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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctgttgtcttcctgcttctctggagttcatttcttttcttcaccagagttcactctagccatttggtatgcgcataattatttaagcttttccatataactcaattagcatgctcactgcttctcagGTCATGACGACATTCATGTCACCACCTCCTGCAGCCACTTTTTTGGCTTTCCATCCTCAAGATAATAATATCATTGCCATAGGAATGGAGGATTCTACAA

Basic information

species Vitis vinifera
transcript Vv16s0039g02410.t01
intron # 20
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv16s0039g02410.t01 (Vitis vinifera), 3'ss of exon 20
lower sequence: LOC_Os08g06480.1 (Oryza sativa), 3'ss of exon 20
gtctgttgtcttcctgcttctctgga-gttcatttcttttcttcaccagagttcactctagccatttggta-tgcgcataattatttaagcttttccata-taactcaattagcatgctc--actgcttctcagGTCATGACGACATTCATGTCACCACCTCCTGCAGCCACTTTTTTGGCTTTCCATCCTCAAGATAATAATATCATTGCCATAGGAATGGAGGATTCTACAA
|| | |  |||    | |     | |   ||| || || |   | | ||||   |     | |||  | || |   |||||  || |  | | ||| ||| |       |||  ||  |   | |  ||| ||||||||||| || |||||| |||| || ||||| || |||||  | || ||||| |||||||| |||||||||||||| || ||||||||||| ||||| |
gtatatgatctcttcggtgtgtagcacaatcaattgttattacc-ctagagcata----ggtcatgagttactttccataaaaatatgtgttattctatagttgtgacgttaaaatttttgaattttttcacagGTCATGACTACTTTCATGGCACCTCCACCTGCTGCAACTTTCCTTGCATTCCACCCTCAAGACAATAATATCATTGCTATTGGAATGGAGGACTCTACCA

upper sequence: Vv16s0039g02410.t01 (Vitis vinifera), 3'ss of exon 20
lower sequence: PP1S316_34V6.1 (Physcomitrella patens), 3'ss of exon 20
gtctgttgtcttcctgcttctctggagttcatttcttttcttcaccagagttcactctagccatttggtatgcgcataattatttaagcttttccatataactcaattagcatgctcactgcttctcagGTCATGACGACATTCATGTCACCACCTCCTGCAGCCACTTTTTTGGCTTTCCATCCTCAAGATAATAATATCATTGCCATAGGAATGGAGGATTCTACAA
           |  |       | ||   ||||| || |  | |  | |  | |||||       ||||    || | |  ||   || | |  ||  |  ||           |  | ||    |||||||||||||||||||||| | |||||||| ||||| |||||| | || |||||||| ||||| || || |||||||||||||||||||||||||| ||||
-----------tattaaaaaaattgaagccattttttattatta--aaaaattactctg-----ctggtg-atgcttgaacatggcagttctgacagttgcctt----------cggattgtgattcagGTCATGACGACATTCATGCCGCCACCTCCAGCAGCTACTTTTCTTGCGTTCCATCCCCAAGACAACAACATCATTGCCATAGGAATGGAGGATTCAACAA

upper sequence: Vv16s0039g02410.t01 (Vitis vinifera), 3'ss of exon 20
lower sequence: PP1S99_260V6.1 (Physcomitrella patens), 3'ss of exon 20
gtctgttgtcttcctgcttc-tctggagttcatttcttttcttcaccagagttcactct---agccatttggtatgcgcataattatttaagcttttccatataactcaattagcatgctcactgctt---ctcagGTCATGACGACATTCATGTCACCACCTCCTGCAGCCACTTTTTTGGCTTTCCATCCTCAAGATAATAATATCATTGCCATAGGAATGGAGGATTCTACAA
    ||    | |  |  || |  |||||  ||||  ||  ||   |  |    |   |   |  | ||| || |  |  ||||| |   || | |    | | | ||        | ||      ||   ||||||||||||||||||||||| |||||||||| ||||| |||||| | || || ||||| ||||| || ||||||||||| || |||||||| ||||| ||||
----gtaaagtccgcgaatcatgaggagtctattttattctttgttctaataatatggtgagaagcgttttgtttttg-gtaattttgacagttgtcaatttttattctgacgcttttcttcggattttgactcagGTCATGACGACATTCATGCCACCACCTCCAGCAGCTACTTTTCTTGCATTTCATCCACAAGACAACAATATCATTGCTATCGGAATGGAAGATTCGACAA

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|71879756|gb|DT028811.1|DT028811
EST:     TGTCTGCATCTGGTGGGAAGGTGTCTTTGTTCAACATGATGACATTTAAG                         GTCATGACGACGTTCATGTCACCACCTCCTGCAGCCACTTTTTTGGCTTTC
genomic: TGTCTGCATCTGGTGGGAAGGTGTCTTTGTTCAACATGATGACATTTAAGgtctgttgtc ... tgcttctcagGTCATGACGACATTCATGTCACCACCTCCTGCAGCCACTTTTTTGGCTTTC
EST: gi|71878707|gb|DT027762.1|DT027762
EST:     TGTCTGCATCTGGTGGGAAGGTGTCTTTGTTCAACATGATGACATTTAAG                         GTCATGACGACGTTCATGTCACCACCTCCTGCAGCCACTTTTTTGGCTTTC
genomic: TGTCTGCATCTGGTGGGAAGGTGTCTTTGTTCAACATGATGACATTTAAGgtctgttgtc ... tgcttctcagGTCATGACGACATTCATGTCACCACCTCCTGCAGCCACTTTTTTGGCTTTC
EST: gi|71880708|gb|DT029763.1|DT029763
EST:     TGTCTGCATCTGGTGGGAAGGTGTCTTTGTTCAACATGATGACATTTAAG                         GTCATGACGACGTTCATGTCACCACCTCCTGCAGCCACTTTTTTGGCTTTC
genomic: TGTCTGCATCTGGTGGGAAGGTGTCTTTGTTCAACATGATGACATTTAAGgtctgttgtc ... tgcttctcagGTCATGACGACATTCATGTCACCACCTCCTGCAGCCACTTTTTTGGCTTTC
EST: gi|71879963|gb|DT029018.1|DT029018
EST:     TGTCTGCATCTGGTGGGAAGGTGTCTTTGTTCAACATGATGACATTTAAG                         GTCATGACGACGTTCATGTCACCACCTCCTGCAGCCACTTTTTTGGCTTTC
genomic: TGTCTGCATCTGGTGGGAAGGTGTCTTTGTTCAACATGATGACATTTAAGgtctgttgtc ... tgcttctcagGTCATGACGACATTCATGTCACCACCTCCTGCAGCCACTTTTTTGGCTTTC
EST: gi|71863790|gb|DT012845.1|DT012845
EST:     TGTCTGCATCTGGTGGGAAGGTGTCTTTGTTCAACATGATGACATTTAAG                         GTCATGACGACATTCATGTCACCACCTCCTGCAGCCACTTTTTTGGCTTTC
genomic: TGTCTGCATCTGGTGGGAAGGTGTCTTTGTTCAACATGATGACATTTAAGgtctgttgtc ... tgcttctcagGTCATGACGACATTCATGTCACCACCTCCTGCAGCCACTTTTTTGGCTTTC
EST: gi|71879582|gb|DT028637.1|DT028637
EST:     TGTCTGCATCTGGTGGGAAGGTGTCTTTGTTCAACATGATGACATTTAAG                         GTCATGACGACGTTCATGTCACCACCTCCTGCAGCCACTTTTTTGGCTTTC
genomic: TGTCTGCATCTGGTGGGAAGGTGTCTTTGTTCAACATGATGACATTTAAGgtctgttgtc ... tgcttctcagGTCATGACGACATTCATGTCACCACCTCCTGCAGCCACTTTTTTGGCTTTC
EST: gi|71879455|gb|DT028510.1|DT028510
EST:     TGTCTGCATCTGGTGGGAAGGTGTCTTTGTTCAACATGATGACATTTAAG                         GTCATGACGACGTTCATGTCACCACCTCCTGCAGCCACTTTTTTGGCTTTC
genomic: TGTCTGCATCTGGTGGGAAGGTGTCTTTGTTCAACATGATGACATTTAAGgtctgttgtc ... tgcttctcagGTCATGACGACATTCATGTCACCACCTCCTGCAGCCACTTTTTTGGCTTTC
EST: gi|71879339|gb|DT028394.1|DT028394
EST:     TGTCTGCATCTGGTGGGAAGGTGTCTTTGTTCAACATGATGACATTTAAG                         GTCATGACGACGTTCATGTCACCACCTCCTGCAGCCACTTTTTTGGCTTTC
genomic: TGTCTGCATCTGGTGGGAAGGTGTCTTTGTTCAACATGATGACATTTAAGgtctgttgtc ... tgcttctcagGTCATGACGACATTCATGTCACCACCTCCTGCAGCCACTTTTTTGGCTTTC
EST: gi|71878846|gb|DT027901.1|DT027901
EST:     TGTCTGCATCTGGTGGGAAGGTGTCTTTGTTCAACATGATGACATTTAAG                         GTCATGACGACGTTCATGTCACCACCTCCTGCAGCCACTTTTTTGGCTTTC
genomic: TGTCTGCATCTGGTGGGAAGGTGTCTTTGTTCAACATGATGACATTTAAGgtctgttgtc ... tgcttctcagGTCATGACGACATTCATGTCACCACCTCCTGCAGCCACTTTTTTGGCTTTC
EST: gi|71880267|gb|DT029322.1|DT029322
EST:     TGTCTGCATCTGGTGGGAAGGTGTCTTTGTTCAACATGATGACATTTAAG                         GTCATGACGACGTTCATGTCACCACCTCCTGCAGCCACTTTTTTGGCTTTC
genomic: TGTCTGCATCTGGTGGGAAGGTGTCTTTGTTCAACATGATGACATTTAAGgtctgttgtc ... tgcttctcagGTCATGACGACATTCATGTCACCACCTCCTGCAGCCACTTTTTTGGCTTTC
EST: gi|71880607|gb|DT029662.1|DT029662
EST:     TGTCTGCATCTGGTGGGAAGGTGTCTTTGTTCAACATGATGACATTTAAG                         GTCATGACGACGTTCATGTCACCACCTCCTGCAGCCACTTTTTTGGCTTTC
genomic: TGTCTGCATCTGGTGGGAAGGTGTCTTTGTTCAACATGATGACATTTAAGgtctgttgtc ... tgcttctcagGTCATGACGACATTCATGTCACCACCTCCTGCAGCCACTTTTTTGGCTTTC
EST: gi|71878134|gb|DT027189.1|DT027189
EST:     TGTCTGCATCTGGTGGGAAGGTGTCTTTGTTCAACATGATGACATTTAAG                         GTCATGACGACGTTCATGTCACCACCTCCTGCAGCCACTTTTTTGGCTTTC
genomic: TGTCTGCATCTGGTGGGAAGGTGTCTTTGTTCAACATGATGACATTTAAGgtctgttgtc ... tgcttctcagGTCATGACGACATTCATGTCACCACCTCCTGCAGCCACTTTTTTGGCTTTC
EST: gi|71879171|gb|DT028226.1|DT028226
EST:     TGTCTGCATCTGGTGGGAAGGTGTCTTTGTTCAACATGATGACATTTAAG                         GTCATGACGACGTTCATGTCACCACCTCCTGCAGCCACTTTTTTGGCTTTC
genomic: TGTCTGCATCTGGTGGGAAGGTGTCTTTGTTCAACATGATGACATTTAAGgtctgttgtc ... tgcttctcagGTCATGACGACATTCATGTCACCACCTCCTGCAGCCACTTTTTTGGCTTTC
EST: gi|71881027|gb|DT030082.1|DT030082
EST:     TGTCTGCATCTGGTGGGAAGGTGTCTTTGTTCAACATGATGACATTTAAG                         GTCATGACGACGTTCATGTCACCACCTCCTGCAGCCACTTTTTTGGCTTTC
genomic: TGTCTGCATCTGGTGGGAAGGTGTCTTTGTTCAACATGATGACATTTAAGgtctgttgtc ... tgcttctcagGTCATGACGACATTCATGTCACCACCTCCTGCAGCCACTTTTTTGGCTTTC
EST: gi|71881083|gb|DT030138.1|DT030138
EST:     TGTCTGCATCTGGTGGGAAGGTGTCTTTGTTCAACATGATGACATTTAAG                         GTCATGACGACGTTCATGTCACCACCTCCTGCAGCCACTTTTTTGGCTTTC
genomic: TGTCTGCATCTGGTGGGAAGGTGTCTTTGTTCAACATGATGACATTTAAGgtctgttgtc ... tgcttctcagGTCATGACGACATTCATGTCACCACCTCCTGCAGCCACTTTTTTGGCTTTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cataattatttaagcttttccatataactcaattagcatgctcactgcttctcagGTCATGACGACATTCATGTCACCACCTCCTGCAGCCACTTTTTTGGCTTTCCATCCTCAAGATAATAATATCATTGCCATAGGAATGGAGGATTCTACAA
                                      tgctcac  putative branch site (score: 2)
                                            ctgcttctc  CT-rich tract
     ttatttaagctttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtctgttgtcttcctgcttctctggagttcatttcttttcttcaccagagttcactctagccatttggtatgcgcataattatttaagcttttccatataactcaattagcatgctcactgcttctcagGTCATGACGACATTCATGTCACCACCTCCTGCAGCCACTTTTTTGGCTTTCCATCCTCAAGATAATAATATCATTGCCATAGGAATGGAGGATTCTACAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT