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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACACAGACTCGCAGTTTCTGTTATGTATCTGACATGGTTGATGGACTTATGCGCCTCATGGAAGGAGATGACACTGGTCCCATCAACATCGGTAACCCAGgtaaagtccgtaatattcctccattagacaaaacacaacccaaccaatctcttgaacttatgctttgtgtccgactctttggtttctcag

Basic information

species Arabidopsis thaliana
transcript AT3G46440.1
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G46440.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: GLYMA12G06980.3 (Glycine max), 5'ss of exon 11
ACACAGACTCGCAGTTTCTGTTATGTATCTGACATGGTTGATGGACTTATGCGCCTCATGGAAGGAGATGACACTGGTCCCATCAACATCGGTAACCCAGgtaaagtccgtaatattcctccattagacaaaacacaacccaaccaatctcttgaacttatgctttgtgtccgactctttggtttctcag
                                    |||||||||||||| || || |||||||| ||  |||||||||| |||||||| || |||||||||           |||    | | | ||  |        |  |    |||    ||    |  | |||||  ||  ||||  | | ||||
------------------------------------GTTGATGGACTTATACGTCTAATGGAAGGGGAAAACACTGGTCCAATCAACATTGGGAACCCAGgt-----------tatattacaactggatcatttgagctctgatttttctgccaaatac-taatatgtgtt-gatactttattatttcag

upper sequence: AT3G46440.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: GLYMA11G15010.1 (Glycine max), 5'ss of exon 11
ACACAGACTCGCAGTTTCTGTTATGTATCTGACATGGTTGATGGACTTATGCGCCTCATGGAAGGAGATGACACTGGTCCCATCAACATCGGTAACCCAGgtaaagtccgtaatattcctccattagacaaaacacaacccaaccaatctcttgaacttatgctttgtgtccgactctttggtttctcag
                                    |||||||||||||| || || |||||||| ||  |||||||||| |||||||| || ||||||||| |  |    ||||      |||| ||           |  ||   |||    ||  | |  | |||||  ||  |||   | |  |||
------------------------------------GTTGATGGACTTATACGTCTAATGGAAGGGGAAAACACTGGTCCAATCAACATTGGGAACCCAGgttatatt-acaata------catttgagtg--------ctgacttttctgccaaatat-taatatgtgtt-gatacttcattcttccag

upper sequence: AT3G46440.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: Vv06s0004g04390.t01 (Vitis vinifera), 5'ss of exon 11
ACACAGACTCGCAGTTTCTGTTATGTATCTGACATGGTTGATGGACTTATGCGCCTCATGGAAGGAGATGACACTGGTCCCATCAACATCGGTAACCCAGgtaaagtccgtaatattcctccattag----acaaaacacaacccaaccaatctcttgaacttatgctttg-tgtccgactctttggtttctcag-----------------
                                    |||||||| || || || ||||||||||||||  ||||||| || |||||||| || ||||||||||   | | |  | ||     |||       | |  |  ||||     | | ||||| ||   ||  ||  ||| | | |       |    |                  
------------------------------------GTTGATGGGCTGATTCGACTCATGGAAGGAGAGAACACTGGGCCAATCAACATTGGAAACCCAGgtagtttacattttttttaattattctcattgctatgcctaacctggaaattttcttgtacacttgagttactgtgctattaccaacctagataatttcttgtacacttcag

upper sequence: AT3G46440.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: Vv06s0004g04390.t01 (Vitis vinifera), 5'ss of exon 10
ACACAGACTCGCAGTTTCTGTTATGTATCTGACATGGTTGATGGACTTATGCGCCTCATGGAAGGAGATGACACTGGTCCCATCAACATCGGTAACCCAGgtaaagtccgtaatattcctccattagacaaaacacaacccaaccaatctcttgaacttatgctttgtgtccgactctttggtttctcag-
                    |  || | ||   |  ||| |  | ||  ||   | ||     | || |    ||  |  |    |||| ||||   ||   | | |    | | |    ||||  ||   | ||          |   | || |  ||||  ||   | || | | | |   |  | |  
--------------------TGGTGAACCTTTGACAGTTCA--GGCTCCTGGAACACAGACTCGCAGTTTCTGCTA-TGTCTCTGACAT-Ggta-tgcaaaaataattataattttatgaccataggattgaccatgtattggtta--ttattaagattat--ttgaagcccaattttcttcatgttaaag

upper sequence: AT3G46440.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: EFJ17446 (Selaginella moellendorffii), 5'ss of exon 10
ACACAGACTCGCAGTTTCTGTTATGTATCTGACATGGTTGATGGACTTATGCGCCTCATGGAAGGAGATGACACTGGTCCCATCAACATCGGTAACCCAGgtaaagt--ccgtaatattcctccattagacaaaacacaacccaaccaatctcttgaacttatgctttgtgtccgactctttggtttctcag
                                    ||||| || || ||    || ||||   | ||||||||||||||||||||| |||| || ||||||||||   | | |  |      | |          ||    |  |   | |   |                                    
------------------------------------GTTGACGGCCTCATCAAACTGATGGCTTGCGATGACACTGGTCCCATCAACCTCGGAAATCCAGgtaaagaaacagaagcaccatctcttcttttctggtactgatcgtctcgttttcag------------------------------------

upper sequence: AT3G46440.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: EFJ35029 (Selaginella moellendorffii), 5'ss of exon 10
ACACAGACTCGCAGTTTCTGTTATGTATCTGACATGGTTGATGGACTTATGCGCCTCATGGAAGGAGATGACACTGGTCCCATCAACATCGGTAACCCAGgtaaagtccgtaatattcctccattagacaaaacacaacccaaccaatctcttgaacttatgctttgtgtccgactctttggtttctcag
                                    ||||| || || ||    || ||||   | ||||||||||||||||||||| |||| || ||||||||||      |    ||  |  |          |    |  |   | |   |                                    
------------------------------------GTTGACGGCCTCATCAAACTGATGGCTTGCGATGACACTGGTCCCATCAACCTCGGAAATCCAGgtaaagaaacagaagcaccatctcttcttttctggctgatcgtctcgttttcag------------------------------------

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|124970021|gb|EL043880.1|EL043880
EST:     TGGAAGGAGATGACACTGGTCCCATCAACATCGGTAACCCAG                         GTGAGTTTACAATGGTGGAGTTGGCTGAGACAGTGAAAGAGCTGATTAA
genomic: TGGAAGGAGATGACACTGGTCCCATCAACATCGGTAACCCAGgtaaagtccg ... ggtttctcagGTGAGTTTACAATGGTGGAGTTGGCTGAGACAGTGAAAGAGCTGATTAA
EST: gi|125135548|gb|EL175810.1|EL175810
EST:     CGCCTCATGGAAGGAGATGACACTGGTCCCATCAACATCGGTAACCCAG                         GTGAGTTTACAATGGTGGAGTTGGCTGAGACAGTGAAAGAGCTGATTAA
genomic: CGCCTCATGGAAGGAGATGACACTGGTCCCATCAACATCGGTAACCCAGgtaaagtccg ... ggtttctcagGTGAGTTTACAATGGTGGAGTTGGCTGAGACAGTGAAAGAGCTGATTAA
EST: gi|47831999|gb|CK121683.1|CK121683
EST:     GCGCCTCATGGAAGGAGATGACACTGGTCCCATCAACATCGGTAACCCAG                         GTGAGTTTACAATGGTGGAGTTGGCTGAGACAGTGAAAGAG
genomic: GCGCCTCATGGAAGGAGATGACACTGGTCCCATCAACATCGGTAACCCAGgtaaagtccg ... ggtttctcagGTGAGTTTACAATGGTGGAGTTGGCTGAGACAGTGAAAGAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACACAGACTCGCAGTTTCTGTTATGTATCTGACATGGTTGATGGACTTATGCGCCTCATGGAAGGAGATGACACTGGTCCCATCAACATCGGTAACCCAGgtaaagtccgtaatattcctccattagacaaaacacaacccaaccaatctcttgaacttatgctttgtgtccgactctttggtttctcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG