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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcattagatgtaatatatgcatgcatgactaacacaaaaatggtgtggacctttcaagttatgcttctcaaatacactgatagtgtttttcttgctttagTGTGAGCCTCCTCGAGATGTTGAAGCTTACATCCATCGATCTGGACGCACAGGAAGAGCAG

Basic information

species Vitis vinifera
transcript Vv16s0022g02110.t01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv16s0022g02110.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA10G38680.1 (Glycine max), 3'ss of exon 8
tcattagatgtaatatatgcatgcatgactaacacaaaaatggtgtggacctttcaagttatgcttctcaaatacactgatagtgtttttcttgctttagTGTGAGCCTCCTCGAGATGTTGAAGCTTACATCCATCGATCTGGACGCACAGGAAGAGCAG
    ||  | | ||  ||| |   |  |     |  | | |  |      ||||    || |  |   |   ||  |||||| | | | | |||  | ||||||| || || |||||||| ||||| || |||||||| ||||||||||||||||||||||
---gtacttttgatgaatgtacatacaat--gtatcagattatt------ctttttttttgtcataacctggtatgctgatatt-tgtattttgtatcagTGTGAACCCCCACGAGATGTAGAAGCCTATATCCATCGTTCTGGACGCACAGGAAGAGCAG

upper sequence: Vv16s0022g02110.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA20G29060.1 (Glycine max), 3'ss of exon 8
tcattagatgtaatatatgcatgcatgactaacacaaaaatggtgtggacctttcaagttatgcttctcaaatacactgatagtgtttttcttgctttagTGTGAGCCTCCTCGAGATGTTGAAGCTTACATCCATCGATCTGGACGCACAGGAAGAGCAG
         ||| | |         | | ||  |   |   | |       |||   || |     ||   || | |||||| | | | | ||| |||||||||| || || || ||||| ||||| || |||||||| ||||||||||||||||||||||
---------gtacttttgatgattgtaaatacaatgtatcagatcattttttttttcgtcac-taccttgtatgc-ctgatatt-tgtattttgatttagTGTGAACCCCCACGGGATGTAGAAGCCTATATCCATCGTTCTGGACGCACAGGAAGAGCAG

upper sequence: Vv16s0022g02110.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: PP1S40_169V6.1 (Physcomitrella patens), 3'ss of exon 6
------------------tcattagatgtaatatatgcatgcatgactaacacaaaaatggtgtggacc---tttcaagttatgcttctcaaatacactgatagtgtttttcttgcttt-----agTGTGAGCCTCCTCGAGATGTTGAAGCTTACATCCATCGATCTGGACGCACAGGAAGAGCAG---------------------------------------
                   | ||||||||  |    ||||| |  |||  | |      |  | | | |   || |  | | |  |     |      |||| |    | | ||| | |     ||||||| |||||||| ||||  ||| | ||||||||||| ||||| || ||||||||||| |                                       
gtacttcacttcgaatgcactttagatgttcttggcgcatgta--actttctctgtctggtagagaatcgtattgctggatgtcgtcactgatcgttttgatcgctactctattgttatttggcagTGTGAACCTCCTCGTGATGCCGAAACCTACATCCATCGGTCTGGGCGGACAGGAAGAGCTGGAAATACTGGTATCTCTGTGTTGTTTTACGACAGGAAGA

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|351046770|gb|FQ454380.1|FQ454380
EST:     ATGTAGCGGCAAGAGGATTGGACATTAATGATGTGCAGTTAATCATCCAG                         TGTGAGCCTCCTCGAGATGTTGAAGCCTACATCCATCGATCTGGACGCACA
genomic: ATGTAGCGGCAAGAGGATTGGACATTAATGATGTGCAGTTAATCATCCAGgtttggcatc ... cttgctttagTGTGAGCCTCCTCGAGATGTTGAAGCTTACATCCATCGATCTGGACGCACA
EST: gi|349818664|gb|FQ403498.1|FQ403498
EST:     ATGTAGCGGCAAGAGGATTGGACATTAATGATGTGCAGTTAATCATCCAG                         TGTGAGCCTCCTCGAGATGTTGAAGCTTACATCCATCGATCTGGACGCACA
genomic: ATGTAGCGGCAAGAGGATTGGACATTAATGATGTGCAGTTAATCATCCAGgtttggcatc ... cttgctttagTGTGAGCCTCCTCGAGATGTTGAAGCTTACATCCATCGATCTGGACGCACA
EST: gi|351040229|gb|FQ425315.1|FQ425315
EST:     ATGTAGCGGCAAGAGGATTGGACATTAATGATGTGCAGCTAATCATCCAG                         TGTGAGCCTCCTCGAGATGTTGAAGCTTACATCCATCGATCTGGACGCACA
genomic: ATGTAGCGGCAAGAGGATTGGACATTAATGATGTGCAGTTAATCATCCAGgtttggcatc ... cttgctttagTGTGAGCCTCCTCGAGATGTTGAAGCTTACATCCATCGATCTGGACGCACA
EST: gi|352790432|gb|FQ478072.1|FQ478072
EST:     ATGTAGCGGCAAGAGGATTGGACATTAATGATGTGCAGTTAATCATCCAG                         TGTGAGCCTCCTCGAGATGTTGAAGCTTACATCCATCGATCTGGACGCACA
genomic: ATGTAGCGGCAAGAGGATTGGACATTAATGATGTGCAGTTAATCATCCAGgtttggcatc ... cttgctttagTGTGAGCCTCCTCGAGATGTTGAAGCTTACATCCATCGATCTGGACGCACA
EST: gi|351048608|gb|FQ448882.1|FQ448882
EST:     ATGTAGCGGCAAGAGGATTGGACATTAATGATGTGCAGTTAATCATCCAG                         TGTGAGCCTCCTCGAGATGTTGAAGCTTACATCCATCGATCTGGACGCACA
genomic: ATGTAGCGGCAAGAGGATTGGACATTAATGATGTGCAGTTAATCATCCAGgtttggcatc ... cttgctttagTGTGAGCCTCCTCGAGATGTTGAAGCTTACATCCATCGATCTGGACGCACA
EST: gi|351033398|gb|FQ462049.1|FQ462049
EST:     ATGTAGCGGCAAGAGGATTGGACATTAATGATGTGCAGTTAATCATCCAG                         TGTGAGCCTCCTCGAGATGTTGAAGCTTACATCCATCGATCTGGACGCACA
genomic: ATGTAGCGGCAAGAGGATTGGACATTAATGATGTGCAGTTAATCATCCAGgtttggcatc ... cttgctttagTGTGAGCCTCCTCGAGATGTTGAAGCTTACATCCATCGATCTGGACGCACA
EST: gi|161720145|gb|FC066753.1|FC066753
EST:     ATGTAGCGGCAAGAGGATTGGACATCAATGATGTGCAGTTAATCATCCAG                         TGTGAGCCTCCTCGAGATGTTGAAGCTTACATCCATCGATCTGGACGCACA
genomic: ATGTAGCGGCAAGAGGATTGGACATTAATGATGTGCAGTTAATCATCCAGgtttggcatc ... cttgctttagTGTGAGCCTCCTCGAGATGTTGAAGCTTACATCCATCGATCTGGACGCACA
EST: gi|161709071|gb|FC058368.1|FC058368
EST:     GTAGCGGCAAGAGGATTGGACATCAATGATGTGCAGTTAATCATCCAG                         TGTGAGCCTCCTCGAGATGTTGAAGCTTACATCCATCGATCTGGACGCACA
genomic: GTAGCGGCAAGAGGATTGGACATTAATGATGTGCAGTTAATCATCCAGgtttggcatc ... cttgctttagTGTGAGCCTCCTCGAGATGTTGAAGCTTACATCCATCGATCTGGACGCACA
EST: gi|351039800|gb|FQ464838.1|FQ464838
EST:     ATGTAGCGGCAAGAGGATTGGACATTAATGATGTGCAGTTAATCATCCAG                         TGTGAGCCTCCTCGAGATGTTGAAGCTTACATCCATCGATCTGGACGCACA
genomic: ATGTAGCGGCAAGAGGATTGGACATTAATGATGTGCAGTTAATCATCCAGgtttggcatc ... cttgctttagTGTGAGCCTCCTCGAGATGTTGAAGCTTACATCCATCGATCTGGACGCACA
EST: gi|349809274|gb|FQ399048.1|FQ399048
EST:     ATGTAGCGGCAAGAGGATTGGACATTAATGACGTGCAGTTAATCATCCAG                         TGTGAGCCTCCTCGAGATGTTGAAGCTTACATCCATCGATCTGGACGCACA
genomic: ATGTAGCGGCAAGAGGATTGGACATTAATGATGTGCAGTTAATCATCCAGgtttggcatc ... cttgctttagTGTGAGCCTCCTCGAGATGTTGAAGCTTACATCCATCGATCTGGACGCACA
EST: gi|352798464|gb|FQ480489.1|FQ480489
EST:     ATGTAGCGGCAAGAGGATTGGACATTAATGATGTGCAGTTAATCATCCAG                         TGTGAGCCTCCTCGAGATGTTGAAGCTTACATCCATCGATCTGGACGCACA
genomic: ATGTAGCGGCAAGAGGATTGGACATTAATGATGTGCAGTTAATCATCCAGgtttggcatc ... cttgctttagTGTGAGCCTCCTCGAGATGTTGAAGCTTACATCCATCGATCTGGACGCACA
EST: gi|349812243|gb|FQ411838.1|FQ411838
EST:     ATGTAGCGGCAAGAGGATTGGACATTAATGATGTGCAGTTAATCATCCAG                         TGTGAGCCTCCTCGAGATGTTGAAGCTTACATCCATCGATCTGGACGCACA
genomic: ATGTAGCGGCAAGAGGATTGGACATTAATGATGTGCAGTTAATCATCCAGgtttggcatc ... cttgctttagTGTGAGCCTCCTCGAGATGTTGAAGCTTACATCCATCGATCTGGACGCACA
EST: gi|351056075|gb|FQ453536.1|FQ453536
EST:     ATGTAGCGGCAAGAGGATTGGACATTAATGATGTGCAGTTAATCATCCAG                         TGTGAGCCTCCTCGAGATGTTGAAGCTTACATCCATCGATCTGGACGCACA
genomic: ATGTAGCGGCAAGAGGATTGGACATTAATGATGTGCAGTTAATCATCCAGgtttggcatc ... cttgctttagTGTGAGCCTCCTCGAGATGTTGAAGCTTACATCCATCGATCTGGACGCACA
EST: gi|71870308|gb|DT019363.1|DT019363
EST:     ATGTAGCGGCAAGAGGATTGGACATCAATGATGTGCAGTTAATCATCCAG                         TGTGAGCCTCCTCGAGATGTTGAAGCTTACATCCATCGATCTGGACGCACA
genomic: ATGTAGCGGCAAGAGGATTGGACATTAATGATGTGCAGTTAATCATCCAGgtttggcatc ... cttgctttagTGTGAGCCTCCTCGAGATGTTGAAGCTTACATCCATCGATCTGGACGCACA
EST: gi|161720948|gb|FC070676.1|FC070676
EST:     ATGTAGCGGCAAGAGGATTGGACATCAATGATGTGCAGTTAATCATCCAG                         TGTGAGCCTCCTCGAGATGTTGAAGCTTACATCCATCGATCTGGACGCACA
genomic: ATGTAGCGGCAAGAGGATTGGACATTAATGATGTGCAGTTAATCATCCAGgtttggcatc ... cttgctttagTGTGAGCCTCCTCGAGATGTTGAAGCTTACATCCATCGATCTGGACGCACA
EST: gi|351055609|gb|FQ452074.1|FQ452074
EST:     ATGTAGCGGCAAGAGGATTGGACATTAATGATGTGCAGTTAATCATCCAG                         TGTGAGCCTCCTCGAGATGTTGAAGCTTACATCCATCGATCTGGACGCACA
genomic: ATGTAGCGGCAAGAGGATTGGACATTAATGATGTGCAGTTAATCATCCAGgtttggcatc ... cttgctttagTGTGAGCCTCCTCGAGATGTTGAAGCTTACATCCATCGATCTGGACGCACA
EST: gi|30253071|gb|CB970622.1|CB970622
EST:     ATGTAGCGGCAAGAGGATTGGACATCAATGATGTGCAGTTAATCATCCAG                         TGTGAGCCTCCTCGAGATGTTGAAGCTTACATCCATCGATCTGGACGCACA
genomic: ATGTAGCGGCAAGAGGATTGGACATTAATGATGTGCAGTTAATCATCCAGgtttggcatc ... cttgctttagTGTGAGCCTCCTCGAGATGTTGAAGCTTACATCCATCGATCTGGACGCACA
EST: gi|351012917|gb|FQ430480.1|FQ430480
EST:     ATGTAGCGGCAAGAGGATTGGACATTAATGATGTGCAGTTAATCATCCAG                         TGTGAGCCTCCTCGAGATGTTGAAGCTTACATCCATCGATCTGGACGCACA
genomic: ATGTAGCGGCAAGAGGATTGGACATTAATGATGTGCAGTTAATCATCCAGgtttggcatc ... cttgctttagTGTGAGCCTCCTCGAGATGTTGAAGCTTACATCCATCGATCTGGACGCACA
EST: gi|110690637|gb|EE067971.1|EE067971
EST:     ATGTAGCGGCAAGAGGATTGGACATCAATGATGTGCAGTTAATCATCCAG                         TGTGAGCCTCCTCGAGATGTTGAAGCTTACATCCATCGATCTGGACGCACA
genomic: ATGTAGCGGCAAGAGGATTGGACATTAATGATGTGCAGTTAATCATCCAGgtttggcatc ... cttgctttagTGTGAGCCTCCTCGAGATGTTGAAGCTTACATCCATCGATCTGGACGCACA
EST: gi|351052845|gb|FQ456573.1|FQ456573
EST:     ATGTAGCGGCAAGAGGATTGGACATTAATGATGTGCAGTTAATCATCCAG                         TGTGAGCCTCCTCGAGATGTTGAAGCTTACATCCATCGATCTGGACGCACA
genomic: ATGTAGCGGCAAGAGGATTGGACATTAATGATGTGCAGTTAATCATCCAGgtttggcatc ... cttgctttagTGTGAGCCTCCTCGAGATGTTGAAGCTTACATCCATCGATCTGGACGCACA
EST: gi|351035558|gb|FQ463403.1|FQ463403
EST:     ATGTAGCGGCAAGAGGATTGGACATTAATGATGTGCAGTTAATCATCCAG                         TGTGAGCCTCCTCGAGATGTTGAAGCTTACACCCATCGATCTGGACGCACA
genomic: ATGTAGCGGCAAGAGGATTGGACATTAATGATGTGCAGTTAATCATCCAGgtttggcatc ... cttgctttagTGTGAGCCTCCTCGAGATGTTGAAGCTTACATCCATCGATCTGGACGCACA
EST: gi|349807331|gb|FQ401323.1|FQ401323
EST:     ATGTAGCGGCAAGAGGATTGGACATTAATGATGTGCAGTTAATCATCCAG                         TGTGAGCCTCCTCGAGATGTTGAAGCTTGCATCCATCGATCTGGACGCACA
genomic: ATGTAGCGGCAAGAGGATTGGACATTAATGATGTGCAGTTAATCATCCAGgtttggcatc ... cttgctttagTGTGAGCCTCCTCGAGATGTTGAAGCTTACATCCATCGATCTGGACGCACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggacctttcaagttatgcttctcaaatacactgatagtgtttttcttgctttagTGTGAGCCTCCTCGAGATGTTGAAGCTTACATCCATCGATCTGGACGCACAGGAAGAGCAG
                             cactgat  putative branch site (score: 3)
                                      tgtttttcttgcttt  putative PPT
                                        tttttctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcattagatgtaatatatgcatgcatgactaacacaaaaatggtgtggacctttcaagttatgcttctcaaatacactgatagtgtttttcttgctttagTGTGAGCCTCCTCGAGATGTTGAAGCTTACATCCATCGATCTGGACGCACAGGAAGAGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG
- - - - - - - - - gcatgca
- - - - - - - - - - - - - - - - -acaaaaa
- - - - - - - - - - - - - - - - - - - - -ggtgtgg
- - - - - - - - - - - - - - - - - - - - - - - - -cctttca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aatacac