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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTGGTGGAGCTGAAAAATGGGGAAACTTACAATGGTCATTTAGTGAATTGTGATACATGGATGAACATCCATCTGCGTGAAGTCATCTGCACTTCAAAAgtatggtatttctttcaatcaattatgtcttatttttctttaatttatttttataatgacttaaaatgatcatcttctgtgattcatggtcacaatgggaattaaaatgtag

Basic information

species Vitis vinifera
transcript Vv14s0060g02240.t01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0060g02240.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA02G17430.2 (Glycine max), 5'ss of exon 3
TTGGTGGAGCTGAAAAATGGGGAAACTTACAATGGTCATTTAGTGAATTGTGATACATGGATGAACATCCATCTGCGTGAAGTCATCTGCACTTCAAAAgtatggtatttctttcaatcaattatgtcttatttttctttaatttatttttataatgacttaaaatgatcatcttctgtgattcatggtcacaa-tgggaattaa-aatgtag
 ||||||| |||||||||||||| ||||| || || || || || ||||||||||||||||||||||||||||| || |||||||| || || || ||||||  |   || ||||| |    |   |    |   |||   || |  | || | |||        |||   | |  ||  | | |   | |||| | | ||||   |||  ||
CTGGTGGAACTGAAAAATGGGGAGACTTATAACGGGCACTTGGTTAATTGTGATACATGGATGAACATCCATCTCCGAGAAGTCATTTGTACCTCTAAAgtaacgatcttttttcactgctctccctgcattcaatctcagatattgtcttctcatgt------gtgaatgtttgttgctactta-acttacaacttgaaattggcaattcag

upper sequence: Vv14s0060g02240.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA03G37170.2 (Glycine max), 5'ss of exon 3
TTGGTGGAGCTGAAAAATGGGGAAACTTACAATGGTCATTTAGTGAATTGTGATACATGGATGAACATCCATCTGCGTGAAGTCATCTGCACTTCAAAAgtatggtatttctttcaatcaattatgtcttatttttctttaatttatttttataatgacttaaaatgatcatcttctgtgattcatggtcacaatgggaattaaaatgtag
|||||||| |||||||||||||| || || || || ||||| || ||||| || ||||||||||||||||||||||| |||||||| || || || ||||||  ||   | || | |||  ||   | || ||||  | |  | || |||  | ||||   |||| | |    ||     | |  |||| |    |               
TTGGTGGAACTGAAAAATGGGGAGACATATAACGGGCATTTGGTTAATTGCGACACATGGATGAACATCCATCTGCGAGAAGTCATTTGTACATCTAAAgtaatgttgcttttacgatcccttgcttgtt-ttttgttgtcttgtaatttggttatgatggaaaaggcttgattt----aaattttggtaatgtag---------------

upper sequence: Vv14s0060g02240.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA19G39780.1 (Glycine max), 5'ss of exon 3
TTGGTGGAGCTGAAAAATGGGGAAACTTACAATGGTCATTTAGTGAATTGTGATACATGGATGAACATCCATCTGCGTGAAGTCATCTGCACTTCAAAAgtatggtatttctttcaatcaattatgtcttatttttctttaatttatttttataatgacttaaaatgatcatcttctgtgattcatggtcacaatgggaattaaaatgtag
|||||||| |||||||||||||| || || || || ||||| || ||||| ||||||||||||||||||||||| || |||||||| || || || ||||||  ||   | || | |||  ||   | || ||||  | |  | || ||| ||  ||| |  ||| | |    |||  |     |||                        
TTGGTGGAACTGAAAAATGGGGAGACATATAACGGGCATTTGGTTAATTGCGATACATGGATGAACATCCATCTCCGAGAAGTCATTTGTACATCTAAAgtaatgttgcttttacgatcccttgcttgtt-ttttgttgtcttgtaatttgattgtga-tggaaaggtttgatttcaattggcaatgtag---------------------

upper sequence: Vv14s0060g02240.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA10G02380.1 (Glycine max), 5'ss of exon 3
TTGGTGGAGCTGAAAAATGGGGAAACTTACAATGGTCATTTAGTGAATTGTGATACATGGATGAACATCCATCTGCGTGAAGTCATCTGCACTTCAAAAgtatggtatttctttcaatcaattatgtcttatttttctttaatttatttttataatgacttaaa-atgatcatcttctgtgattcatggtcacaatg-ggaattaa-aatgtag
 | ||||| |||||||||||||| ||||| || || || || || ||||||||||||||||||||||| ||||| || |||||||| || || || ||||||  |   || ||||| |   || |  ||   ||  || | |  |||| |  |     || | |  |||   |||  |   | | |   | |||||  | ||||   |||  ||
CTAGTGGAACTGAAAAATGGGGAGACTTATAACGGGCACTTGGTTAATTGTGATACATGGATGAACATTCATCTCCGAGAAGTCATTTGTACCTCTAAAgtaacgatcttttttcact--gttctccctgcattcactctcagatattgtctt-----ctcatatgtgaatgtctgttacaactta-acttacaatttgaaattggcaattcag

upper sequence: Vv14s0060g02240.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: AT5G27720.1 (Arabidopsis thaliana), 5'ss of exon 4
TTGGTGGAGCTGAAAAATGGGGAAACTTACAATGGTCATTTAGTGAATTGTGATACATGGATGAACATCCATCTGCGTGAAGTCATCTGCACTTCAAAAgta---tggtatttctttcaatcaattatgtcttatttttctttaatttatttttataatgacttaaa----atgatcatcttctgtgattcatggtcacaatgggaattaaaatgtag
 | |||||||| || ||||| || || |||||||| ||||| |||||||||||||| ||||||||||||||||||||||||||||| || || ||||| ||    |  | |||   |   |  ||       || |||  ||  | ||  |  |  |||    |  |    |   |||| |  | || | | || | ||  | |              
CTCGTGGAGCTTAAGAATGGAGAGACATACAATGGGCATTTGGTGAATTGTGATACTTGGATGAACATCCATCTGCGTGAAGTCATATGTACATCAAAGgttatcttatgttttcatatgttgatacaaatatactttgtttagacttcgtgatgaaattttgtgtagctgacactcatatattttgctgcttgattactctag--------------

upper sequence: Vv14s0060g02240.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: PP1S36_327V6.2 (Physcomitrella patens), 5'ss of exon 2
TTGGTGGAGCTGAAAAATGGGGAAACTTACAATGGTCATTTAGTGAATTGTGATACATGGATGAACATCCATCTGCGTGAAGTCATCTGCACTTCAAAAgt-atggtatttctttcaatcaattat----gtctt-------atttttctt-----------taatttatttttata------atgacttaaaatga--tcatcttctgtgattcatggtcacaatgggaattaaaatgtag---------------
 | || ||||| |||||||| || ||||| || || |||||||| || |||||||||||||||||||| || || |||||||| || ||||| ||||| || ||  | |||  | | || |  |||    || ||       || |  ||            |  || || ||||||      |||| ||||  |||  |  |||||  |  ||  || |  |  | ||  ||| |||| |                
CTTGTCGAGCTCAAAAATGGAGAGACTTATAACGGCCATTTAGTAAACTGTGATACATGGATGAACATTCACCTACGTGAAGTTATTTGCACCTCAAAGgtgattatttttgctaccattatctattagggttttcaaagtgatctgcctcgtcccagctgctggttcatatttatattgcagatgaattaatttgagttattcttcgattgttattgattccttttggttttataatggatatgtgggcattgtag

upper sequence: Vv14s0060g02240.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: EFJ10085 (Selaginella moellendorffii), 5'ss of exon 2
TTGGTGGAGCTGAAAAATGGGGAAACTTACAATGGTCATTTAGTGAATTGTGATACATGGATGAACATCCATCTGCGTGAAGTCATCTGCACTTCAAAAgta--tggtatttctttcaatcaattatgtcttatttttctttaatttatttttataatgacttaaaatgatcatcttctgtgattcatggtcacaatgggaattaaaatgtag
        ||| || ||||| || ||||||||||| ||||| ||||  || ||||  ||||||||||||||||| || ||||| || |||||||| || |    || | |||  | |   |  |  | ||| ||  |||||   |  |                                                                 
--------GCTCAAGAATGGAGAGACTTACAATGGGCATTTGGTGAGCTGCGATAGCTGGATGAACATCCATCTACGAGAAGTTATTTGCACTTCCAAGGCGAGTGATgttttctccttcctttcttttctcatccttcttctctccag----------------------------------------------------------------

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|37189618|gb|CF608967.1|CF608967
EST:     GTGATACATGGATGAACATCCATCTGCGTGAAGTCATCTGCACTTCAAAA                         GATGGAGATAGGTTTTGGAGAATGCCAGAATGCTACATTCGTGGGAATACA
genomic: GTGATACATGGATGAACATCCATCTGCGTGAAGTCATCTGCACTTCAAAAgtatggtatt ... taaaatgtagGATGGAGATAGGTTTTGGAGAATGCCAGAATGCTACATTCGTGGGAATACA
EST: gi|71866659|gb|DT015714.1|DT015714
EST:     GTGATACATGGATGAACATCCATCTGCGTGAAGTCATCTGCACTTCAAAA                         GATGGAGATAGGTTTTGGAGAATGCCAGAATGCTACATTCGTGGGAATACA
genomic: GTGATACATGGATGAACATCCATCTGCGTGAAGTCATCTGCACTTCAAAAgtatggtatt ... taaaatgtagGATGGAGATAGGTTTTGGAGAATGCCAGAATGCTACATTCGTGGGAATACA
EST: gi|37189144|gb|CF608493.1|CF608493
EST:     GTGATACATGGATGAACATCCATCTGCGTGAAGTCATCTGCACTTCAAAA                         GATGGAGATAGGTTTTGGAGAATGCCAGAATGCTACATTCGTGGGAATACA
genomic: GTGATACATGGATGAACATCCATCTGCGTGAAGTCATCTGCACTTCAAAAgtatggtatt ... taaaatgtagGATGGAGATAGGTTTTGGAGAATGCCAGAATGCTACATTCGTGGGAATACA
EST: gi|110368812|gb|EC932903.1|EC932903
EST:     GTGATACATGGATGAACATCCATCTGCGTGAAGTCATCTGCACTTCAAAA                         GATGGAGATAGGTTTTGGAGAATGCCAGAATGCTACATTCGTGGGAATACA
genomic: GTGATACATGGATGAACATCCATCTGCGTGAAGTCATCTGCACTTCAAAAgtatggtatt ... taaaatgtagGATGGAGATAGGTTTTGGAGAATGCCAGAATGCTACATTCGTGGGAATACA
EST: gi|71886236|gb|DT035291.1|DT035291
EST:     GTGATACATGGATGAACATCCATCTGCGTGAAGTCATCTGCACTTCAAAA                         GATGGAGATAGGTTTTGGAGAATGCCAGAATGCTACATTCGTGGGAATACA
genomic: GTGATACATGGATGAACATCCATCTGCGTGAAGTCATCTGCACTTCAAAAgtatggtatt ... taaaatgtagGATGGAGATAGGTTTTGGAGAATGCCAGAATGCTACATTCGTGGGAATACA
EST: gi|37184974|gb|CF604327.1|CF604327
EST:     GTGATACATGGATGAACATCCATCTGCGTGAAGTCATCTGCACTTCAAAA                         GATGGAGATAGGTTTTGGAGAATGCCAGAATGCTACATTCGTGGGAATACA
genomic: GTGATACATGGATGAACATCCATCTGCGTGAAGTCATCTGCACTTCAAAAgtatggtatt ... taaaatgtagGATGGAGATAGGTTTTGGAGAATGCCAGAATGCTACATTCGTGGGAATACA
EST: gi|110400007|gb|EC966544.1|EC966544
EST:     TGAACATCCATCTGCGTGAAGTCATCTGCACTTCAAAA                         GATGGAGATAGGTTTTGGAGAATGCCAGAATGCTACATTCGTGGGAATACA
genomic: TGAACATCCATCTGCGTGAAGTCATCTGCACTTCAAAAgtatggtatt ... taaaatgtagGATGGAGATAGGTTTTGGAGAATGCCAGAATGCTACATTCGTGGGAATACA
EST: gi|37189131|gb|CF608480.1|CF608480
EST:     GTGATACATGGATGAACATCCATCTGCGTGAAGTCATCTGCACTTCAAAA                         GATGGAGATAGGTTTTGGAGAATGCCAGAATGCTACATTCGTGGGAATACA
genomic: GTGATACATGGATGAACATCCATCTGCGTGAAGTCATCTGCACTTCAAAAgtatggtatt ... taaaatgtagGATGGAGATAGGTTTTGGAGAATGCCAGAATGCTACATTCGTGGGAATACA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTGGTGGAGCTGAAAAATGGGGAAACTTACAATGGTCATTTAGTGAATTGTGATACATGGATGAACATCCATCTGCGTGAAGTCATCTGCACTTCAAAAgtatggtatttctttcaatcaattatgtcttatttttctttaatttatttttataatgacttaaaatgatcatcttctgtgattcatggtcacaatgggaattaaaatgtag

- - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA