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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCACGTCACAATGGCCAAAATTATGTCTTTGCTCTGTTGACTGGTTATCGTGATCCTCCTGCTGGAATTTCGgtaaatttctctcctatttttgctttagacttgttattacaacttcaaattgttggaagttagaaataatcctgtgactaacgggtacag

Basic information

species Arabidopsis thaliana
transcript AT5G40810.2
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G40810.2 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: LOC_Os01g70960.1 (Oryza sativa), 5'ss of exon 5
GCACGTCACAATGGCCAAAATTATGTCTTTGCTCTGTTGACTGGTTATCGTGATCCTCCTGCTGGAATTTCGgtaaatttctctcctatttttgctttagacttgttattacaacttcaaattgttggaagttagaaataatcctgtgactaacgggtacag----------
||  | ||||||||||| || ||||| ||||||||  | ||||||||||||||||| ||||||||  |||||||||   |||||| ||  | |  ||| |   | ||| |     |    | |  | |   | | | || || || ||| || | | |              
GCCAGGCACAATGGCCAGAACTATGTTTTTGCTCTTCTCACTGGTTATCGTGATCCACCTGCTGGTGTTTCGgtaaccctctctcatacatattgttttgttattttagtgttggtcgctacttgtaggtttcacatatgattctctgagtatctgatttgttagatttgta

upper sequence: AT5G40810.2 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA05G07020.1 (Glycine max), 5'ss of exon 5
GCACGTCACAATGGCCAAAATTATGTCTTTGCTCTGTTGACTGGTTATCGTGATCCTCCTGCTGGAATTTCGgtaaatttctctcc-----tatttttgctt--tagacttgttattacaacttcaaattgttggaagttagaaataatcctgtg-actaacgggtacag-----
|| ||||||||||| || || ||||| ||||| ||  | |||||||||||||| |||||||||||  ||||||||||||  | ||       ||||||  ||  ||  ||| ||  |  |||||       ||  |      || |  || | |     ||  | || |      
GCTCGTCACAATGGTCAGAACTATGTGTTTGCACTTCTAACTGGTTATCGTGACCCTCCTGCTGGTGTTTCGgtaaattgttgtctattaacatttttaattattatgcttattgctgtaacttttgcacattcta---ccaaagttgtcttatatgtcaattgctagactacgt

upper sequence: AT5G40810.2 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA16G06700.2 (Glycine max), 5'ss of exon 5
GCACGTCACAATGGCCAAAATTATGTCTTTGCTCTGTTGACTGGTTATCGTGATCCTCCTGCTGGAATTTCGgtaaatttctctcctatttttgctttagacttgttattacaact--tcaaattgttggaagttagaaataatcctgt-gactaacgggtacag--------------
|| ||||||||||| || || ||||| ||||| ||  |||||||||||||||| || ||||||||  ||||||||||||  |||    || ||   |||    |  || |  |  |  | || |  ||  |   || |  |    | || |||| | ||  |  |              
GCCCGTCACAATGGTCAGAACTATGTTTTTGCCCTTCTGACTGGTTATCGTGACCCACCTGCTGGTGTTTCGgtaaattcttct----ttcttatcttaagtcttctactttatttagtaaagtaatttta---tacattttgctcagttgactgatggaaaatgctaggccaccaata

upper sequence: AT5G40810.2 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA19G22530.2 (Glycine max), 5'ss of exon 5
GCACGTCACAATGGCCAAAATTATGTCTTTGCTCTGTTGACTGGTTATCGTGATCCTCCTGCTGGAATTTCGgtaaatttctctcctatttttgctttagac--ttgttattacaacttcaaattgttggaagtta----gaaataatcctg--tgactaacgggtacag----
|| || |||||||| || || ||||| ||| | ||  | || ||||||||||| |||||||||||  |||||||||||||  ||| ||||     |||| |   || |  |||   ||  || || ||| |  ||      || |  || |   ||   ||  | || |     
GCTCGCCACAATGGTCAGAACTATGTGTTTTCCCTTCTAACCGGTTATCGTGACCCTCCTGCTGGTGTTTCGgtaaattttgctc-tattaacattttaaataattatgcttattgctgtaactt-ttgcacattctactaaagttgtcttatatggaaaattgctagactacg

upper sequence: AT5G40810.2 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: Vv14s0171g00330.t01 (Vitis vinifera), 5'ss of exon 5
GCACGTCACAATGGCCAAAATTATGTCTTTGCTCTGTTGACTGGTTATCGTGATCCTCCTGCTGGAATTTCGgtaaatttctctcctatttttgctttagactt----gttattacaacttca-aattgttggaagttagaaataatcctgtgactaacgggtacag-----
|| || |||||||| ||||| ||||| ||||| ||| | |||||||| |||||||| |||||||| |||||||||||||  ||| |  |  |    ||||  ||    |||| |       || |    |   || ||    |||| | |     | |||  |         
GCTCGCCACAATGGTCAAAACTATGTATTTGCACTGCTAACTGGTTACCGTGATCCACCTGCTGGCATTTCGgtaaattcttcttcactgatgatattagttttcatggttaattttgtgacacagacttcataattttcttataaactttaacatcacgactttgtatttt

upper sequence: AT5G40810.2 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: Vv09s0002g05950.t01 (Vitis vinifera), 5'ss of exon 4
GCACGTCACAATGGCCAAAATTATGTCTTTGCTCTGTTGACTGGTTATCGTGATCCTCCTGCTGGAATTTCGgtaaatttctc-tcctatttttgctttagacttgttattaca-acttcaaattgttggaagttagaaataatcctgtgactaacgggtacag--------
|| || |||||||| || |||||||| |||||||| || |||||||| ||||||||||| |||||  |||| |||| ||  |  ||  |  ||   | || || ||| ||   | |   | |  |  || ||  |     ||        | |  | | ||           
GCCCGCCACAATGGTCAGAATTATGTATTTGCTCTTTTAACTGGTTACCGTGATCCTCCAGCTGGTGTTTCAgtaagttctttatctcagattatatataaacatgtaatagaacatacctaggtactgaaatctgagtttatctgccatattttcagttatgtgatgatgt

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|116466135|gb|EG508727.1|EG508727
EST:     ATGTCTTTGCTCTGTTGACTGGTTATCGTGATCCTCCTGCTGGAATTTCG                         ATCAGAGAGGGGCTACACTACAATCCTTATTTCCCTGGTGGAGCAATCGCT
genomic: ATGTCTTTGCTCTGTTGACTGGTTATCGTGATCCTCCTGCTGGAATTTCGgtaaatttct ... acgggtacagATCAGAGAGGGGCTACACTACAATCCTTATTTCCCTGGTGGAGCAATCGCT
EST: gi|125007689|gb|EL079958.1|EL079958
EST:     CGTGAT-CTCCTGCTGGAATTTCG                         T
genomic: CGTGATCCTCCTGCTGGAATTTCGgtaaatttct ... acgggtacag-
EST: gi|125007689|gb|EL079958.1|EL079958
EST:     CGTGAT-CTCCTGCTGGAATTTCG                         T
genomic: CGTGATCCTCCTGCTGGAATTTCGgtaaatttct ... acgggtacag-
EST: gi|86078839|gb|DR374596.1|DR374596
EST:     ATGTCTTTGCTCTGTTGACTGGTTATCGTGATCCTCCTGCTGGAATTTCA                         ATCAGAGAGGGGCTACACTACAATCCTTATTTCCCTGGTGGAGCAATCGCT
genomic: ATGTCTTTGCTCTGTTGACTGGTTATCGTGATCCTCCTGCTGGAATTTCGgtaaatttct ... acgggtacagATCAGAGAGGGGCTACACTACAATCCTTATTTCCCTGGTGGAGCAATCGCT
EST: gi|86083864|gb|DR379623.1|DR379623
EST:     GTCCTTTGCTCTGTTGACTGGTTATCGGTGATCCTCCTGCTGGAATTTCA                         ATCAGAGAGGGGCTACACTACAATCCTTATTTCCCTGGTGGAGCAAATCGC
genomic: GT-CTTTGCTCTGTTGACTGGTTATC-GTGATCCTCCTGCTGGAATTTCGgtaaatttct ... acgggtacagATCAGAGAGGGGCTACACTACAATCCTTATTTCCCTGGTGGAGC-AATCGC
EST: gi|86080213|gb|DR375970.1|DR375970
EST:     ATGTCTTTGCTCTGTTGACTGGTTATCGTGATCCTCCTGCTGGAATTTCA                         ATCAGAGAGGGGCTACACTACAATCCTTATTTCCCTGGTGGAGCAATCGCT
genomic: ATGTCTTTGCTCTGTTGACTGGTTATCGTGATCCTCCTGCTGGAATTTCGgtaaatttct ... acgggtacagATCAGAGAGGGGCTACACTACAATCCTTATTTCCCTGGTGGAGCAATCGCT
EST: gi|124989417|gb|EL061736.1|EL061736
EST:     GTTGACTGGTTATCGTGATCCTCCTGCTTTGGAATTTCG                         ATCAGAGAGGGGCTACACTACAATCCTTATTTCCCTGGTGGAGCAATCGCT
genomic: GTTGACTGGTTATCGTGATCCTCCTGC--TGGAATTTCGgtaaatttct ... acgggtacagATCAGAGAGGGGCTACACTACAATCCTTATTTCCCTGGTGGAGCAATCGCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCACGTCACAATGGCCAAAATTATGTCTTTGCTCTGTTGACTGGTTATCGTGATCCTCCTGCTGGAATTTCGgtaaatttctctcctatttttgctttagacttgttattacaacttcaaattgttggaagttagaaataatcctgtgactaacgggtacag

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