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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttttttcttcgctcaaccattctacttaagcatgattatgatgtctaactgttttctaacttgccaagataatcatcatgtttccatgtgttggttgcagAACTTCCCTTGTCAAGAAGTTGAAAGGCATAACAAACCAGAGGTTGAACTAAA

Basic information

species Vitis vinifera
transcript Vv05s0029g01310.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0029g01310.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA08G11740.1 (Glycine max), 3'ss of exon 2
---ttttttcttcgctcaaccattctacttaagcatgattatgatgtctaactgttttctaacttgccaagataatcatcatgtttccatgtgttggttgcagAACTTCCCTTGTCAAGAAGTTGAAAGGCATAACAAACCAGAGGTTGAACTAAA
   |   ||||||| | |||    ||    |    || ||||  | ||  |  | |    || |   || |       |  |  |||   |   ||||| |||||||| || ||||||||||| |||||||||||||| || ||||||||||| ||
gtatcacttcttcgtt-aacgccactctcaatatttgtttat--tttcgcatcgat----aaataatcacgtgttgtgttgttcttcttcgctatggttccagAACTTTCCGTGTCAAGAAGTCGAAAGGCATAACAAGCCCGAGGTTGAACTCAA

upper sequence: Vv05s0029g01310.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA05G28650.1 (Glycine max), 3'ss of exon 2
---ttttttcttcgctcaaccattctacttaagcatgattatgatgtctaactgttttctaacttgccaagataatcatcatgtttccatgtgttggttgcagAACTTCCCTTGTCAAGAAGTTGAAAGGCATAACAAACCAGAGGTTGAACTAAA
   |   | ||||       | ||   | | | ||  || || |  |||   | | ||||    ||    | |  |  |  |  |||   |   || || |||||||| || || |||||||| |||||||||||||| || ||||||||||| ||
gtatcactccttcttcgtttcttttggcatcaacaaaataatcacctct---tctgttctgttctgttctgttgttttt--ttcttcttcgctatgcttccagAACTTTCCCTGCCAAGAAGTCGAAAGGCATAACAAGCCCGAGGTTGAACTCAA

upper sequence: Vv05s0029g01310.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT4G14147.1 (Arabidopsis thaliana), 3'ss of exon 3
ttttttcttcgctcaaccattctacttaagcatgattatgatgtctaactgttttctaacttgccaagataatcatcat----gtttccatgtgt---tggttgcagAACTTCCCTTGTCAAGAAGTTGAAAGGCATAACAAACCAGAGGTTGAACTAAA
       |||| | ||  |    |     ||     |    | | | |     |||    || |   | | ||  || |    | ||| ||   |   |  |||||||| || |||||||||||||||||||||||||| ||||||||||||||| ||||
------tttcgttaaagtaggtgaaaggggc-catgtggagtctttgaaaacattcagctttacatggtttatattcctgaaagcttctatacttctctacttgcagAATTTTCCTTGTCAAGAAGTTGAAAGGCATAATAAACCAGAGGTTGAATTAAA

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|29785136|gb|CB341880.2|CB341880
EST:     TGTATTTCACTTGCATACGGAACACTCTTGAAGCTGCCATGTGCTTGCAG                         AACTTCCCTTGTCAAGAAGTTGAAAGGCATAACAAACCAGAGGTTGAACTA
genomic: TGTATTTCACTTGCATACGGAACACTCTTGAAGCTGCCATGTGCCTGCAGgtatgctgta ... ttggttgcagAACTTCCCTTGTCAAGAAGTTGAAAGGCATAACAAACCAGAGGTTGAACTA
EST: gi|71855533|gb|DT004588.1|DT004588
EST:     TGTATTTCACTTGCATACGGAACACTCTTGAAGCTGCCATGTGCCTGCAG                         AACTTCCCTTGTCAAGAAGTTGAAAGGCATAACAAACCAGAGGTTGAACTA
genomic: TGTATTTCACTTGCATACGGAACACTCTTGAAGCTGCCATGTGCCTGCAGgtatgctgta ... ttggttgcagAACTTCCCTTGTCAAGAAGTTGAAAGGCATAACAAACCAGAGGTTGAACTA
EST: gi|351046852|gb|FQ454462.1|FQ454462
EST:     TGTATTTCACTTGCATGCGGAACACTCTTGAAGCTGCCATGTGCCTGCAG                         AACTTCCCTTGTCAAGAAGTTGAAAGGCATAACAAACCAGAGGTTGAACTA
genomic: TGTATTTCACTTGCATACGGAACACTCTTGAAGCTGCCATGTGCCTGCAGgtatgctgta ... ttggttgcagAACTTCCCTTGTCAAGAAGTTGAAAGGCATAACAAACCAGAGGTTGAACTA
EST: gi|71857830|gb|DT006885.1|DT006885
EST:     TGTATTTCACTTGCATACGGAACACTCTTGAAGCTGCCATGTGCCTGCAG                         AACTTCCCTTGTCAAGAAGTTGAAAGGCATAACAAACCAGAGGTTGAACTA
genomic: TGTATTTCACTTGCATACGGAACACTCTTGAAGCTGCCATGTGCCTGCAGgtatgctgta ... ttggttgcagAACTTCCCTTGTCAAGAAGTTGAAAGGCATAACAAACCAGAGGTTGAACTA
EST: gi|110693326|gb|EE069458.1|EE069458
EST:     TGTATTTCACTTGCATACGGAACACTCTTGAAGCTGCCATGTGCCTGCAG                         AACTTCCCTTGTCAAGAAGTTGAAAGGCATAACAAACCAGAGGTTGAACTA
genomic: TGTATTTCACTTGCATACGGAACACTCTTGAAGCTGCCATGTGCCTGCAGgtatgctgta ... ttggttgcagAACTTCCCTTGTCAAGAAGTTGAAAGGCATAACAAACCAGAGGTTGAACTA
EST: gi|349826081|gb|FQ415886.1|FQ415886
EST:     TGTATTTCACTTGCATACGGAACACTCTTGAAGCTGCCATGTGCCCGCAG                         AACTTCCCTTGTCAAGAAGTTGAAAGGCATAACAAACCAGAGGTTGAACTA
genomic: TGTATTTCACTTGCATACGGAACACTCTTGAAGCTGCCATGTGCCTGCAGgtatgctgta ... ttggttgcagAACTTCCCTTGTCAAGAAGTTGAAAGGCATAACAAACCAGAGGTTGAACTA
EST: gi|33405119|gb|CF210746.1|CF210746
EST:     TGTATTTCACTTGCATACGGAACACTCTTGAAGCTGCCATGTGCCTGCAG                         AACTTCCCTTGTCAAGAAGTTGAAAGGCATAACAAACCAGAGGTTGAACTA
genomic: TGTATTTCACTTGCATACGGAACACTCTTGAAGCTGCCATGTGCCTGCAGgtatgctgta ... ttggttgcagAACTTCCCTTGTCAAGAAGTTGAAAGGCATAACAAACCAGAGGTTGAACTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taactgttttctaacttgccaagataatcatcatgtttccatgtgttggttgcagAACTTCCCTTGTCAAGAAGTTGAAAGGCATAACAAACCAGAGGTTGAACTAAA
        ttctaac  putative branch site (score: 1)
      ttttctaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttttttcttcgctcaaccattctacttaagcatgattatgatgtctaactgttttctaacttgccaagataatcatcatgtttccatgtgttggttgcagAACTTCCCTTGTCAAGAAGTTGAAAGGCATAACAAACCAGAGGTTGAACTAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - tcaacca
- - - - - - - - - - - - - - -gcatgat
- - - - - - - - - - - - - - - - - - - tgatgtc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cttgcca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -catcatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccatgtg