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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaacaaaaactagagtcttctctctgttcttgatgccaaaaccctaagatttttcgattttttccctgcagCTAGAGGTTTTGTTCAATGGTAATTCACCTCATGAAGTTGCTCATATCGCAAATGGTTCACATCCTGGAAATTGCATCTCTCTTCTTCGAATCAAT

Basic information

species Arabidopsis thaliana
transcript AT5G46880.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G46880.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: LOC_Os10g42490.1 (Oryza sativa), 3'ss of exon 10
--------------------------gtaaacaaaaactagagtcttctctctgttcttgatg--ccaaaaccctaagatttttcgattttttccctgcagCTAGAGGTTTTGTTCAATGGTAATTCACCTCATGAAGTTGCTCATATCGCAAATGGTTCACATCCTGGAAATTGCATCTCTCTTCTTCGAATCAAT
                            |  | | |   | | |  |   | |   | | ||    |       | |  ||| |  ||||      ||||||| ||| ||||||  || ||    || | |||||| || || ||||| |||||||| ||||||||  | |||||||||||||||||||| || || 
gtacaatgaagagccatataatatactcagtccatactgaaaattgttgttgttcaccttataattcgttgtggtcatgtttgttaatttgccttttgcagCTTGAGATTTTGTCAAACGGCGGCTCCCTTCATGAGGTGGCACATATTGCAAATGGATCACATCCAAGGAATTGCATCTCTCTTCTTCGCATTAAC

upper sequence: AT5G46880.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA09G34070.1 (Glycine max), 3'ss of exon 9
----------------gtaaacaaaaactagagtctt--ctctctg---ttcttgatgccaaaaccctaag-----atttttcgattttttccctg-cagCTAGAGGTTTTGTTCAATGGTAATTCACCTCATGAAGTTGCTCATATCGCAAATGGTTCACATCCTGGAAATTGCATCTCTCTTCTTCGAATCAAT
                  ||   || | |  | ||||    |  ||   || || | |   ||    | |      | |||    ||| ||   || ||| | || | | | | |||||| || |||    ||||||| |||||||| |||||||| |||||||| ||||| ||||| ||||||||||| || |||
gtagtgcaaaccctttacaattcaatattcaactcttaatccattgcattttttaacggttaactgatgaatatccactttcttttttcttttttgtcagATGGATGCTCTTTCCAATGGGAACTCATTGAATGAAGTGGCTCATATTGCAAATGGCTCACATCCAGGAAACTGCATTTCTCTTCTTCGCATAAAT

upper sequence: AT5G46880.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA01G01850.1 (Glycine max), 3'ss of exon 9
---------------------------------------------gtaaacaaaaactagagtctt--ctctctg---ttcttgatgccaaaaccct-aagattt-ttcgattttttccctgcagCTAGAGGTTTTGTTCAATGGTAATTCACCTCATGAAGTTGCTCATATCGCAAATGGTTCACATCCTGGAAATTGCATCTCTCTTCTTCGAATCAAT
                                              | ||  || |||  | | ||    |  ||   || || | |   ||    | || || | ||   || |||    |||| | ||   | | |  || || || |||    ||||||| |||||||| |||||||| |||||||| ||||| ||||| ||||||||||| || |||
gtagtgcaaacccatgtatcagatccaatctgcaatcatttataattcaattaatactcaactattaatccattgcattttttaacggttaactgatgaatatctatttttttattttttggcagATGGATACTCTTTCAAACGGGAACTCATTGAATGAAGTGGCTCATATTGCAAATGGCTCACATCCAGGAAACTGCATTTCTCTTCTTCGCATAAAT

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|164154028|gb|EL993200.1|EL993200
EST:     GTCTTTGATCTTATCCGTGATCAACATCACCAATCTCTG                         CTAGAGGTTTTGTTCAATGGTAATTCACCTCATGAAGTTGCTCATATCG
genomic: GTCTTTGATCTTATCCGTGATCAACATCACCAATCTCTGgtaaacaaaa ... ttccctgcagCTAGAGGTTTTGTTCAATGGTAATTCACCTCATGAAGTTGCTCATATCG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttctctctgttcttgatgccaaaaccctaagatttttcgattttttccctgcagCTAGAGGTTTTGTTCAATGGTAATTCACCTCATGAAGTTGCTCATATCGCAAATGGTTCACATCCTGGAAATTGCATCTCTCTTCTTCGAATCAAT
           tcttgat  putative branch site (score: 4)
                                 tttttcgattttttcc  putative PPT
                                atttttcgatttttt  TA-rich tract