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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ataatgctccttaccccttgatcctaattcaaaatgatgtttaatgaaaaattcttctgcttagtggaagtgtgaatgcttaaacaattttttactccagGTATAGGCTTTGGTCCTGGGATTCCCGGATTACAGCTGGGTGTTGGATTTGGTGCTGGATGTGGGGTTGGTTTAGGATTTGGTTATGGTGTGGGGAGGGG

Basic information

species Vitis vinifera
transcript Vv18s0089g01180.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0089g01180.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA09G28210.1 (Glycine max), 3'ss of exon 1
---ataatgctccttaccccttgatcctaattcaaaatgatgtttaatgaaaaattcttctgcttagtggaagtgtgaatgcttaaacaattttttactccagGTATAGGCTTTGGTCCTGGGATTCCCGGATTACAGCTGGGTGTTGGATTTGGTGCTGGATGTGGGGTTGGTTTAGGATTTGGTTATGGTGTGGGGAGGGG
|| || | | || ||| | | | || || || | || || ||||| | ||| | || || | ||| |||||||| | || |||| ||||| ||||| ||||| || | ||| |||||||||||||||||||||| ||||||||||| ||||| ||||||||||||| ||
ttaatgatctggttcatgttttaatcttcaagtgtgaacatacttcctgcatcgtt-ttatgcttcatagaatctc--acgcaaaatatttgtttgactccagGAGTGGGTGTTGGCCCTGGAATTCCTGGATTCCAAGTTGGTTTTGGATTTGGTGCTGGATGTGGTGTTGGTTTAGGGTTTGGCTATGGTGTGGGGAAAGG

upper sequence: Vv18s0089g01180.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA16G33040.1 (Glycine max), 3'ss of exon 1
-ataatgctccttaccccttgatcct-aattcaaaatgatgtttaatgaaaaattcttctgcttagtggaagtgtgaatgcttaaacaattttttactccagGTATAGGCTTTGGTCCTGGGATTCCCGGATTACAGCTGGGTGTTGGATTTGGTGCTGGATGTGGGGTTGGTTTAGGATTTGGTTATGGTGTGGGGAGGGG
| || | | | || ||| | || | ||| | | | || ||||| | ||| | | || || | ||| |||||||| | || ||||| ||||| ||||| || || || | ||| |||||||||| ||||||||||| |||||||| || ||||| ||||||||||||| ||
actgatcttgttcatgttttaatctttaagtttgtttgaacatacttcctgttgttttatgcttcatagaatctt--acgcaaaatatttgtttgactccagGAGTGGGTTTTGGCCCTGGAATTCCTGGTTTCCAAGTTGGTTTTGGATTTGGAGCTGGATGTGGAGTTGGTTTTGGGTTTGGCTATGGTGTGGGGAAAGG
















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|110398953|gb|EC965437.1|EC965437
EST:     CGGCTTCGGCGCCGGCTGCGGCATCGGCCTTGGCGTTGGCCTCCTTGGAG                         GTATAGGCTTTGGTCCTGGGATTCCCGGATTACAGCTGGGTGTTGGATTTG
genomic: CGGCTTCGGCGCCGGCTGCGGCATCGGCCTTGGCGTTGGCCTCCTTGGAGgtacatctct ... tttactccagGTATAGGCTTTGGTCCTGGGATTCCCGGATTACAGCTGGGTGTTGGATTTG
EST: gi|110360979|gb|EC924425.1|EC924425
EST:     CGGCTTCGGCGCCGGCTGCGGCATCGGCCTTGGCGTTGGCCTCCTCGGAG                         GTATAGGCCTTGGTCCTGGGATTCCCGGATTACAGCTGGGTGTTGGATTTG
genomic: CGGCTTCGGCGCCGGCTGCGGCATCGGCCTTGGCGTTGGCCTCCTTGGAGgtacatctct ... tttactccagGTATAGGCTTTGGTCCTGGGATTCCCGGATTACAGCTGGGTGTTGGATTTG
EST: gi|110377077|gb|EC942138.1|EC942138
EST:     CGGCTTCGGCGCCGGCTGCGGCATCGGCCTTGGCGCCGGCCTCCTTGGAG                         GTATAGGCTTTGGTCCTGGGATTCCCGGATTACAGCTGGGTGTTGGATTTG
genomic: CGGCTTCGGCGCCGGCTGCGGCATCGGCCTTGGCGTTGGCCTCCTTGGAGgtacatctct ... tttactccagGTATAGGCTTTGGTCCTGGGATTCCCGGATTACAGCTGGGTGTTGGATTTG
EST: gi|110409299|gb|EC974959.1|EC974959
EST:     CGGCTTCGGCGCCGGCTGCGGCATCGGCCTTGGCGTTGGCCTCCTTGGAG                         GTATAGGCTTTGGTCCTGGGATTCCCGGATTACAGCTGGGTGTTGGATTTG
genomic: CGGCTTCGGCGCCGGCTGCGGCATCGGCCTTGGCGTTGGCCTCCTTGGAGgtacatctct ... tttactccagGTATAGGCTTTGGTCCTGGGATTCCCGGATTACAGCTGGGTGTTGGATTTG
EST: gi|110399462|gb|EC965969.1|EC965969
EST:     CGGCTTCGGCGCCGGCTGCGGCATCGGCCTTGGCGTTGGCCTCCTTGGAG                         GTATAGGCTTTGGTCCTGGGATTCCCGGATTACAGCTGGGTGTTGGATTTG
genomic: CGGCTTCGGCGCCGGCTGCGGCATCGGCCTTGGCGTTGGCCTCCTTGGAGgtacatctct ... tttactccagGTATAGGCTTTGGTCCTGGGATTCCCGGATTACAGCTGGGTGTTGGATTTG
EST: gi|110402585|gb|EC960503.1|EC960503
EST:     CGGCTTCGGCGCCGGCTGCGGCATCGGCCTTGGCGTTGGCCTCCTTGGAG                         GTATAGGCTTTGGTCCTGGGATTCCCGGATTACAGCTGGGTGTTGGATTTG
genomic: CGGCTTCGGCGCCGGCTGCGGCATCGGCCTTGGCGTTGGCCTCCTTGGAGgtacatctct ... tttactccagGTATAGGCTTTGGTCCTGGGATTCCCGGATTACAGCTGGGTGTTGGATTTG
EST: gi|294966623|gb|GW839614.1|GW839614
EST:     CGGCTTCGGCGCCGGCTGCGGCATCGGCCTTGGCGTTGGCCTCCTTGGAG                         GTATAGGCTTTGGTCCTGGGATTCCCGGATTACAGCTGGGTGTTGGATTTG
genomic: CGGCTTCGGCGCCGGCTGCGGCATCGGCCTTGGCGTTGGCCTCCTTGGAGgtacatctct ... tttactccagGTATAGGCTTTGGTCCTGGGATTCCCGGATTACAGCTGGGTGTTGGATTTG
EST: gi|37189101|gb|CF608450.1|CF608450
EST:     CGGCTTCGGCGCCGGCTGCGGCATCGGCCTTGGCGTTGGCCTCCTTGGAG                         GTATAGGCTTTGGTCCTGGGATTCCCGGATTACAGCTGGGTGTTGGATTTG
genomic: CGGCTTCGGCGCCGGCTGCGGCATCGGCCTTGGCGTTGGCCTCCTTGGAGgtacatctct ... tttactccagGTATAGGCTTTGGTCCTGGGATTCCCGGATTACAGCTGGGTGTTGGATTTG
EST: gi|110371245|gb|EC935106.1|EC935106
EST:     CGGCTTCGGCGCCGGCTGCGGCATCGGCCTTGGCGTTGGCCTCCTTGGAG                         GTATAGGCTTTGGTCCTGGGATTCCCGGATTACAGCTGGGTGTTGGATTTG
genomic: CGGCTTCGGCGCCGGCTGCGGCATCGGCCTTGGCGTTGGCCTCCTTGGAGgtacatctct ... tttactccagGTATAGGCTTTGGTCCTGGGATTCCCGGATTACAGCTGGGTGTTGGATTTG
EST: gi|110387778|gb|EC952474.1|EC952474
EST:     CGGCTTCGGCGCCGGCTGCGGCATCGGCCTTGGCGTTGGCCTCCTTGGAG                         GTATAGGCTTTGGTCCTGGGATTCCCGGATTACAGCTGGGTGTTGGATTTG
genomic: CGGCTTCGGCGCCGGCTGCGGCATCGGCCTTGGCGTTGGCCTCCTTGGAGgtacatctct ... tttactccagGTATAGGCTTTGGTCCTGGGATTCCCGGATTACAGCTGGGTGTTGGATTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaaaaattcttctgcttagtggaagtgtgaatgcttaaacaattttttactccagGTATAGGCTTTGGTCCTGGGATTCCCGGATTACAGCTGGGTGTTGGATTTGGTGCTGGATGTGGGGTTGGTTTAGGATTTGGTTATGGTGTGGGGAGGGG
                                          ttttttactcc  CT-rich tract
 ttaaacaattttttac  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ataatgctccttaccccttgatcctaattcaaaatgatgtttaatgaaaaattcttctgcttagtggaagtgtgaatgcttaaacaattttttactccagGTATAGGCTTTGGTCCTGGGATTCCCGGATTACAGCTGGGTGTTGGATTTGGTGCTGGATGTGGGGTTGGTTTAGGATTTGGTTATGGTGTGGGGAGGGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- aatgctc
- - - - - ttacccc
- - - - - - - - - - - - - - - aaaatga
- - - - - - - - - - - - - - - - - - - - - - tgaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaatgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaacaat