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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gattcttactcttgaaagtatcatatgtggccatgtagaaatgaatgctattgcttcctttatccttttcatatggggttcatcttttacattgctgcagCAACACTGGGAGCAACTTTAGCGAGGCACCGTTCAAAACCTAGGATTTACATTGGATGCATGAAATCTGGACCTGTTCTAGCTCAAAA

Basic information

species Vitis vinifera
transcript Vv19s0090g00560.t01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv19s0090g00560.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: LOC_Os02g06840.2 (Oryza sativa), 3'ss of exon 8
---gattcttactcttgaaagtatcatatgtggccatgtagaaatgaatgctattgct-tcctttatccttttcatatggggttcatcttttacattgctgcagCAACACTGGGAGCAACTTTAGCGAGGCACCGTTCAAAACCTAGGATTTACATTGGATGCATGAAATCTGGACCTGTTCTAGCTCAAAA
    | ||| |    || |  | | ||   | || ||||||||| |      | |||| |     ||   ||   ||||   ||  | |||| | ||  |||||||||||| |||   | |||| | |  ||    |  || || ||  | || |||||||||||||||||||||||||| ||| || | ||
agctagtctcatcaatgcatatttgattcattgc-atgtagaaa-gggcatcactgctatagacaattgattctttatgacattggtgttttgcttt--tgcagCAACACTTGGACAGATTTTATCTAATCATGCATTGAAGCCCAGAGTATATATTGGATGCATGAAATCTGGACCTGTCCTAACTGAGAA

upper sequence: Vv19s0090g00560.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GRMZM2G132866_T02 (Zea mays), 3'ss of exon 6
---gattcttactcttgaaagtatcatatgtggccatgtagaaatgaatgctattgcttcctttatccttttcatatggggttcatcttttacattgctgcagCAACACTGGGAGCAACTTTAGCGAGGCACCGTTCAAAACCTAGGATTTACATTGGATGCATGAAATCTGGACCTGTTCTAGCTCAAAA
    |    ||    |  |||  | || ||||    || | |||  |  ||   || |    |    |    ||  |   |   |  ||   ||||  ||||||||| || |||   | | |  |||  ||    |  || || ||  | ||||| |||||||||||||||||||||||  || |  ||||
ttaaaaaactagaagtacaagc-tgatgtgtgaatctgcataaaaaatagcatatgataagctctggcaaagcaactaacgccaaagttcggcatt--tgcagCAACGCTCGGACAGATTCTGTCGAAACATGCATTGAAGCCGAGAGTGTACATCGGATGCATGAAATCTGGACCTGTCTTATCCGAAAA

upper sequence: Vv19s0090g00560.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: AT4G26940.1 (Arabidopsis thaliana), 3'ss of exon 7
---gattcttactct-tgaaagtatcatatgtggccatgtagaaatgaatgctattgcttcctttatccttttcatatggggttcatcttttacattgctgcagCAACACTGGGAGCAACTTTAGCGAGGCACCGTTCAAAACCTAGGATTTACATTGGATGCATGAAATCTGGACCTGTTCTAGCTCAAAA
    ||    ||||| | |||||||| |   | |   |||     |   ||  ||  |    ||   ||||| |  |     |   || |  | ||| ||||||| || || ||||||   ||||| ||  ||||    || ||  |  | |||||||| ||||||||||||||||||||||| ||||| ||
gtgaatataaactctcttaaagtatc-tgaattgttttgt-----ttcttgtcatctcaagtttgtgcctttgctcact---tctgtcatggatatttctgcagCCACGCTTGGAGCAGAATTAGCAAGATACCGGATGAAGCCCCGAGTGTACATTGGTTGCATGAAATCTGGACCTGTTCTTGCTCAGAA

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|34544134|gb|CF512366.1|CF512366
EST:     GGATGCAGATTTCTATGTCAAAGTAGATGATGATGTCCATGTAAATATAG                         CAACACTGGGAGCAACTTTAGCGAGGCACCGTTCAAAACCTAGGATTTACA
genomic: GGATGCAGATTTCTATGTCAAAGTAGATGATGATGTCCATGTAAATATAGgtaaagatgc ... attgctgcagCAACACTGGGAGCAACTTTAGCGAGGCACCGTTCAAAACCTAGGATTTACA
EST: gi|349826233|gb|FQ416038.1|FQ416038
EST:     GGATGCAGATTTCTATGTCAAAGTAGATGATGATGTCCATGTAAATATAG                         CAACACTGGGAGCAACTTTAGCGAGGCACCGTTCAAAACCTAGGATTTACA
genomic: GGATGCAGATTTCTATGTCAAAGTAGATGATGATGTCCATGTAAATATAGgtaaagatgc ... attgctgcagCAACACTGGGAGCAACTTTAGCGAGGCACCGTTCAAAACCTAGGATTTACA
EST: gi|71875910|gb|DT024965.1|DT024965
EST:     GGATGCAGATTTCTATGTCAAAGTAGATGATGATGTCCATGTAAATATAG                         CAACACTGGGAGCAACTTTAGCGAGGCACCGTTCAAAACCTAGGATTTACA
genomic: GGATGCAGATTTCTATGTCAAAGTAGATGATGATGTCCATGTAAATATAGgtaaagatgc ... attgctgcagCAACACTGGGAGCAACTTTAGCGAGGCACCGTTCAAAACCTAGGATTTACA
EST: gi|77583730|gb|DV220900.1|DV220900
EST:     GGATGCAGATTTCTATGTCAAAGTAGATGATGATGTCCATGTAAATATAG                         CAACACTGGGAGCAACTTTAGCGAGGCACCGTTCAAAACCTAGGATTTACA
genomic: GGATGCAGATTTCTATGTCAAAGTAGATGATGATGTCCATGTAAATATAGgtaaagatgc ... attgctgcagCAACACTGGGAGCAACTTTAGCGAGGCACCGTTCAAAACCTAGGATTTACA
EST: gi|71875911|gb|DT024966.1|DT024966
EST:     GGATGCAGATTTCTATGTCAAAGTAGATGATGATGTCCATGTAAATATAG                         CAACACTGGGAGCAACTTTAGCGAGGCACCGTTCAAAACCTAGGATTTACA
genomic: GGATGCAGATTTCTATGTCAAAGTAGATGATGATGTCCATGTAAATATAGgtaaagatgc ... attgctgcagCAACACTGGGAGCAACTTTAGCGAGGCACCGTTCAAAACCTAGGATTTACA
EST: gi|351046999|gb|FQ454609.1|FQ454609
EST:     GGATGCAGATTTCTATGTCAAAGTAGATGATGATGTCCATGTAAATATAG                         CAACACTGGGAGCAACTTTAGCGAGGCACCGTTCAAAACCTAGGATTTACA
genomic: GGATGCAGATTTCTATGTCAAAGTAGATGATGATGTCCATGTAAATATAGgtaaagatgc ... attgctgcagCAACACTGGGAGCAACTTTAGCGAGGCACCGTTCAAAACCTAGGATTTACA
EST: gi|110712361|gb|EE089898.1|EE089898
EST:     GGATGCAGATTTCTATGTCAAAGTAGATGATGATGTCCATGTAAATATAG                         CAACACTGGGAGCAACTTTAGCGAGGCACCGTTCAAAACCTAGGATTTACA
genomic: GGATGCAGATTTCTATGTCAAAGTAGATGATGATGTCCATGTAAATATAGgtaaagatgc ... attgctgcagCAACACTGGGAGCAACTTTAGCGAGGCACCGTTCAAAACCTAGGATTTACA
EST: gi|351056608|gb|FQ442436.1|FQ442436
EST:     GGATGCAGATTTCTATGTCAAAGTAGATGATGATGTCCATGTAAATATAG                         CAACACTGGGAGCAACTTTAGCGAGGCACCGTTCAAAACCTAGGATTTACA
genomic: GGATGCAGATTTCTATGTCAAAGTAGATGATGATGTCCATGTAAATATAGgtaaagatgc ... attgctgcagCAACACTGGGAGCAACTTTAGCGAGGCACCGTTCAAAACCTAGGATTTACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgctattgcttcctttatccttttcatatggggttcatcttttacattgctgcagCAACACTGGGAGCAACTTTAGCGAGGCACCGTTCAAAACCTAGGATTTACATTGGATGCATGAAATCTGGACCTGTTCTAGCTCAAAA
                    ttttcatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gattcttactcttgaaagtatcatatgtggccatgtagaaatgaatgctattgcttcctttatccttttcatatggggttcatcttttacattgctgcagCAACACTGGGAGCAACTTTAGCGAGGCACCGTTCAAAACCTAGGATTTACATTGGATGCATGAAATCTGGACCTGTTCTAGCTCAAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
- - - - - - -gaaagta
- - - - - - - - - - - - - - - ccatgta
- - - - - - - - - - - - - - - - - - - aaatgaa