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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tggaaaatagctcctaaatttagcatgaatgaattctggatagtggattttttactgctcttctttcccactgtcataatttattaatttctttttgcagATTGGAAAGCATGGTATAATTATTGAGTTTACTGATCCTGACTATAATACAAGGCGAAGTGCCACATATTTGCCCGAGGTGGCTGCCCATGAAG

Basic information

species Vitis vinifera
transcript Vv13s0101g00100.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv13s0101g00100.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os10g42250.2 (Oryza sativa), 3'ss of exon 3
tggaaaatagctcctaaatttagcatgaatgaattctggatagtggattttttactgctcttctttcccactgtcataatttattaatttctttttgcagATTGGAAAGCATGGTATAATTATTGAGTTTACTGATCCTGACTATAATACAAGGCGAAGTGCCACATATTTGCCCGAGGTGGCTGCCCATGAAG
                          | ||| |  ||  | | |||  ||||    | ||||     |   | | ||||| |  |  |       ||||| | || ||||||||  |||||||||| || |||||||| |||||||| |  ||||| ||||| || ||||| || ||||| |||||||||||||
--------------------------gtatgcaa-ctacacattgg--ttttagtcgttctttcactctcttctaataatcttgtggtac-----tgcagGTGGGTAAGCATGGGTTAATTATTGAATTCACTGATCCAGACTATAACATGAGGCGCAGTGCAACTTATTTACCTGAGGTTGCTGCCCATGAAG

upper sequence: Vv13s0101g00100.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA20G18290.1 (Glycine max), 3'ss of exon 3
tggaaaatagctcctaa-atttagcatgaatgaattctggatagtggattttttactgctc-ttctttcccactgtcataatttattaatttctttttgcagATTGGAAAGCATGGTATAATTATTGAGTTTACTGATCCTGACTATAATACAAGGCGAAGTGCCACATATTTGCCCGAGGTGGCTGCCCATGAAG
 | |  |||      ||  || ||    |   |||  | | |   |||   | |  |  |  | || |  || | | |  |||      ||  || |||||||| | ||||||||||||||||||||| ||| ||||||||| |||||| |||||||| ||||| |||||  |||| || ||||||||| ||||||
-gcaggatattgtaaaatgttaagtgatataaaatattagctctaggacactattgtatttatactattgcattttta-gattccgagtttctttcttgcagATAGAAAAGCATGGTATAATTATTGAATTTTCTGATCCTGTCTATAACACAAGGCGTAGTGCTACATACCTGCCTGAAGTGGCTGCCAATGAAG

upper sequence: Vv13s0101g00100.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA10G24340.1 (Glycine max), 3'ss of exon 3
tggaaaatagctcctaaatttagcatga-atgaattctggatagtggatt--ttttactgctcttctttcccactgtcataatttattaatttcttt-ttgcagATTGGAAAGCATGGTATAATTATTGAGTTTACTGATCCTGACTATAATACAAGGCGAAGTGCCACATATTTGCCCGAGGTGGCTGCCCATGAAG
   || |||  |   |||| ||   ||| || || | |   |  | |     | ||     | |  |||  |||| | | | | | | | ||||||| |||||||| | ||||||||||||||||||||| ||| ||||||||| |||||| |||||| | ||||| |||||  |||| || ||||| ||| ||||||
---aagata-ttgtaaaatgtaaagtgatataaagtattagttctaggacactattgtatttataattttgcacttttagattctgtcagtttctttcttgcagATAGAAAAGCATGGTATAATTATTGAATTTTCTGATCCTGTCTATAACACAAGGTGTAGTGCTACATACCTGCCTGAAGTGGCCGCCAATGAAG

upper sequence: Vv13s0101g00100.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT2G38710.2 (Arabidopsis thaliana), 3'ss of exon 3
-tggaaaatagctcctaaatttagcatgaatgaattctggatagtggattttttactgctcttctttcccactgtcataatttattaatttctttttgcagATTGGAAAGCATGGTATAATTATTGAGTTTACTGATCCTGACTATAATACAAGGCGAAGTGCCACATATTTGCCCGAGGTGGCTGCCCATGAAG
 | |   ||  |     | |||  |         || |   ||||   | || |||       | ||     | |  |  ||| |  |||||  | |  || |||| |||||||||||||| |||||||||||||| |||||   |||||||| |||||| |||||||||||||| |||||| | || |||||||
cttgctcatgacattgtagtttgtcgaattcttcttgtttgtagtttgtcttatacattgtcccgttggtgatattttgttttgt-gatttcactctaaagGTTGGTAAGCATGGTATAATCATTGAGTTTACTGAACCTGAGACTAATACAAAGCGAAGCGCCACATATTTGCCTGAGGTGCCAGCTCATGAAG

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|34544770|gb|CF513002.1|CF513002
EST:     TTTCCATTCTGACTGATTATGAAACTGGGCTCAACTACCTTGATTGGGAG                         ATTGGAAAGCATGGTATAATTATTGAGTTTACTGATCCTGACTATAATACA
genomic: TTTCCATTCTGACTGATTATGAAACTGGGCTCAACTACCTTGATTGGGAGgtatgggttt ... ctttttgcagATTGGAAAGCATGGTATAATTATTGAGTTTACTGATCCTGACTATAATACA
EST: gi|110411687|gb|EC977410.1|EC977410
EST:     TTTCCATTCTGACTGATTATGAAACTGGGCTCAACTACCTTGATTGGGAG                         ATTGGAAAGCATGGTATAATTATTGAGTTTACTGATCCTGACTATAATACA
genomic: TTTCCATTCTGACTGATTATGAAACTGGGCTCAACTACCTTGATTGGGAGgtatgggttt ... ctttttgcagATTGGAAAGCATGGTATAATTATTGAGTTTACTGATCCTGACTATAATACA
EST: gi|110410525|gb|EC976208.1|EC976208
EST:     TTTCCATTCTGACTGATTATGAAACTGGGCTCAACTACCTTGATTGGGAG                         ATTGGAAAGCATGGTATAATTATTGAGTTTACTGATCCTGACTATAATACA
genomic: TTTCCATTCTGACTGATTATGAAACTGGGCTCAACTACCTTGATTGGGAGgtatgggttt ... ctttttgcagATTGGAAAGCATGGTATAATTATTGAGTTTACTGATCCTGACTATAATACA
EST: gi|30305062|gb|CB981856.1|CB981856
EST:     TTTCCATTCTGTCTGATTATGAAACTGGGCTCAACTACCTTGATTGGGAG                         ATTGGAAAGCATGGTATAATTATTGAGTTTACTGATCCTGACTATAATACA
genomic: TTTCCATTCTGACTGATTATGAAACTGGGCTCAACTACCTTGATTGGGAGgtatgggttt ... ctttttgcagATTGGAAAGCATGGTATAATTATTGAGTTTACTGATCCTGACTATAATACA
EST: gi|349827778|gb|FQ422646.1|FQ422646
EST:     TTTCCATTCTGACTGATTATGAAACTGGGCTCAACTACCTTGATTGGGAG                         ATTGGAAAGCATGGTATAATTATTGAGTTTACTGATCCTGACTATAATACA
genomic: TTTCCATTCTGACTGATTATGAAACTGGGCTCAACTACCTTGATTGGGAGgtatgggttt ... ctttttgcagATTGGAAAGCATGGTATAATTATTGAGTTTACTGATCCTGACTATAATACA
EST: gi|110401758|gb|EC968377.1|EC968377
EST:     TTTCCATTCTGACTGATTATGAAACTGGGCTCAACTACCTTGATTGGGAG                         ATTGGAAAGCATGGTATAATTATTGAGTTTACTGATCCTGACTATAATACA
genomic: TTTCCATTCTGACTGATTATGAAACTGGGCTCAACTACCTTGATTGGGAGgtatgggttt ... ctttttgcagATTGGAAAGCATGGTATAATTATTGAGTTTACTGATCCTGACTATAATACA
EST: gi|110422162|gb|EC988477.1|EC988477
EST:     TTTCCATTCTGACTGATTATGAAACTGGGCTCAACTACCTTGATTGGGAG                         ATTGGAAAGCATGGTATAATTATTGAGTTTACTGATCCTGACTATAATACA
genomic: TTTCCATTCTGACTGATTATGAAACTGGGCTCAACTACCTTGATTGGGAGgtatgggttt ... ctttttgcagATTGGAAAGCATGGTATAATTATTGAGTTTACTGATCCTGACTATAATACA
EST: gi|110384273|gb|EC948699.1|EC948699
EST:     TTTCCATTCTGACTGATTATGAAACTGGGCTCAACTACCTTGATTGGGAG                         ATTGGAAAGCATGGTATAATTATTGAGTTTACTGATCCTGACTATAATACA
genomic: TTTCCATTCTGACTGATTATGAAACTGGGCTCAACTACCTTGATTGGGAGgtatgggttt ... ctttttgcagATTGGAAAGCATGGTATAATTATTGAGTTTACTGATCCTGACTATAATACA
EST: gi|30305004|gb|CB981798.1|CB981798
EST:     TTTCCATTCTGACTGATTATGAAACTGGGCTCAACTACCTTGATTGGGAG                         ATTGGAAAGCATGGTATAATTATTGAGTTTACTGATCCTGACTATAATACA
genomic: TTTCCATTCTGACTGATTATGAAACTGGGCTCAACTACCTTGATTGGGAGgtatgggttt ... ctttttgcagATTGGAAAGCATGGTATAATTATTGAGTTTACTGATCCTGACTATAATACA
EST: gi|26258672|gb|CA809735.1|CA809735
EST:     TTTCCATTCTGACTGATTATGAAACTGGGCTCAACTACCTTGATTGGGAG                         ACTTGGAAAGCATGGTATAATTATTGAGTTTACTGATCCTGACTATAATAC
genomic: TTTCCATTCTGACTGATTATGAAACTGGGCTCAACTACCTTGATTGGGAGgtatgggttt ... ctttttgcagA-TTGGAAAGCATGGTATAATTATTGAGTTTACTGATCCTGACTATAATAC
EST: gi|110379714|gb|EC944932.1|EC944932
EST:     TTTCCATTCTGACTGATTATGAAACTGGGCTCAACTACCTTGATTGGGAG                         ATTGGAAAGCATGGTATAATTATTGAGTTTACTGATCCTGACTATAATACA
genomic: TTTCCATTCTGACTGATTATGAAACTGGGCTCAACTACCTTGATTGGGAGgtatgggttt ... ctttttgcagATTGGAAAGCATGGTATAATTATTGAGTTTACTGATCCTGACTATAATACA
EST: gi|22011850|gb|BQ796884.1|BQ796884
EST:     TTTCCATTCTGACTGATTATGAAACTGGGCTCAACTACCTTGATTGGGAG                         ATTGGAAAGCATGGTATAATTATTGAGTTTACTGATCCTGACTATAATACA
genomic: TTTCCATTCTGACTGATTATGAAACTGGGCTCAACTACCTTGATTGGGAGgtatgggttt ... ctttttgcagATTGGAAAGCATGGTATAATTATTGAGTTTACTGATCCTGACTATAATACA
EST: gi|110360228|gb|EC923056.1|EC923056
EST:     TTTCCATTCTGACTGATTATGAAACTGGGCTCAACTACCTTGATTGGGAG                         ATTGGAAAGCATGGTATAATTATTGAGTTTACTGATCCTGACTATAATACA
genomic: TTTCCATTCTGACTGATTATGAAACTGGGCTCAACTACCTTGATTGGGAGgtatgggttt ... ctttttgcagATTGGAAAGCATGGTATAATTATTGAGTTTACTGATCCTGACTATAATACA
EST: gi|26267150|gb|CA818213.1|CA818213
EST:     TTTCCATTCTGACTGATTATGAAACTGGGCTCAACTACCTTGATTGGGAG                         ATTGGAAAGCATGGTATAATTATTGAGTTTACTGATCCTGACTATAATACA
genomic: TTTCCATTCTGACTGATTATGAAACTGGGCTCAACTACCTTGATTGGGAGgtatgggttt ... ctttttgcagATTGGAAAGCATGGTATAATTATTGAGTTTACTGATCCTGACTATAATACA
EST: gi|26257860|gb|CA808923.1|CA808923
EST:     TTTCCATTCTGACTGATTATGAAACTGGGCTCAACTACCTTGATTGGGAG                         ACTTGGAAAGCATGGTATAATTATTGAGTTTACTGATCCTGACTATAATAC
genomic: TTTCCATTCTGACTGATTATGAAACTGGGCTCAACTACCTTGATTGGGAGgtatgggttt ... ctttttgcagA-TTGGAAAGCATGGTATAATTATTGAGTTTACTGATCCTGACTATAATAC
EST: gi|110373876|gb|EC938294.1|EC938294
EST:     TTTCCATTCTGACTGATTATGAAACTGGGCTCAACTACCTTGATTGGGAG                         ATTGGAAAGCATGGTATAATTATTGAGTTTACTGATCCTGACTATAATACA
genomic: TTTCCATTCTGACTGATTATGAAACTGGGCTCAACTACCTTGATTGGGAGgtatgggttt ... ctttttgcagATTGGAAAGCATGGTATAATTATTGAGTTTACTGATCCTGACTATAATACA
EST: gi|110390064|gb|EC954950.1|EC954950
EST:     TTTCCATTCTGACTGATTATGAAACTGGGCTCAACTACCTTGATTGGGAG                         ATTGGAAAGCATGGTATAATTATTGAGTTTACTGATCCTGACTATAATACA
genomic: TTTCCATTCTGACTGATTATGAAACTGGGCTCAACTACCTTGATTGGGAGgtatgggttt ... ctttttgcagATTGGAAAGCATGGTATAATTATTGAGTTTACTGATCCTGACTATAATACA
EST: gi|34544852|gb|CF513084.1|CF513084
EST:     TTTCCATTCTGACTGATTATGAAACTGGGCTCAACTCCCTTGATTGGGAG                         ATTGGAAAGCATGGTATAATTATTGAGTTTACTGATCCTGACTATAATACA
genomic: TTTCCATTCTGACTGATTATGAAACTGGGCTCAACTACCTTGATTGGGAGgtatgggttt ... ctttttgcagATTGGAAAGCATGGTATAATTATTGAGTTTACTGATCCTGACTATAATACA
EST: gi|110362338|gb|EC925866.1|EC925866
EST:     TTTCCATTCTGACTGATTATGAAACTGGGCTCAACTACCTTGATTGGGAG                         ATTGGAAAGCATGGTATAATTATTGAGTTTACTGATCCTGACTATAATACA
genomic: TTTCCATTCTGACTGATTATGAAACTGGGCTCAACTACCTTGATTGGGAGgtatgggttt ... ctttttgcagATTGGAAAGCATGGTATAATTATTGAGTTTACTGATCCTGACTATAATACA
EST: gi|26258698|gb|CA809761.1|CA809761
EST:     TTTCCATTCTGACTGATTATGAAACTGGGCTCAACTACCTTGATTGGGAG                         ATTGGAAAGCATGGTATAATTATTGAGTTTACTGATCCTGACTATAATACA
genomic: TTTCCATTCTGACTGATTATGAAACTGGGCTCAACTACCTTGATTGGGAGgtatgggttt ... ctttttgcagATTGGAAAGCATGGTATAATTATTGAGTTTACTGATCCTGACTATAATACA
EST: gi|26265055|gb|CA816118.1|CA816118
EST:     TGACTGATTATGAAACTGGGCTCAACTACCCTTGATTGGGAG                         ATTGGAAAGCATGGTATAATTATTGAGTTTACTGATCCTGACTATAATACA
genomic: TGACTGATTATGAAACTGGGCTCAACTA-CCTTGATTGGGAGgtatgggttt ... ctttttgcagATTGGAAAGCATGGTATAATTATTGAGTTTACTGATCCTGACTATAATACA
EST: gi|161713972|gb|FC063157.1|FC063157
EST:     TTTCCATTCTGACTGATTATGAAACTGGGCTCAACTACCTTGATTGGGAG                         ATTGGAAAGCATGGTATAATT
genomic: TTTCCATTCTGACTGATTATGAAACTGGGCTCAACTACCTTGATTGGGAGgtatgggttt ... ctttttgcagATTGGAAAGCATGGTATAATT
EST: gi|26265515|gb|CA816578.1|CA816578
EST:     CTTCCATTCTGACTGATTATGAAACTGGGCTCAACTACCTTGATTGGGAG                         ATTGGAAAGCATGGTATAATTATTGAGTTTACTGATCCTGACTATAATACA
genomic: TTTCCATTCTGACTGATTATGAAACTGGGCTCAACTACCTTGATTGGGAGgtatgggttt ... ctttttgcagATTGGAAAGCATGGTATAATTATTGAGTTTACTGATCCTGACTATAATACA
EST: gi|33408857|gb|CF214484.1|CF214484
EST:     TTTCCATTCTGACTGATTATGAAACTGGGCTCAACTACCTTGATTGGGAG                         ATTGGAAAGCATGGTATAATTATTGAGTTTACTGATCCTGACTATAATACA
genomic: TTTCCATTCTGACTGATTATGAAACTGGGCTCAACTACCTTGATTGGGAGgtatgggttt ... ctttttgcagATTGGAAAGCATGGTATAATTATTGAGTTTACTGATCCTGACTATAATACA
EST: gi|26257886|gb|CA808949.1|CA808949
EST:     TTTCCATTCTGACTGATTATGAAACTGGGCTCAACTACCTTGATTGGGAG                         ATTGGAAAGCATGGTATAATTATTGAGTTTACTGATCCTGACTATAATACA
genomic: TTTCCATTCTGACTGATTATGAAACTGGGCTCAACTACCTTGATTGGGAGgtatgggttt ... ctttttgcagATTGGAAAGCATGGTATAATTATTGAGTTTACTGATCCTGACTATAATACA
EST: gi|110358301|gb|EC922414.1|EC922414
EST:     TTTCCATTCTGACTGATTATGAAACTGGGCTCAACTACCTTGATTGGGAG                         ATGGGAAAGCATGGTATAATTATTGAGTTTACTGATCCTGACTATAATACA
genomic: TTTCCATTCTGACTGATTATGAAACTGGGCTCAACTACCTTGATTGGGAGgtatgggttt ... ctttttgcagATTGGAAAGCATGGTATAATTATTGAGTTTACTGATCCTGACTATAATACA
EST: gi|33410301|gb|CF215928.1|CF215928
EST:     TTTCCATTCTGACTGATTATGAAACTGGGCTCAACTACCTTGATTGGGAG                         ATTGGAAAGCATGGTATAATTATTGAGTTTACTGATCCTGACTATAATACA
genomic: TTTCCATTCTGACTGATTATGAAACTGGGCTCAACTACCTTGATTGGGAGgtatgggttt ... ctttttgcagATTGGAAAGCATGGTATAATTATTGAGTTTACTGATCCTGACTATAATACA
EST: gi|33410379|gb|CF216006.1|CF216006
EST:     TTTCCATTCTGACTGATTATGAAACTGGGCTCAACTACCTTGATTGGGAG                         ATTGGAAAGCATGGTATAATTATTGAGTTTACTGATCCTGACTATAATACA
genomic: TTTCCATTCTGACTGATTATGAAACTGGGCTCAACTACCTTGATTGGGAGgtatgggttt ... ctttttgcagATTGGAAAGCATGGTATAATTATTGAGTTTACTGATCCTGACTATAATACA
EST: gi|294966108|gb|GW837475.1|GW837475
EST:     TTTCCATTCTGACTGATTATGAAACTGGGCTCAGCTACCTTGATTGGGAG                         ATTGGAAAGCATGGTATAATTATTGAGTTTACTGATCCTGACTATAATACA
genomic: TTTCCATTCTGACTGATTATGAAACTGGGCTCAACTACCTTGATTGGGAGgtatgggttt ... ctttttgcagATTGGAAAGCATGGTATAATTATTGAGTTTACTGATCCTGACTATAATACA
EST: gi|110369937|gb|EC934110.1|EC934110
EST:     TTTCCATTCTGACTGATTATGAAACTGGGCTCAACTACCTTGATTGGGAG                         ATTGGAAAGCATGGTATAATTATTGAGTTTACTGATCCTGACTATAATACA
genomic: TTTCCATTCTGACTGATTATGAAACTGGGCTCAACTACCTTGATTGGGAGgtatgggttt ... ctttttgcagATTGGAAAGCATGGTATAATTATTGAGTTTACTGATCCTGACTATAATACA
EST: gi|34549687|gb|CF517919.1|CF517919
EST:     TTTCCATTCTGACTGATTATGAAACTGGGCTCAACTACCTTGATTGGGAG                         ATTGGAAAGCATGGTATAATTATTGAGTTTACTGATCCTGACTATAATACA
genomic: TTTCCATTCTGACTGATTATGAAACTGGGCTCAACTACCTTGATTGGGAGgtatgggttt ... ctttttgcagATTGGAAAGCATGGTATAATTATTGAGTTTACTGATCCTGACTATAATACA
EST: gi|26267720|gb|CA818783.1|CA818783
EST:     CTTCCATTCTGACTGATTATGAAACTGGGCTCAACTACCTTGATTGGGAG                         ATTGGAAAGCATGGTATAATTATTGAGTTTACTGATCCTGACTATAATACA
genomic: TTTCCATTCTGACTGATTATGAAACTGGGCTCAACTACCTTGATTGGGAGgtatgggttt ... ctttttgcagATTGGAAAGCATGGTATAATTATTGAGTTTACTGATCCTGACTATAATACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gattttttactgctcttctttcccactgtcataatttattaatttctttttgcagATTGGAAAGCATGGTATAATTATTGAGTTTACTGATCCTGACTATAATACAAGGCGAAGTGCCACATATTTGCCCGAGGTGGCTGCCCATGAAG
                                    tattaat  putative branch site (score: 2)
                                          tttctttttgc  CT-rich tract
                        actgtcataatttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tggaaaatagctcctaaatttagcatgaatgaattctggatagtggattttttactgctcttctttcccactgtcataatttattaatttctttttgcagATTGGAAAGCATGGTATAATTATTGAGTTTACTGATCCTGACTATAATACAAGGCGAAGTGCCACATATTTGCCCGAGGTGGCTGCCCATGAAG

-ggaaaat
- - - - - ctcctaa
- - - - - - - - - - - gcatgaa
- - - - - - - - - - - - - - - - attctgg