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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cataatgaaccataataaaagatcggaactacttttggtcttccaacttttctttttctggtaatattctgtcaaataatgtttactattcatgttttagGTTTTCCCCTGAGAAAATATGGTACATTGATCAGATGCTCAAGGTTCTTTCTGAG

Basic information

species Vitis vinifera
transcript Vv01s0026g00310.t01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv01s0026g00310.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA02G03800.1 (Glycine max), 3'ss of exon 7
cataatgaaccataataaaagatcggaactacttttggtcttccaacttttctttttctggtaatattctgtcaaataatgtttact-attcatgttttagGTTTTCCCCTGAGAAAATATGGTACATTGATCAGATGCTCAAGGTTCTTTCTGAG
  | |    |  | |    ||| |  ||  | ||  | | |||      ||      ||    |||||  ||  | |||  |||| | ||| ||| || |||| |||||| ||||| || ||||| ||||||||||||||||||||||| ||||||
tgtcaccccctgtcaatgtagaact-aataagttgagattttctttaaattgcacaactcaatatatttggttgactaacatttatttattaatgcttcagGTATTCCCCAGAGAAGATCTGGTATATTGATCAGATGCTCAAGGTTCTGTCTGAG

upper sequence: Vv01s0026g00310.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA08G39930.1 (Glycine max), 3'ss of exon 8
cataatgaaccataataaaagatcggaactactt-ttggtcttccaacttttctt-tttctggtaatat-tctgtcaaataatgtttact-attcatgttttagGTTTTCCCCTGAGAAAATATGGTACATTGATCAGATGCTCAAGGTTCTTTCTGAG
     | | || | || |  | |  ||| || |   | || ||  |  ||| |     |||   ||| | | ||    ||||  |||||| |||  || || ||||||||||| ||||| || |||||||||||||| ||||| |||||||| ||||||
--ctgttaccctttatca--gtttagaagtagtagctagtgttttatttttccccacatctataaatgtatttggtttataacatttacttatttgtgcttcagGTTTTCCCCAGAGAAGATCTGGTACATTGATCAAATGCTGAAGGTTCTGTCTGAG

upper sequence: Vv01s0026g00310.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA01G03890.1 (Glycine max), 3'ss of exon 8
cataatgaaccataataaaagatcggaactacttttggtcttccaacttttctttttctggtaatattctgtcaaataatgtttact-attcatgttttagGTTTTCCCCTGAGAAAATATGGTACATTGATCAGATGCTCAAGGTTCTTTCTGAG
  | |    |  | |    ||| | ||   | |   | | ||       ||      ||    |||||  ||  | |||  |||| | ||| ||| || |||| |||||| ||||| || ||||| ||||||||||||||||||||||| ||| ||
tgtcacctcctgtcaatttagaactga-taagtagagattttatttaaattgcacaactaaatatatttggttgactaacatttatttattaatgcttcagGTATTCCCCAGAGAAGATCTGGTATATTGATCAGATGCTCAAGGTTCTGTCTCAG

upper sequence: Vv01s0026g00310.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: AT1G60070.2 (Arabidopsis thaliana), 3'ss of exon 8
--------------------------------------------------------------------------------------------------cataatgaaccataataa---aagatcggaactacttttggtcttccaacttttctttttctggtaatattctgtcaaataatgtttactattcatgttttagGTTTTCCCCTGAGAAAATATGGTACATTGATCAGATGCTCAAGGTTCTTTCTGAG
                                                                                                  |  ||| ||   ||||     ||| |    |  |   | |       || |  | |   || |    || |  || |   |||   || |     | |  ||||||| | || |||||||| |||||||||||||| ||||| |||||||| ||||||
gtaagttgcgcaactcttcagccagcatgtacagagatttcattcttctagtatatggtaactgaacattttaatttgtatcaaagttgtgcgttaagctcaattaatagtaatcccttaagtttatcagaatgctggcctggataaatggtgtccatcagacc-taattggttactgaattagtatttcctttctgctagGTTTGCTCCAGAGAAAATCTGGTACATTGATCAAATGCTAAAGGTTCTATCTGAG

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|71889458|gb|DT038513.1|DT038513
EST:     CCAGAATTCAAGGGAGATCTGACCGCCAAAATTTGCTCAATTGTTGAAAA                         GTTTTCCCCTGAGAAAATATGGTACATTGATCAGATGCTCAAGGTTCTTTC
genomic: CCAGAATTCAAGGGAGATCTGACCGCCAAAATTTGCTCAATTGTTGAAAAgtaagttaaa ... catgttttagGTTTTCCCCTGAGAAAATATGGTACATTGATCAGATGCTCAAGGTTCTTTC
EST: gi|110416791|gb|EC982796.1|EC982796
EST:     CCAGAATTCAAGGGAGATCTGACCGCCAAAATTTGCTCAATTGTTGAAAA                         GTTTTCCCCTGAGAAAATATGGTACATTGATCAGATGCTCAAGGTTCTTTC
genomic: CCAGAATTCAAGGGAGATCTGACCGCCAAAATTTGCTCAATTGTTGAAAAgtaagttaaa ... catgttttagGTTTTCCCCTGAGAAAATATGGTACATTGATCAGATGCTCAAGGTTCTTTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acttttctttttctggtaatattctgtcaaataatgtttactattcatgttttagGTTTTCCCCTGAGAAAATATGGTACATTGATCAGATGCTCAAGGTTCTTTCTGAG
                            aaataatgtttactat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cataatgaaccataataaaagatcggaactacttttggtcttccaacttttctttttctggtaatattctgtcaaataatgtttactattcatgttttagGTTTTCCCCTGAGAAAATATGGTACATTGATCAGATGCTCAAGGTTCTTTCTGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- -aatgaac
- - - - - - -aataaaa
- - - - - - - - - - - - - - - -cttttgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caaataa