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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgattgctttgtatatcattctttctcagtgtttttgtttttggtttctatgtgttttgtgtgaatgatttgatttttgaatgaattgtagGGATTTAAATGAGGTTTTGGATGCCTATGAGAGAGGAGACAAGTTTTACTTGTACACAGGCAGAGGACCTTCTTCTGAGGCTTTGCATTTGGGGCATTTG

Basic information

species Vitis vinifera
transcript Vv12s0028g03370.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv12s0028g03370.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA03G25740.1 (Glycine max), 3'ss of exon 1
gtatgattgctttgtatatcattctttctcagtgtttttgtttttggtttctatgtgttttgtgtgaatgatttgatttttgaatgaattgtagGGATTTAAATGAGGTTTTGGATGCCTATGAGAGAGGAGACAAGTTTTACTTGTACACAGGCAGAGGACCTTCTTCTGAGGCTTTGCATTTGGGGCATTTG
          |   |  |||  | |    |  | | |   |   |  |||   |    | |   |  ||||| |  ||| |   ||  | | || |||||    ||| || |||| || |||||||| ||||| ||||| ||||||||||| ||  | |||||||| ||||| || ||||||||||| || |||
---------gtacctccatccatttcctcccttctctccttcccttattttcttaaactataatttgatgatgtcgtttctttgtg--tcgcagCGATTTCGCGGAGATTCTGGACGCGTATGAGAGGGGAGATAAGTTCTACTTGTACACCGGACGCGGACCTTCCTCTGAAGCCTTGCATTTGGGACACTTG

upper sequence: Vv12s0028g03370.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT3G04600.2 (Arabidopsis thaliana), 3'ss of exon 2
gtatgattgctttgtatatcattctttctcagtgtttttgtttttggtttctatgtgttttgtgtgaatgatttgatttttgaatgaattgtagGGATTTAAATGAGGTTTTGGATGCCTATGAGAGAGGAGACAAGTTTTACTTGTACACAGGCAGAGGACCTTCTTCTGAGGCTTTGCATTTGGGGCATTTG
                  | |  | ||| |  ||||||  ||  | || |  |  | | | || |   |  ||| | || |||     |   |||||||| |||||| ||||||| || |||||||||||||||||||| ||  | ||||| || ||||||||||| || || || ||||||||||||||||||
-----------------gttagacattcac--tgttttaattaattgtgtagaaatttctcgtcttgcttgttttaattgtgaggttttaacagGGATTTCAATGAGATTTTGGACGCTTATGAGAGAGGAGACAAGTTCTATCTCTACACTGGAAGAGGACCTTCATCAGAAGCATTGCATTTGGGGCATTTG
















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|161717337|gb|FC065270.1|FC065270
EST:     TCTCGCCCTCCTCACGTCTTTCTCCGCCGCGGTGTTTTCTTCGCTCACCG                         GGATTTGAATGAGGTTTTGGGTGCCTATGAGAGAGGAGACAAGTTTTACTT
genomic: TCTCGCCCTCCTCACGTCTTTCTCCGCCGCGGTGTCTTCTTCGCTCACCGgtatgattgc ... tgaattgtagGGATTTAAATGAGGTTTTGGATGCCTATGAGAGAGGAGACAAGTTTTACTT
EST: gi|110709548|gb|EE085106.1|EE085106
EST:     TCTCGCCCTCCTCACGTCTTTCTCCGCCGCGGTGTCTTCTTCGCTCACCG                         GGATTTAAATGAGGTTTTGGATGCCTATGAGAGAGGAGACAAGTTTTACTT
genomic: TCTCGCCCTCCTCACGTCTTTCTCCGCCGCGGTGTCTTCTTCGCTCACCGgtatgattgc ... tgaattgtagGGATTTAAATGAGGTTTTGGATGCCTATGAGAGAGGAGACAAGTTTTACTT
EST: gi|71855398|gb|DT004453.1|DT004453
EST:     TCTCGCCCTCCTCACGTCTTTCTCCGCCGCGGTGTCTTCTTCGCTCACCG                         GGATTTAAATGAGGTTT-GGATGTCTATGAGAGAGGAGACAAGTTTTACTT
genomic: TCTCGCCCTCCTCACGTCTTTCTCCGCCGCGGTGTCTTCTTCGCTCACCGgtatgattgc ... tgaattgtagGGATTTAAATGAGGTTTTGGATGCCTATGAGAGAGGAGACAAGTTTTACTT
EST: gi|294967200|gb|GW840075.1|GW840075
EST:     CTCGCCCTCCTCACGTCTTTCTCCGCCGCGG-GTGCTCCTTCGCTCACCG                         GGATTTAAATGAGGTTTTGGATGCCTATGAGAGAGGAGACAAGTTTTACTT
genomic: CTCGCCCTCCTCACGTCTTTCTCCGCCGCGGTGT-CTTCTTCGCTCACCGgtatgattgc ... tgaattgtagGGATTTAAATGAGGTTTTGGATGCCTATGAGAGAGGAGACAAGTTTTACTT
EST: gi|110710091|gb|EE086125.1|EE086125
EST:     TCTCGCCCTCCTCACGTCTTTCTCCGCCGCGGTGTCTTCTTCGCTCACCG                         GGATTTAAATGAGGTTTTGGATGCCTATGAGAGAGGAGACAAGTTTTACTT
genomic: TCTCGCCCTCCTCACGTCTTTCTCCGCCGCGGTGTCTTCTTCGCTCACCGgtatgattgc ... tgaattgtagGGATTTAAATGAGGTTTTGGATGCCTATGAGAGAGGAGACAAGTTTTACTT
EST: gi|71860975|gb|DT010030.1|DT010030
EST:     TCTCGCCCTCCTCACGTCTTTCTCCGCCGCGGTGTCTTCTTCGCTCACCG                         GGATTTAAATGAGGTTTTGGATGCCTATGAGAGAGGAGACAAGTTTTACTT
genomic: TCTCGCCCTCCTCACGTCTTTCTCCGCCGCGGTGTCTTCTTCGCTCACCGgtatgattgc ... tgaattgtagGGATTTAAATGAGGTTTTGGATGCCTATGAGAGAGGAGACAAGTTTTACTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttttggtttctatgtgttttgtgtgaatgatttgatttttgaatgaattgtagGGATTTAAATGAGGTTTTGGATGCCTATGAGAGAGGAGACAAGTTTTACTTGTACACAGGCAGAGGACCTTCTTCTGAGGCTTTGCATTTGGGGCATTTG
                               atttgat  putative branch site (score: 5)
                           aatgatttgattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgattgctttgtatatcattctttctcagtgtttttgtttttggtttctatgtgttttgtgtgaatgatttgatttttgaatgaattgtagGGATTTAAATGAGGTTTTGGATGCCTATGAGAGAGGAGACAAGTTTTACTTGTACACAGGCAGAGGACCTTCTTCTGAGGCTTTGCATTTGGGGCATTTG

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