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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atcacaaactctgaactctagaggataacttcttgtgtgctctataatgtatgcttcttaaattttatttttctctaccttatcttttatttgcattcagTGAGGTGGCTAAAGCAGTTGCACGGATCATAGCTCTTGCCCTTGACCTTGAACGTGATTTCTTTGATAAACCAGAAATGCTTGGTGACCCTATTGCAACC

Basic information

species Vitis vinifera
transcript Vv11s0016g03200.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv11s0016g03200.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os01g09300.3 (Oryza sativa), 3'ss of exon 4
-------atcacaaactctgaactctagaggataacttcttgtg-tgctctataatgtatgcttcttaaattttatttttctctaccttatcttttatttgcattcagTGAGGTGGCTAAAGCAGTTGCACGGATCATAGCTCTTGCCCTTGACCTTGAACGTGATTTCTTTGATAAACCAGAAATGCTTGGTGACCCTATTGCAACC
|| | || |||| || | || || || | ||| |||||| | |||||| || | | | | || || | || || || | | |||||| |||||| ||| || ||||| |||| || || ||||| || |||| ||| || |||||||||||||||||||||||||| || || || || ||
ctagccgttctctaaacctga-ctttgcag--caagttttggtgatgctctttt-tgtatgatttattactgtaatgatt---tgatttgcattctaat-gaattcagGAGGGTGGCAAAATCAATTGCAAGGATTATTGCCCTTGCTCTAAACCTAGAAGAGGACTTCTTTGATAAACCAGAAATGCTTGGCGAGCCCATAGCCACA
















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|71860593|gb|DT009648.1|DT009648
EST:     CGCTTGCCAGAATGGAGGCAGACTATGGAGAAATTCCATCAAGAGGCGCT                         TGAGGTGGCTAAAGCAGTTGCACGGATCATAGCTCTTGCTCTTGACCTTGA
genomic: CGCTTGCCAGAATGGAGGCAGACTATGGAGAAATTCCATCAAGAGGCGCTgtaagttctg ... ttgcattcagTGAGGTGGCTAAAGCAGTTGCACGGATCATAGCTCTTGCCCTTGACCTTGA
EST: gi|71862772|gb|DT011827.1|DT011827
EST:     CGCTTGCCAGAATGGAGGCAGACTATGGAGAAATTCCATCAAGAGGCGCT                         TGAGGTGGCTAAAGCAGTTGCACGGATCATAGCTCTTGCTCTTGACCTTGA
genomic: CGCTTGCCAGAATGGAGGCAGACTATGGAGAAATTCCATCAAGAGGCGCTgtaagttctg ... ttgcattcagTGAGGTGGCTAAAGCAGTTGCACGGATCATAGCTCTTGCCCTTGACCTTGA
EST: gi|71861743|gb|DT010798.1|DT010798
EST:     CGCTTGCCAGAATGGAGGCAGACTATGGAGAAATTCCATCAAGAGGCGCT                         TGAGGTGGCTAAAGCAGTTGCACGGATCATAGCTCTTGCTCTTGACCTTGA
genomic: CGCTTGCCAGAATGGAGGCAGACTATGGAGAAATTCCATCAAGAGGCGCTgtaagttctg ... ttgcattcagTGAGGTGGCTAAAGCAGTTGCACGGATCATAGCTCTTGCCCTTGACCTTGA
EST: gi|71862499|gb|DT011554.1|DT011554
EST:     CGCTTGCCAGAATGGAGGCAGACTATGGAGAAATTCCATCAAGAGGCGCT                         TGAGGTGGCTAAAGCAGTTGCACGGATCATAGCTCTTGCTCTTGACCTTGA
genomic: CGCTTGCCAGAATGGAGGCAGACTATGGAGAAATTCCATCAAGAGGCGCTgtaagttctg ... ttgcattcagTGAGGTGGCTAAAGCAGTTGCACGGATCATAGCTCTTGCCCTTGACCTTGA
EST: gi|71881554|gb|DT030609.1|DT030609
EST:     TGGAGAAATTCCATCAAGAGGCGCT                         TGAGGTGGCTAAAGCAGTTGCGCGGATCATAGCTCTTGCCCTTGACCTTGA
genomic: TGGAGAAATTCCATCAAGAGGCGCTgtaagttctg ... ttgcattcagTGAGGTGGCTAAAGCAGTTGCACGGATCATAGCTCTTGCCCTTGACCTTGA
EST: gi|71864491|gb|DT013546.1|DT013546
EST:     CGCTTGCCAGAATGGAGGCAGACTATGGAGAAATTCCATCAAGAGGCGCT                         TGAGGTGGCTAAAGCAGTTGCACGGATCATAGCTCTTGCTCTTGACCTTGA
genomic: CGCTTGCCAGAATGGAGGCAGACTATGGAGAAATTCCATCAAGAGGCGCTgtaagttctg ... ttgcattcagTGAGGTGGCTAAAGCAGTTGCACGGATCATAGCTCTTGCCCTTGACCTTGA
EST: gi|71887181|gb|DT036236.1|DT036236
EST:     TGGAGAAATTCCATCAAGAGGCGCT                         TGAGGTGGCTAAAGCAGTTGCGCGGATCATAGCTCTTGCCCTTGACCTTGA
genomic: TGGAGAAATTCCATCAAGAGGCGCTgtaagttctg ... ttgcattcagTGAGGTGGCTAAAGCAGTTGCACGGATCATAGCTCTTGCCCTTGACCTTGA
EST: gi|71864483|gb|DT013538.1|DT013538
EST:     CGCTTGCCAGAATGGAGGCAGACTATGGAGAAATTCCATCAAGAGGCGCT                         TGAGGTGGCTAA
genomic: CGCTTGCCAGAATGGAGGCAGACTATGGAGAAATTCCATCAAGAGGCGCTgtaagttctg ... ttgcattcagTGAGGTGGCTAA
EST: gi|77589174|gb|DV223847.1|DV223847
EST:     TGGAGAAATTCCATCAAGAGGCGCT                         TGAGGTGGCTAAAGCAGTTGCGCGGATCATAGCTCTTGCCCTTGACCTTGA
genomic: TGGAGAAATTCCATCAAGAGGCGCTgtaagttctg ... ttgcattcagTGAGGTGGCTAAAGCAGTTGCACGGATCATAGCTCTTGCCCTTGACCTTGA
EST: gi|71863373|gb|DT012428.1|DT012428
EST:     CGCTTGCCAGAATGGAGGCAGACTATGGAGAAATTCCATCAAGAGGCGCT                         TGAGGTGGCTAAAGCAGTTGCACGGATCATAGCTCTTGCTCTTGACCTTGA
genomic: CGCTTGCCAGAATGGAGGCAGACTATGGAGAAATTCCATCAAGAGGCGCTgtaagttctg ... ttgcattcagTGAGGTGGCTAAAGCAGTTGCACGGATCATAGCTCTTGCCCTTGACCTTGA
EST: gi|294965788|gb|GW839243.1|GW839243
EST:     CGCTTGCCAGAATGGAGGCAGACTATGGAGAAATTCCATCAAGAGGCGCT                         TGAGGTGGCTAAAGCAGTTGCACGGATCATAGCTCTTGCCCTTGACCTTGA
genomic: CGCTTGCCAGAATGGAGGCAGACTATGGAGAAATTCCATCAAGAGGCGCTgtaagttctg ... ttgcattcagTGAGGTGGCTAAAGCAGTTGCACGGATCATAGCTCTTGCCCTTGACCTTGA
EST: gi|110690968|gb|EE068534.1|EE068534
EST:     CGCTTGCCAGAATGGAGGCAGACTATGGAGAAATTCCATCAAGAGGCGCT                         TGAGGTGGCTAAAGCAGTTGCACGGATCATAGCTCTTGCCCTTGACCTTGA
genomic: CGCTTGCCAGAATGGAGGCAGACTATGGAGAAATTCCATCAAGAGGCGCTgtaagttctg ... ttgcattcagTGAGGTGGCTAAAGCAGTTGCACGGATCATAGCTCTTGCCCTTGACCTTGA
EST: gi|71884795|gb|DT033850.1|DT033850
EST:     TGGAGAAATTCCATCAAGAGGCGCT                         TGAGGTGGCTAAAGCAGTTGCGCGGATCATAGCTCTTGCCCTTGACCTTGA
genomic: TGGAGAAATTCCATCAAGAGGCGCTgtaagttctg ... ttgcattcagTGAGGTGGCTAAAGCAGTTGCACGGATCATAGCTCTTGCCCTTGACCTTGA
EST: gi|110404543|gb|EC969762.1|EC969762
EST:     CGCTTGCCAGAATGGAGGCAGACTATGGAGAAATTCCATCAAGAGGCGCT                         TGAGGTGGCTAAAGCAGTTGCACGGATCATAGCTCTTGCCCTTGACCTTGA
genomic: CGCTTGCCAGAATGGAGGCAGACTATGGAGAAATTCCATCAAGAGGCGCTgtaagttctg ... ttgcattcagTGAGGTGGCTAAAGCAGTTGCACGGATCATAGCTCTTGCCCTTGACCTTGA
EST: gi|71863525|gb|DT012580.1|DT012580
EST:     CGCTTGCCAGAATGGAGGCAGACTATGGAGAAATTCCATCAAGAGGCGCT                         TGAGGTGGCTAAAGCAGTTGCACGGATCATAGCTCTTGCCCTTGACCTTGA
genomic: CGCTTGCCAGAATGGAGGCAGACTATGGAGAAATTCCATCAAGAGGCGCTgtaagttctg ... ttgcattcagTGAGGTGGCTAAAGCAGTTGCACGGATCATAGCTCTTGCCCTTGACCTTGA
EST: gi|71884047|gb|DT033102.1|DT033102
EST:     TGGAGAAATTCCATCAAGAGGCGCT                         TGAGGTGGCTAAAGCAGTTGCGCGGATCATAGCTCTTGCCCTTGACCTTGA
genomic: TGGAGAAATTCCATCAAGAGGCGCTgtaagttctg ... ttgcattcagTGAGGTGGCTAAAGCAGTTGCACGGATCATAGCTCTTGCCCTTGACCTTGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatgtatgcttcttaaattttatttttctctaccttatcttttatttgcattcagTGAGGTGGCTAAAGCAGTTGCACGGATCATAGCTCTTGCCCTTGACCTTGAACGTGATTTCTTTGATAAACCAGAAATGCTTGGTGACCCTATTGCAACC
                 ttttatttttctctac  CT-rich tract
 ttaaattttatttttc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atcacaaactctgaactctagaggataacttcttgtgtgctctataatgtatgcttcttaaattttatttttctctaccttatcttttatttgcattcagTGAGGTGGCTAAAGCAGTTGCACGGATCATAGCTCTTGCCCTTGACCTTGAACGTGATTTCTTTGATAAACCAGAAATGCTTGGTGACCCTATTGCAACC

- - caaactc
- - - - - - - - - - -aggataa
- - - - - - - - - - - - - - - - -tgtgtgc
- - - - - - - - - - - - - - - - - - - - - - - - gtatgct