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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggtgaggtcgattatttattgatgtttaagaatttcaaattattggttttgagaaaagtttggtcagttaattgattctgttttaacaaattaaatgcagGACTATCTAAATTGAAGACAGGAGATAGGCAATGGTTCTTTTTTAGCCCCAGAGACAGGAAGTACCCTAATGGAGCTAGGTCTAATAGGGCAACCAGGCA

Basic information

species Vitis vinifera
transcript Vv18s0001g01820.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0001g01820.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA10G36360.1 (Glycine max), 3'ss of exon 1
ggtgaggtcgattatttattgatgtttaa-gaatttcaaattattggtt--ttgagaaaagtttggtcagttaattgattctgttttaacaaattaaatgcagGACTATCTAAATTGAAGACAGGAGATAGGCAATGGTTCTTTTTTAGCCCCAGAGACAGGAAGTACCCTAATGGAGCTAGGTCTAATAGGGCAACCAGGCA
| | | | || || | || || || |||| | || ||||| | | ||| | | || || | ||| |||||| | ||||| |||||| || ||||||||||||||||||||||| | | |||||| |||||||| |||||||| | |||||||| | |||||||| |
tatactcccaaaatatctttaatctgaaataaaactctgattacccttcaatttcttcttgtttgatta-ctaactaacaatggcttgtaatattt--tgcagGGCAATCTATATTGAAAACTGGAGATAGGCAATGGTTCTTTTTCTGTCACAGAGATAGGAAGTATCCTAATGGTGGAAGGTCTAACCGAGCAACCAGACG

upper sequence: Vv18s0001g01820.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA20G31210.1 (Glycine max), 3'ss of exon 1
ggtgaggtcgattatttattgatgtttaa---gaatttcaaatt--attggttttgagaaaagtttggtcagttaattgattctgttttaacaaattaaatgcagGACTATCTAAATTGAAGACAGGAGATAGGCAATGGTTCTTTTTTAGCCCCAGAGACAGGAAGTACCCTAATGGAGCTAGGTCTAATAGGGCAACCAGGCA
| | | | | || ||||| ||| | || | | | | || | | | | || | | | ||| | | || | |||||| | ||||| |||||| || ||||||||||||||||||||||| | | |||||| ||||| || |||||||| | |||||||| | |||||||| |
----atatatactcccaaaatatctttaatctgaaataaaactctgactagccttcaatatgttcttgtttgattactgactaaaggcttgtaatattt-tgcagGGCAATCTATATTGAAAACGGGAGATAGGCAATGGTTCTTTTTCTGTCACAGAGATAGGAAATATCCTAATGGTGGAAGGTCTAACCGAGCAACCAGACG
















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|161709113|gb|FC061348.1|FC061348
EST:     TATCATCGCCGACGTCGATGTCTACAAGTGGGACCCCGAGGATTTGCCTG                         GACTATCTAAATTGAAGACAGG
genomic: TATCATCGCCGAGGTCGATGTCTACAAGTGGGACCCCGAGGATTTGCCTGgtatcaaacc ... ttaaatgcagGACTATCTAAATTGAAGACAGG
EST: gi|161720508|gb|FC070907.1|FC070907
EST:     TATCATCGCCGAGGTCGATGTCTACAAGTGGGACCCCGAGGATTTGCCTG                         GACTATCTAAATTGAAGACAGGAGATAGGCAATGGTTCTTTTTTAGCCCCA
genomic: TATCATCGCCGAGGTCGATGTCTACAAGTGGGACCCCGAGGATTTGCCTGgtatcaaacc ... ttaaatgcagGACTATCTAAATTGAAGACAGGAGATAGGCAATGGTTCTTTTTTAGCCCCA
EST: gi|161716141|gb|FC068060.1|FC068060
EST:     TATCATCGCCGAGGTCGATGTCTACAAGTGGGACCCCGAGGATTTGCCTG                         GACTATCTAAATTGAAGACAGGAGATAGGCAATGGTTCTTTTTTAGCCCCA
genomic: TATCATCGCCGAGGTCGATGTCTACAAGTGGGACCCCGAGGATTTGCCTGgtatcaaacc ... ttaaatgcagGACTATCTAAATTGAAGACAGGAGATAGGCAATGGTTCTTTTTTAGCCCCA
EST: gi|161720743|gb|FC070650.1|FC070650
EST:     TATCATCGCCGAGGTCGATGTCTACAAGTGGGACCCCGAGGATTTGCCTG                         GACTATCTAAATTGAAGACAGGAGATAGGCAATGGTTCTTTTTTAGCCCCA
genomic: TATCATCGCCGAGGTCGATGTCTACAAGTGGGACCCCGAGGATTTGCCTGgtatcaaacc ... ttaaatgcagGACTATCTAAATTGAAGACAGGAGATAGGCAATGGTTCTTTTTTAGCCCCA
EST: gi|71860524|gb|DT009579.1|DT009579
EST:     TATCATCGCCGAGGTCGATGTCTACAAGTGGGACCCCGAGGATTTGCCTG                         GGCTATCTAAATTGAAGACAGGAGATAGGCAATGGTTCTTTTTTAGCCCCA
genomic: TATCATCGCCGAGGTCGATGTCTACAAGTGGGACCCCGAGGATTTGCCTGgtatcaaacc ... ttaaatgcagGACTATCTAAATTGAAGACAGGAGATAGGCAATGGTTCTTTTTTAGCCCCA
EST: gi|71862727|gb|DT011782.1|DT011782
EST:     TATCATCGCCGAGGTCGATGTCTACAAGTGGGACCCCGAGGATTTGCCTG                         GGCTATCTAAATTGAAGACAGGAGATAGGCAATGGTTCTTTTTTAGCCCCA
genomic: TATCATCGCCGAGGTCGATGTCTACAAGTGGGACCCCGAGGATTTGCCTGgtatcaaacc ... ttaaatgcagGACTATCTAAATTGAAGACAGGAGATAGGCAATGGTTCTTTTTTAGCCCCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttttgagaaaagtttggtcagttaattgattctgttttaacaaattaaatgcagGACTATCTAAATTGAAGACAGGAGATAGGCAATGGTTCTTTTTTAGCCCCAGAGACAGGAAGTACCCTAATGGAGCTAGGTCTAATAGGGCAACCAGGCA
                                   ttttaac  putative branch site (score: 2)
 ttaattgattctgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggtgaggtcgattatttattgatgtttaagaatttcaaattattggttttgagaaaagtttggtcagttaattgattctgttttaacaaattaaatgcagGACTATCTAAATTGAAGACAGGAGATAGGCAATGGTTCTTTTTTAGCCCCAGAGACAGGAAGTACCCTAATGGAGCTAGGTCTAATAGGGCAACCAGGCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
ggtgagg
- - - - - - - - - - - - - - - - - -caaatta
- - - - - - - - - - - - - - - - - - - - - - - - - gagaaaa