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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atcatcaatttaattgacataagtcatagatttagattagattttgggatttttcttccctgaatttgctgagtcttgagattatatcgggtgtttccagGTTTTGAGATCTTAGCATTTCCATGCAATCAATTTCTGAAGCAAGAGCCTGGGTCGAGTGAGCAGGCACAAGAATTTGCATGTACAAGATACAAGGCTGA

Basic information

species Vitis vinifera
transcript Vv07s0104g00320.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv07s0104g00320.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA10G03000.1 (Glycine max), 3'ss of exon 3
atcatcaatttaatt-gacataagtcatagatttagattagattttgggatttttcttccctgaatttgctgagtcttgagattatatcgggtgtttccagGTTTTGAGATCTTAGCATTTCCATGCAATCAATTTCTGAAGCAAGAGCCTGGGTCGAGTGAGCAGGCACAAGAATTTGCATGTACAAGATACAAGGCTGA
 |     ||| | || ||  | | | | |    | |   | |    |  |||  || |   ||||         ||||    || | |  |||| |   |||  ||||||| || |||||||||||||| |||||| ||||| ||||||| ||| | ||  || |||||||||||||||||||||||||||| ||||||||
gtatggtattcattttgaacttaattagattggtgggccaaaaag-gaaattgatcatagttgaaaaaat---atctt----ttttttttggtgatgttagGACTTGAGATATTGGCATTTCCATGCAACCAATTTTTGAAGAAAGAGCCAGGGACTAGCCAGGAGGCACAAGAATTTGCATGTACAAGATATAAGGCTGA

upper sequence: Vv07s0104g00320.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA02G16800.1 (Glycine max), 3'ss of exon 3
atcatcaatttaattgacataagtcatagatttagattag--attttgggatttttcttccctgaatttgctgagtcttgagattatatcgggtgtttccagGTTTTGAGATCTTAGCATTTCCATGCAATCAATTTCTGAAGCAAGAGCCTGGGTCGAGTGAGCAGGCACAAGAATTTGCATGTACAAGATACAAGGCTGA
        | |  |   |||     |   ||||||||| |      |   ||     |   |  | ||     | | |     || | |  |||| |   |||  ||||||| || ||||||||||| || |||||| ||||| ||||||| ||| | ||  || |||||||||| ||||| ||||||||||| ||||||||
-------gtatgctattcattttcaacttatttagattggtgggcctaaaatgaaattgatcatagttgagaaaatatc----ttttttttggtgatgttagGACTTGAGATATTGGCATTTCCATGTAACCAATTTTTGAAGAAAGAGCCAGGGACAAGCCAGGAGGCACAAGACTTTGCTTGTACAAGATATAAGGCTGA

upper sequence: Vv07s0104g00320.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA19G33650.3 (Glycine max), 3'ss of exon 3
---------------------------------------------------atcatcaatttaattgacataagtcataga----tttagattagattttgggatttttct--tccctgaatttgctgagtcttgaga---ttatatcgggtgtttccagGTTTTGAGATCTTAGCATTTCCATGCAATCAATTTCTGAAGCAAGAGCCTGGGTCGAGTGAGCAGGCACAAGAATTTGCATGTACAAGATACAAGGCTGA
                                                   ||    |||||        | ||| |   |    |||   ||| | |   |||||           | || ||| |    |||||||   || | | || || |  ||||| |||||||  | |||||||||||||| || |||||||| |||||||| |||   ||  || ||||| | |||||||| |||||||| |||||||||||
gtatggtttttttaggtttacagagcagttggtgcacttgcatgttattggattccaaatttgtgccttttcagtgaccaaatacttttagttaaactgaaggattaaaagaaattattaaattgatctcacttgagaatgttttgttggttgatctcagGTCTTGAGATACTGGCATTTCCATGCAACCAGTTTCTGAAACAAGAGCCCGGGAGTAGCCAGGAGGCAGAGGAATTTGCCTGTACAAGGTACAAGGCTGA

upper sequence: Vv07s0104g00320.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA03G30800.1 (Glycine max), 3'ss of exon 3
-------------------------------------------------------------atcatcaatttaattgacataagtcatagatttagattagattttgggatttttct---tccctgaatttgctgagtcttgag-attatatcgggtgtttccagGTTTTGAGATCTTAGCATTTCCATGCAATCAATTTCTGAAGCAAGAGCCTGGGTCGAGTGAGCAGGCACAAGAATTTGCATGTACAAGATACAAGGCTGA
                                                                  |  ||   |   || |     | ||  |   ||| | |   ||||| |  |   | | | ||||  || | |  |||   || ||| || || |  ||||  |||||||  | |||||||||||||| || ||||||||||| |||||||||   ||  || | | | | |||||||| || |||||||||||||| | 
gtatggtttttttaggtttacagagcagttggtgcacttgcatgttattggattctaaatttgtgccttttcggtgaccaaatacttttgaacttagttaaactgaaggattataataaattcttaaattgtctcacttatgaatgttttattggttgatctcagGCCTTGAGATACTGGCATTTCCATGCAACCAGTTTCTGAAGCAGGAGCCTGGGAGTAGCCAGGACGTAGAGGAATTTGCCTGCACAAGATACAAGGCCGC

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|32270831|gb|CD719990.1|CD719990
EST:     TTCGAATTACACCCAATTGACTGAGCTCTACAACAAATACAAGGACAGAG                         GTTTTGAGATCTTAGCATTTCCATGCAATCAATTTCTGAAGCAAGAGCCTG
genomic: TTCGAATTACACCCAATTGACTGAGCTCTACAACAAATACAAGGACAGAGgtagatgatt ... gtgtttccagGTTTTGAGATCTTAGCATTTCCATGCAATCAATTTCTGAAGCAAGAGCCTG
EST: gi|18458555|gb|BM436833.1|BM436833
EST:     TTCGAATTACACCCAATTGACTGAGCTCTACAACAAATACAAGGACAGAG                         GTTTTGAGATCTTAGCATTTCCATGCAATCAATTTCTGAAGCAAGAGCCTG
genomic: TTCGAATTACACCCAATTGACTGAGCTCTACAACAAATACAAGGACAGAGgtagatgatt ... gtgtttccagGTTTTGAGATCTTAGCATTTCCATGCAATCAATTTCTGAAGCAAGAGCCTG
EST: gi|71871438|gb|DT020493.1|DT020493
EST:     TTCGAATTACACCCAATTGACTGAGCTCTACAACAAATACAAGGACAGAG                         GTTTTGAGATCTTAGCGTTTCCATGCAATCAATTTCTGAAGCAAGAGCCTG
genomic: TTCGAATTACACCCAATTGACTGAGCTCTACAACAAATACAAGGACAGAGgtagatgatt ... gtgtttccagGTTTTGAGATCTTAGCATTTCCATGCAATCAATTTCTGAAGCAAGAGCCTG
EST: gi|33406214|gb|CF211841.1|CF211841
EST:     TTCGAATTACACCCAATTGACTGAGCTCTACAACAAATACAAGGACAGAG                         GTTTTGAGATCTTAGCATTTCCATGCAATCAATTTCTGAAGCAAGAGCCTG
genomic: TTCGAATTACACCCAATTGACTGAGCTCTACAACAAATACAAGGACAGAGgtagatgatt ... gtgtttccagGTTTTGAGATCTTAGCATTTCCATGCAATCAATTTCTGAAGCAAGAGCCTG
EST: gi|32248717|gb|CD714536.1|CD714536
EST:     TTCGAATTACACCCAATTGACTGAGCTCTACAACAAATACAAGGACAGAG                         GTTTTGAGATCTTAGCATTTCCATGCAATCAATTTCTGAAGCAAGAGCCTG
genomic: TTCGAATTACACCCAATTGACTGAGCTCTACAACAAATACAAGGACAGAGgtagatgatt ... gtgtttccagGTTTTGAGATCTTAGCATTTCCATGCAATCAATTTCTGAAGCAAGAGCCTG
EST: gi|32247920|gb|CD713739.1|CD713739
EST:     TTCGAATTACACCCAATTGACTGAGCTCTACAACAAATACAAGGACAGAG                         GTTTTGAGATCTTAGCATTTCCATGCAATCAATTTCTGAAGCAAGAGCCTG
genomic: TTCGAATTACACCCAATTGACTGAGCTCTACAACAAATACAAGGACAGAGgtagatgatt ... gtgtttccagGTTTTGAGATCTTAGCATTTCCATGCAATCAATTTCTGAAGCAAGAGCCTG
EST: gi|32270478|gb|CD719637.1|CD719637
EST:     TTCGAATTACACCCAATTGACTGAGCTCTACAACAAATACAAGGACAGAG                         GTTTTGAGATCTTAGCATTTCCATGCAATCAATTTCTGAAGCAAGAGCCTG
genomic: TTCGAATTACACCCAATTGACTGAGCTCTACAACAAATACAAGGACAGAGgtagatgatt ... gtgtttccagGTTTTGAGATCTTAGCATTTCCATGCAATCAATTTCTGAAGCAAGAGCCTG
EST: gi|30327074|gb|CD010336.1|CD010336
EST:     TTCGAATTACACCCAATTGACTGAGCTCTACAACAAATACAAGGACAGAG                         GTTTTGAGATCTTAGCATTTCCATGCAATCAATTTCTGAAGCAAGAGCCTG
genomic: TTCGAATTACACCCAATTGACTGAGCTCTACAACAAATACAAGGACAGAGgtagatgatt ... gtgtttccagGTTTTGAGATCTTAGCATTTCCATGCAATCAATTTCTGAAGCAAGAGCCTG
EST: gi|30326869|gb|CD010131.1|CD010131
EST:     TTCGAATTACACCCAATTGACTGAGCTCTACAACAAATACAAGGACAGAG                         GTTTTGAGATCTTAGCATTTCCATGCAATCAATTTCTGAAGCAAGAGCCTG
genomic: TTCGAATTACACCCAATTGACTGAGCTCTACAACAAATACAAGGACAGAGgtagatgatt ... gtgtttccagGTTTTGAGATCTTAGCATTTCCATGCAATCAATTTCTGAAGCAAGAGCCTG
EST: gi|110730026|gb|EE106638.1|EE106638
EST:     TTCGAATTACACCCAATTGACTGAGCTCTACAACAAATACAAGGACAGAG                         GTTTTGAGATCTTAGCATTTCCATGCAATCAATTTCTGAAGCAAGAGCCTG
genomic: TTCGAATTACACCCAATTGACTGAGCTCTACAACAAATACAAGGACAGAGgtagatgatt ... gtgtttccagGTTTTGAGATCTTAGCATTTCCATGCAATCAATTTCTGAAGCAAGAGCCTG
EST: gi|110360010|gb|EC922487.1|EC922487
EST:     TTCGAATTACACCCAATTGACTGAGCTCTACAACAAATACAAGGACAGAG                         GTTTGGAGATCTTAGCATTTCCATGCAATCAATTTCTGAAGCAAGAGCCTG
genomic: TTCGAATTACACCCAATTGACTGAGCTCTACAACAAATACAAGGACAGAGgtagatgatt ... gtgtttccagGTTTTGAGATCTTAGCATTTCCATGCAATCAATTTCTGAAGCAAGAGCCTG
EST: gi|32268850|gb|CD718009.1|CD718009
EST:     TTCGAATTACACCCAATTGACTGAGCTCTACAACAAATACAAGGACAGAG                         GTTTTGAGATCTTAGCATTTCCATGCAATCAATTTCTGAAGCAAGAGCCTG
genomic: TTCGAATTACACCCAATTGACTGAGCTCTACAACAAATACAAGGACAGAGgtagatgatt ... gtgtttccagGTTTTGAGATCTTAGCATTTCCATGCAATCAATTTCTGAAGCAAGAGCCTG
EST: gi|33406296|gb|CF211923.1|CF211923
EST:     TTCGAATTACACCCAATTGACTGAGCTCTACAACAAATACAAGGACAGAG                         GTTTTGAGATCTTAGCATTTCCATGCAATCAATTTCTGAAGCAAGAGCCTG
genomic: TTCGAATTACACCCAATTGACTGAGCTCTACAACAAATACAAGGACAGAGgtagatgatt ... gtgtttccagGTTTTGAGATCTTAGCATTTCCATGCAATCAATTTCTGAAGCAAGAGCCTG
EST: gi|110374752|gb|EC939679.1|EC939679
EST:     TTCGAATTACACCCAATTGACTGAGCTCTACAACAAATACAAGGACAGAG                         GTTTTGAGATCTTAGCATTTCCATGCAATCAATTTCTGAAGCAAGAGCCTG
genomic: TTCGAATTACACCCAATTGACTGAGCTCTACAACAAATACAAGGACAGAGgtagatgatt ... gtgtttccagGTTTTGAGATCTTAGCATTTCCATGCAATCAATTTCTGAAGCAAGAGCCTG
EST: gi|30325164|gb|CD008426.1|CD008426
EST:     TTCGAATTACACCCAATTGACTGAGCTCTACAACAAATACAAGGACAGAG                         GTTTTGAGATCTTAGCATTTCCATGCAATCAATTTCTGAAGCAAGAGCCTG
genomic: TTCGAATTACACCCAATTGACTGAGCTCTACAACAAATACAAGGACAGAGgtagatgatt ... gtgtttccagGTTTTGAGATCTTAGCATTTCCATGCAATCAATTTCTGAAGCAAGAGCCTG
EST: gi|110360267|gb|EC923156.1|EC923156
EST:     TTCGAATTACACCCAATTGACTGAGCTCTACAACAAATACAAGGACAGAG                         GTTTTGAGATCTTAGCATTTCCATGCAATCAATTTCTGAAGCAAGAGCCTG
genomic: TTCGAATTACACCCAATTGACTGAGCTCTACAACAAATACAAGGACAGAGgtagatgatt ... gtgtttccagGTTTTGAGATCTTAGCATTTCCATGCAATCAATTTCTGAAGCAAGAGCCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gggatttttcttccctgaatttgctgagtcttgagattatatcgggtgtttccagGTTTTGAGATCTTAGCATTTCCATGCAATCAATTTCTGAAGCAAGAGCCTGGGTCGAGTGAGCAGGCACAAGAATTTGCATGTACAAGATACAAGGCTGA
                                              tgtttcc  CT-rich tract
                                 agattatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atcatcaatttaattgacataagtcatagatttagattagattttgggatttttcttccctgaatttgctgagtcttgagattatatcgggtgtttccagGTTTTGAGATCTTAGCATTTCCATGCAATCAATTTCTGAAGCAAGAGCCTGGGTCGAGTGAGCAGGCACAAGAATTTGCATGTACAAGATACAAGGCTGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG
-tcatcaa
- - - - - - - - - - - - - - - - - - - - -ttttggg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttgctga