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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcaaatcatctcttctttcatctatatagtcttaaaagatatggagttgtttttaatcttgcaagtcttccagATATTCAACGAGTTCAACGCAAGAAAACCTGATGAAATGAATGTATTCCGGGGAGTAAATAAGAACCCTCTCTTCGTAGCAATTGTTGGAGTCACTTTTA

Basic information

species Arabidopsis thaliana
transcript AT3G21180.1
intron # 29
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G21180.1 (Arabidopsis thaliana), 3'ss of exon 29
lower sequence: GLYMA13G44990.1 (Glycine max), 3'ss of exon 31
--------gtaagcaaatcatctcttctttcatctat-atagtcttaaaagatatggagttgttttta-----------atcttgcaa---gtcttccagATATTCAACGAGTTCAACGCAAGAAAACCTGATGAAATGAATGTATTCCGGGGAGTAAATAAGAACCCTCTCTTCGTAGCAATTGTTGGAGTCACTTTTA
        ||      ||  |  |    || ||  ||   | |||||    | || ||||| | | ||           ||  | |||    | || |||||||||||||||||||| ||  ||||||| || || |||||||| ||||||||||| | |||||||| ||||||| | | |||||||||| | || ||  
atatttgggttgatggattgtacccctctttattaattggattcttattgaagatcgagttttatatataataataatgattattcaattgattttacagATATTCAACGAGTTCAATGCTCGAAAACCAGAAGAGATGAATGTCTTCCGGGGAGTGACTAAGAACCGTCTCTTCATGGGAATTGTTGGAATGACCTTCG

upper sequence: AT3G21180.1 (Arabidopsis thaliana), 3'ss of exon 29
lower sequence: GLYMA15G00340.1 (Glycine max), 3'ss of exon 31
gtaagcaaatcatctcttctttcatctatatagtcttaaaagatatggagttgtttttaatcttgcaagtcttccagATATTCAACGAGTTCAACGCAAGAAAACCTGATGAAATGAATGTATTCCGGGGAGTAAATAAGAACCCTCTCTTCGTAGCAATTGTTGGAGTCACTTTTA
|||||  |   |    |      || |   | ||  | |  ||| || |    | | |||||     | | || |||||||||||||||||||| ||  ||||||| || || |||||||| ||||||||||| | |||||||  ||||||| | | |||||||||| | || ||  
gtaagtgagatagtagt------atttggctggt--tgatggat-tgaaaccctctataatcaattga-ttttacagATATTCAACGAGTTCAATGCTCGAAAACCAGAAGAGATGAATGTCTTCCGGGGAGTGACTAAGAACGGTCTCTTCATGGGAATTGTTGGAATGACCTTCG

upper sequence: AT3G21180.1 (Arabidopsis thaliana), 3'ss of exon 29
lower sequence: Vv09s0018g02130.t01 (Vitis vinifera), 3'ss of exon 31
-------------------------------------------------------------------------------------------------------gtaagc--aaatcatctcttctttcatctatatagtcttaaaagatatggagttgtttttaatcttgcaagtc--ttccagATATTCAACGAGTTCAACGCAAGAAAACCTGATGAAATGAATGTATTCCGGGGAGTAAATAAGAACCCTCTCTTCGTAGCAATTGTTGGAGTCACTTTTA
                                                                                                        |||     ||| ||  ||| | |    | | || | ||  ||  ||   |       |||  |   ||  ||  || |||||||||||||||||||| || ||||| || |||||||| ||||| ||    ||||| | ||| ||    || ||  | |  ||  ||||| |||| ||| 
gtaagtagtctggggtaagctgagtaaaacaggaatgagtcgttaaaaaataaataaaaatgtcatgacctaagtttttctttttccaggtcacattataaaattaattttgaataattacttatgtttgttttttactatttcaaagtaccaaacaaaaattagccaaccatttcatttgcagATATTCAACGAGTTCAATGCCAGAAAGCCAGATGAAATTAATGTCTTTACTGGAGTGACTAAAAATTACCTATTTATGGGGATCATTGGAATCACCTTTG

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|86084426|gb|DR380185.1|DR380185
EST:     CAATGCCTTTGTCATGTGTCAA                         ATATTCAACGAGTTCAACGCAAGAAAACCTGATGAAATGAATGTATTCCGG
genomic: CAATGCCTTTGTCATGTGTCAAgtaagcaaat ... agtcttccagATATTCAACGAGTTCAACGCAAGAAAACCTGATGAAATGAATGTATTCCGG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catctatatagtcttaaaagatatggagttgtttttaatcttgcaagtcttccagATATTCAACGAGTTCAACGCAAGAAAACCTGATGAAATGAATGTATTCCGGGGAGTAAATAAGAACCCTCTCTTCGTAGCAATTGTTGGAGTCACTTTTA
                                ttttaat  putative branch site (score: 3)
                                               tcttcc  putative PPT
     atatagtcttaaaa  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagcaaatcatctcttctttcatctatatagtcttaaaagatatggagttgtttttaatcttgcaagtcttccagATATTCAACGAGTTCAACGCAAGAAAACCTGATGAAATGAATGTATTCCGGGGAGTAAATAAGAACCCTCTCTTCGTAGCAATTGTTGGAGTCACTTTTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG