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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTTGGTCCTTACTTATGCCAACCTGTGATTGCTGGCTTGGGAGATGATGACAAGCCTTTCATTTGCACGATGGACTCTATCGGAGCCAAgtatgttcacatctattcttggttataatctctgatttgtatggacgattttcgctcttacatgttaatgtcattagcttggttagtgtggtctgtatag...

Basic information

species Arabidopsis thaliana
transcript AT1G21720.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G21720.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA06G11930.1 (Glycine max), 5'ss of exon 2
ATTTGGTCCTTACTTATGCCAACCTGTGATTGCTGGCTTGGGAGATGATGACAAGCCTTTCATTTGCACGATGGACTCTATCGGAGCCAAgtatgttcacatctattcttggttataatctctgatttgtatggacgattttcgctcttacatgttaatgtcattagcttggttagtgtggtctgtatag-------
 |||||||| ||||| ||||| ||||| ||||||||  | ||||||||||||||||| ||||||||||| |||||  | || ||||| ||||| ||| |  |  ||| |||  |||||||| ||   |   |    | |    | |     | |||| ||| ||  |   | || |  |     || |||       
GTTTGGTCCATACTTTTGCCAGCCTGTAATTGCTGGACTAGGAGATGATGACAAGCCATTCATTTGCACAATGGATGCCATTGGAGCAAAgtaagtttaagt--attattg--tataatctgtgcccttatttactgttcagtgttgaggaaagttagtgttatagg---gattggcatatcacgtctagatttctt

upper sequence: AT1G21720.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA04G42830.1 (Glycine max), 5'ss of exon 2
ATTTGGTCCTTACTTATGCCAACCTGTGATTGCTGGCTTGGGAGATGATGACAAGCCTTTCATTTGCACGATGGACTCTATCGGAGCCAAgtatgttcacatctattcttggttataatctctgatttgtatggacgattttcgctcttacatgttaatgtcattagcttggttagtgtggtctgta-tag-----
 |||||||| ||||| ||||| ||||| ||||||||  | |||||||||||||| || ||||||||||| |||||  | || ||||| ||||| ||| |  |  ||   ||    || |  ||| || || | || ||   |   | ||     ||| ||  |||  ||   |   | |  ||| || |||     
GTTTGGTCCATACTTTTGCCAGCCTGTAATTGCTGGACTAGGAGATGATGACAAACCATTCATTTGCACAATGGATGCCATTGGAGCAAAgtaagtttaagta-atctgtgcccttatttactgtttagtgttgaggaaggttagtgtt-----ttagtgatattcactgcatacatttcttctataatagatttc

upper sequence: AT1G21720.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA14G24270.2 (Glycine max), 5'ss of exon 3
ATTTGGTCCTTACTTATGCCAACCTGTGATTGCTGGCTTGGGAGATGATGACAAGCCTTTCATTTGCACGATGGACTCTATCGGAGCCAAgtatgttcacatctattcttggttataatctctgatttgtatggacgattttcgctctta--catgttaatgtcattagcttggttagtgtggtctgtatag-
 |||||||| || || ||||| ||||| |||||||| || || ||||| ||||| || ||||||||||| ||||| | ||| || || ||||| ||| |  | |      |   ||| | |||  |       |     |   |  |  |  | ||  ||||| |  |   ||  |||| |  | ||||||  
GTTTGGTCCATATTTTTGCCAGCCTGTAATTGCTGGATTAGGGGATGAAGACAAACCATTCATTTGCACAATGGATTGTATTGGCGCAAAgtaagttgaattattagacagtccatattttcttgtagagggaggttggtgatgtgcaaaatcttgcaaatgttagcaatgtg--tagtata-tatgtataat

upper sequence: AT1G21720.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: Vv18s0001g02260.t01 (Vitis vinifera), 5'ss of exon 4
ATTTGGTCCTTACTTATGCCAACCTGTGATTGCTGGCTTGGGAGATGATGACAAGCCTTTCATTTGCACGATGGACTCTATCGGAGCCAAgtatgttcacatctattcttggttataatctctgatttgtatggacgattttcgctcttacatgttaatgtcattagcttg-gttagtgtggtctgtatag-
 |||||||| ||||| ||||| |||||||||||||| ||||||||||| |||||||| ||||||||||| ||||| || || ||||||||||||||| | || | |||     | ||| ||      || |   |   || |   | |  ||   || ||   |   | || || ||  |  |  | ||   
GTTTGGTCCATACTTCTGCCAGCCTGTGATTGCTGGATTGGGAGATGAAGACAAGCCATTCATTTGCACAATGGATTCAATTGGAGCCAAgtatgttga-atttcttcgcttgtgtaaccttct-cgtggactcatagttgtacatatgtcagcatactgagttgtacatgtgtcagcatactgaggattct

upper sequence: AT1G21720.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: EFJ05723 (Selaginella moellendorffii), 5'ss of exon 4
ATTTGGTCCTTACTTATGCCAACCTGTGATTGCTGGCTTGGGAGATGATGACAAGCCTTTCATTTGCACGATGGACTCTATCGGAGCCAAgtatgttcacatctattcttggttataatctctgatttgtatggacgattttcgctcttacatgttaatgtcattagcttggttagtgtggtctgtatag
||||||||| |||||    || ||| | ||||||||  | ||||  ||  ||||||||| ||| ||||||||||||||||||||||| | ||  ||   |  || |  |  | |   ||   ||| ||   |    | ||| |||                                             
ATTTGGTCCCTACTTCGTTCAGCCTCTCATTGCTGGGCTCGGAGCAGACAACAAGCCTTACATCTGCACGATGGACTCTATCGGAGCAATgtgagtgtccgactttcgtaagctc--ataagtgacttactt----gttttacgcag-------------------------------------------

upper sequence: AT1G21720.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: EFJ32896 (Selaginella moellendorffii), 5'ss of exon 4
ATTTGGTCCTTACTTATGCCAACCTGTGATTGCTGGCTTGGGAGATGATGACAAGCCTTTCATTTGCACGATGGACTCTATCGGAGCCAAgtatgttcacatctattcttggtt-ataatctctgatttgtatggacgattttcgctcttacatgttaatgtcattagcttggttagtgtggtctgtatag
||||||||| |||||    || ||| | ||||||||  | ||||  ||  ||||||||| ||| ||||||||||||||||||||||| | ||  ||   |  || |  |  | | ||||      | |||| |     |                                                    
ATTTGGTCCCTACTTCGTTCAGCCTCTCATTGCTGGGCTCGGAGCAGACAACAAGCCTTACATCTGCACGATGGACTCTATCGGAGCAATgtgagtgtccgactttcgtaagctcataagtgactacttgttttacgcag---------------------------------------------------

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|86039655|gb|DR335410.1|DR335410
EST:     GGAGATGATGACAAGCCTTTCATTTGCACGATGGACTCTATCGGAGCCAA                         AGAGTTAGCTAAAGATTTTGTTGTATCTGGAACTGCTTCAGAATCACTCTA
genomic: GGAGATGATGACAAGCCTTTCATTTGCACGATGGACTCTATCGGAGCCAAgtatgttcac ... cgaaatgcagAGAGTTAGCTAAAGATTTTGTTGTATCTGGAACTGCTTCAGAATCACTCTA
EST: gi|86039666|gb|DR335421.1|DR335421
EST:     GGAGATGATGACAAGCCTTTCATTTGCACGATGGACTCTATCGGAGCCAA                         AGAGTTAGCTAAAGATTTTGTT
genomic: GGAGATGATGACAAGCCTTTCATTTGCACGATGGACTCTATCGGAGCCAAgtatgttcac ... cgaaatgcagAGAGTTAGCTAAAGATTTTGTT
EST: gi|86039651|gb|DR335406.1|DR335406
EST:     GGAGATGATGACAAGCCTTTCATTTGCACGATGGACTCTATCGGAGCCAA                         AGAGTTAGCTAAAGATTTTGTTGTATCTGGAACTGCTTCAGAATCACTCTA
genomic: GGAGATGATGACAAGCCTTTCATTTGCACGATGGACTCTATCGGAGCCAAgtatgttcac ... cgaaatgcagAGAGTTAGCTAAAGATTTTGTTGTATCTGGAACTGCTTCAGAATCACTCTA
EST: gi|86039663|gb|DR335418.1|DR335418
EST:     GGAGATGATGACAAGCCTTTCATTTGCACGATGGACTCTATCGGAGCCAA                         AGAGTTAGCTAAAGATTTTGTTGTATCTGGAACTGCTTCAGAATCACTCTA
genomic: GGAGATGATGACAAGCCTTTCATTTGCACGATGGACTCTATCGGAGCCAAgtatgttcac ... cgaaatgcagAGAGTTAGCTAAAGATTTTGTTGTATCTGGAACTGCTTCAGAATCACTCTA
EST: gi|86076686|gb|DR372443.1|DR372443
EST:     GGAGATGATGACAAGCCTTTCATTTGCACGATGGACTCTATCGGAGCCAA                         AGAGTTAGCTAAAGATTTTGTTGTATCTGGAACTGCTTCAGAATCACTCTA
genomic: GGAGATGATGACAAGCCTTTCATTTGCACGATGGACTCTATCGGAGCCAAgtatgttcac ... cgaaatgcagAGAGTTAGCTAAAGATTTTGTTGTATCTGGAACTGCTTCAGAATCACTCTA
EST: gi|86039659|gb|DR335414.1|DR335414
EST:     GGAGATGATGACAAGCCTTTCATTTGCACGATGGACTCTATCGGAGCCAA                         AGAGTTAGCTAAAGATTTTGTTGTATCTGGAACTGCTTCAGAATCACTCTA
genomic: GGAGATGATGACAAGCCTTTCATTTGCACGATGGACTCTATCGGAGCCAAgtatgttcac ... cgaaatgcagAGAGTTAGCTAAAGATTTTGTTGTATCTGGAACTGCTTCAGAATCACTCTA
EST: gi|86039656|gb|DR335411.1|DR335411
EST:     GGAGATGATGACAAGCCTTTCATTTGCACGATGGACTCTATCGGAGCCAA                         AGAGTTAGCTAAAGATTTTGT-GTATCTGGAACTGCTTCAGAATCACTCTA
genomic: GGAGATGATGACAAGCCTTTCATTTGCACGATGGACTCTATCGGAGCCAAgtatgttcac ... cgaaatgcagAGAGTTAGCTAAAGATTTTGTTGTATCTGGAACTGCTTCAGAATCACTCTA
EST: gi|124775988|gb|EH866115.1|EH866115
EST:     GGAGATGATGACAAGCCTTTCATTTGCACGATGGACTCTATCGGAGCCAA                         AGAGTTAGCTAAAGATTTTGTTGTATCTGGAAC
genomic: GGAGATGATGACAAGCCTTTCATTTGCACGATGGACTCTATCGGAGCCAAgtatgttcac ... cgaaatgcagAGAGTTAGCTAAAGATTTTGTTGTATCTGGAAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATTTGGTCCTTACTTATGCCAACCTGTGATTGCTGGCTTGGGAGATGATGACAAGCCTTTCATTTGCACGATGGACTCTATCGGAGCCAAgtatgttcacatctattcttggttataatctctgatttgtatggacgattttcgctcttacatgttaatgtcattagcttggttagtgtggtctgtatag

- - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - -  GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttcgctct