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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCGCTGGGATAAATTTGAAGATTCATACAGAACTATGCTGTTTTCAAATGGCGAAAAATGCTGGAATGGACCTGATAGGAGTTTGAAGgtaacgaccataatgttcttacattggatcatgtattcattggtttataataatggtgacacgactgccttgcacctttaactagcttttgaactggtag...

Basic information

species Vitis vinifera
transcript Vv06s0004g00140.t01
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0004g00140.t01 (Vitis vinifera), 5'ss of exon 13
lower sequence: LOC_Os01g16970.1 (Oryza sativa), 5'ss of exon 13
GCGCTGGGATAAATTTGAAGATTCATACAGAACTATGCTGTTTTCAAATGGCGAAAAATGCTGGAATGGACCTGATAGGAGTTTGAAGgtaacgaccataatgttcttacattggatcatgtattcattggttta--taataatggtgacacgactgccttgcacctt--taac---tagcttttgaactggtag--
||||||||| ||||||||||| || ||||||   ||||  ||||||||||| || | |||||||||||| |||||  | ||| | |||||   |    |  | ||| | | || |  |  ||  || |  | |    |     |        |   | |||| | |||  |||    | ||||      || ||   
GCGCTGGGACAAATTTGAAGAATCCTACAGAGTAATGCAATTTTCAAATGGAGACAGATGCTGGAATGGCCCTGACCGAAGTCTAAAGgt---gcttctccttttcatgccttcgtgcccgttatcttaagatggattgtctgtttctgtttgcaggtcttgaaacttaataaaatatggcttgccttatgatacag

upper sequence: Vv06s0004g00140.t01 (Vitis vinifera), 5'ss of exon 13
lower sequence: AC213600.3_FGT002 (Zea mays), 5'ss of exon 13
GCGCTGGGATAAATTTGAAGATTCATACAGAACTATGCTGTTTTCAAATGGCGAAAAATGCTGGAATGGACCTGATAGGAGTTTGAAGgtaacgaccataatgttcttacattggatcatgtattcattggtttataataatggtgacacgactgccttgcacctttaactagcttttgaactggtag
||| ||||| |||||||||||||| ||||||   ||||  ||||||| ||| || |||||||||||||| |||||  | ||  | ||||||       ||       | ||| |     | |  |    ||||   |||  |          |||   |  ||  |     ||               
GCGGTGGGACAAATTTGAAGATTCGTACAGAGTGATGCACTTTTCAAGTGGAGACAAATGCTGGAATGGTCCTGACCGAAGCCTAAAGgtagtatgtcta-----tctgcat-gccctttctggttgcaggttctaaattctaactcttt--ctgttgtttacactcgtgcag---------------

upper sequence: Vv06s0004g00140.t01 (Vitis vinifera), 5'ss of exon 13
lower sequence: GLYMA07G35090.1 (Glycine max), 5'ss of exon 14
GCGCTGGGATAAATTTGAAGATTCATACAGAACTATGCTGTTTTCAAATGGCGAAAAATGCTGGAATGGACCTGATAGGAGTTTGAAGgtaacgaccataatgttcttacattggatcatgtattcattggtttataataatggtgacacgactgccttgcacctttaactagcttttgaactggtag---
| ||||||| |||||||| ||||||||||||   ||| ||||||| ||||| || |||||||||||||| |||||||||||||||||||| |      | |  || | | | ||    |||   |||||   ||| |||  |||  | |  | || ||     | ||   ||    || ||      |   
GAGCTGGGACAAATTTGAGGATTCATACAGAGTAATGGTGTTTTCTAATGGTGATAAATGCTGGAATGGTCCTGATAGGAGTTTGAAGgttatatttttcaaattttaaaaatga--tatgctgtcattt-cttacaattttggctagattattgtctctattcattctataatgattaaataaactgtct

upper sequence: Vv06s0004g00140.t01 (Vitis vinifera), 5'ss of exon 13
lower sequence: GLYMA20G02950.2 (Glycine max), 5'ss of exon 11
GCGCTGGGATAAATTTGAAGATTCATACAGAACTATGCTGTTTTCAAATGGCGAAAAATGCTGGAATGGACCTGATAGGAGTTTGAAGgtaacg-accataatgttcttacattggatcatgtattcattggtttataataatggtgacacgact--gccttgcacctttaactagcttttgaactggtag
| ||||||| |||||||| ||||| ||||||   ||| ||||||| ||||| || |||||||||||||| || ||||||||||||||||| |       | |  || | | | ||   |||| | |||||   ||| |||  |||  | |  | |  | ||     | ||   ||    || ||      |
GAGCTGGGACAAATTTGAGGATTCGTACAGAGTAATGGTGTTTTCTAATGGTGATAAATGCTGGAATGGTCCAGATAGGAGTTTGAAGgttatatgttttcaaattttaaaaatga--catgcagtcattt-cttacaattttggctagattattttgtctctattcattctgtaatgcttaaataaactg

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|294964262|gb|GW838065.1|GW838065
EST:     TGTTTTCAAATGGCGAAAAATGCTGGAATGGACCTGATAGGAGTTTGAAG                         GTCAAGCTAAGATGTGGGTTGAAAAATGAGGTTACTGATGTTGATGAACCA
genomic: TGTTTTCAAATGGCGAAAAATGCTGGAATGGACCTGATAGGAGTTTGAAGgtaacgacca ... tttttaacagGTCAAGCTAAGATGTGGGTTGAAAAATGAGGTTACTGATGTTGATGAACCA
EST: gi|29783023|gb|CB348862.2|CB348862
EST:     TGTTTTCAAATGGCGAAAAATGCTGGAATGGACCTGATAGGAGTTTGAAG                         GTCAAGCTAAGATGTGGGTTGAAAAATGAGGTTACTGATGTTGATGAACCA
genomic: TGTTTTCAAATGGCGAAAAATGCTGGAATGGACCTGATAGGAGTTTGAAGgtaacgacca ... tttttaacagGTCAAGCTAAGATGTGGGTTGAAAAATGAGGTTACTGATGTTGATGAACCA
EST: gi|29782985|gb|CB348782.2|CB348782
EST:     TGTTTTCAAATGGCGAAAAATGCTGGAATGGACCTGATAGGAGTTTGAAG                         GTCAAGCTAAGATGTGGGTTGAAAAATGAGGTTACTGATGTTGATGAACCA
genomic: TGTTTTCAAATGGCGAAAAATGCTGGAATGGACCTGATAGGAGTTTGAAGgtaacgacca ... tttttaacagGTCAAGCTAAGATGTGGGTTGAAAAATGAGGTTACTGATGTTGATGAACCA
EST: gi|33406825|gb|CF212452.1|CF212452
EST:     TGTTTTCAAATGGCGAAAAATGCTGGAATGGACCTGATAGGAGTTTGAAG                         GTCAAGCTAAGATGTGGGTTGAAAAATGAGGTTACTGATGTTGATGAACCA
genomic: TGTTTTCAAATGGCGAAAAATGCTGGAATGGACCTGATAGGAGTTTGAAGgtaacgacca ... tttttaacagGTCAAGCTAAGATGTGGGTTGAAAAATGAGGTTACTGATGTTGATGAACCA
EST: gi|110687364|gb|EE064720.1|EE064720
EST:     TGTTTTCAAATGGCGAAAAATGCTGGAATGGACCTGATAGGAGTTTGAAG                         GTCAAGCTAAGATGTGGGTTGAAAAATGAGGTTACTGATGTTGATGAACCA
genomic: TGTTTTCAAATGGCGAAAAATGCTGGAATGGACCTGATAGGAGTTTGAAGgtaacgacca ... tttttaacagGTCAAGCTAAGATGTGGGTTGAAAAATGAGGTTACTGATGTTGATGAACCA
EST: gi|29786143|gb|CB343671.2|CB343671
EST:     TGTTTTCAAATGGCGAAAAATGCTGGAATGGACCTGATAGGAGTTTGAAG                         GTCAAGCTAAGATGTGGGTTGAAAAATGAGGTTACTGATGTTGATGAACCA
genomic: TGTTTTCAAATGGCGAAAAATGCTGGAATGGACCTGATAGGAGTTTGAAGgtaacgacca ... tttttaacagGTCAAGCTAAGATGTGGGTTGAAAAATGAGGTTACTGATGTTGATGAACCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCGCTGGGATAAATTTGAAGATTCATACAGAACTATGCTGTTTTCAAATGGCGAAAAATGCTGGAATGGACCTGATAGGAGTTTGAAGgtaacgaccataatgttcttacattggatcatgtattcattggtttataataatggtgacacgactgccttgcacctttaactagcttttgaactggtag

- - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG