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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGTTGAGAGTTCCTCGTTTCTTTGATCCTTGGGGTGGTTATGATATGATTGGCTTTGGGGACATTCTCTTCCCTGGTTTGCTCATTTCATTTGCTTTCAGgtactctttacactgtcaagtttccagtaagtgagataacagtgaaggttatgattatggatcctatattttcctttaagtttttttaataaaaatcaac...

Basic information

species Vitis vinifera
transcript Vv05s0062g01250.t01
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0062g01250.t01 (Vitis vinifera), 5'ss of exon 11
lower sequence: LOC_Os11g24540.2 (Oryza sativa), 5'ss of exon 11
TGTTGAGAGTTCCTCGTTTCTTTGATCCTTGGGGTGGTTATGATATGATTGGCTTTGGGGACATTCTCTTCCCTGGTTTGCTCATTTCATTTGCTTTCAGgtactctttacactgtcaagtttccagtaagtgagataacagtgaaggttatgat-tatggatcctatattttcctttaagtttttttaat---aaaaatcaac-
| || ||| | ||||||||||||||||| |||||||| ||||| ||||| |||||||| |||||| | |||||||| |||||  || ||||    | ||||||    ||| ||| |  |  || | | ||   |  |   |       || ||||   | | |   |  |   |  | |||| |   ||       ||||  || 
TCTTAAGAATACCTCGTTTCTTTGATCCATGGGGTGGCTATGACATGATAGGCTTTGGTGACATTATTTTCCCTGGATTGCTAGTTGCATTCAGCTACAGgta----ttatactatatatattgctgcaatataagttgtaacttctcttttgatgccttggtttcac-tggacgctaaagtgtcggtaggttggtaaatatact

upper sequence: Vv05s0062g01250.t01 (Vitis vinifera), 5'ss of exon 11
lower sequence: GRMZM2G082330_T01 (Zea mays), 5'ss of exon 11
TGTTGAGAGTTCCTCGTTTCTTTGATCCTTGGGGTGGTTATGATATGATTGGCTTTGGGGACATTCTCTTCCCTGGTTTGCTCATTTCATTTGCTTTCAGgtactc---tttacactgtcaagtttccagtaagtgagataacagtgaaggttatgattatggatcctatattttcctttaagtttttttaataaaaatcaac
|  | ||  | || || ||||||||||| |||||||||||||||||||| |||||||| |||||| |||||||||| |||||  ||  |||    |  |||||      ||| |  | |  | | |  | |   |       || |    |||    | | |  ||   |||    |  ||   || |    |     || | 
TCCTAAGGATACCCCGCTTCTTTGATCCATGGGGTGGTTATGATATGATAGGCTTTGGTGACATTATCTTCCCTGGATTGCTTGTTGGATTCAGCTATAGgtatgtgattttgccatatacattatttacttccttgtgatccatta---gttccactaaggcttcacgtatagaacaatatagttgtgcgctggttgtctat

upper sequence: Vv05s0062g01250.t01 (Vitis vinifera), 5'ss of exon 11
lower sequence: GLYMA20G39260.1 (Glycine max), 5'ss of exon 10
TGTTGAGAGTTCCTCGTTTCTTTGATCCTTGGGGTGGTTATGATATGATTGGCTTTGGGGACATTCTCTTCCCTGGTTTGCTCATTTCATTTGCTTTCAGgtact-----ctttacactgtcaagt--ttccagtaagtgaga----taacag-------tgaaggttatgattatggatcctatattttcctttaagtttttttaataaaaatcaac--------------------------------------------
| |||||| |||||||| | | ||||||||||||||| |||||||||||||| ||||| || |||||||| |||||||||||  |||| ||||||   ||||| |     | ||     |||||     |  | ||| ||  |    | | |        ||||| | |   || |      ||| |  |  | |  |||||| |  |     | ||                                             
TTTTGAGATTTCCTCGTCTTTCTGATCCTTGGGGTGGCTATGATATGATTGGATTTGGAGATATTCTCTTTCCTGGTTTGCTTGTTTCCTTTGCTCGTAGgtattgaattccttttttggtcaaaaaacttgaataaatggaagattttataaacttctttgaagataacacttgttttcaatatttgcttttgtgtgtttttcttcttctttttaatgtacatttgagaagatgcattgttatggtttttgattgtctcag

upper sequence: Vv05s0062g01250.t01 (Vitis vinifera), 5'ss of exon 11
lower sequence: GLYMA10G44490.1 (Glycine max), 5'ss of exon 11
TGTTGAGAGTTCCTCGTTTCTTTGATCCTTGGGGTGGTTATGATATGATTGGCTTTGGGGACATTCTCTTCCCTGGTTTGCTCATTTCATTTGCTTTCAGgt-----actctttacactgtcaag--tttccagtaagtgagataacagtgaa---------ggttatgattatggatcctatattttcctttaagtttttttaataaaaatcaac-------------------------------------------------
| |||||| |||||||| | | ||||||||||||||| |||||||||||||| ||||| || |||||||| |||||||||||  |||| ||| ||   ||||     | || |||    |||||     |  | ||| ||  | |  | | ||          | |||     ||  | | |||||| ||||   || | | |  |     ||                                                    
TTTTGAGATTTCCTCGTCTTTCTGATCCTTGGGGTGGCTATGATATGATTGGATTTGGAGATATTCTCTTTCCTGGTTTGCTTGTTTCCTTTACTCGTAGgtattgaattccttatttggtcaaaaaacttgaataaatggaagattaataaacttctctgaagatatacacttgttttcaatatttgccttcgtgtgtgtgtgtttttcttctttttaatgtacatttgagaagatacattgttatggttttttattgtctcag

upper sequence: Vv05s0062g01250.t01 (Vitis vinifera), 5'ss of exon 11
lower sequence: GLYMA18G53880.1 (Glycine max), 5'ss of exon 10
-TGTTGAGAGTTCCTCGTTTCTTTGATCCTTGGGGTGGTTATGATATGATTGGCTTTGGGGACATTCTCTTCCCTGGTTTGCTCATTTCATTTGCTTTCAGgtactctttacactgtcaagtttccagtaagtgagataacagtgaaggttatg--attatggatcctatattttcctttaagtttttttaataaaaatcaac
 | |||||| |||||||| | |||||||| ||||| |||||||| |||||||| ||||| || ||||| || ||||||||||| ||||| ||||||   ||||| |   | |  | |  ||||  ||  |  |   ||||  |  |   |||    |||   |||        |   | | | |  ||    || |  |   |
CTTTTGAGATTTCCTCGTCTTTTTGATCCCTGGGGAGGTTATGACATGATTGGATTTGGAGATATTCTGTTTCCTGGTTTGCTTATTTCCTTTGCTCATAggtattgaattccttatttagttaacatcatat---ataaatgcaagatttacaaaattgaagatgtagataatagatatgaatgattactgtatattttggc

upper sequence: Vv05s0062g01250.t01 (Vitis vinifera), 5'ss of exon 11
lower sequence: GLYMA08G47600.1 (Glycine max), 5'ss of exon 10
TGTTGAGAGTTCCTCGTTTCTTTGATCCTTGGGGTGGTTATGATATGATTGGCTTTGGGGACATTCTCTTCCCTGGTTTGCTCATTTCATTTGCTTTCAGgtactctttacactgtcaagtttccagtaagtgagataacagtgaaggttatgattatggatcctatattttcctttaagtttttttaataaaaatcaac----
| |||||| |||||||| | |||||||| ||||| |||||||| |||||||| ||||| || ||||| || ||||||||||| ||||| ||||||   |||||||   | |  | |  |||   ||  |  |   ||||  |  |   |||  |  || ||   | ||  |     |   | ||||   | |  |  ||     
TTTTGAGATTTCCTCGTCTTTTTGATCCCTGGGGAGGTTATGACATGATTGGATTTGGAGATATTCTGTTTCCTGGTTTGCTTATTTCCTTTGCTCATAGgtactgaattccttattgagtcaacatcatat---ataaatgctagatttacaac-attgaagatgtagatgtgaatggatattttggcttaccacaaaagaca

upper sequence: Vv05s0062g01250.t01 (Vitis vinifera), 5'ss of exon 11
lower sequence: AT2G43070.1 (Arabidopsis thaliana), 5'ss of exon 11
TGTTGAGAGTTCCTCGTTTCTTTGATCCTTGGGGTGGTTATGATATGATTGGCTTTGGGGACATTCTCTTCCCTGGTTTGCTCATTTCATTTGCTTTCAGgtactctttacactgtcaagtttccagtaagtgagataacagtgaaggttatgattatggatcctatattttcctttaagtttttttaataaaaatcaac--------------------------------------------------
|  | ||  ||||||| |||||||||||||||||||||||||| |||||||| ||||||||||| |||||||| |||||||||||||| ||||||| |||||||| ||||  | || |  ||   ||    | | | ||||     |  |   ||  | |  || ||| ||||     ||| | |||   ||  ||   |                                                  
TACTAAGGATTCCTCGGTTCTTTGATCCTTGGGGTGGTTATGACATGATTGGTTTTGGGGACATCCTCTTCCCCGGTTTGCTCATTTCCTTTGCTTCCAGgtact-tttagtcagtgacattcttagagcttcaaagaacaacttggaattccatctttg--cccatactttctccagagtgtctttctcaacgattctctcatccaatcctctcccacgattaatacttgctccactctttgatctcag

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|110367857|gb|EC931810.1|EC931810
EST:     GGCTTTGGGGACATTCTCTTCCCTGGTTTGCTCATTTCATTTGCTTTCAG                         ATTTGACAAAACAAATAAAAGGGGCATGACAAATGGATATTTCCTTTGGTT
genomic: GGCTTTGGGGACATTCTCTTCCCTGGTTTGCTCATTTCATTTGCTTTCAGgtactcttta ... attgtcacagATTTGACAAAACAAATAAAAGGGGCATGACAAATGGATATTTCCTTTGGTT
EST: gi|30128129|gb|CB913468.1|CB913468
EST:     CTGGTTTGCTCATTTCATTTGCTTTCAG                         ATTTGACGAAACAAATAAAAGGGGCATGACAAATGGATATTTCCTTTGGTT
genomic: CTGGTTTGCTCATTTCATTTGCTTTCAGgtactcttta ... attgtcacagATTTGACAAAACAAATAAAAGGGGCATGACAAATGGATATTTCCTTTGGTT
EST: gi|30137132|gb|CB922470.1|CB922470
EST:     GCTCATTTCATTTGCTTTCAG                         ATTTGACAAAACAAATAAAAGGGGCATGACAAATGGATATTTCCTTTGGTT
genomic: GCTCATTTCATTTGCTTTCAGgtactcttta ... attgtcacagATTTGACAAAACAAATAAAAGGGGCATGACAAATGGATATTTCCTTTGGTT
EST: gi|110688633|gb|EE067409.1|EE067409
EST:     GGCTTTGGGGACATTCTCTTCCCTGGTTTGCTCATTTCATTTGCTTTCAG                         ATTTGACAAAACAAATAAAAGGGGCATGACAAATGGATATTTCCTTTGGTT
genomic: GGCTTTGGGGACATTCTCTTCCCTGGTTTGCTCATTTCATTTGCTTTCAGgtactcttta ... attgtcacagATTTGACAAAACAAATAAAAGGGGCATGACAAATGGATATTTCCTTTGGTT
EST: gi|110731688|gb|EE106318.1|EE106318
EST:     GGCTTTGGGGACATTCTCTTCCCTGGTTTGCTCATTTCATTTGCTTTCAG                         ATTTGACAAAACAAATAAAAGGGGCATGACAAATGGATATTTCCTTTGGTT
genomic: GGCTTTGGGGACATTCTCTTCCCTGGTTTGCTCATTTCATTTGCTTTCAGgtactcttta ... attgtcacagATTTGACAAAACAAATAAAAGGGGCATGACAAATGGATATTTCCTTTGGTT
EST: gi|110687402|gb|EE064779.1|EE064779
EST:     GGCTTTGGGGACATTCTCTTCCCTGGTTTGCTCATTTCATTTGCTTTCAG                         ATTTGACAAAACAAATAAAAGGGGCATGACAAATGGATATTTCCTTTGGTT
genomic: GGCTTTGGGGACATTCTCTTCCCTGGTTTGCTCATTTCATTTGCTTTCAGgtactcttta ... attgtcacagATTTGACAAAACAAATAAAAGGGGCATGACAAATGGATATTTCCTTTGGTT
EST: gi|110395316|gb|EC960974.1|EC960974
EST:     GGCTTTGGGGACATTCTCTTCCCTGGTTTGCTCATTTCATTTGCTTTCAG                         ATTTGACAAAACAAATAAAAGGGGCATGACAAATGGATATTTCCTTTGGTT
genomic: GGCTTTGGGGACATTCTCTTCCCTGGTTTGCTCATTTCATTTGCTTTCAGgtactcttta ... attgtcacagATTTGACAAAACAAATAAAAGGGGCATGACAAATGGATATTTCCTTTGGTT
EST: gi|110697095|gb|EE073781.1|EE073781
EST:     GGCTTTGGGGACATTCTCTTCCCTGGTTTGCTCATTTCATTTGCTTTCAG                         ATTTGACAAAACAAATAAAAGGGGCATGACAAATGGATATTTCCTTTGGTT
genomic: GGCTTTGGGGACATTCTCTTCCCTGGTTTGCTCATTTCATTTGCTTTCAGgtactcttta ... attgtcacagATTTGACAAAACAAATAAAAGGGGCATGACAAATGGATATTTCCTTTGGTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGTTGAGAGTTCCTCGTTTCTTTGATCCTTGGGGTGGTTATGATATGATTGGCTTTGGGGACATTCTCTTCCCTGGTTTGCTCATTTCATTTGCTTTCAGgtactctttacactgtcaagtttccagtaagtgagataacagtgaaggttatgattatggatcctatattttcctttaagtttttttaataaaaatcaac

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gagataa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aataaaa