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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtgaaggttgtttgatcatttggttttgggccaccaggcctgtatgatgatgttcttcattctccctgttgtttagttttcattggttctttcatgggtcagGTTCGAGGTATTGAAACAGTTACCACATATGACTCAAAAACTGGAGAGTTTGTTATTAACAGTCCCTGTGAATCAGCTCAGAAGTACTGGATAGGAGGAG

Basic information

species Vitis vinifera
transcript Vv12s0028g02660.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv12s0028g02660.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os06g24704.1 (Oryza sativa), 3'ss of exon 2
gtatgtgaaggttgtttgatcatttggttttgggccaccaggcctgtatgatgatgttcttcattctccctgttgtttagttttcattggttctttcatgggtcagGTTCGAGGTATTGAAACAGTTACCACATATGACTCAAAAACTGGAGAGTTTGTTATTAACAGTCCCTGTGAATCAGCTCAGAAGTACTGGATAGGAGGAG
|||||||| | |  |||| |||     ||   |      ||   |||  | || ||||  | |   |     |||  |  |||  | |  ||      ||    |||| ||||| ||||| |||||  | || |||||    |||||  |||||||||| || || | ||| ||||||||||| |||||||||||||| || ||||
gtatgtgatgatattttggtca---aattactgaattgtagttttgttagctg-tgttgatgagatttttctttgccttatttg-actaatt------tga---agGTCCGAGGAATTGAGACAGTGGCTACTTATGATATTAAAACAAGAGAGTTTGTGATAAATACTCCTTGTGAATCAGCCCAGAAGTACTGGATTGGTGGAG

upper sequence: Vv12s0028g02660.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G014136_T01 (Zea mays), 3'ss of exon 2
gtatgtgaaggttgtttgatcatttggttttgggccaccaggcctgtatgatgatgttcttcattctccctgttgtttagttttcattgg---ttctttcatgggtcagGTTCGAGGTATTGAAACAGTTACCACATATGACTCAAAAACTGGAGAGTTTGTTATTAACAGTCCCTGTGAATCAGCTCAGAAGTACTGGATAGGAGGAG
             ||  |  |||  | ||| ||   | ||  | | |      ||  ||| || |  |  || || |||  ||   |||    ||||||  |     |||| ||||| || |||||| |  | || ||||| ||| ||||  |||||||  | || || | ||| |||||||||||||||||||||||||| || ||||
-------------gtacgtgcata-gatttgggctaagcatactttttacggtataatct-cactaactgtgctgattaagttctgttgctgtttctttgttacaaaagGTGCGAGGAATAGAAACAATAGCAACTTATGATTCAGAAACAAGAGAGTTCATCATAAATACTCCATGTGAATCAGCTCAGAAGTACTGGATTGGTGGAG

upper sequence: Vv12s0028g02660.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA12G14060.1 (Glycine max), 3'ss of exon 2
gtatgtgaaggttgtttgatcatttggttttgggccaccaggcctgtatgatgatgttctt-cattctccctgttgtttagttttcattggttctttcatgggtcagGTTCGAGGTATTGAAACAGTTACCACATATGACTCAAAAACTGGAGAGTTTGTTATTAACAGTCCCTGTGAATCAGCTCAGAAGTACTGGATAGGAGGAG
||||||||||||||    || | |||| |        | |    |  || || ||| | || | || || || ||  | |   ||    |  |  ||        |||||||||| ||||||||||| || || ||||| ||||| || || || ||||| || || | ||| |||||||| | ||||||||| ||||| || || |
gtatgtgaaggttgcccaataagttgggtcattaggtctacatgtaaattattatgcttttgccttgtcacttttaataatcctttccagactaattttca---tagGTTCGAGGAATTGAAACAGTCACTACTTATGATTCAAACACCGGGGAATTTGTCATCAATACTCCATGTGAATCGGGTCAGAAGTATTGGATTGGTGGTG

upper sequence: Vv12s0028g02660.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA06G43840.1 (Glycine max), 3'ss of exon 2
gtatgtgaaggttgtttgatcatttggttttgg-gccaccaggcctgtatgatgatgttctt-cattctccctgttgtttagttttcattggttctttcatgggtcagGTTCGAGGTATTGAAACAGTTACCACATATGACTCAAAAACTGGAGAGTTTGTTATTAACAGTCCCTGTGAATCAGCTCAGAAGTACTGGATAGGAGGAG
|||||||||||||| |  || | ||||  |        |||    |  || || ||| | || | || || || ||  | |    |    |  |  ||        |||||||||| ||||||||||| || || ||||| ||||| || ||||| ||||| || || |  || |||||||| | ||||||||| ||||| || || |
gtatgtgaaggttgctcaataagttggggtcattagttccacatgtaaattattatgcttttgccttgtcacttttaataatcccttccagactaattttca---tagGTTCGAGGAATTGAAACAGTCACTACTTATGATTCAAACACCGGAGAATTTGTCATCAATACCCCATGTGAATCGGGTCAGAAGTATTGGATTGGTGGTG

upper sequence: Vv12s0028g02660.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT1G06290.1 (Arabidopsis thaliana), 3'ss of exon 2
gtatgtgaaggttgtttgatcatttggttttgggccaccaggcctgtatgatgatgttcttcattctccctgttgtttagttttcattggttctttcatgggtcagGTTCGAGGTATTGAAACAGTTACCACATATGACTCAAAAACTGGAGAGTTTGTTATTAACAGTCCCTGTGAATCAGCTCAGAAGTACTGGATAGGAGGAG
||| |   |  ||  |||||       ||||    | |||    |  ||| |||| |||  ||||        | || |||| |  ||  ||||||  ||    |||| || || ||||||||||| || || |||||| ||||||||| ||||||||| || || | ||| |||||||| ||||||||||| ||||| || || |
gtaggcatatttt-cttgattgcc--attttttttctccatatgt-catggtgatcttccacattta------tattgagttctatttatttcttt--tgatatagGTACGGGGAATTGAAACAGTGACAACTTATGACCCAAAAACTGAAGAGTTTGTGATAAATACTCCTTGTGAATCTGCTCAGAAGTATTGGATTGGTGGGG

upper sequence: Vv12s0028g02660.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT1G06310.1 (Arabidopsis thaliana), 3'ss of exon 2
gtatgtgaaggttgtttgatcatttggttttgggccaccaggcctgtatgatgatgttcttcattctccctgttgtttagttttcattggttctttcatgggtcagGTTCGAGGTATTGAAACAGTTACCACATATGACTCAAAAACTGGAGAGTTTGTTATTAACAGTCCCTGTGAATCAGCTCAGAAGTACTGGATAGGAGGAG
                             | ||   |          ||  ||   || | ||  ||   | |   || ||  || ||| ||   |      |||||| || || ||||||||||| || || |||||| ||| ||||| ||||||||| || || | ||| |||||||| ||||||||||| ||||| || |  |
----------------------------gtaggcatattgcagtgtcattttgcatttatccagactatatatgtattggtgatctttgatttggtggctt-tcagGTACGGGGAATTGAAACAGTGACTACTTATGACCCAACAACTGAAGAGTTTGTGATAAATACTCCTTGTGAATCTGCTCAGAAGTATTGGATCGGTGAGG

upper sequence: Vv12s0028g02660.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: EFJ04838 (Selaginella moellendorffii), 3'ss of exon 3
gtatgtgaaggttgtttgatcatttggttttgggccaccaggcctgtatgatgatgttcttcattctccctgttgtttagttttcattggttctttcatgggtcagGTTCGAGGTATTGAAACAGTTACCACATATGACTCAAAAACTGGAGAGTTTGTTATTAACAGTCCCTGTGAATCAGCTCAGAAGTACTGGATAGGAGGAG
                                         |   ||| | |  | || |   || |   | || |||    || | |||||  |       |||||| ||||| ||||||||  | ||    || ||  ||  |||    ||||||||||| |||| ||| || || || |||||||| ||||||||||||||||
-----------------------------------------gttcgta-gct--tcttttctcttttttgttttctttgtgcttgagtggtttatgatcttttcagGTCCGAGGGATTGAAACTATAACTGTGTACGATCCATCAACACAGGAGTTTGTTATCAACACTCCATGCGAGTCTGCTCAGAAATACTGGATAGGAGGAG

upper sequence: Vv12s0028g02660.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: EFJ13387 (Selaginella moellendorffii), 3'ss of exon 3
gtatgtgaaggttgtttgatcatttggttttgggccaccaggcctgtatgatgatgttcttcattctccctgttgtttagttttcattggttctttcatgggtcagGTTCGAGGTATTGAAACAGTTACCACATATGACTCAAAAACTGGAGAGTTTGTTATTAACAGTCCCTGTGAATCAGCTCAGAAGTACTGGATAGGAGGAG
                                         |   ||| | |  | || |   || |   | || |||    || | |||||  |       |||||| ||||| ||||||||  | ||    || ||  ||  |||    ||||||||||| |||| ||| || || || |||||||| ||||||||||||||||
-----------------------------------------gttcgta-gct--tcttttctcttttttgttttctttgtgcttgagtggtttatgatcttttcagGTCCGAGGGATTGAAACTATAACTGTGTACGATCCATCAACAAAGGAGTTTGTTATCAACACTCCATGCGAGTCTGCTCAGAAATACTGGATAGGAGGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgatgttcttcattctccctgttgtttagttttcattggttctttcatgggtcagGTTCGAGGTATTGAAACAGTTACCACATATGACTCAAAAACTGGAGAGTTTGTTATTAACAGTCCCTGTGAATCAGCTCAGAAGTACTGGATAGGAGGAG
                                       ttctttcat  CT-rich tract
                        tttagtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtgaaggttgtttgatcatttggttttgggccaccaggcctgtatgatgatgttcttcattctccctgttgtttagttttcattggttctttcatgggtcagGTTCGAGGTATTGAAACAGTTACCACATATGACTCAAAAACTGGAGAGTTTGTTATTAACAGTCCCTGTGAATCAGCTCAGAAGTACTGGATAGGAGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG