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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgcaatctgctgttacaaagaatgatttgtcaaaacttaaatattttttccaactgatttattagaataaactttctgcattaatgcagGCTGGAGCCTGTAATCATTGAGCTTGAACGGCAACGAGCACCTGTTGTAGTGATATCTCACCAG

Basic information

species Vitis vinifera
transcript Vv06s0004g06920.t01
intron # 20
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0004g06920.t01 (Vitis vinifera), 3'ss of exon 20
lower sequence: LOC_Os03g18310.1 (Oryza sativa), 3'ss of exon 19
-----------gtttgcaatctgctgttacaaagaatgatttgtcaaaacttaaatattttttcca--actgattta-ttagaataaactttctgcattaatgcagGCTGGAGCCTGTAATCATTGAGCTTGAACGGCAACGAGCACCTGTTGTAGTGATATCTCACCAG
            | ||  |  |  |   |   |||   || |  |  || | |  |||| |  | |  |  | |  | ||    |  ||  ||| |  |  | |||  | || |||||||| ||||||||||||||||| || || || ||||| || ||||||||||||
gttaattcaggctatgtgaaattatcacatgcagacatatattacgtaattcacctattgtaactattatcggtgcactttatctttacagtcttctctgtt-cagATTAGAACCTGTAATTATTGAGCTTGAACGGCAGCGTGCTCCAGTTGTTGTCATATCTCACCAG

upper sequence: Vv06s0004g06920.t01 (Vitis vinifera), 3'ss of exon 20
lower sequence: GLYMA14G37520.1 (Glycine max), 3'ss of exon 31
gtttgcaatctgctgttacaaagaatgatttgtcaaaacttaaatattttttccaactgatttattagaataaactttctgcattaatgcagGCTGGAGCCTGTAATCATTGAGCTTGAACGGCAACGAGCACCTGTTGTAGTGATATCTCACCAG
||          ||  |   || | |  || ||   ||   |  || ||  |  |  | | | | | ||||    |||    | ||||||||| | || |||||||| ||||||||||| || ||||||||||||||||| |||||||||||||||
gtagatgcatcacttcttttaacattatttagttccaaaccac-tacttgcttgatgtaaataacttgaat----ttttaataataatgcagGTTAGAACCTGTAATTATTGAGCTTGAGCGACAACGAGCACCTGTTGTTGTGATATCTCACCAG

upper sequence: Vv06s0004g06920.t01 (Vitis vinifera), 3'ss of exon 20
lower sequence: GLYMA02G39390.1 (Glycine max), 3'ss of exon 20
gtttgcaatctgctgttacaaagaatgatttgtcaaaacttaaatattttttccaactgatttattagaataaactttctgcattaatgcagGCTGGAGCCTGTAATCATTGAGCTTGAACGGCAACGAGCACCTGTTGTAGTGATATCTCACCAG
||        | ||  |   || | |  || ||   ||      || || ||     |||| ||      | || |||    | ||||||||| | || |||||||| ||||| ||||| || ||||||||||||||||| |||||||||||||||
gtagatgcattacttcttttaacattatttagttccaaac-ggctacttgtt-----tgatgtaaataggttaaattttaataataatgcagGTTAGAACCTGTAATTATTGAACTTGAGCGACAACGAGCACCTGTTGTTGTGATATCTCACCAG

upper sequence: Vv06s0004g06920.t01 (Vitis vinifera), 3'ss of exon 20
lower sequence: GLYMA11G27870.1 (Glycine max), 3'ss of exon 21
gtttgcaatctgctgttacaaagaatgatttgtcaaaacttaaatattttttccaactgatttattagaataaactttctgcattaatgcagGCTGGAGCCTGTAATCATTGAGCTTGAACGGCAACGAGCACCTGTTGTAGTGATATCTCACCAG
   |  | | |    ||| ||| | |  || ||     |||   |    || | |   ||| ||    | | || |||  | | |||| |||  | || |||||||| || |||||||| || ||||||||||||||||| |||||||||||||||
--gtatattttatc-ttataaatattatttagttc---cttgcttcaacttgcta---gatataaataactcaagttttagtaataatacagATTAGAACCTGTAATTATAGAGCTTGAGCGCCAACGAGCACCTGTTGTTGTGATATCTCACCAG

upper sequence: Vv06s0004g06920.t01 (Vitis vinifera), 3'ss of exon 20
lower sequence: GLYMA18G06770.1 (Glycine max), 3'ss of exon 22
gtttgcaatctgctgttacaaagaatgatttgtcaaaacttaaatattttttccaactgatttattagaataaactttctgcattaatgcagGCTGGAGCCTGTAATCATTGAGCTTGAACGGCAACGAGCACCTGTTGTAGTGATATCTCACCAG-
   |  | | |    ||| ||| | |  ||      | ||    |  |         |||| ||    | | || |||  | | |||| |||| | || |||||||| || |||||||| || ||||||||||||||||| ||||||||||||||| 
---tatattttatc-ttataaacattattt------agctcctttcctcaacttgtttgatataaataactcaagttttagtaataatacaggTTAGAACCTGTAATTATAGAGCTTGAGCGACAACGAGCACCTGTTGTTGTGATATCTCACCAGG

upper sequence: Vv06s0004g06920.t01 (Vitis vinifera), 3'ss of exon 20
lower sequence: GLYMA11G27410.1 (Glycine max), 3'ss of exon 27
gtttgcaatctgctgttacaaagaatgatttgtcaaaacttaaatattttttccaactgatttattagaataaactttctgcattaatgcagGCTGGAGCCTGTAATCATTGAGCTTGAACGGCAACGAGCACCTGTTGTAGTGATATCTCACCAG
   |  | | |    ||| ||| | |  || ||     |||   |    || |    |||| ||    | | || |||  | | |||| |||  | || |||||||| || |||||| | || ||||||||||||||||| |||||||||||||||
--gtatattttatc-ttataaatattatttagttc---cttgcttcaacttgct---tgatataaataactcaagttttagtaataatacagATTAGAACCTGTAATTATAGAGCTTAAGCGCCAACGAGCACCTGTTGTTGTGATATCTCACCAG

upper sequence: Vv06s0004g06920.t01 (Vitis vinifera), 3'ss of exon 20
lower sequence: AT1G07110.1 (Arabidopsis thaliana), 3'ss of exon 20
gtttgcaatctgctgttacaaagaatgatttgtcaaaacttaaatattttttccaactgatttattagaataaactttctgcattaatgcagGCTGGAGCCTGTAATCATTGAGCTTGAACGGCAACGAGCACCTGTTGTAGTGATATCTCACCAG
   |    ||| || ||  |     |  |  || ||  | ||||          |||    | |  | ||||    | ||     |||||||||| || ||||| ||||||||| | ||||| ||| |||| ||||| || |||||||||||||||
--gtatgttcttctcttctacttctttctacgtgaagtcataaac-------taaacc---tcaggaaaatatcgctactttgacaatgcagGCTTGAACCTGTGATCATTGAGTTAGAACGACAAAGAGCTCCTGTCGTCGTGATATCTCACCAG

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|352764397|gb|FQ472754.1|FQ472754
EST:     CTGAGGTATCGGTATCCTCGTGGTGAATCTTACCTGGATGTTATCCAAAG                         GCTGGAGCCTGTAATCATTGAGCTTGAACGGCAACGAGCACCTGTTGTAGT
genomic: CTGAGGTATCGGTATCCTCGTGGTGAATCTTACCTGGATGTTATCCAAAGgtttgcaatc ... attaatgcagGCTGGAGCCTGTAATCATTGAGCTTGAACGGCAACGAGCACCTGTTGTAGT
EST: gi|71882349|gb|DT031404.1|DT031404
EST:     CTGAGGTATCGGTATCCTCGTGGTGAATCTTACCTGGATGTTATCCAAAG                         GCTGGAGCCTGTAATCATTGAGCTTGAACGGCAACGAGCACCTGTTGTAGT
genomic: CTGAGGTATCGGTATCCTCGTGGTGAATCTTACCTGGATGTTATCCAAAGgtttgcaatc ... attaatgcagGCTGGAGCCTGTAATCATTGAGCTTGAACGGCAACGAGCACCTGTTGTAGT
EST: gi|352769630|gb|FQ468558.1|FQ468558
EST:     CTGAGGTATCGGTATCCTCGTGGTGAATCTTACCTGGATGTTATCCAAAG                         GCTGGAGCCTGTAATCATTGAGCTTGAACGGCAACGAGCACCTGTTGTAGT
genomic: CTGAGGTATCGGTATCCTCGTGGTGAATCTTACCTGGATGTTATCCAAAGgtttgcaatc ... attaatgcagGCTGGAGCCTGTAATCATTGAGCTTGAACGGCAACGAGCACCTGTTGTAGT
EST: gi|71888454|gb|DT037509.1|DT037509
EST:     CTGAGGTATCGGTATCCTCGTGGTGAATCTTACCTGGATGTTATCCAAAG                         GCTGGAGCCTGTAATCATTGAGCTTGAACGGCAACGAGCACCTGTTGTAGT
genomic: CTGAGGTATCGGTATCCTCGTGGTGAATCTTACCTGGATGTTATCCAAAGgtttgcaatc ... attaatgcagGCTGGAGCCTGTAATCATTGAGCTTGAACGGCAACGAGCACCTGTTGTAGT
EST: gi|352768928|gb|FQ468119.1|FQ468119
EST:     CTGAGGTATCGGTATCCTCGTGGTGAATCTTACCTGGATGTTATCCAAAG                         GCTGGAGCCTGTAATCATTGAGCTTGAACGGCAACGAGCACCTGTTGTAGT
genomic: CTGAGGTATCGGTATCCTCGTGGTGAATCTTACCTGGATGTTATCCAAAGgtttgcaatc ... attaatgcagGCTGGAGCCTGTAATCATTGAGCTTGAACGGCAACGAGCACCTGTTGTAGT
EST: gi|71889378|gb|DT038433.1|DT038433
EST:     CTGAGGTATCGGTATCCTCGTGGTGAATCTTACCTGGATGTTATCCAAAG                         GCTGGAGCCTGTAATCATTGAGCTTGAACGGCAACGAGCACCTGTTGTAGT
genomic: CTGAGGTATCGGTATCCTCGTGGTGAATCTTACCTGGATGTTATCCAAAGgtttgcaatc ... attaatgcagGCTGGAGCCTGTAATCATTGAGCTTGAACGGCAACGAGCACCTGTTGTAGT
EST: gi|71887336|gb|DT036391.1|DT036391
EST:     CTGAGGTATCGGTATCCTCGTGGTGAATCTTACCTGGATGTTATCCAAAG                         GCTGGAGCCTGTAATCATTGAGCTTGAACGGCAACGAGCACCTGTTGTAGT
genomic: CTGAGGTATCGGTATCCTCGTGGTGAATCTTACCTGGATGTTATCCAAAGgtttgcaatc ... attaatgcagGCTGGAGCCTGTAATCATTGAGCTTGAACGGCAACGAGCACCTGTTGTAGT
EST: gi|71887343|gb|DT036398.1|DT036398
EST:     CTGAGGTATCGGTATCCTCGTGGTGAATCTTACCTGGATGTTATCCAAAG                         GCTGGAGCCTGTAATCATTGAGCTTGAACGGCAACGAGCACCTGTTGTAGT
genomic: CTGAGGTATCGGTATCCTCGTGGTGAATCTTACCTGGATGTTATCCAAAGgtttgcaatc ... attaatgcagGCTGGAGCCTGTAATCATTGAGCTTGAACGGCAACGAGCACCTGTTGTAGT
EST: gi|71890359|gb|DT039414.1|DT039414
EST:     CTGAGGTATCGGTATCCTCGTGGTGAATCTTACCTGGATGTTATCCAAAG                         GCTGGAGCCTGTAATCATTGAGCTTGAACGGCAACGAGCACCTGTTGTAGT
genomic: CTGAGGTATCGGTATCCTCGTGGTGAATCTTACCTGGATGTTATCCAAAGgtttgcaatc ... attaatgcagGCTGGAGCCTGTAATCATTGAGCTTGAACGGCAACGAGCACCTGTTGTAGT
EST: gi|34362375|gb|CF403960.1|CF403960
EST:     CTGAGGTATCGGTATCCTCGTGGTGAATCTTACCTGGATGTTATCCAAAG                         GCTGGAGCCTGTAATCATTGAGCTTGAACGGCAACGAGCACCTGTTGTAGT
genomic: CTGAGGTATCGGTATCCTCGTGGTGAATCTTACCTGGATGTTATCCAAAGgtttgcaatc ... attaatgcagGCTGGAGCCTGTAATCATTGAGCTTGAACGGCAACGAGCACCTGTTGTAGT
EST: gi|71887083|gb|DT036138.1|DT036138
EST:     TTACCTGGATGTTATCCAAAG                         GCTGGAGCCTGTAATCATTGAGCTTGAACGGCAACGAGCACCTGTTGTAGT
genomic: TTACCTGGATGTTATCCAAAGgtttgcaatc ... attaatgcagGCTGGAGCCTGTAATCATTGAGCTTGAACGGCAACGAGCACCTGTTGTAGT
EST: gi|110360631|gb|EC923892.1|EC923892
EST:     CTGAGGTATCGGTATCCTCGTGGTGAATCTTACCTGGATGTTATCCAAAG                         GCTGGAGCCTGTAATCATTGAGCTTGAACGGCAACGAGCACCTGTTGTAGT
genomic: CTGAGGTATCGGTATCCTCGTGGTGAATCTTACCTGGATGTTATCCAAAGgtttgcaatc ... attaatgcagGCTGGAGCCTGTAATCATTGAGCTTGAACGGCAACGAGCACCTGTTGTAGT
EST: gi|110415443|gb|EC981352.1|EC981352
EST:     CTGAGGTATCGGTATCCTCGTGGTGAATCTTACCTGGATGTTATCCAAAG                         GCTGGAGCCTGTAATCATTGAGCTTGAACGGCAACGAGCACCTGTTGTAGT
genomic: CTGAGGTATCGGTATCCTCGTGGTGAATCTTACCTGGATGTTATCCAAAGgtttgcaatc ... attaatgcagGCTGGAGCCTGTAATCATTGAGCTTGAACGGCAACGAGCACCTGTTGTAGT
EST: gi|77581485|gb|DV219679.1|DV219679
EST:     CTGAGGTATCGGTATCCTCGTGGTGAATCTTACCTGGATGTTATCCAAAG                         GCTGGAGCCTGTAATCATTGAGCTTGAACGGCAACGAGCACCTGTTGTAGT
genomic: CTGAGGTATCGGTATCCTCGTGGTGAATCTTACCTGGATGTTATCCAAAGgtttgcaatc ... attaatgcagGCTGGAGCCTGTAATCATTGAGCTTGAACGGCAACGAGCACCTGTTGTAGT
EST: gi|352781433|gb|FQ468277.1|FQ468277
EST:     CTGAGGTATCGGTATCCTCGTGGTGAATCTTACCTGGATGTTATCCAAAG                         GCTGGAGCCTGTAATCATTGAGCTTGAACGGCAACGAGCACCTGTTGTAGT
genomic: CTGAGGTATCGGTATCCTCGTGGTGAATCTTACCTGGATGTTATCCAAAGgtttgcaatc ... attaatgcagGCTGGAGCCTGTAATCATTGAGCTTGAACGGCAACGAGCACCTGTTGTAGT
EST: gi|71888451|gb|DT037506.1|DT037506
EST:     CTGAGGTATCGGTATCCTCGTGGTGAATCTTACCTGGATGTTATCCAAAG                         GCTGGAGCCTGTAATCATTGAGCTTGAACGGCAACGAGCACCTGTTGTAGT
genomic: CTGAGGTATCGGTATCCTCGTGGTGAATCTTACCTGGATGTTATCCAAAGgtttgcaatc ... attaatgcagGCTGGAGCCTGTAATCATTGAGCTTGAACGGCAACGAGCACCTGTTGTAGT
EST: gi|71881182|gb|DT030237.1|DT030237
EST:     CTGAGGTATCGGTATCCTCGTGGTGAATCTTACCTGGATGTTATCCAAAG                         GCTGGAGCCTGTAATCATTGAGCTTGAACGGCAACGAGCACCTGTTGTAGT
genomic: CTGAGGTATCGGTATCCTCGTGGTGAATCTTACCTGGATGTTATCCAAAGgtttgcaatc ... attaatgcagGCTGGAGCCTGTAATCATTGAGCTTGAACGGCAACGAGCACCTGTTGTAGT
EST: gi|71885715|gb|DT034770.1|DT034770
EST:     CTGAGGTATCGGTATCCTCGTGGTGAATCTTACCTGGATGTTATCCAAAG                         GCTGGAGCCTGTAATCATTGAGCTTGAACGGCAACGAGCACCTGTTGTAGT
genomic: CTGAGGTATCGGTATCCTCGTGGTGAATCTTACCTGGATGTTATCCAAAGgtttgcaatc ... attaatgcagGCTGGAGCCTGTAATCATTGAGCTTGAACGGCAACGAGCACCTGTTGTAGT
EST: gi|27582400|gb|CB005095.1|CB005095
EST:     CTGAGGTATCGGTATCCTCGTGGTGAATCTTACCTGGATGTTATCCAAAG                         GCTGGAGCCTGTAATCATTGAGCTTGAACGGCAACGAGCACCTGTTGTAGT
genomic: CTGAGGTATCGGTATCCTCGTGGTGAATCTTACCTGGATGTTATCCAAAGgtttgcaatc ... attaatgcagGCTGGAGCCTGTAATCATTGAGCTTGAACGGCAACGAGCACCTGTTGTAGT
EST: gi|352774206|gb|FQ474729.1|FQ474729
EST:     CTGAGGTATCGGTATCCTCGTGGTGAATCTTACCTGGATGTTATCCAAAG                         GCTGGAGCCTGTAATCATTGAGCTTGAACGGCAACGAGCACCTGTTGTAGT
genomic: CTGAGGTATCGGTATCCTCGTGGTGAATCTTACCTGGATGTTATCCAAAGgtttgcaatc ... attaatgcagGCTGGAGCCTGTAATCATTGAGCTTGAACGGCAACGAGCACCTGTTGTAGT
EST: gi|352768854|gb|FQ468045.1|FQ468045
EST:     CTGAGGTATCGGTATCCTCGTGGTGAATCTTACCTGGATGTTATCCAAAG                         GCTGGAGCCTGTAATCATTGAGCTTGAACGGCAACGAGCACCTGTTGTAGT
genomic: CTGAGGTATCGGTATCCTCGTGGTGAATCTTACCTGGATGTTATCCAAAGgtttgcaatc ... attaatgcagGCTGGAGCCTGTAATCATTGAGCTTGAACGGCAACGAGCACCTGTTGTAGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acttaaatattttttccaactgatttattagaataaactttctgcattaatgcagGCTGGAGCCTGTAATCATTGAGCTTGAACGGCAACGAGCACCTGTTGTAGTGATATCTCACCAG
                                            cattaat  putative branch site (score: 3)
                    tgatttattagaataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgcaatctgctgttacaaagaatgatttgtcaaaacttaaatattttttccaactgatttattagaataaactttctgcattaatgcagGCTGGAGCCTGTAATCATTGAGCTTGAACGGCAACGAGCACCTGTTGTAGTGATATCTCACCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT