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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactattctgatctgataatccggataagttgatgatttatctgttgatataatttaatttctttgttagCTTGATGATTGGGTGCTATGTCGAATCTACAAGAAGAACAACACGCATAGAACGCTGGATCCTGACAAGGATGACTCCATGGACGACATGCTTGGGCCGG

Basic information

species Vitis vinifera
transcript Vv19s0014g03300.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv19s0014g03300.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA13G35560.1 (Glycine max), 3'ss of exon 2
-----------------------------gtactattctgatctgataatccggataagttgatgatttatctgttgatata-atttaatttctttgttagCTTGATGATTGGGTGCTATGTCGAATCTACAAGAAGAACAACACGCATAGAACGC---TGGATCCTGACAAGGATGACTCCATGGACGACATGCTTGGGCCGG
                               | |||| || | |    ||||   |  ||   |  |  || || || | |  ||||  | | | | | ||||||||||||||||||| || |||||||||||||||| ||||||||||||  | |   |||| | ||||| ||| || || ||||| |||||| ||||     
attctattatctaagttttgttcatgaattaaatattgtgctttatatatccctttgggtgatttctgaatttggtgctttggattttgtgtgtctat-agCTTGATGATTGGGTGCTGTGCCGAATCTACAAGAAGAGCAACACGCATAGGTCACCCATGGAGCATGACAGGGAAGATTCAATGGATGACATGATTGGAG---

upper sequence: Vv19s0014g03300.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA12G34990.1 (Glycine max), 3'ss of exon 2
-------------------gtactattctgatctgataatccggataagttgatgatttatctgttgatataatttaatttc---tttgt-------tagCTTGATGATTGGGTGCTATGTCGAATCTACAAGAAGAACAACACGCATAGAACGC---TGGATCCTGACAAGGATGACTCCATGGACGACATGCTTGGGCCGG
                      || |    ||||    ||||   |  ||   |  |  || || || |    || |||||    || ||       |||||||||||||||||||| || |||||||||||||||| ||||||||||||  | |   |||| | ||| | ||| || || ||||| |||||| ||||     
tgtccatgaattaaatattacgctttatatatctatccatccctttgggtaatttctgaatttggtggtgcttttgaattttgtgttggtgtgtgtctagCTTGATGATTGGGTGCTGTGCCGAATCTACAAGAAGAGCAACACGCATAGGTCACCCATGGAGCATGAAAGGGAAGATTCAATGGATGACATGATTGGAG---

upper sequence: Vv19s0014g03300.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT3G15510.1 (Arabidopsis thaliana), 3'ss of exon 2
gtactattc-------tgatctgataatccggat----aagttgatgatttatctgttgatataatttaatttctttgt---tagCTTGATGATTGGGTGCTATGTCGAATCTACAAGAAGAACAACACGCATAGAACGCTGGATCCTGACAAGGATGACTCCATGGACGACATGCTTGGGCCGG-
|||  ||||       |  ||  ||| ||  |||     | ||  |||| |   | |||  |  ||||  ||  | |||   |||||||||||||||||| ||||| |||||||||||||||||||| |   | ||    | |||   || |||||| |    |||  |||  | | |   | || 
gtatgattcatcgaaattttcaaatattcttgattcttgaattcttgatcttgattttgggaatatttttttattgtgtgtgtagCTTGATGATTGGGTGTTATGTAGAATCTACAAGAAGAACAACGCAAGTCGACATGTTGATAACGATAAGGATCATGATATGATCGAT-TACATTTTCAGGA

upper sequence: Vv19s0014g03300.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT1G52880.1 (Arabidopsis thaliana), 3'ss of exon 2
-----gtactattctgatctgataatccggat----------aagt--tgatgatttatctgttgatataatttaatttctttgttagCTTGATGATTGGGTGCTATGTCGAATCTACAAGAAGAACAACACGCATAGAACGCTGGATCCTGACAAGGATGACTCCATGGACGACATGCTTGGGCCGG--
      || |||  |  ||| | ||||  |||          ||||  ||||    ||  | ||||| |  ||| ||| || ||| ||||||||||||||||| | ||||| ||||||||||| ||||| | | | || |  || ||      ||       |  |||   |  |  | |   |      
gtatattattataatattcttaaaatcttgattttaaaagaaaagttttgattggctaatttttgat-tctttttattactatgt-agCTTGATGATTGGGTGTTGTGTCGTATCTACAAGAAAAACAATA-GTACAGCAT-CTAGACATCATCATCATCTTCATCATATTCATCTAGATAATGATCATC

