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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CACGCTGGGAATGATAAGTCTTGTGTATGGCACGCTCGTGATTTCTCCGATGGTGAATTGAAGGATGAGCTCTTCTGTATCCGGTTTGCTTCAGTTGAGAgtgagtgtgaattttgcttttgtgtttttttatttctcagttgattggatcttactacgtaattgttgcttatagtagcactgctctgtctcgtttttgt...

Basic information

species Arabidopsis thaliana
transcript AT2G30060.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G30060.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA01G29410.1 (Glycine max), 5'ss of exon 3
CACGCTGGGAATGATAAGTCTTGTGTATGGCACGCTCGTGATTTCTCCGATGGTGAATTGAAGGATGAGCTCTTCTGTATCCGGTTTGCTTCAGTTGAGAgtgagtgt----gaattttgcttttgtg-tttttttatttctcagttgattggatcttactacgta-attgttgcttatagtagcactgctctgtctcgtttttgt
||  |||||||||| || || ||||| ||||| |||  ||||||  | ||||| ||||||||||||||||| ||||||||  ||||| | || ||||||||||||| |    |  || |||| |||    || | ||| |   | ||  ||  |  | ||| | |  ||| ||    ||| | | | |||    | |  |      
CATTCTGGGAATGAGAAATCGTGTGTGTGGCATGCTTCTGATTTTGCAGATGGGGAATTGAAGGATGAGCTGTTCTGTATTAGGTTTCCCTCTGTTGAGAgtgagtctctaggctttgtgctgttggaacttctctatgttgaattttgttttagttcacttcttccatttttatggataattgaaatgcaaattttgat------

upper sequence: AT2G30060.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA20G31070.1 (Glycine max), 5'ss of exon 3
CACGCTGGGAATGATAAGTCTTGTGTATGGCACGCTCGTGATTTCTCCGATGGTGAATTGAAGGATGAGCTCTTCTGTATCCGGTTTGCTTCAGTTGAGAgtgagtgtgaattttgcttttgtgtttttttatttctcagttgattggatcttactacgtaattgttgcttata---gtagcactgctctgtctcgtttttgt
||||||||||| || || ||||| || ||||||||| | |||||  | ||||||||| | ||||| ||||| ||||| ||||| ||| ||||  |||| ||||||| ||    ||  |||||    |  | || | | | |  |     | ||  |       ||||||| ||     | |   |  | ||  || | ||| |
CACGCTGGGAACGAGAAATCTTGCGTTTGGCACGCTAGGGATTTTGCTGATGGTGAACTCAAGGACGAGCTTTTCTGCATCCGTTTTCCTTCTATTGAAAgtgagt-tgtgcctt-tttttggagctaataatattttattgaagatatttttcgtttagttctgttgctaatgtgtttggtgtttttgtggttc-tctttat

upper sequence: AT2G30060.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: Vv06s0004g06880.t01 (Vitis vinifera), 5'ss of exon 3
CACGCTGGGAATGATAAGTCTTGTGTATGGCACGCTCGTGATTTCTCCGATGGTGAATTGAAGGATGAGCTCTTCTGTATCCGGTTTGCTTCAGTTGAGAgtgagtgtgaattttgcttttgtgtttttttatttctcagttgattggatcttactacgtaattgttgcttatagtagcactgctctgtctcgtttttgt---
|| ||||| || |||||||| ||||| ||||| ||   ||||||  | ||||| ||||||||||||||||| ||||||||  | ||||| |||||||| ||||||| | |||||     ||  | | | || | | | |  || ||  || ||  |   | |   | | | | |       |  | ||  | |   |  |   
CATGCTGGTAACGATAAGTCCTGTGTCTGGCATGCCACTGATTTTGCTGATGGAGAATTGAAGGATGAGCTTTTCTGTATAAGATTTGCATCAGTTGAAAgtgagtat-aatttgttcattacggtctgttctctgt-aactgttttcatattgttttttgaa-atagatcaaacgcattttcttgtgattggaactgcttga

upper sequence: AT2G30060.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: PP1S25_241V6.2 (Physcomitrella patens), 5'ss of exon 3
CACGCTGGGAATGATAAGTCTTGTGTATGGCACGCTCGTGATTTCTCCGATGGTGAATTGAAGGATGAGCTCTTCTGTATCCGGTTTGCTTCAGTTGAGAgtgagtgtgaattttgcttttgtgtttttttatttctcagttgattggatcttactacgtaattgttgcttatagtagcactgctctgtctcgtttttgt---------------------------------------------------------------------------------------
|||||||| | |||||||||||| || ||||| || || |||||||| ||||||||  ||||||| || || ||||| || |||||||     ||||| ||| |||   |  |     |   |  | || | | ||  |||| || |  | || |   | | |    | ||     |    || ||||| |  ||   |                                                                                        
CACGCTGGCAGTGATAAGTCTTGGGTCTGGCATGCACGGGATTTCTCAGATGGTGAGCTGAAGGAGGAACTTTTCTGCATGCGGTTTGGAAGTGTTGAAAgtaagttccatctgcatatccatcctcttctttctcgaagttaat-gcttgttgcagtgcagt----gtttgcgacaatgttgttctgtatgtttccaggaattttgatgtaatacaagatctattcaaggtatgtgttgtctctatattgcttttttcttcaatctcaaggctattgtatgaacag

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|124787162|gb|EH876841.1|EH876841
EST:     CCGGTTTGCTTCAGTTGAGA                         ATTGCAAAGCATTTATGCAAAAGTTCAAGGAAGTAGCTGAA
genomic: CCGGTTTGCTTCAGTTGAGAgtgagtgtga ... acatgatcagATTGCAAAGCATTTATGCAAAAGTTCAAGGAAGTAGCTGAA




















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
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CACGCTGGGAATGATAAGTCTTGTGTATGGCACGCTCGTGATTTCTCCGATGGTGAATTGAAGGATGAGCTCTTCTGTATCCGGTTTGCTTCAGTTGAGAgtgagtgtgaattttgcttttgtgtttttttatttctcagttgattggatcttactacgtaattgttgcttatagtagcactgctctgtctcgtttttgt

- - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgtctcg