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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaatctttgtcatattcctgaattccaaatttatggatcattaaaaggtctcagtacgagttgccttgcaaagctaatgatggagtccgattgatgccagGTTGAAGCAAAGAAGTTTGGGATGCTGGCAAATTGGCAGCGGGAGTTCACAATGGAAGACATATTGACGCAGCTGAAGAAAGAAATGGCAGCCCCCCACA

Basic information

species Vitis vinifera
transcript Vv06s0080g01080.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0080g01080.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA03G35790.1 (Glycine max), 3'ss of exon 3
---aaatctttgtcatattcctgaattccaaatttatggatcattaaaaggtctcagtacgagttgccttgcaaagctaatgatggagtccgattgatgccagGTTGAAGCAAAGAAGTTTGGGATGCTGGCAAATTGGCAGCGGGAGTTCACAATGGAAGACATATTGACGCAGCTGAAGAAAGAAATGGCAGCCCCCCACA
   || |  ||  |  || | |  | ||| | | | | |  | | | |    ||   ||  |  | |||     || |  | ||||| |   | |     ||||||||| ||||||| |||||  | || ||||||||||| |||  ||| || |||||||| ||| |||| ||||||||||| |||||||| ||  | || |
atgaactagtttgccaatacatatactcctattat-tagtccctgatacaaacttgataataaattcctaatttagat--ttatggatttgtaattgaaacagGTTGAATCAAAGAAATTTGGTCTTCTTGCAAATTGGCAACGGAGGTTTACCATGGAAGATATACTGACCCAGCTGAAGAAGGAAATGGCGGCTTCACATA

upper sequence: Vv06s0080g01080.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA19G38450.1 (Glycine max), 3'ss of exon 3
aaatctttgtcatattcctgaattccaaatttatggatcattaaaaggtctcagtacgagttgccttgcaaagct-----aatgatggagtc-cgattgatgccagGTTGAAGCAAAGAAGTTTGGGATGCTGGCAAATTGGCAGCGGGAGTTCACAATGGAAGACATATTGACGCAGCTGAAGAAAGAAATGGCAGCCCCCCACA
|||||| |||  |  |||  | | | | | |  |  ||| |||   |  |    ||| |  |   |   |||        | | ||||| |  | |||||  | |||||||| ||||||| |||||  | || ||||||||||| | |  ||| || |||||||| ||| |||| ||||||||||| |||||||| ||  | || |
aaatctatgttttcatcccaagtcctatactcct--atcgtta---gtccatgttacaaacttgataataaattccttagatttatggatttgcaattgaaac-agGTTGAATCAAAGAAATTTGGTCTTCTTGCAAATTGGCAACAGAGGTTTACCATGGAAGATATACTGACCCAGCTGAAGAAGGAAATGGCGGCTTCACATA

upper sequence: Vv06s0080g01080.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA15G21780.1 (Glycine max), 3'ss of exon 2
aaatctttgtcatattcctgaat-tccaaatttatggatcattaaaaggtctcagta-cgagttgcctt-gcaaagctaatgatggagtccgattgatgccagGTTGAAGCAAAGAAGTTTGGGATGCTGGCAAATTGGCAGCGGGAGTTCACAATGGAAGACATATTGACGCAGCTGAAGAAAGAAATGGCAGCCCCCCACA
  |   || |||| ||  ||| | |   ||  | | |   |||  |  | || | || | | ||  ||| |  |    | | || || |   ||  |    |||||||| ||||||| |||||  | || |||||||||||  | |||| ||| ||||| |||||| |||| ||| ||||||| |||||||| || || || |
-gacacttctcatgtttatgattatgagaaaatttagtctattttattggcttaataactaattatctttgtgacaagatttatagacttgaatgaaa--tagGTTGAACCAAAGAAATTTGGTCTTCTTGCAAATTGGCAAAGAGAGTACACCATGGAGGACATACTGACACAGTTGAAGAAGGAAATGGCCGCTCCTCATA

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|110710128|gb|EE086190.1|EE086190
EST:     GGTTCCATTCACGCATCAACATGATTTGTGTGAATCATGAGACTGGAGTG                         GTTGAAGCAAAGAAGTTTGGGATGCTGGCAAATTGGCAGCGGGAGTTCACA
genomic: GGTTCCATTCACGCATCAACATGATTTGTGTGAATCATGAGACTGGAGTGgtaaagttgt ... ttgatgccagGTTGAAGCAAAGAAGTTTGGGATGCTGGCAAATTGGCAGCGGGAGTTCACA
EST: gi|29786222|gb|CB343829.2|CB343829
EST:     GGTTCCATTCACGCATCAACATGATTTGTGTGAATCATGAGACTGGAGTG                         GTTGAAGCAAAGAAGCTTGGGATGCTGGCAAATTGGCAGCGGGAGTTCACA
genomic: GGTTCCATTCACGCATCAACATGATTTGTGTGAATCATGAGACTGGAGTGgtaaagttgt ... ttgatgccagGTTGAAGCAAAGAAGTTTGGGATGCTGGCAAATTGGCAGCGGGAGTTCACA
EST: gi|110380195|gb|EC945441.1|EC945441
EST:     GGTTCCATTCACGCATCAACATGATTTGTGTGAATCATGAGACTGGAGTG                         GTTGAAGCAAAGAAGTTTGGGATGCTGGCAAATTGGCAGCGGGAGTTCACA
genomic: GGTTCCATTCACGCATCAACATGATTTGTGTGAATCATGAGACTGGAGTGgtaaagttgt ... ttgatgccagGTTGAAGCAAAGAAGTTTGGGATGCTGGCAAATTGGCAGCGGGAGTTCACA
EST: gi|110375015|gb|EC939967.1|EC939967
EST:     GGTTCCATTCACGCATCAACATGATTTGTGTGAATCATGAGACTGGAGTG                         GTTGAAGCAAAGAAGTTTGGGATGCTGGCAAATTGGCAGCGG
genomic: GGTTCCATTCACGCATCAACATGATTTGTGTGAATCATGAGACTGGAGTGgtaaagttgt ... ttgatgccagGTTGAAGCAAAGAAGTTTGGGATGCTGGCAAATTGGCAGCGG
EST: gi|110396671|gb|EC962365.1|EC962365
EST:     GGTTCCATTCACGCATCAACATGATTTGTGTGAATCATGAGACTGGAGTG                         GTTGAAGCAAAGAAGTTTGGGATGCTGGCAAATTGGCAGCGGGAGTTCACA
genomic: GGTTCCATTCACGCATCAACATGATTTGTGTGAATCATGAGACTGGAGTGgtaaagttgt ... ttgatgccagGTTGAAGCAAAGAAGTTTGGGATGCTGGCAAATTGGCAGCGGGAGTTCACA
EST: gi|32267862|gb|CD717021.1|CD717021
EST:     GGTTCCATTCACGCATCAACATGATTTGTGTGAATCATGAGACTGGAGTG                         GTTGAAGCAAAGAAGTTTGGGATGCTGGCAAATTGGCAGCGGGAGTTCACA
genomic: GGTTCCATTCACGCATCAACATGATTTGTGTGAATCATGAGACTGGAGTGgtaaagttgt ... ttgatgccagGTTGAAGCAAAGAAGTTTGGGATGCTGGCAAATTGGCAGCGGGAGTTCACA
EST: gi|51989701|gb|CV179156.1|CV179156
EST:     GGTTCCATTCACGCATCAACATGATTTGTGTGAATCATGAGACTGGAGTG                         GTTGAAGCAAAGAAGTTTGGGATGCTGGCAAATTGGCAGCGGGAGTTCGCA
genomic: GGTTCCATTCACGCATCAACATGATTTGTGTGAATCATGAGACTGGAGTGgtaaagttgt ... ttgatgccagGTTGAAGCAAAGAAGTTTGGGATGCTGGCAAATTGGCAGCGGGAGTTCACA
EST: gi|28964729|gb|CB343762.1|CB343762
EST:     GGTTCCATTCACGCATCAACATGATTTGTGTGAATCATGAGACTGGAGTG                         GTTGAAGCAAAGAAGCTTGGGATGCTGGCAAATTGGCAGCGGGAGTTCACA
genomic: GGTTCCATTCACGCATCAACATGATTTGTGTGAATCATGAGACTGGAGTGgtaaagttgt ... ttgatgccagGTTGAAGCAAAGAAGTTTGGGATGCTGGCAAATTGGCAGCGGGAGTTCACA
EST: gi|110422039|gb|EC988350.1|EC988350
EST:     GGTTCCATTCACGCATCAACATGATTTGTGTGAATCATGAGACTGGAGTG                         GTTGAAGCAAAGAAGTTTGGGATGCTGGCAAATTGGCAGCGGGAGTTCACA
genomic: GGTTCCATTCACGCATCAACATGATTTGTGTGAATCATGAGACTGGAGTGgtaaagttgt ... ttgatgccagGTTGAAGCAAAGAAGTTTGGGATGCTGGCAAATTGGCAGCGGGAGTTCACA
EST: gi|32269983|gb|CD719142.1|CD719142
EST:     GGTTCCATTCACGCATCAACATGATTTGTGTGAATCATGAGACTGGAGTG                         GTTGAAGCAAAGAAGTTTGGGATGCTGGCAAATTGGCAGCGGGAGTTCACA
genomic: GGTTCCATTCACGCATCAACATGATTTGTGTGAATCATGAGACTGGAGTGgtaaagttgt ... ttgatgccagGTTGAAGCAAAGAAGTTTGGGATGCTGGCAAATTGGCAGCGGGAGTTCACA
EST: gi|110695956|gb|EE074565.1|EE074565
EST:     GTTCCATTCACGCATCACCACCCATTTGTGTGAATCATGAGACTGGAGTG                         GTTGAAGCAAAGAAGTTTGGGATGCTGGCAAATTGGCAGCGGGAGTTCACA
genomic: GTTCCATTCACGCATCAACATG-ATTTGTGTGAATCATGAGACTGGAGTGgtaaagttgt ... ttgatgccagGTTGAAGCAAAGAAGTTTGGGATGCTGGCAAATTGGCAGCGGGAGTTCACA
EST: gi|37184157|gb|CF603511.1|CF603511
EST:     GGTTCCATTCACGCATCAACATGATTTGTGTGAATCATGAGACTGGAGTG                         GTTGAAGCAAAGAAGTTTGGGATGCTGGCAAATTGGCAGCGGGAGTTCACA
genomic: GGTTCCATTCACGCATCAACATGATTTGTGTGAATCATGAGACTGGAGTGgtaaagttgt ... ttgatgccagGTTGAAGCAAAGAAGTTTGGGATGCTGGCAAATTGGCAGCGGGAGTTCACA
EST: gi|33408882|gb|CF214509.1|CF214509
EST:     GGTTCCATTCACGCATCAACATGATTTGTGTGAATCATGAGACTGGAGTG                         GTTGAAGCAAAGAAGTTTGGGATGCTGGCAAATTGGCAGCGGGAGTTCACA
genomic: GGTTCCATTCACGCATCAACATGATTTGTGTGAATCATGAGACTGGAGTGgtaaagttgt ... ttgatgccagGTTGAAGCAAAGAAGTTTGGGATGCTGGCAAATTGGCAGCGGGAGTTCACA
EST: gi|32272011|gb|CD721170.1|CD721170
EST:     GGTTCCATTCACGCATCAACATGATTTGTGTGAATCATGAGACTGGAGTG                         GTTGAAGCAAAGAAGTTTGGGATGCTGGCAAATTGGCAGCGGGAGTTCACA
genomic: GGTTCCATTCACGCATCAACATGATTTGTGTGAATCATGAGACTGGAGTGgtaaagttgt ... ttgatgccagGTTGAAGCAAAGAAGTTTGGGATGCTGGCAAATTGGCAGCGGGAGTTCACA
EST: gi|71874414|gb|DT023469.1|DT023469
EST:     GGTTCCATTCACGCATCAACATGATTTGTGTGAATCATGAGACTGGAGTG                         GTTGAAGCAAAGAAGTTTGGGATGCTGGCAAATTGGCAGCGGGAGTTCACA
genomic: GGTTCCATTCACGCATCAACATGATTTGTGTGAATCATGAGACTGGAGTGgtaaagttgt ... ttgatgccagGTTGAAGCAAAGAAGTTTGGGATGCTGGCAAATTGGCAGCGGGAGTTCACA
EST: gi|87583905|gb|DY473274.1|DY473274
EST:     GGTTCCATTCACGCATCAACATGATTTGTGTGAATCATGAGACTGGAGTG                         GTTGAAGCAAAGAAGTTTGGGATGCTGGCAAATTGGCAGCGGGAGTTCACA
genomic: GGTTCCATTCACGCATCAACATGATTTGTGTGAATCATGAGACTGGAGTGgtaaagttgt ... ttgatgccagGTTGAAGCAAAGAAGTTTGGGATGCTGGCAAATTGGCAGCGGGAGTTCACA
EST: gi|110705394|gb|EE082194.1|EE082194
EST:     GGTTCCATTCACGCATCAACATGATTTGTGTGAATCATGAGACTGGAGTG                         GTTGAAGCAAAGAAGTTTGGGATGCTGGCAAATTGGCAGCGGGAGTTCACA
genomic: GGTTCCATTCACGCATCAACATGATTTGTGTGAATCATGAGACTGGAGTGgtaaagttgt ... ttgatgccagGTTGAAGCAAAGAAGTTTGGGATGCTGGCAAATTGGCAGCGGGAGTTCACA
EST: gi|30323103|gb|CD006365.1|CD006365
EST:     GGTTCCATTCACGCATCAACATGATTTGTGTGAATCATGAGACTGGAGTG                         GTTGAAGCAAAGAAGTTTGGGATGCTGGCAAATTGGCAGCGGGAGTTCACA
genomic: GGTTCCATTCACGCATCAACATGATTTGTGTGAATCATGAGACTGGAGTGgtaaagttgt ... ttgatgccagGTTGAAGCAAAGAAGTTTGGGATGCTGGCAAATTGGCAGCGGGAGTTCACA
EST: gi|110417859|gb|EC983955.1|EC983955
EST:     GGTTCCATTCACGCATCAACATGATTTGTGTGAATCATGAGACTGGAGTG                         GTTGAAGCAAAGAAGTTTGGGATGCTGGCAAATTGGCAGCGGGAGTTCACA
genomic: GGTTCCATTCACGCATCAACATGATTTGTGTGAATCATGAGACTGGAGTGgtaaagttgt ... ttgatgccagGTTGAAGCAAAGAAGTTTGGGATGCTGGCAAATTGGCAGCGGGAGTTCACA
EST: gi|71890414|gb|DT039469.1|DT039469
EST:     GGTTCCATTCACGCATCAACATGATTTGTGTGAATCATGAGACTGGAGTG                         GTTGAAGCAAAGAAGTTTGGGATGCTGGCAAATTGGCAGCGGGAGTTCACA
genomic: GGTTCCATTCACGCATCAACATGATTTGTGTGAATCATGAGACTGGAGTGgtaaagttgt ... ttgatgccagGTTGAAGCAAAGAAGTTTGGGATGCTGGCAAATTGGCAGCGGGAGTTCACA
EST: gi|30323096|gb|CD006358.1|CD006358
EST:     GGTTCCATTCACGCATCAACATGATTTGTGTGAATCATGAGACTGGAGTG                         GTTGAAGCAAAGAAGTTTGGGATGCTGGCAAATTGGCAGCGGGAGTTCACA
genomic: GGTTCCATTCACGCATCAACATGATTTGTGTGAATCATGAGACTGGAGTGgtaaagttgt ... ttgatgccagGTTGAAGCAAAGAAGTTTGGGATGCTGGCAAATTGGCAGCGGGAGTTCACA
EST: gi|110717402|gb|EE093225.1|EE093225
EST:     GGTTCCATTCACGCATCAACATGATTTGTGTGAATCATGAGACTGGAGTG                         GTTGAAGCAAAGAAGTTTGGGATGCTGGCAAATTGGCAGCGGGAGTTCACA
genomic: GGTTCCATTCACGCATCAACATGATTTGTGTGAATCATGAGACTGGAGTGgtaaagttgt ... ttgatgccagGTTGAAGCAAAGAAGTTTGGGATGCTGGCAAATTGGCAGCGGGAGTTCACA
EST: gi|110717466|gb|EE093345.1|EE093345
EST:     GGTTCCATTCACGCATCAACATGATTTGTGTGAATCATGAGACTGGAGTG                         GTTGAAGCAAAGAAGTTTGGGATGCTGGCAAATTGGCAGCGGGAGTTCACA
genomic: GGTTCCATTCACGCATCAACATGATTTGTGTGAATCATGAGACTGGAGTGgtaaagttgt ... ttgatgccagGTTGAAGCAAAGAAGTTTGGGATGCTGGCAAATTGGCAGCGGGAGTTCACA
EST: gi|110702625|gb|EE078761.1|EE078761
EST:     GGTTCCATTCACGCATCAACATGATTTGTGTGAATCATGAGACTGGAGTG                         GTTGAAGCAAAGAAGTTTGGGATGCTGGCAAATTGGCAGCGGGAGTTCACA
genomic: GGTTCCATTCACGCATCAACATGATTTGTGTGAATCATGAGACTGGAGTGgtaaagttgt ... ttgatgccagGTTGAAGCAAAGAAGTTTGGGATGCTGGCAAATTGGCAGCGGGAGTTCACA
EST: gi|30125506|gb|CB910845.1|CB910845
EST:     GGTTCCATTCACGCATCAACATGATTTGTGTGAATCATGAGACTGGAGTG                         GTTGAAGCAAAGAAGTTTGGGATGCTGGCAAATTGGCAGCGGGAGTTCACA
genomic: GGTTCCATTCACGCATCAACATGATTTGTGTGAATCATGAGACTGGAGTGgtaaagttgt ... ttgatgccagGTTGAAGCAAAGAAGTTTGGGATGCTGGCAAATTGGCAGCGGGAGTTCACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aggtctcagtacgagttgccttgcaaagctaatgatggagtccgattgatgccagGTTGAAGCAAAGAAGTTTGGGATGCTGGCAAATTGGCAGCGGGAGTTCACAATGGAAGACATATTGACGCAGCTGAAGAAAGAAATGGCAGCCCCCCACA
                             taatgat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaatctttgtcatattcctgaattccaaatttatggatcattaaaaggtctcagtacgagttgccttgcaaagctaatgatggagtccgattgatgccagGTTGAAGCAAAGAAGTTTGGGATGCTGGCAAATTGGCAGCGGGAGTTCACAATGGAAGACATATTGACGCAGCTGAAGAAAGAAATGGCAGCCCCCCACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - ttcctga
- - - - - - - - - - - - ccaaatt
- - - - - - - - - - - - - - - - - - - -attaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gctaatg