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|110698654|gb|EE076400.1|EE076400
EST:     ACACAAAGCCTCCCGGATGCGATATGGGCAACAAGAAGAACTCTTTGCGG                         CTTGATGATTGGGTGCTATGTCGAATCTACAAGAAGAACAACACGCATAGA
genomic: ACACAAAGCCTCCCGGATGCGATATGGGCAACAAGAAGAACTCTTTGCGGgtactattct ... tctttgttagCTTGATGATTGGGTGCTATGTCGAATCTACAAGAAGAACAACACGCATAGA
EST: gi|110695778|gb|EE074187.1|EE074187
EST:     GATGCGATATGGGCAACAAGAAGAACTCTTTGCGG                         CTTGATGATTGGGTGCTATGTCGAATCTACAAGAAGAACAACACGCATAGA
genomic: GATGCGATATGGGCAACAAGAAGAACTCTTTGCGGgtactattct ... tctttgttagCTTGATGATTGGGTGCTATGTCGAATCTACAAGAAGAACAACACGCATAGA
EST: gi|110392391|gb|EC957779.1|EC957779
EST:     ACACAAAGCCTCCCGGATGCGATATGGGCAACAAGAAGAACTCTTTGCGG                         CTTGATGATTGGGTGCTATGTCGAATCTACAAGAAGAACAACACGCATAGA
genomic: ACACAAAGCCTCCCGGATGCGATATGGGCAACAAGAAGAACTCTTTGCGGgtactattct ... tctttgttagCTTGATGATTGGGTGCTATGTCGAATCTACAAGAAGAACAACACGCATAGA
EST: gi|110715066|gb|EE092691.1|EE092691
EST:     ACACAAAGCCTCCCGGATGCGATATGGGCAACAAGAAGAACTCTTTGCGG                         CTTGATGATTGGGTGCTATGTCGAATCTACAAGAAGAACAACACGCATAGA
genomic: ACACAAAGCCTCCCGGATGCGATATGGGCAACAAGAAGAACTCTTTGCGGgtactattct ... tctttgttagCTTGATGATTGGGTGCTATGTCGAATCTACAAGAAGAACAACACGCATAGA
EST: gi|30133635|gb|CB918974.1|CB918974
EST:     ACACAAAGCCTCCCGGATGCGATATGGGCAACAAGAAGAACTCTTTGCGG                         CTTGATGATTGGGTGCTATGTCGAATCTACAAGAAGAACAACACGCATAGA
genomic: ACACAAAGCCTCCCGGATGCGATATGGGCAACAAGAAGAACTCTTTGCGGgtactattct ... tctttgttagCTTGATGATTGGGTGCTATGTCGAATCTACAAGAAGAACAACACGCATAGA
EST: gi|110715806|gb|EE094279.1|EE094279
EST:     ACACAAAGCCTCCCGGATGCGATATGGGCAACAAGAAGAACTCTTTGCGG                         CTTGATGATTGGGTGCTATGTCGAATCTACAAGAAGAACAACACGCATAGA
genomic: ACACAAAGCCTCCCGGATGCGATATGGGCAACAAGAAGAACTCTTTGCGGgtactattct ... tctttgttagCTTGATGATTGGGTGCTATGTCGAATCTACAAGAAGAACAACACGCATAGA
EST: gi|30299010|gb|CB975804.1|CB975804
EST:     ACACAAAGCCTCCCGGATGCGATATGGGCAACAAGAAGAACTCTTTGCGG                         CTTGATGATTGGGTGCTATGTCGAATCTACAAGAAGAACAACACGCATAGA
genomic: ACACAAAGCCTCCCGGATGCGATATGGGCAACAAGAAGAACTCTTTGCGGgtactattct ... tctttgttagCTTGATGATTGGGTGCTATGTCGAATCTACAAGAAGAACAACACGCATAGA
EST: gi|110724037|gb|EE099512.1|EE099512
EST:     ACACAAAGCCTCCCGGATGCGATATGGGCAACAAGAAGAACTCTTTGCGG                         CTTGATGATTGGGTGCTATGTCGAATCTACAAGAAGAACAACACGCATAGA
genomic: ACACAAAGCCTCCCGGATGCGATATGGGCAACAAGAAGAACTCTTTGCGGgtactattct ... tctttgttagCTTGATGATTGGGTGCTATGTCGAATCTACAAGAAGAACAACACGCATAGA
EST: gi|30130874|gb|CB916213.1|CB916213
EST:     ACACAAAGCCTCCCGGATGCGATATGGGCAACAAGAAGAACTCTTTGCGG                         CTTGATGATTGGGTGCTATGTCGAATCTACNAGAAGAACAACACGCATAGA
genomic: ACACAAAGCCTCCCGGATGCGATATGGGCAACAAGAAGAACTCTTTGCGGgtactattct ... tctttgttagCTTGATGATTGGGTGCTATGTCGAATCTACAAGAAGAACAACACGCATAGA
EST: gi|110725159|gb|EE101550.1|EE101550
EST:     ACACAAAGCCTCCCGGATGCGATATGGGCAACAAGAAGAACTCTTTGCGG                         CTTGATGATTGGGTGCTATGTCGAATCTACAAGAAGAACAACACGCATAGA
genomic: ACACAAAGCCTCCCGGATGCGATATGGGCAACAAGAAGAACTCTTTGCGGgtactattct ... tctttgttagCTTGATGATTGGGTGCTATGTCGAATCTACAAGAAGAACAACACGCATAGA
EST: gi|110709962|gb|EE085891.1|EE085891
EST:     ACACAAAGCCTCCCGGATGCGATATGGGCAACAAGAAGAACTCTTTGCGG                         CTTGATGATTGGGTGCTATGTCNAATCTACAAGAAGAACAACACGCATAGA
genomic: ACACAAAGCCTCCCGGATGCGATATGGGCAACAAGAAGAACTCTTTGCGGgtactattct ... tctttgttagCTTGATGATTGGGTGCTATGTCGAATCTACAAGAAGAACAACACGCATAGA
EST: gi|26264640|gb|CA815703.1|CA815703
EST:     ACACAA-GCCTCCCGGATGCGATATGGGCAACAAGAAGAACTCTTTGCGG                         CTTGATGATTGGGTGCTATGTCGAATCTACAAGAAGAACAACACGCATAGA
genomic: ACACAAAGCCTCCCGGATGCGATATGGGCAACAAGAAGAACTCTTTGCGGgtactattct ... tctttgttagCTTGATGATTGGGTGCTATGTCGAATCTACAAGAAGAACAACACGCATAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ataatccggataagttgatgatttatctgttgatataatttaatttctttgttagCTTGATGATTGGGTGCTATGTCGAATCTACAAGAAGAACAACACGCATAGAACGCTGGATCCTGACAAGGATGACTCCATGGACGACATGCTTGGGCCGG
                                     atttaat  putative branch site (score: 4)
                                           tttctttgtt  CT-rich tract
                    atttatctgttgatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtactattctgatctgataatccggataagttgatgatttatctgttgatataatttaatttctttgttagCTTGATGATTGGGTGCTATGTCGAATCTACAAGAAGAACAACACGCATAGAACGCTGGATCCTGACAAGGATGACTCCATGGACGACATGCTTGGGCCGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA