGGAATTCTCTTGGACACCGTCTGGTATGAA
EST: gi|351044375|gb|FQ452927.1|FQ452927
EST:     TGCTTTTATCTCATGCGGCAGCCGCTCAGAGATACCGTGAGAAATATCAA                         GAAAAACAGAAGGGGAAGATTGGAATTCTCTTGGACACCGTCTGGTATGAA
genomic: TGCTTTTATCTCATGCGGCAGCCGCTCAGAGATACCGTGAGAAATATCAAgtacattcta ... gaatttttagGAAAAACAGAAGGGGAAGATTGGAATTCTCTTGGACACCGTCTGGTATGAA
EST: gi|349815167|gb|FQ410390.1|FQ410390
EST:     TGCTTTTATCTCATGCGGCAGCCGCTCAGAGATACCGTGAGAAATATCAA                         GAAAAACAGAAGGGGAAGATTGGAATTCTCTTGGACACCGTCTGGTATGAA
genomic: TGCTTTTATCTCATGCGGCAGCCGCTCAGAGATACCGTGAGAAATATCAAgtacattcta ... gaatttttagGAAAAACAGAAGGGGAAGATTGGAATTCTCTTGGACACCGTCTGGTATGAA
EST: gi|352790248|gb|FQ481447.1|FQ481447
EST:     TGCTTTTATCTCATGCGGCAGCCGCTCAGAGATACCGTGAGAAATATCAA                         GAAAAACAGAAGGGGAAGATTGGAATTCTCTTGGACACCGTCTGGTATGAA
genomic: TGCTTTTATCTCATGCGGCAGCCGCTCAGAGATACCGTGAGAAATATCAAgtacattcta ... gaatttttagGAAAAACAGAAGGGGAAGATTGGAATTCTCTTGGACACCGTCTGGTATGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgagcttaaaccatctggatttctcatctatgcaaaattttatgaatttttagGAAAAACAGAAGGGGAAGATTGGAATTCTCTTGGACACCGTCTGGTATGAACCTCTTACCAGATCGAAGGATGACCAGCAAGCAGCTCAGAGAGCCATAG
                                                ttttt  CT-rich tract
                           atctatgcaaaatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacattctacttctttttattttttgttttttaacttttggtttgagcttaaaccatctggatttctcatctatgcaaaattttatgaatttttagGAAAAACAGAAGGGGAAGATTGGAATTCTCTTGGACACCGTCTGGTATGAACCTCTTACCAGATCGAAGGATGACCAGCAAGCAGCTCAGAGAGCCATAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA