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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATATTGTCATGTATGTTAATTCTCCTGGTGGATCAGTTACAGCTGgtaataacaactttgtcagcttactctttatcttttttccggttttatggttaatgactcgtgcatctcttactttacccag

Basic information

species Arabidopsis thaliana
transcript AT1G02560.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G02560.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: LOC_Os03g19510.1 (Oryza sativa), 5'ss of exon 5
GATATTGTCATGTATGTTAATTCTCCTGGTGGATCAGTTACAGCTGgtaataacaactttgtcagcttactctttatcttttttccggttttatggttaatgactcgtgc---atctcttactttacccag
|||||  | |||||||| ||||||||||| |||||||| |||||||||||||||   |    ||  ||  |   || ||   |  |  | ||        ||  ||   |   |   | |  | |    ||
GATATCATTATGTATGTGAATTCTCCTGGAGGATCAGTGACAGCTGgtaataac---tcatccattttttttcatagctccatctcactcttggaacatttgtttcacaccaaactgcattttgtgtttag

upper sequence: AT1G02560.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GLYMA02G01510.2 (Glycine max), 5'ss of exon 5
GATATTGTCATGTATGTTAATTCTCCTGGTGGATCAGTTACAGCTGgtaataacaactttgtcagcttactctt----tatctttt-ttccggttttatggttaatgactcgtgc--atctcttactttacccag---------------------------------------
||||||||||||||||| |||||||| || || ||||||||||||||||||||    || || |      ||||    | |||||| ||    | ||||  | |   ||  | ||  |     || | || |                                          
GATATTGTCATGTATGTAAATTCTCCAGGAGGGTCAGTTACAGCTGgtaataattttttagttaaaactatcttgcattgtcttttattattatattatattcatctacatgggctgaaaatatattgtatctcaaatattaaaatgctttctttgttattcttttccccttag

upper sequence: AT1G02560.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GLYMA10G01550.1 (Glycine max), 5'ss of exon 5
GATATTGTCATGTATGTTAATTCTCCTGGTGGATCAGTTACAGCTGgtaataacaactttgtcag------cttactctttatctttt-ttccggttttatggttaatgactcgtgc--atctcttactttacccag---------------------------------------
||||||||||||||||| |||||||| || || || ||||||||||||||||     || || |       ||| || | | | |||| ||    | ||||  | |   ||  | ||  |     || | || ||                                         
GATATTGTCATGTATGTAAATTCTCCAGGAGGGTCGGTTACAGCTGgtaatagttttttagttaaaactatcttgctttgttttttttattattatattatattcatctacatgggctaaaaatatattgtatcccaaatattaaaatgctttctttgttattcttttccccttag

upper sequence: AT1G02560.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GLYMA19G40480.1 (Glycine max), 5'ss of exon 4
GATATTGTCATGTATGTTAATTCTCCTGGTGGATCAGTTACAGCTGgtaataacaactt--tgtcagcttactctttatcttttttccg-----gttttatggttaa--tgactcgtgca-tctcttactttacccag----------------------------------
|||||||||||||| || |||||||  || ||||||||| |||||||||||||  | ||  ||| |   | | ||  ||   ||| | |       | ||||  ||   | |    |||| |   ||| ||||                                       
GATATTGTCATGTACGTAAATTCTCTGGGAGGATCAGTTGCAGCTGgtaataattattttttgtgaatctgccctgcattagtttactgtattcaatctatgcctagacttaaaaatgcaatgcattattttattttaaaatatgatgtgcttcacttttcctttttgtcag

upper sequence: AT1G02560.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GLYMA03G37880.1 (Glycine max), 5'ss of exon 4
GATATTGTCATGTATGTTAATTCTCCTGGTGGATCAGTTACAGCTGgtaataacaacttt--gtcagcttactctttatcttttttccg-----gttttatggttaa--tgactcgtgcatctc-ttactttacccag----------------------------------
                    |||||| || |||||||||||||||||||||||  | |||  || |   | | ||  ||   ||| | |       | ||||  ||   | |    ||||   | ||| ||||                                       
--------------------TTCTCCGGGAGGATCAGTTACAGCTGgtaataattattttatgtgaatctgccctgcattagtttactgtattcaatctatgcctagacttaaaaatgcaatgcgttattttattttaaaaactaatgtgcttcacttttcctttctgttag

upper sequence: AT1G02560.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: Vv07s0005g01530.t01 (Vitis vinifera), 5'ss of exon 5
GATATTGTCATGTATGTTAATTCTCCTGGTGGATCAGTTACAGCTGgtaataacaactttgt--cagcttactctttatcttttttccggttt-------tatggttaatgactcgtgcat-ctcttactttacccag-----------------------
||||||||||||||||| || ||||| || |||||||||||||||||||||  |    ||     |  ||  |||| |   |  | |  ||||       |  |  |   |||| || ||   ||||| |||    |                        
GATATTGTCATGTATGTGAACTCTCCAGGAGGATCAGTTACAGCTGgtaatttctgtcttacaataaatttttcttcacactggtactagtttatttaactgagcatggagacttgtacaggttcttattttcttgaattcttccttatttatcccctcag

upper sequence: AT1G02560.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: PP1S49_191V6.1 (Physcomitrella patens), 5'ss of exon 5
GATATTGTCATGTATGTTAATTCTCCTGGTGGATCAGTTACAGCTGgtaa--------taacaact-ttgtcagcttactctttatcttttttccggttttatggttaatgactcgtgcatctcttactttacccag---------
||||||||||||||||||||||| |||||||| || || ||||| |||||        | ||| |  |    | | ||   |  || | |||    ||||  | |||  |   |  ||  |   || |||| ||            
GATATTGTCATGTATGTTAATTCACCTGGTGGTTCTGTCACAGCAGgtaaagcatacatgacagcaatcaaaatcataacatggatttgtttgtttgtttgtttgtttgtttgttttgttttgttttcttttccgctttctgcact

upper sequence: AT1G02560.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: EFJ35520 (Selaginella moellendorffii), 5'ss of exon 4
GATATTGTCATGTATGTTAATTCTCCTGGTGGATCAGTTACAGCTGgtaataacaactttgtcagcttactctttatcttttttccggttttatggttaatgactcgtgcatctcttactttacccag
||||||||||||||||| ||||| ||||| || || ||||| |||||||               | ||  | ||| | |   |  ||  ||    | |||  | |  |   | ||||  | | | |||
GATATTGTCATGTATGTAAATTCACCTGGAGGTTCCGTTACCGCTGgta-------------tggttttttttttttttccctatcgagttgtcagctaacaatttat---tttctt--tctgctcag

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|125289367|gb|EL303452.1|EL303452
EST:     GATATTGTCATGTATGTTAATTCTCCTGGTGGATCAGTTACAGCTG                         GCATGGCTATATTCGATACTATGAGGCACAT
genomic: GATATTGTCATGTATGTTAATTCTCCTGGTGGATCAGTTACAGCTGgtaataacaa ... ctttacccagGCATGGCTATATTCGATACTATGAGGCACAT
EST: gi|125166336|gb|EL192182.1|EL192182
EST:     GGTGGATCAGTTACAGCTG                         GCATGGC-ATATTCGATACTATGAGGCACATCCGGCCTGATGTGTCCACTG
genomic: GGTGGATCAGTTACAGCTGgtaataacaa ... ctttacccagGCATGGCTATATTCGATACTATGAGGCACATCCGGCCTGATGTGTCCACTG
EST: gi|124709267|gb|EH800669.1|EH800669
EST:     CTGGTGGATCAGTTACAGCTG                         GCATGGCTATATTCGATACTATGAGGCACATCCGGCCTGATGTGTCCACTG
genomic: CTGGTGGATCAGTTACAGCTGgtaataacaa ... ctttacccagGCATGGCTATATTCGATACTATGAGGCACATCCGGCCTGATGTGTCCACTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATATTGTCATGTATGTTAATTCTCCTGGTGGATCAGTTACAGCTGgtaataacaactttgtcagcttactctttatcttttttccggttttatggttaatgactcgtgcatctcttactttacccag

- - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - CAGCTG