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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttagctttaattccatttttcccatcacaattatcaaagtcattgtttctctgacttgttttatgttgacatgcttgattcagGATGAAAATAGGAGATCAGAGGAAAGAGAGTGGATGGGACAGAAGTATTTGATTCATTTCTTCGACTACGAAATGGAGAATAAGAAGTATTTAATATGGG

Basic information

species Vitis vinifera
transcript Vv10s0003g00880.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv10s0003g00880.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA13G24060.1 (Glycine max), 3'ss of exon 3
gtttagctttaattccatttttcccatcacaattatcaaagtcattgtttctctgacttgttttatgttgacatgcttgattcagGATGAAAATAGGAGATCAGAGGAAAGAGAGTGGATGGGACAGAAGTATTTGATTCATTTCTTCGACTACGAAATGGAGAATAAGAAGTATTTAATATGGG
||  |   ||| ||  |||||   | |||    |       ||||| ||  | | |||||| | ||||    |  ||| |  |||||||||||| |||||   || || || |||||||||||| ||||||||||| | |||||||| ||||| || || | | |||| || ||  | |||||||
gtccatgcttatttttattttgatc-tcatgtct-------tcattcttgatatcacttgtctgatgtcatta--ctttaagcagGATGAAAATCGGAGACAGGATGAGAGGGAGTGGATGGGAGAGAAGTATTTGTTGCATTTCTTTGACTATGATATCGGGCATAAAAAATACATCATATGGG

upper sequence: Vv10s0003g00880.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT1G28960.5 (Arabidopsis thaliana), 3'ss of exon 3
----gtttagctttaattcca--tttttcccatcacaattatcaaagtcattgtttc---tctgacttgttttatgttgacatgcttgattcagGATGAAAATAGGAGATCAGAGGAAAGAGAGTGGATGGGACAGAAGTATTTGATTCATTTCTTCGACTACGAAATGGAGAATAAGAAGTATTTAATATGGG
     | | | |||  | |||  ||  |        | || |     |     | ||     | | |  ||  |  ||    |  ||| |||||||||| ||| | ||||| || || ||||||||||||||  | ||||||||||| |||| ||| ||||||  ||  |   ||||| | ||| | |||||||
gttgctcttgttttcttaccaagttactttagctgtagttgtgttttttcccttctcaagcatcattacttgaacctttttttttttgtttcagGATGAGAATCGAAGATCTGAAGAGAGAGAGTGGATGGGTGAAAAGTATTTGATCCATTACTTTGACTACAGAACAGGAGATAAGGATTATATGATATGGG
















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|110712360|gb|EE089889.1|EE089889
EST:     CTGATGAAGTGGATGCNGTATTTGATGCCCCTTTGGAGATGTTCATCAAG                         GATGAAAATANGAGATCAGAGGAAAGAGAGTGGATGGGACAGAAGTATTTG
genomic: CTGATGAAGTGGATGCGGTATTTGATGCCCCTTTGGAGATGTTCATCAAGgtttagcttt ... cttgattcagGATGAAAATAGGAGATCAGAGGAAAGAGAGTGGATGGGACAGAAGTATTTG
EST: gi|110709463|gb|EE084944.1|EE084944
EST:     CTGATGAAGTGGATGCGGTATTTGATGCCCCTTTGGAGATGTTCATCAAG                         GATGAAAATAGGAGATCAGAGGAAAGAGAGTGGATGGGACAGAAGTATTTG
genomic: CTGATGAAGTGGATGCGGTATTTGATGCCCCTTTGGAGATGTTCATCAAGgtttagcttt ... cttgattcagGATGAAAATAGGAGATCAGAGGAAAGAGAGTGGATGGGACAGAAGTATTTG
EST: gi|110698121|gb|EE075771.1|EE075771
EST:     CTGATGAAGTGGATGCGGTATTTGATGCCCCTTTGGAGATGTTCATCAAG                         GATGAAAATAGGAGATCAGAGGAAAGAGAGTGGATGGGACAGAAGTATTTG
genomic: CTGATGAAGTGGATGCGGTATTTGATGCCCCTTTGGAGATGTTCATCAAGgtttagcttt ... cttgattcagGATGAAAATAGGAGATCAGAGGAAAGAGAGTGGATGGGACAGAAGTATTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aattatcaaagtcattgtttctctgacttgttttatgttgacatgcttgattcagGATGAAAATAGGAGATCAGAGGAAAGAGAGTGGATGGGACAGAAGTATTTGATTCATTTCTTCGACTACGAAATGGAGAATAAGAAGTATTTAATATGGG
                           ttgttttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttagctttaattccatttttcccatcacaattatcaaagtcattgtttctctgacttgttttatgttgacatgcttgattcagGATGAAAATAGGAGATCAGAGGAAAGAGAGTGGATGGGACAGAAGTATTTGATTCATTTCTTCGACTACGAAATGGAGAATAAGAAGTATTTAATATGGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT