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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCACATTGAGCAGTGGATTGATTTTGCATCATTGGAGATTGATGCTAATATTGGGCATTGGTTTAGACCAAGGATTGGACGTGCTGTATACCTTCCACCGgttggtccattatcatctttaataatttttctcatttctctgctatgcttcactccacgcctagaggcaagaaaggaaagggggttgggtggaatcaata...

Basic information

species Vitis vinifera
transcript Vv12s0035g01130.t01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv12s0035g01130.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA17G00470.4 (Glycine max), 5'ss of exon 5
CCACATTGAGCAGTGGATTGATTTTGCATCATTGGAGATTGATGCTAATATTGGGCATTGGTTTAGACCAAGGATTGGACGTGCTGTATACCTTCCACCGgttggtc-cattatcatctttaataatttttctcatttctctgctatgcttcactccacgcctagaggcaagaaaggaaagggggttgggtggaatcaata-
||||||||| ||||||||||||||| ||||||||||||||||||||||||||    | |||| |   |||||  ||||||| |    ||| ||||| || ||  ||  ||     || ||| ||| | |     |||  | ||  |  || ||       |||  |  ||| || |  |     |||   |        |  
CCACATTGAACAGTGGATTGATTTTTCATCATTGGAGATTGATGCTAATATTATCAAGTGGTATGCCCCAAGAGTTGGACGAGGACCATATCTTCCTCCAgtaagttacaaaggaattttttatactatggaaaattgatatgaca-actccatgttgaccctccattcaa-aatgtcagtttagttcttttatcctgttgg

upper sequence: Vv12s0035g01130.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA07G40330.1 (Glycine max), 5'ss of exon 6
CCACATTGAGCAGTGGATTGATTTTGCATCATTGGAGATTGATGCTAATATTGGGCATTGGTTTAGACCAAGGATTGGACGTGCTGTATACCTTCCACCGgttggtc-cattatcatctttaataatttttctcatttctctgctatgcttcactccacgcctagaggcaagaaaggaaagggggttgggtggaatcaata
||||||||| || |||||||||||| ||||||||||||||||||||||||||    | |||| |   |||||  ||||||| |    ||| ||||| || ||  ||  ||      | ||| ||| |   |   |||  | ||      | ||       |||  |  ||| | |         |||   |        | 
CCACATTGAACAATGGATTGATTTTTCATCATTGGAGATTGATGCTAATATTATCAAGTGGTATGCCCCAAGAGTTGGACGAGGACCATATCTTCCTCCAgtaagttacaaagaatttttttatactacgtaaaattgatatggcg-attccatgttgaccctccattcaaaatatctgttttagttcttttatcctgttg

upper sequence: Vv12s0035g01130.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA12G28670.1 (Glycine max), 5'ss of exon 5
CCACATTGAGCAGTGGATTGATTTTGCATCATTGGAGATTGATGCTAATATTGGGCATTGGTTTAGACCAAGGATTGGACGTGCTGTATACCTTCCACCGgttggtccattatcatctttaataatttttctcatttctctgctatgcttcactccacgcctagaggcaagaaaggaaagggggttgggtggaatcaata
||||||||| ||||||||||||||| |||| |||||||| ||||||||| |   | | | | |   ||||||  |||||  |||   ||||||||| || ||  | | |||    | |  | |    | |    | ||  |    ||| ||| |  | | | |      | | |  |     |  ||  || |       
CCACATTGACCAGTGGATTGATTTTTCATCCTTGGAGATCGATGCTAATCTCATGAAATTGCTCCTACCAAGACTTGGATTTGCCCCATACCTTCCTCCAgtaag-ctattgctttgtacattctagtcttgagtatccatatgttgcatca-tgtatgtccaattctgaaataatac----gtctgcatgaag------

upper sequence: Vv12s0035g01130.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA16G00360.1 (Glycine max), 5'ss of exon 5
CCACATTGAGCAGTGGATTGATTTTGCATCATTGGAGATTGATGCTAATATTGGGCATTGGTTTAGACCAAGGATTGGACGTGCTGTATACCTTCCACCGgttgg-tccattatcatctttaataatttttctcatttctctgctatgcttcac-tccacgcctagaggcaagaaaggaaagggggttgggtggaatcaata
||||||||| ||||||||||| ||| |||| |||||||| ||||||||||||  | | |  |    ||||||  |||||  |||   ||||||||| || ||  | |  ||  | |||| ||      ||||| ||   | || |||  |   | |  | | |||      | | | |||    |  ||  || |       
CCACATTGACCAGTGGATTGACTTTTCATCCTTGGAGATCGATGCTAATATTATGAAATTATACCTACCAAGACTTGGATTTGCCCCATACCTTCCTCCAgtaagctatatattgatctgta-----ctttcttatccatatgttatattcgtcatgtatgtctaattctgaaataagaataatg--tgaatgaag------

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|351055139|gb|FQ440478.1|FQ440478
EST:     TTGGGCATTGGTTTAGACCAAGGATGGGACGTGCTGTATACCTTCCACCG                         TTTGAGGAGGCTGCAATTGCTGCATTGAAGAGAGCATTAGGTGCTTTGAAC
genomic: TTGGGCATTGGTTTAGACCAAGGATTGGACGTGCTGTATACCTTCCACCGgttggtccat ... ctgtgtatagTTTGAGGAGGCTGCAATTGCTGCATTGAAGAGAGCATTAGGTGCTTTGAAC
EST: gi|110372574|gb|EC936754.1|EC936754
EST:     GGACGTGCTGTATACCTTCCACCG                         TTTGAGGAGGCTGCAATTGCTGCATTGAAGAGAGCATTAGGTGCTTTGAAC
genomic: GGACGTGCTGTATACCTTCCACCGgttggtccat ... ctgtgtatagTTTGAGGAGGCTGCAATTGCTGCATTGAAGAGAGCATTAGGTGCTTTGAAC
EST: gi|161712238|gb|FC061612.1|FC061612
EST:     TTGGGCATTGGTTTAGACCAAGGATGGGACGTGCTGTATACCTTCCACCG                         TTTGAGGAGGCTGCAATTGCTGCATTGAAGAGAGCATTAGGTGCTTTGAAC
genomic: TTGGGCATTGGTTTAGACCAAGGATTGGACGTGCTGTATACCTTCCACCGgttggtccat ... ctgtgtatagTTTGAGGAGGCTGCAATTGCTGCATTGAAGAGAGCATTAGGTGCTTTGAAC
EST: gi|110368464|gb|EC932441.1|EC932441
EST:     TTGGGCATTGGTTTAGACCAAGGATTGGACGTGCTGTATACCTTCCACCG                         TTTGAGGAGGCTGCAATTGCTGCATTGAAGAGAGCATTAGGTGCTTTGAAC
genomic: TTGGGCATTGGTTTAGACCAAGGATTGGACGTGCTGTATACCTTCCACCGgttggtccat ... ctgtgtatagTTTGAGGAGGCTGCAATTGCTGCATTGAAGAGAGCATTAGGTGCTTTGAAC
EST: gi|161719271|gb|FC068941.1|FC068941
EST:     TTGGGCATTGGTTTAGACCAAGGATTGGACGTGCTGTATACCTTCCACCG                         TTTGAGGAGGCTGCAATTGCTGCATTGAAGAGAGCATTAGGTGCTTTGAAC
genomic: TTGGGCATTGGTTTAGACCAAGGATTGGACGTGCTGTATACCTTCCACCGgttggtccat ... ctgtgtatagTTTGAGGAGGCTGCAATTGCTGCATTGAAGAGAGCATTAGGTGCTTTGAAC
EST: gi|110727170|gb|EE103626.1|EE103626
EST:     TTGGGCATTGGTTTAGACCAAGGATGGGACGTGCTGTATACCTTCCACCG                         TTTGAGGAGGCTGCAATTGCTGCATTGAAGAGAGCATTANGTGCTTTGAAC
genomic: TTGGGCATTGGTTTAGACCAAGGATTGGACGTGCTGTATACCTTCCACCGgttggtccat ... ctgtgtatagTTTGAGGAGGCTGCAATTGCTGCATTGAAGAGAGCATTAGGTGCTTTGAAC
EST: gi|351042107|gb|FQ456317.1|FQ456317
EST:     TTGGGCATTGGTTTAGACCAAGGATGGGACGTGCTGTATACCTTCCACCG                         TTTGAGGAGGCTGCAATTGCTGCATTGAAGAGAGCATTAGGTGCTTTGAAC
genomic: TTGGGCATTGGTTTAGACCAAGGATTGGACGTGCTGTATACCTTCCACCGgttggtccat ... ctgtgtatagTTTGAGGAGGCTGCAATTGCTGCATTGAAGAGAGCATTAGGTGCTTTGAAC
EST: gi|110727691|gb|EE104738.1|EE104738
EST:     TTGGGCATTGGTTTAGACCAAGGATGGGACGTGCTGTATACCTTCCACCG                         TTTGAGGAGGCTGCAATTGCTGCATTGAAGAGAGCATTAGGTGCTTTGAAC
genomic: TTGGGCATTGGTTTAGACCAAGGATTGGACGTGCTGTATACCTTCCACCGgttggtccat ... ctgtgtatagTTTGAGGAGGCTGCAATTGCTGCATTGAAGAGAGCATTAGGTGCTTTGAAC
EST: gi|351017433|gb|FQ435786.1|FQ435786
EST:     TTGGGCATTGGTTTAGACCAAGGATGGGACGTGCTGTATACCTTCCACCG                         TTTGAGGAGGCTGCAATTGCTGCATTGAAGAGAGCATTAGGTGCTTTGAAC
genomic: TTGGGCATTGGTTTAGACCAAGGATTGGACGTGCTGTATACCTTCCACCGgttggtccat ... ctgtgtatagTTTGAGGAGGCTGCAATTGCTGCATTGAAGAGAGCATTAGGTGCTTTGAAC
EST: gi|110381916|gb|EC937999.1|EC937999
EST:     TTGGGCATTGGTTTAGACCAAGGATGGGACGTGCTGTATACCTTCCACCG                         TTTGAGGAGGCTGCAATTGCTGCATTGAAGAGAGCATTAGGTGCTTTGAAC
genomic: TTGGGCATTGGTTTAGACCAAGGATTGGACGTGCTGTATACCTTCCACCGgttggtccat ... ctgtgtatagTTTGAGGAGGCTGCAATTGCTGCATTGAAGAGAGCATTAGGTGCTTTGAAC
EST: gi|37183980|gb|CF603334.1|CF603334
EST:     TTGGGCATTGGTTTAGACCAAGGATTGGACGTGCTGTATACCTTCCACCG                         TTTGAGGAGGCTGCAATTGCTGCATTGAAGAGAGCATTAGGTGCTTTGAAC
genomic: TTGGGCATTGGTTTAGACCAAGGATTGGACGTGCTGTATACCTTCCACCGgttggtccat ... ctgtgtatagTTTGAGGAGGCTGCAATTGCTGCATTGAAGAGAGCATTAGGTGCTTTGAAC
EST: gi|37183445|gb|CF602799.1|CF602799
EST:     TTGGGCATTGGTTTAGACCAAGGATTGGACGTGCTGTATACCTTCCACCG                         TTTGAGGAGGCTGCAATTGCTGCATTGAAGAGAGCATTAGGTGCTTTGAAC
genomic: TTGGGCATTGGTTTAGACCAAGGATTGGACGTGCTGTATACCTTCCACCGgttggtccat ... ctgtgtatagTTTGAGGAGGCTGCAATTGCTGCATTGAAGAGAGCATTAGGTGCTTTGAAC
EST: gi|351028342|gb|FQ427238.1|FQ427238
EST:     TTGGGCATTGGTTTAGACCAAGGATGGGACGTGCTGTATACCTTCCACCG                         TTTGAGGAGGCTGCAATTGCTGCATTGAAGAGAGCATTAGGTGCTTTGAAC
genomic: TTGGGCATTGGTTTAGACCAAGGATTGGACGTGCTGTATACCTTCCACCGgttggtccat ... ctgtgtatagTTTGAGGAGGCTGCAATTGCTGCATTGAAGAGAGCATTAGGTGCTTTGAAC
EST: gi|110374475|gb|EC939254.1|EC939254
EST:     TTGGGCATTGGTTTAGACCAAGGATGGGACGTGCTGTATACCTTCCACCG                         TTTGAGGAGGCTGCAATTGCTGCATTGAAGAGAGCATTAGGTGCTTTGAAC
genomic: TTGGGCATTGGTTTAGACCAAGGATTGGACGTGCTGTATACCTTCCACCGgttggtccat ... ctgtgtatagTTTGAGGAGGCTGCAATTGCTGCATTGAAGAGAGCATTAGGTGCTTTGAAC
EST: gi|110381825|gb|EC935490.1|EC935490
EST:     TTGGGCATTGGTTTAGACCAAGGATTGGACGTGCTGTATACCTTCCACCG                         TTTGAGGAGGCTGCAATTGCTGCATTGAAGAGAGCATTAGGTGCTTTGAAC
genomic: TTGGGCATTGGTTTAGACCAAGGATTGGACGTGCTGTATACCTTCCACCGgttggtccat ... ctgtgtatagTTTGAGGAGGCTGCAATTGCTGCATTGAAGAGAGCATTAGGTGCTTTGAAC
EST: gi|110699423|gb|EE076408.1|EE076408
EST:     TTGGGCATTGGTTTAGACCAAGGATGGGACGTGCTGTATACCTTCCACCG                         TTTGAGGAGGCTGCAATTGCTGCATTGAAGAGAGCATTAGGTGCTTTGAAC
genomic: TTGGGCATTGGTTTAGACCAAGGATTGGACGTGCTGTATACCTTCCACCGgttggtccat ... ctgtgtatagTTTGAGGAGGCTGCAATTGCTGCATTGAAGAGAGCATTAGGTGCTTTGAAC
EST: gi|110392524|gb|EC958004.1|EC958004
EST:     TTGGGCATTGGTTTAGACCAAGGATGGGACGTGCTGTATACCTTCCACCG                         TTTGAGGAGGCTGCAATTGCTGCATTGAAGAGAGCATTAGGTGCTTTGAAC
genomic: TTGGGCATTGGTTTAGACCAAGGATTGGACGTGCTGTATACCTTCCACCGgttggtccat ... ctgtgtatagTTTGAGGAGGCTGCAATTGCTGCATTGAAGAGAGCATTAGGTGCTTTGAAC
EST: gi|351025275|gb|FQ434288.1|FQ434288
EST:     TTGGGCATTGGTTTAGACCAAGGATGGGACGTGCTGTATACCTTCCACCG                         TTTGAGGAGGCTGCAATTGCTGCATTGAAGAGAGCATTAGGTGCTTTGAAC
genomic: TTGGGCATTGGTTTAGACCAAGGATTGGACGTGCTGTATACCTTCCACCGgttggtccat ... ctgtgtatagTTTGAGGAGGCTGCAATTGCTGCATTGAAGAGAGCATTAGGTGCTTTGAAC
EST: gi|71855580|gb|DT004635.1|DT004635
EST:     TTGGGCATTGGTTTAGACCAAGGATTGGACGTGCTGTATACCTTCCACCG                         TTTGAGGAGGCTGCAATTGCTGCATTGAAGAGAGCATTAGGTGCTTTGAAC
genomic: TTGGGCATTGGTTTAGACCAAGGATTGGACGTGCTGTATACCTTCCACCGgttggtccat ... ctgtgtatagTTTGAGGAGGCTGCAATTGCTGCATTGAAGAGAGCATTAGGTGCTTTGAAC
EST: gi|71859460|gb|DT008515.1|DT008515
EST:     TTGGGCATTGGTTTAGACCAAGGATGGGACGTGCTGTATACCTTCCACCG                         TTTGAGGAGGCTGCAATTGCTGCATTGAAGAGAGCATTAGGTGCTTTGAAC
genomic: TTGGGCATTGGTTTAGACCAAGGATTGGACGTGCTGTATACCTTCCACCGgttggtccat ... ctgtgtatagTTTGAGGAGGCTGCAATTGCTGCATTGAAGAGAGCATTAGGTGCTTTGAAC
EST: gi|71858356|gb|DT007411.1|DT007411
EST:     TTGGGCATTGGTTTAGACCAAGGATGGGACGTGCTGTATACCTTCCACCG                         TTTGAGGAGGCTGCAATTGCTGCATTGAAGAGAGCATTAGGTGCTTTGAAC
genomic: TTGGGCATTGGTTTAGACCAAGGATTGGACGTGCTGTATACCTTCCACCGgttggtccat ... ctgtgtatagTTTGAGGAGGCTGCAATTGCTGCATTGAAGAGAGCATTAGGTGCTTTGAAC
EST: gi|294965707|gb|GW839162.1|GW839162
EST:     TGGGCATTGGTTTAGACCAAGGATGGGACCGTGCTGTATACCTTCCACCG                         TTTGAGGAGGCTGCAATT
genomic: TGGGCATTGGTTTAGACCAAGGATTGGAC-GTGCTGTATACCTTCCACCGgttggtccat ... ctgtgtatagTTTGAGGAGGCTGCAATT
EST: gi|34544508|gb|CF512740.1|CF512740
EST:     TTGGGCATTGGTTTAGACCAAGGATGGGACGTGCTGTATACCTTCCACCG                         TTTGAGGAGGCTGCAATTGCTGCATTGAAGAGAGCATTAGGTGCTTTGAAC
genomic: TTGGGCATTGGTTTAGACCAAGGATTGGACGTGCTGTATACCTTCCACCGgttggtccat ... ctgtgtatagTTTGAGGAGGCTGCAATTGCTGCATTGAAGAGAGCATTAGGTGCTTTGAAC
EST: gi|351027331|gb|FQ444580.1|FQ444580
EST:     TTGGGCATTGGTTTAGACCAAGGATGGGACGTGCTGTATACCTTCCACCG                         TTTGAGGAGGCTGCAATTGCTGCATTGAAGAGAGCATTAGGTGCTTTGAAC
genomic: TTGGGCATTGGTTTAGACCAAGGATTGGACGTGCTGTATACCTTCCACCGgttggtccat ... ctgtgtatagTTTGAGGAGGCTGCAATTGCTGCATTGAAGAGAGCATTAGGTGCTTTGAAC
EST: gi|161714380|gb|FC063221.1|FC063221
EST:     TTGGGCATTGGTTTAGACCAAGGATTGGACGTGCTGTATACCTTCCACCG                         TTTGAGGAGGCTGCAATTGCTGCATTGAAGAGAGCATTAGGTGCTTTGAAC
genomic: TTGGGCATTGGTTTAGACCAAGGATTGGACGTGCTGTATACCTTCCACCGgttggtccat ... ctgtgtatagTTTGAGGAGGCTGCAATTGCTGCATTGAAGAGAGCATTAGGTGCTTTGAAC
EST: gi|351016802|gb|FQ424229.1|FQ424229
EST:     TTGGGCATTGGTTTAGACCAAGGATGGGACGTGCTGTATACCTTCCACCG                         TTTGAGGAGGCTGCAATTGCTGCATTGAAGAGAGCATTAGGTGCTTTGAAC
genomic: TTGGGCATTGGTTTAGACCAAGGATTGGACGTGCTGTATACCTTCCACCGgttggtccat ... ctgtgtatagTTTGAGGAGGCTGCAATTGCTGCATTGAAGAGAGCATTAGGTGCTTTGAAC
EST: gi|352794288|gb|FQ479530.1|FQ479530
EST:     TTGGGCATTGGTTTAGACCAAGGATGGGACGTGCTGTATACCTTCCACCG                         TTTGAGGAGGCTGCAATTGCTGCATTGAAGAGAGCATTAGGTGCTTTGAAC
genomic: TTGGGCATTGGTTTAGACCAAGGATTGGACGTGCTGTATACCTTCCACCGgttggtccat ... ctgtgtatagTTTGAGGAGGCTGCAATTGCTGCATTGAAGAGAGCATTAGGTGCTTTGAAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCACATTGAGCAGTGGATTGATTTTGCATCATTGGAGATTGATGCTAATATTGGGCATTGGTTTAGACCAAGGATTGGACGTGCTGTATACCTTCCACCGgttggtccattatcatctttaataatttttctcatttctctgctatgcttcactccacgcctagaggcaagaaaggaaagggggttgggtggaatcaata

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcaagaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aggaaag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaatcaa