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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...caaagagctagagtcaagtgagtaacatatgatgcatgtcacgcacttctctcaatcaaaatttattagcttactctgaattttgttctcttattatcagGCCCTTCTTCATTCCTCCCACATGTACCATGAAGCCAAGCATTCATTTGCCAGCCATGGTGTGAAGTTCCCATCTGTTGAGGTTGATCTACCTGCCATGA

Basic information

species Vitis vinifera
transcript Vv05s0020g00380.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0020g00380.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA17G04210.1 (Glycine max), 3'ss of exon 1
caaaga-gctagagtcaagtgagtaacatatgatgcatgtcacgcacttctctcaatcaaaatttattagcttact--ctgaattttgttctcttattatcagGCCCTTCTTCATTCCTCCCACATGTACCATGAAGCCAAGCATTCATTTGCCAGCCATGGTGTGAAGTTCCCATCTGTTGAGGTTGATCTACCTGCCATGA
    ||   |  | |    |   ||   |   | | ||       |      || |   | |   ||   || | |  | | |  ||  | | ||  || ||||| ||||| ||||| ||||||||||| ||||| || || ||| ||||||||| |||||| || |||||  ||||||||||||||||| | || |||||||
tgctgacattgtaattccatatatagttttaaaagaataatggatataatattcta--gagacccatgtactcatttgcggtaccttcatattttggta-cagGCACTTCTGCATTCTTCCCACATGTATCATGAGGCTAAACATGCATTTGCCAACCATGGGGTCAAGTTTTCATCTGTTGAGGTTGATTTGCCAGCCATGA

upper sequence: Vv05s0020g00380.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA07G36040.1 (Glycine max), 3'ss of exon 1
caaagagctagagtcaagtgagtaacatatgatgcatgtcacgcacttctctcaatcaaaatttattagcttact--ctgaattttgttctcttattatcagGCCCTTCTTCATTCCTCCCACATGTACCATGAAGCCAAGCATTCATTTGCCAGCCATGGTGTGAAGTTCCCATCTGTTGAGGTTGATCTACCTGCCATGA
      | |  | |    |   |||  ||  |   |  | | | |  |       |  | |   ||   || | |  | | |  ||  | | ||  || ||||| ||| | ||||| ||||||||||| ||||| || || ||| ||||||||| |||||| || |||||  ||||||| ||||||||| | || |||||||
gttgatgttgtaattccatatataatttaaaaaaga-ataatggatataatattctagagacccatgcactcatttacggtaccttcatattttggta-cagGCACTTTTGCATTCTTCCCACATGTATCATGAGGCTAAACATGCATTTGCCAACCATGGGGTCAAGTTTTCATCTGTCGAGGTTGATTTGCCAGCCATGA

upper sequence: Vv05s0020g00380.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT3G17240.3 (Arabidopsis thaliana), 3'ss of exon 1
--caaagagctagagtcaagtgagtaacatatgatgcatgtcac-gcacttctctcaatcaaaatttattagcttactctgaattttgttctcttattatcagGCCCTTCTTCATTCCTCCCACATGTACCATGAAGCCAAGCATTCATTTGCCAGCCATGGTGTGAAGTTCCCATCTGTTGAGGTTGATCTACCTGCCATGA
  ||     || |  |    ||  |     ||  ||   ||| | |        |  || || || ||| | | || ||| | ||| |||       ||| ||||||||||||| || || ||||||||||||||||| |||||    ||||| | ||||||||| ||| || | || |||||||| ||||| ||||| ||| 
atcacgatcctcgcattttttgttttgtg-attgtgttagtctctgtttgagatttgattaatatatatga-cataatct-agtttagtttctgctgtattagGCCCTTCTTCACTCTTCTCACATGTACCATGAAGCAAAGCACGTTTTTGCTAACCATGGTGTTAAGGTCTCTTCGGTTGAGGTAGATCTTCCTGCTATGT

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|352781168|gb|FQ466481.1|FQ466481
EST:     GCGGCACTCTCGGCGGTACCTGTCTCAACGTCGGTTGTATTCCTTCCAAG                         GCCCTTCTTCATTCCTCCCACATGTACCATGAAGCCAAGCATTCATTTGCC
genomic: GCGGCACTCTCGGCGGTACCTGTCTCAACGTCGGTTGTATTCCTTCCAAGgtaatatagg ... ttattatcagGCCCTTCTTCATTCCTCCCACATGTACCATGAAGCCAAGCATTCATTTGCC
EST: gi|110712782|gb|EE088127.1|EE088127
EST:     GCGGCACTCTCGGCGGTACCTGTCTCAACGTCGGTTGTATTCCTTCCAAG                         GCCCTTCTTCATTCCTCCCACATGTACCATGAAGCCAAGCATTCATTTGCC
genomic: GCGGCACTCTCGGCGGTACCTGTCTCAACGTCGGTTGTATTCCTTCCAAGgtaatatagg ... ttattatcagGCCCTTCTTCATTCCTCCCACATGTACCATGAAGCCAAGCATTCATTTGCC
EST: gi|294966285|gb|GW837536.1|GW837536
EST:     GCGGCACTCTCGGCGGTACCTGTCTCAACGTCGGTTGTATTCCTTCCAAG                         GCCCTTCTTCATTCCTCCCACATGTACCATGAAGCCAAGCATTCATTTGCC
genomic: GCGGCACTCTCGGCGGTACCTGTCTCAACGTCGGTTGTATTCCTTCCAAGgtaatatagg ... ttattatcagGCCCTTCTTCATTCCTCCCACATGTACCATGAAGCCAAGCATTCATTTGCC
EST: gi|351022044|gb|FQ437831.1|FQ437831
EST:     GCGGCACTCTCGGCGGTACCTGTCTCAACGTCGGTTGTATTCCTTCCAAG                         GCCCTTCTTCATTCCTCCCACATGTACCATGAAGCCAAGCATTCATTTGCC
genomic: GCGGCACTCTCGGCGGTACCTGTCTCAACGTCGGTTGTATTCCTTCCAAGgtaatatagg ... ttattatcagGCCCTTCTTCATTCCTCCCACATGTACCATGAAGCCAAGCATTCATTTGCC
EST: gi|349823721|gb|FQ415132.1|FQ415132
EST:     GCGGCACTCTCGGCGGTACCTGTCTCAACGTCGGTTGTATTCCTTCCAAG                         GCCCTTCTTCATTCCTCCCACATGTACCATGAAGCCAAGCATTCATTTGCC
genomic: GCGGCACTCTCGGCGGTACCTGTCTCAACGTCGGTTGTATTCCTTCCAAGgtaatatagg ... ttattatcagGCCCTTCTTCATTCCTCCCACATGTACCATGAAGCCAAGCATTCATTTGCC
EST: gi|110712231|gb|EE089616.1|EE089616
EST:     GCGGCACTCTCGGCGGTACCTGTCTCAACGTCGGTTGTATTCCTTCCAAG                         GCCCTTCTTCATTCCTCCCACATGTACCATGAAGCCAAGCATTCATTTGCC
genomic: GCGGCACTCTCGGCGGTACCTGTCTCAACGTCGGTTGTATTCCTTCCAAGgtaatatagg ... ttattatcagGCCCTTCTTCATTCCTCCCACATGTACCATGAAGCCAAGCATTCATTTGCC
EST: gi|110412873|gb|EC978636.1|EC978636
EST:     GCGGCACTCTCGGCGGTACCTGTCTCAACGTCGGTTGTATTCCTTCCAAG                         GCCCTTCTTCATTCCTCCCACATGTACCATGAAGCCAAGCATTCATTTGCC
genomic: GCGGCACTCTCGGCGGTACCTGTCTCAACGTCGGTTGTATTCCTTCCAAGgtaatatagg ... ttattatcagGCCCTTCTTCATTCCTCCCACATGTACCATGAAGCCAAGCATTCATTTGCC
EST: gi|110718447|gb|EE095288.1|EE095288
EST:     GCGGCACTCTCGGCGGTACCTGTCTCAACGTCGGTTGTATTCCTTCCAAG                         GCCCTTCTTCATTCCTCCCACATGTACCATGAAGCCAAGCATTCATTTGCC
genomic: GCGGCACTCTCGGCGGTACCTGTCTCAACGTCGGTTGTATTCCTTCCAAGgtaatatagg ... ttattatcagGCCCTTCTTCATTCCTCCCACATGTACCATGAAGCCAAGCATTCATTTGCC
EST: gi|30251404|gb|CB969137.1|CB969137
EST:     GCGGCACTCTCGGCGGTACCTGTCTCAACGTCGGTTGTATTCCTTCCAAG                         GCCCTTCTTCATTCCTCCCACATGTACCATGAAGCCAAGCATTCATTTGCC
genomic: GCGGCACTCTCGGCGGTACCTGTCTCAACGTCGGTTGTATTCCTTCCAAGgtaatatagg ... ttattatcagGCCCTTCTTCATTCCTCCCACATGTACCATGAAGCCAAGCATTCATTTGCC
EST: gi|110710824|gb|EE087321.1|EE087321
EST:     GCGGCACTCTCGGCGGTACCTGTCTCAACGTCGGTTGTATTCCTTCCAAG                         GCCCTTCTTCATTCCTCCCACATGTACCATGAAGCCAAGCATTCATTTGCC
genomic: GCGGCACTCTCGGCGGTACCTGTCTCAACGTCGGTTGTATTCCTTCCAAGgtaatatagg ... ttattatcagGCCCTTCTTCATTCCTCCCACATGTACCATGAAGCCAAGCATTCATTTGCC
EST: gi|110720802|gb|EE097045.1|EE097045
EST:     GCGGCACTCTCGGCGGTACCTGTCTCAACGTCGGTTGTATTCCTTCCAAG                         GCCCTTCTTCATTCCTCCCACATGTACCATGAAGCCAAGCATTCATTTGCC
genomic: GCGGCACTCTCGGCGGTACCTGTCTCAACGTCGGTTGTATTCCTTCCAAGgtaatatagg ... ttattatcagGCCCTTCTTCATTCCTCCCACATGTACCATGAAGCCAAGCATTCATTTGCC
EST: gi|110711226|gb|EE087511.1|EE087511
EST:     GCGGCACTCTCGGCGGTACCTGTCTCAACGTCGGTTGTATTCCTTCCAAG                         GCCCTTCTTCATTCCTCCCACATGTACCATGAAGCCAAGCATTCATTTGCC
genomic: GCGGCACTCTCGGCGGTACCTGTCTCAACGTCGGTTGTATTCCTTCCAAGgtaatatagg ... ttattatcagGCCCTTCTTCATTCCTCCCACATGTACCATGAAGCCAAGCATTCATTTGCC
EST: gi|110720297|gb|EE096106.1|EE096106
EST:     GCGGCACTCTCGGCGGTACCTGTCTCAACGTCGGTTGTATTCCTTCCAAG                         GCCCTTCTTCATTCCTCCCACATGTACCATGAAGCCAAGCATTCATTTGCC
genomic: GCGGCACTCTCGGCGGTACCTGTCTCAACGTCGGTTGTATTCCTTCCAAGgtaatatagg ... ttattatcagGCCCTTCTTCATTCCTCCCACATGTACCATGAAGCCAAGCATTCATTTGCC
EST: gi|110375938|gb|EC940968.1|EC940968
EST:     GCGGCACGCTCGGCGGTACCTGTCTCAACGTCGGTTGTATTCCTTCCAAG                         GCCCTTCTTCATTCCTCCCACATGTACCATGAAGCCAAGCATTCATTTGCC
genomic: GCGGCACTCTCGGCGGTACCTGTCTCAACGTCGGTTGTATTCCTTCCAAGgtaatatagg ... ttattatcagGCCCTTCTTCATTCCTCCCACATGTACCATGAAGCCAAGCATTCATTTGCC
EST: gi|110690663|gb|EE068018.1|EE068018
EST:     GCGGCACTCTCGGCGGTACCTGTCTCAACGTCGGTTGTATTCCTTCCAAG                         GCCCTTCTTCATTCCTCCCACATGTACCATGAAGCCAAGCATTCATTTGCC
genomic: GCGGCACTCTCGGCGGTACCTGTCTCAACGTCGGTTGTATTCCTTCCAAGgtaatatagg ... ttattatcagGCCCTTCTTCATTCCTCCCACATGTACCATGAAGCCAAGCATTCATTTGCC
EST: gi|110713757|gb|EE089955.1|EE089955
EST:     GCGGCACTCTCGGCGGTACCTGTCTCAACGTCGGTTGTATTCCTTCCAAG                         GCCCTTCTTCATTCCTCCCACATGTACCATGAAGCCAAGCATTCATTTGCC
genomic: GCGGCACTCTCGGCGGTACCTGTCTCAACGTCGGTTGTATTCCTTCCAAGgtaatatagg ... ttattatcagGCCCTTCTTCATTCCTCCCACATGTACCATGAAGCCAAGCATTCATTTGCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttctctcaatcaaaatttattagcttactctgaattttgttctcttattatcagGCCCTTCTTCATTCCTCCCACATGTACCATGAAGCCAAGCATTCATTTGCCAGCCATGGTGTGAAGTTCCCATCTGTTGAGGTTGATCTACCTGCCATGA
                      agcttac  putative branch site (score: 3)
                                   ttttgttctcttatt  putative PPT
      tcaatcaaaatttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
caaagagctagagtcaagtgagtaacatatgatgcatgtcacgcacttctctcaatcaaaatttattagcttactctgaattttgttctcttattatcagGCCCTTCTTCATTCCTCCCACATGTACCATGAAGCCAAGCATTCATTTGCCAGCCATGGTGTGAAGTTCCCATCTGTTGAGGTTGATCTACCTGCCATGA

-aaagagc
- - - - - - - - - - agtaaca
- - - - - - - - - - - - - - - - -gcatgtc
- - - - - - - - - - - - - - - - - - - - - - - - - - -aatcaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctctgaa