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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtcattgttatctattgtaatggtgactgtggaagaattaattaattattcctttattcaattatgctcatgagaatggtgtgttgtatccatgccttagGTAACCAAAGAATGCCTAGACAAAGCAATATCAATATGTGCACCTGGGGTGGAGTTCAAGAAAATTGGAAAAACCATACA

Basic information

species Vitis vinifera
transcript Vv07s0031g00820.t01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv07s0031g00820.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA01G39200.1 (Glycine max), 3'ss of exon 6
gtcattgttatctattgtaatggtgactgtggaagaattaattaattattcctttattcaattatgctcatgagaatggtgtgttgtatccat-gccttagGTAACCAAAGAATGCCTAGACAAAGCAATATCAATATGTGCACCTGGGGTGGAGTTCAAGAAAATTGGAAAAACCATACA
 |   | || |  | |||  |  |   |     |||||| |   ||| | |   |  |  ||| ||  | | | |   ||| ||| |||  ||      ||||||| |||||||||||||| ||||||||||||||||||||||| || |||||||||||||||||||| ||||| || ||
tttggttttgtgaaatgtttttttttgttgttgagaattgagacattgtcctcgtcatttattttgtgcttaataggagtgggtt-tatatattaatacagGTAACTAAAGAATGCCTAGATAAAGCAATATCAATATGTGCACCAGGAGTGGAGTTCAAGAAAATTGGCAAAACAATTCA
















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|34546470|gb|CF514702.1|CF514702
EST:     CAACNNNNNNNNGTGGAGATGTTGATGATAAAGCCAGAAAATTGGTAGAG                         GTAACCAAAGAATGCCTAGACAAAGCAATATCAATATGTGCACCTGGGGTG
genomic: CAACTTTTTTTTGTGGAGATGTTGATGATAAAGCCAGAAAATTGGTAGAGgtagtgttct ... catgccttagGTAACCAAAGAATGCCTAGACAAAGCAATATCAATATGTGCACCTGGGGTG
EST: gi|110381974|gb|EC938149.1|EC938149
EST:     CAACNNNNNNNNGTGGAGATGTTGATGATAAAGCCAGAAAATTGGTAGAG                         GTAACCAAAGAATGCCTAGACAAAGCAATATCAATATGTGCACCTGGGGTG
genomic: CAACTTTTTTTTGTGGAGATGTTGATGATAAAGCCAGAAAATTGGTAGAGgtagtgttct ... catgccttagGTAACCAAAGAATGCCTAGACAAAGCAATATCAATATGTGCACCTGGGGTG
EST: gi|110711473|gb|EE087994.1|EE087994
EST:     CAACNNNNNNNNGTGGAGATGTTGATGATAAAGCCAGAAAATTGGTAGAG                         GTAACCAAAGAATGCCTAGACAAAGCAATATCAATATGTGCACCTGGGGTG
genomic: CAACTTTTTTTTGTGGAGATGTTGATGATAAAGCCAGAAAATTGGTAGAGgtagtgttct ... catgccttagGTAACCAAAGAATGCCTAGACAAAGCAATATCAATATGTGCACCTGGGGTG
EST: gi|34546385|gb|CF514617.1|CF514617
EST:     CAACNNNNNNNNGTGGAGATGTTGATGATAAAGCCAGAAAATTGGTAGAG                         GTAACCAAAGAATGCCTAGACAAAGCAATATCAATATGTGCACCTGGGGTG
genomic: CAACTTTTTTTTGTGGAGATGTTGATGATAAAGCCAGAAAATTGGTAGAGgtagtgttct ... catgccttagGTAACCAAAGAATGCCTAGACAAAGCAATATCAATATGTGCACCTGGGGTG
EST: gi|110429644|gb|EC996143.1|EC996143
EST:     CAACNNNNNNNNGTGGAGATGTTGATGATAAAGCCAGAAAATTGGTAGAG                         GTAACCAAAGAATGCCTAGACAAAGCAATATCAATATGTGCACCTGGGGTG
genomic: CAACTTTTTTTTGTGGAGATGTTGATGATAAAGCCAGAAAATTGGTAGAGgtagtgttct ... catgccttagGTAACCAAAGAATGCCTAGACAAAGCAATATCAATATGTGCACCTGGGGTG
EST: gi|33405491|gb|CF211118.1|CF211118
EST:     CAACNNNNNNNNGTGGAGATGTTGATGATAAAGCCAGAAAATTGGTAGAG                         GTAACCAAAGAATGCCTAGACAAAGCAATATCAATATGTGCACCTGGGGTG
genomic: CAACTTTTTTTTGTGGAGATGTTGATGATAAAGCCAGAAAATTGGTAGAGgtagtgttct ... catgccttagGTAACCAAAGAATGCCTAGACAAAGCAATATCAATATGTGCACCTGGGGTG
EST: gi|110387367|gb|EC952027.1|EC952027
EST:     CAACNNNNNNNNGTGGAGATGTTGATGATAAAGCCAGAAAATTGGTAGAG                         GTAACCAAAGAATGCCTAGACAAAGCAATATCAATATGTGCACCTGGGGTG
genomic: CAACTTTTTTTTGTGGAGATGTTGATGATAAAGCCAGAAAATTGGTAGAGgtagtgttct ... catgccttagGTAACCAAAGAATGCCTAGACAAAGCAATATCAATATGTGCACCTGGGGTG
EST: gi|33405428|gb|CF211055.1|CF211055
EST:     CAACNNNNNNNNGTGGAGATGTTGATGATAAAGCCAGAAAATTGGTAGAG                         GTAACCAAAGAATGCCTAGACAAAGCAATATCAATATGTGCACCTGGGGTG
genomic: CAACTTTTTTTTGTGGAGATGTTGATGATAAAGCCAGAAAATTGGTAGAGgtagtgttct ... catgccttagGTAACCAAAGAATGCCTAGACAAAGCAATATCAATATGTGCACCTGGGGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttattcctttattcaattatgctcatgagaatggtgtgttgtatccatgccttagGTAACCAAAGAATGCCTAGACAAAGCAATATCAATATGTGCACCTGGGGTGGAGTTCAAGAAAATTGGAAAAACCATACA
       tttattcaattat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcattgttatctattgtaatggtgactgtggaagaattaattaattattcctttattcaattatgctcatgagaatggtgtgttgtatccatgccttagGTAACCAAAGAATGCCTAGACAAAGCAATATCAATATGTGCACCTGGGGTGGAGTTCAAGAAAATTGGAAAAACCATACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - -tgactgt
- - - - - - - - - - - - - - - ggaagaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - catgaga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tggtgtg