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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcttcatgtggtatattttctctattgataggggtcagtatattgatacagtttttgagtcattctttcttgaaacagGCAAAGATGGGTATGACAGAAGATTTTGAAGCTTCTTTGCAAGTTCTTCGGGGGTTTGATACTGATATTACTTTTGAAGTGAATGAAATCAAG

Basic information

species Vitis vinifera
transcript Vv18s0001g12560.t01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0001g12560.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA17G36950.1 (Glycine max), 3'ss of exon 8
-gtaagcttcatgtggtatattttctctattgataggggtcagtatattgatacagtttttg--agtcattctttcttg----aaacagGCAAAGATGGGTATGACAGAAGATTTTGAAGCTTCTTTGCAAGTTCTTCGGGGGTTTGATACTGATATTACTTTTGAAGTGAATGAAATCAAG
 |||| ||| |||   |   | ||||  | ||     |  || ||| |    ||||||| |   ||| | | | | |||    | | ||||||| ||||| ||||||||||| |||||| |||| |||||||| || || || ||||||||||||||| || |||||||||||||||| || 
ggtaaactttatgaattg-gtattcttgagtgtc---gtccaatatgtgttgacagtttctaaaagtgaatttgttttgttgaatataGGCAAAAATGGGAATGACAGAAGAATTTGAAACTTCCTTGCAAGTGCTCCGAGGCTTTGATACTGATATTTCTGTTGAAGTGAATGAAATTAA-

upper sequence: Vv18s0001g12560.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA14G08070.1 (Glycine max), 3'ss of exon 8
gtaagcttcatgtggtatattttctctattgataggggtcagtatattgatacagtttttgagtcattctttcttg----aaacagGCAAAGATGGGTATGACAGAAGATTTTGAAGCTTCTTTGCAAGTTCTTCGGGGGTTTGATACTGATATTACTTTTGAAGTGAATGAAATCAAG
||||||||  ||    |  | ||||  | ||  |  |   | | | ||| ||   | |   ||| | | | | |||    | | ||||||| ||||| ||||||||||| |||||| |||| |||||||| || || || ||||| ||||||||| || |||||||||||||||| |||
gtaagctttgtgaatca-gtattcttgagtgtgatcgaata-tgtgttgttagtttctaaaagtgaatttgttttgctgaatatagGCAAAAATGGGAATGACAGAAGAATTTGAAACTTCCTTGCAAGTGCTCCGAGGCTTTGAGACTGATATTTCTGTTGAAGTGAATGAAATTAAG

upper sequence: Vv18s0001g12560.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: AT1G19450.1 (Arabidopsis thaliana), 3'ss of exon 8
gtaagcttcatgtggtatattttctctattgataggggtcagtatattgatacagtttttgagtcattctt-tcttgaaac---agGCAAAGATGGGTATGACAGAAGATTTTGAAGCTTCTTTGCAAGTTCTTCGGGGGTTTGATACTGATATTACTTTTGAAGTGAATGAAATCAAG
||| || ||        ||||   | ||||| | | | |   |  |||  |     |  | | |  || |  | ||| ||    |||||||||||||| ||||||| ||||| ||| |||| |||||||||||||| || ||||| |||||||||||  |||| || ||||||||||||
gtatgcctctacaaccgtattgcttatattgtt-gagtttgttgcattattggttatcctaaattgttttggtgttgtaattgtagGCAAAGATGGGTTTGACAGATGATTTCGAAACTTCATTGCAAGTTCTTCGTGGATTTGAGACTGATATTACCGTTGAGGTTAATGAAATCAAG

upper sequence: Vv18s0001g12560.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: AT1G75220.1 (Arabidopsis thaliana), 3'ss of exon 8
-----------------------------------------gtaagcttcatgtggtatattttctctattgataggggtcagtatattgat-acagtttttgagtcattc---tttcttgaaac--agGCAAAGATGGGTATGACAGAAGATTTTGAAGCTTCTTTGCAAGTTCTTCGGGGGTTTGATACTGATATTACTTTTGAAGTGAATGAAATCAAG
                                         | |   ||    |  |  | | | | | ||  |     | |    ||| || |    |  || |  | |    ||  || |||   ||||||| |||||||||||||| || |||||| |||| || ||||||||||| || ||||| |||||||||||  ||||||| ||||||||||||
gtaagccttacagtagtttgcttattcttcttgagtttagtgcatattttggttactccactcttttttttttttttaataacatcattaatcatctctgatgggatacttgatttcgttaaaatgtagGCAAAAATGGGTATGACAGATGAATTTGAAACTTCATTACAAGTTCTTCGAGGATTTGAGACTGATATTACCGTTGAAGTTAATGAAATCAAG

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|110701968|gb|EE080148.1|EE080148
EST:     CAATTTTGATACCTGGCCTATTTTTTATCCCAAAATCTCCTCGGTGGCTT                         GCAAAGATGGGTATGACAGAAGATTTTGAAGCTTCTTTGCAAGTTCTTCGG
genomic: CAATTTTGATACCTGGCCTATTTTTTATCCCAGAATCTCCTCGGTGGCTTgtaagcttca ... cttgaaacagGCAAAGATGGGTATGACAGAAGATTTTGAAGCTTCTTTGCAAGTTCTTCGG
EST: gi|110699858|gb|EE077237.1|EE077237
EST:     CAATTTTGATACCTGGCCTATTTTTTATCCCAGAATCTCCTCGGTGGCTT                         GCAAAGATGGGTATGACAGAAGATTTTGAAGCTTCTTTGCA
genomic: CAATTTTGATACCTGGCCTATTTTTTATCCCAGAATCTCCTCGGTGGCTTgtaagcttca ... cttgaaacagGCAAAGATGGGTATGACAGAAGATTTTGAAGCTTCTTTGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attgataggggtcagtatattgatacagtttttgagtcattctttcttgaaacagGCAAAGATGGGTATGACAGAAGATTTTGAAGCTTCTTTGCAAGTTCTTCGGGGGTTTGATACTGATATTACTTTTGAAGTGAATGAAATCAAG
                 tattgat  putative branch site (score: 3)
                                    tcattctttctt  putative PPT
               tatattgata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagcttcatgtggtatattttctctattgataggggtcagtatattgatacagtttttgagtcattctttcttgaaacagGCAAAGATGGGTATGACAGAAGATTTTGAAGCTTCTTTGCAAGTTCTTCGGGGGTTTGATACTGATATTACTTTTGAAGTGAATGAAATCAAG

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