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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggagattgagatttagattaaagttcactttgatgccataattttttgaatgtgggagaaggtacatgggtgactgaaatgttatgttatgttttgttagCTTTCTCACTGGTGATCGAAATGCAAGATTCAGCTATGGGTATTCCAGTTTCAAGGGTAAAAGGCCTTCCATGGAGGATTTCTACGAGACTAGAATATCA

Basic information

species Vitis vinifera
transcript Vv18s0001g15050.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0001g15050.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA10G43810.4 (Glycine max), 3'ss of exon 1
ggagattgagatttagattaaagttcactttgatgccataattttttgaatgtgggaga--aggtacatgggtgactgaaatgttatg---ttatgttttgttagCTTTCTCACTGGTGATCGAAATGCAAGATTCAGCTATGGGTATTCCAGTTTCAAGGGTAAAAGGCCTTCCATGGAGGATTTCTACGAGACTAGAATATCA
     |||| ||||   | |    ||  ||| ||    | | |  | | ||          |  ||          | |||||   ||   |||| | |   |||||||||| ||||    ||||||| ||| ||||||||||| |||||||||||||||||||||||| | || |||||||||||||  ||||| | |||||||
-----ttgaaatttgtttcaggcatcctttttatttttttaataatggcattccaactctcaaatattcaaaattttaaaatgaagtgctcttatttctgtctagCTTTCTCTCTGGAAGCCGAAATGGAAGGTTCAGCTATGGATATTCCAGTTTCAAGGGTAAAAGGTCATCAATGGAGGATTTCTTTGAGACCAAAATATCA

upper sequence: Vv18s0001g15050.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA20G38500.1 (Glycine max), 3'ss of exon 1
ggagattgagatttagattaaagttcactttgatgcc---------ataattttttgaatgtgggagaaggtacatgggtgactgaaatgttatgttatgttttgttagCTTTCTCACTGGTGATCGAAATGCAAGATTCAGCTATGGGTATTCCAGTTTCAAGGGTAAAAGGCCTTCCATGGAGGATTTCTACGAGACTAGAATATCA
       || ||||   | |    ||  |||||||           ||    ||   | | |   | |    | ||     | |||| || | |  ||| | |   |||||||||| ||||    ||||||| ||| ||||||||||| |||||||||||||||||||||||| | || |||||||||||||  ||||| | |||||||
-------gaaatttgtttcaggcatccttttgatgtttttttaataatggcattccaactctcaaatattcaaaattttgaaatgaagtgctct--tatttctgtctagCTTTCTCTCTGGAAGCCGAAATGGAAGGTTCAGCTATGGATATTCCAGTTTCAAGGGTAAAAGGTCATCAATGGAGGATTTCTTTGAGACCAAAATATCA
















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|110712077|gb|EE089286.1|EE089286
EST:     ATGATTCTCTCTAGAGATCCCGCCGCCATCTTCAGCGGTGGCGGTATCAG                         CTTTCTCACTGGTGATCGAAATGCAAGATTCAGCTATGGGTATTCCAGTTT
genomic: ATGATTCTCTCTAGAGATCCCGCCGCCATCTTCAGCGGCGGCGGTATCAGgtttcctgtc ... gttttgttagCTTTCTCACTGGTGATCGAAATGCAAGATTCAGCTATGGGTATTCCAGTTT
EST: gi|351048563|gb|FQ448837.1|FQ448837
EST:     ATGATTCTCTCTAGAGATCCCGCCGCCATCTTCAGCGGCGGCGGTATCAG                         CTTTCTCACTGGTGATCGAAATGCAAGATTCAGCTATGGGTATTCCAGTTT
genomic: ATGATTCTCTCTAGAGATCCCGCCGCCATCTTCAGCGGCGGCGGTATCAGgtttcctgtc ... gttttgttagCTTTCTCACTGGTGATCGAAATGCAAGATTCAGCTATGGGTATTCCAGTTT
EST: gi|161716302|gb|FC064648.1|FC064648
EST:     ATGATTCTCTCTAGAGATCCCGCCGCCATCTTCAGCGGCGGCGGTATCAG                         CTTTCTCACTGGTGATCGAAATGCAAGATTCAGCTATGGGTATTCCAGTTT
genomic: ATGATTCTCTCTAGAGATCCCGCCGCCATCTTCAGCGGCGGCGGTATCAGgtttcctgtc ... gttttgttagCTTTCTCACTGGTGATCGAAATGCAAGATTCAGCTATGGGTATTCCAGTTT
EST: gi|71858300|gb|DT007355.1|DT007355
EST:     ATGATTCTCTCTAGAGATCCCGCCGCCATCTTCAGCGGCGGCGGTATCAG                         CTTTCTCACTGGTGATCGAAATGCAAGATTCAGCTATGGGTATTCCAGTTT
genomic: ATGATTCTCTCTAGAGATCCCGCCGCCATCTTCAGCGGCGGCGGTATCAGgtttcctgtc ... gttttgttagCTTTCTCACTGGTGATCGAAATGCAAGATTCAGCTATGGGTATTCCAGTTT
EST: gi|352791261|gb|FQ474951.1|FQ474951
EST:     ATGATTCTCTCTAGAGATCCCGCCGCCATCTTCAGCGGCGGCGGTATCAG                         CTTTCTCACTGGTGATCGAAATGCAAGATTCAGCTATGGGTATTCCAGTTT
genomic: ATGATTCTCTCTAGAGATCCCGCCGCCATCTTCAGCGGCGGCGGTATCAGgtttcctgtc ... gttttgttagCTTTCTCACTGGTGATCGAAATGCAAGATTCAGCTATGGGTATTCCAGTTT
EST: gi|27584677|gb|CB007372.1|CB007372
EST:     ATGATTCTCTCTAGAGATCCCGCCGCCATCTTCAGCGGCGGCGGTATCAG                         CTTTCTCACTGGTGATCGAAATGCAAGATTCAGCTATGGGTATTCCAGTTT
genomic: ATGATTCTCTCTAGAGATCCCGCCGCCATCTTCAGCGGCGGCGGTATCAGgtttcctgtc ... gttttgttagCTTTCTCACTGGTGATCGAAATGCAAGATTCAGCTATGGGTATTCCAGTTT
EST: gi|161717197|gb|FC066571.1|FC066571
EST:     ATGATTCTCTCTAGAGATCCCGCCGCCATCTTCAGCGGCGGCGGTATCAG                         CTTTCTCACTGGTGATCGAAATGCAAGATTCAGCTATGGGTATTCCAGTTT
genomic: ATGATTCTCTCTAGAGATCCCGCCGCCATCTTCAGCGGCGGCGGTATCAGgtttcctgtc ... gttttgttagCTTTCTCACTGGTGATCGAAATGCAAGATTCAGCTATGGGTATTCCAGTTT
EST: gi|351036088|gb|FQ463933.1|FQ463933
EST:     ATGATTCTCTCTAGAGATCCCGCCGCCATCTTCGGCGGCGGCGGTATCAG                         CTTTCTCACTGGTGATCGAAATGCAAGATTCAGCTATGGGTATTCCAGTTT
genomic: ATGATTCTCTCTAGAGATCCCGCCGCCATCTTCAGCGGCGGCGGTATCAGgtttcctgtc ... gttttgttagCTTTCTCACTGGTGATCGAAATGCAAGATTCAGCTATGGGTATTCCAGTTT
EST: gi|110711257|gb|EE087557.1|EE087557
EST:     ATGATTCTCTCTAGAGATCCCGCCGCCATCTTCAGCGGTGGCGGTATCAG                         CTTTCTCACTGGTGATCGAAATGCAAGATTCAGCTATGGGTATTCCAGTTT
genomic: ATGATTCTCTCTAGAGATCCCGCCGCCATCTTCAGCGGCGGCGGTATCAGgtttcctgtc ... gttttgttagCTTTCTCACTGGTGATCGAAATGCAAGATTCAGCTATGGGTATTCCAGTTT
EST: gi|161719283|gb|FC064823.1|FC064823
EST:     ATGATTCTCTCTAGAGATCCCGCCGCCATCTTCAGCGGCGGCGGTATCAG                         CTTTCTCACTGGTGATCGAAATGCAAGATTCAGCTATGGGTATTCCAGTTT
genomic: ATGATTCTCTCTAGAGATCCCGCCGCCATCTTCAGCGGCGGCGGTATCAGgtttcctgtc ... gttttgttagCTTTCTCACTGGTGATCGAAATGCAAGATTCAGCTATGGGTATTCCAGTTT
EST: gi|71856207|gb|DT005262.1|DT005262
EST:     ATGATTCTCTCTAGAGATCCCGCCGCCATCTTCAGCGGCGGCGGTATCAG                         CTTTCTCACTGGTGATCGAAATGCAAGATTCAACTATGGGTATTCCAGTTT
genomic: ATGATTCTCTCTAGAGATCCCGCCGCCATCTTCAGCGGCGGCGGTATCAGgtttcctgtc ... gttttgttagCTTTCTCACTGGTGATCGAAATGCAAGATTCAGCTATGGGTATTCCAGTTT
EST: gi|71858998|gb|DT008053.1|DT008053
EST:     ATGATTCTCTCTAGAGATCCCGCCGCCATCTTCAGCGGCGGCGGTATCAG                         CTTTCTCACTGGTGATCGAAATGCAAGATTCAGCTATGGGTATTCCAGTTT
genomic: ATGATTCTCTCTAGAGATCCCGCCGCCATCTTCAGCGGCGGCGGTATCAGgtttcctgtc ... gttttgttagCTTTCTCACTGGTGATCGAAATGCAAGATTCAGCTATGGGTATTCCAGTTT
EST: gi|351033310|gb|FQ446542.1|FQ446542
EST:     ATGATTCTCTCTAGAGATCCCGCCGCCATCTTCAGCGGCGGCGGTATCAG                         CTTTCTCACTGGTGATCGAAATGCAAGATTCAGCTATGGGTATTCCAGTTT
genomic: ATGATTCTCTCTAGAGATCCCGCCGCCATCTTCAGCGGCGGCGGTATCAGgtttcctgtc ... gttttgttagCTTTCTCACTGGTGATCGAAATGCAAGATTCAGCTATGGGTATTCCAGTTT
EST: gi|71855048|gb|DT004103.1|DT004103
EST:     ATGATTCTCTCTAGAGATCCCGCCGCCATCTTCAGCGGCGGCGGTATCAG                         CTTTCTCACTGGTGATCGAAATGCAAGATTCAGCTATGGGTATTCCAGTTT
genomic: ATGATTCTCTCTAGAGATCCCGCCGCCATCTTCAGCGGCGGCGGTATCAGgtttcctgtc ... gttttgttagCTTTCTCACTGGTGATCGAAATGCAAGATTCAGCTATGGGTATTCCAGTTT
EST: gi|71855402|gb|DT004457.1|DT004457
EST:     ATGATTCTCTCTAGAGATCCCGCCGCCATCTTCAGCGGCGGCGGTATCAG                         CTTTCTCACTGGTGATCGAAATGCAAGATTCAGCTATGGGTATTCCAGTTT
genomic: ATGATTCTCTCTAGAGATCCCGCCGCCATCTTCAGCGGCGGCGGTATCAGgtttcctgtc ... gttttgttagCTTTCTCACTGGTGATCGAAATGCAAGATTCAGCTATGGGTATTCCAGTTT
EST: gi|161715035|gb|FC063620.1|FC063620
EST:     ATGATTCTCTCTAGAGATCCCGCCGCCATCTTCAGCGGCGGCGGTATCAG                         CTTTCTCACTGGTGATCGAAATGCAAGATTCAGCTATGGGTATTCCAGTTT
genomic: ATGATTCTCTCTAGAGATCCCGCCGCCATCTTCAGCGGCGGCGGTATCAGgtttcctgtc ... gttttgttagCTTTCTCACTGGTGATCGAAATGCAAGATTCAGCTATGGGTATTCCAGTTT
EST: gi|161711260|gb|FC060764.1|FC060764
EST:     ATGATTCTCTCTAGAGATCCCGCCGCCATCTTCAGCGGCGGCGGTATCAG                         CTTTCTCACTGGTGATCGAAATGCAAGATTCAGCTATGGGTATTCCAGTTT
genomic: ATGATTCTCTCTAGAGATCCCGCCGCCATCTTCAGCGGCGGCGGTATCAGgtttcctgtc ... gttttgttagCTTTCTCACTGGTGATCGAAATGCAAGATTCAGCTATGGGTATTCCAGTTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgaatgtgggagaaggtacatgggtgactgaaatgttatgttatgttttgttagCTTTCTCACTGGTGATCGAAATGCAAGATTCAGCTATGGGTATTCCAGTTTCAAGGGTAAAAGGCCTTCCATGGAGGATTTCTACGAGACTAGAATATCA
                                              ttttgtt  CT-rich tract
                               aaatgttatgttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggagattgagatttagattaaagttcactttgatgccataattttttgaatgtgggagaaggtacatgggtgactgaaatgttatgttatgttttgttagCTTTCTCACTGGTGATCGAAATGCAAGATTCAGCTATGGGTATTCCAGTTTCAAGGGTAAAAGGCCTTCCATGGAGGATTTCTACGAGACTAGAATATCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - atgccat
- - - - - - - - - - - - - - - - - - - - - - - -gaatgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - ggagaagg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tacatgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgactga