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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagttttggaagaactattatattgttttgttttctaaatgaaatatcagttatcttacaatatttatcttgtccttaaaaattcgatttcctgtaatcagaaggaatttagtcatttgttctattgcttgtatcttggctgtgatatttaactctttgcatctttagGTATGTTGCAACTTCAGTTACTTCAGTTCATGAGATGGAAAATGGCTTTAACATATGGTCCTTCAACGGCAAGCTCCTGTATCGGATACTAAAGGATCAC

Basic information

species Vitis vinifera
transcript Vv04s0008g07070.t01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0008g07070.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GRMZM2G174757_T01 (Zea mays), 3'ss of exon 9
gtagttttggaagaactattatattgttttgttttctaaatgaaatatcagttatcttacaatatttatcttgtccttaaaaattcgatttcctgtaatcagaaggaat-ttagtcatttgttctattgcttgtatcttggctgtgatatt-taactctttgcatctttagGTATGTTGCAACTTCAGTTACTTCAGTTCATGAGATGGAAAATGGCTTTAACATATGGTCCTTCAACGGCAAGCTCCTGTATCGGATACTAAAGGATCAC
                                                              ||| | |||     ||       | |    | ||| ||| |  |  | || |  |    |     |   ||||     |   |||| ||  ||||| ||   ||   || ||| | || ||| ||||||| ||||||||||| ||||| ||||||||| | |||||||||||||  |||||||  || ||   | |   ||||||||| 
-------------------------------------------------------------gtatatttctaaattttgg-----ccacagtcagtagtcatactgtgtcttgggtacccatagccctaaatgtact---gaaatgattttgcaactccttttgtcc--agATATCTCGCGACTGCAGTTACCTCAGTTCATGAAATGGAGAATGGCTTTCAAATATGGTCCTTCAGTGGCAAGCATCTTTACAAGGTGTCAAAGGATCAT

upper sequence: Vv04s0008g07070.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: AT5G27640.1 (Arabidopsis thaliana), 3'ss of exon 10
gtagttttggaagaactattatattgttttgttttctaaatgaaatatcagttatcttacaatatttatcttgtccttaaaaattcgatttcctgtaatcagaaggaatttagtcatttgttctatt-gcttgtatcttggctgtgatatttaactctttgcatctttagGTATGTTGCAACTTCAGTTACTTCAGTTCATGAGATGGAAAATGGCTTTAACATATGGTCCTTCAACGGCAAGCTCCTGTATCGGATACTAAAGGATCAC
                                                                                   | | | |  || |||  | ||  | |    |  ||  ||||||| | |   ||    | |||  | |  |  | |||   |    ||||| ||||||||  |||| || ||||| ||||||||||| ||||| || | ||||||||| |||||||| |   | || || |||||| | |||||||| 
----------------------------------------------------------------------------------gtcctactgtct-taacta-aaccagtcctttggttgtttctatttgttccaattgctgatgttgtttgcacttttttattttcaaagGTACGTTGCAACCGCAGTGACATCAGTCCATGAGATGGAGAATGGGTTCACCATATGGTCTTTCAACGGGATTATGCTTTACCGGATATTGAAGGATCAT
















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|349828093|gb|FQ415421.1|FQ415421
EST:     ACTGCTGAACATTTCATGGCTACAGATATTGAATGGGATCCTACTGGAAG                         GTATGTTGCAACTTCAGTTACTTCAGTTCATGAGATGGAAAATGGCTTCAA
genomic: ACTGCTGAACATTTCATGGCTACAGATATTGAATGGGATCCTACTGGAAGgtagttttgg ... gcatctttagGTATGTTGCAACTTCAGTTACTTCAGTTCATGAGATGGAAAATGGCTTTAA
EST: gi|351017906|gb|FQ439072.1|FQ439072
EST:     ACTGCTGAACATTTCATGGCTACAGATATTGAATGGGATCCTACTGGAAG                         GTATGTTGCAACTTCAGTTACTTCAGTTCATGAGATGGAAAATGGCTTCAA
genomic: ACTGCTGAACATTTCATGGCTACAGATATTGAATGGGATCCTACTGGAAGgtagttttgg ... gcatctttagGTATGTTGCAACTTCAGTTACTTCAGTTCATGAGATGGAAAATGGCTTTAA
EST: gi|71866867|gb|DT015922.1|DT015922
EST:     ACTGCTGAACATTTCATGGCTACAGATATTGAATGGGATCCTACTGGAAG                         GTATGTTGCAACTTCAGTTACTTCAGTTCATGAGATGGAAAATGGCTTCAA
genomic: ACTGCTGAACATTTCATGGCTACAGATATTGAATGGGATCCTACTGGAAGgtagttttgg ... gcatctttagGTATGTTGCAACTTCAGTTACTTCAGTTCATGAGATGGAAAATGGCTTTAA
EST: gi|26267174|gb|CA818237.1|CA818237
EST:     ACTGCTGAACATTTCATGGCTACAGATATTGAATGGGATCCTACTGGAAG                         GTATGTTGCAACTTCAGTTACTTCAGTTCATGAGATGGAAAATGGCTTCAA
genomic: ACTGCTGAACATTTCATGGCTACAGATATTGAATGGGATCCTACTGGAAGgtagttttgg ... gcatctttagGTATGTTGCAACTTCAGTTACTTCAGTTCATGAGATGGAAAATGGCTTTAA
EST: gi|351030721|gb|FQ438559.1|FQ438559
EST:     ACTGCTGAACATTTCATGGCTACAGATATTGAATGGGATCCTACTGGAAG                         GTATGTTGCAACTTCAGTTACTTCAGTTCATGAGATGGAAAATGGCTTCAA
genomic: ACTGCTGAACATTTCATGGCTACAGATATTGAATGGGATCCTACTGGAAGgtagttttgg ... gcatctttagGTATGTTGCAACTTCAGTTACTTCAGTTCATGAGATGGAAAATGGCTTTAA
EST: gi|71868401|gb|DT017456.1|DT017456
EST:     ACTGCTGAACATTTCATGGCTACAGATATTGAATGGGATCCTACTGGAAG                         GTATGTTGCAACTTCAGTTACTTCAGTTCATGAGATGGAAAATGGCTTCAA
genomic: ACTGCTGAACATTTCATGGCTACAGATATTGAATGGGATCCTACTGGAAGgtagttttgg ... gcatctttagGTATGTTGCAACTTCAGTTACTTCAGTTCATGAGATGGAAAATGGCTTTAA
EST: gi|351013418|gb|FQ425449.1|FQ425449
EST:     ACTGCTGAACATTTCATGGCTACAGATATTGAATGGGATCCTACTGGAAG                         GTATGTTGCAACTTCAGTTACTTCAGTTCATGAGATGGAAAATGGCTTCAA
genomic: ACTGCTGAACATTTCATGGCTACAGATATTGAATGGGATCCTACTGGAAGgtagttttgg ... gcatctttagGTATGTTGCAACTTCAGTTACTTCAGTTCATGAGATGGAAAATGGCTTTAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catttgttctattgcttgtatcttggctgtgatatttaactctttgcatctttagGTATGTTGCAACTTCAGTTACTTCAGTTCATGAGATGGAAAATGGCTTTAACATATGGTCCTTCAACGGCAAGCTCCTGTATCGGATACTAAAGGATCAC
                                 atttaac  putative branch site (score: 3)
                                       ctctttgcatcttt  CT-rich tract
                               atatttaactcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagttttggaagaactattatattgttttgttttctaaatgaaatatcagttatcttacaatatttatcttgtccttaaaaattcgatttcctgtaatcagaaggaatttagtcatttgttctattgcttgtatcttggctgtgatatttaactctttgcatctttagGTATGTTGCAACTTCAGTTACTTCAGTTCATGAGATGGAAAATGGCTTTAACATATGGTCCTTCAACGGCAAGCTCCTGTATCGGATACTAAAGGATCAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT