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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcaggcatctcttgtttaaaaagacctgaaaaactttccctttcgctgtcttgtaatttatttttctctttttttactatgcagTTTATATTCTCAACCGCTCTTGATGGAAAGATCAAGGCGTGGCTCTATGATAATGTTGGTTCTCGGGTTGATTATGACGCACCGGGACAGTGGTGTACAA

Basic information

species Arabidopsis thaliana
transcript AT3G16830.1
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G16830.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: PP1S316_34V6.1 (Physcomitrella patens), 3'ss of exon 13
-------gtgcaggcatctc--ttgtttaaaaagacctgaaaaactttccctttcgc-tgtcttgtaatttatttttctct---ttttttactatg-cagTTTATATTCTCAACCGCTCTTGATGGAAAGATCAAGGCGTGGCTCTATGATAATGTTGGTTCTCGGGTTGATTATGACGCACCGGGACAGTGGTGTACAA
         || | || |    | |||  ||| |  ||   |    | |    | |     | ||     ||   || | |   |    ||| ||  ||||||||||||||||| ||| ||||||| ||||| || || ||||||||||||    |||| ||| | ||||| || || ||||| || || ||||| || |
cttatttaagctgccaacgaggtagttagaaatgtgcttctatctgtactgcattgtacagcatgagccctaaaattgtttgaatggcctacaatttcagTTTATATTCTCAACAGCTATTGATGGCAAGATAAAAGCTTGGCTCTATGATCTCCTTGGATCTAGAGTTGACTACGATGCACCTGGTCATTGGTGCACTA

upper sequence: AT3G16830.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: PP1S99_260V6.1 (Physcomitrella patens), 3'ss of exon 13
gtgcaggcatctcttgtttaaaa-agacctgaaaaactttcccttt--------cgctgtcttgtaatttatttttctctttt------tttactatgc-agTTTATATTCTCAACCGCTCTTGATGGAAAGATCAAGGCGTGGCTCTATGATAATGTTGGTTCTCGGGTTGATTATGACGCACCGGGACAGTGGTGTACAA
    || |   | |   |||||| | |  || |  | ||    | |        || |||  |||     |  | |  | |||        |  ||||| |||||||||||||||| ||| | ||||| ||||| || || ||||||||||||  | |||||||| | ||||| ||||| ||||| || || ||||| || |
--ttagccccatgtgaattaaaacaaaaatggagtaattcgtatctgaaatgtgcggtgtggtgtgtaaaacctctgacctttggatgacctcgtatgccagTTTATATTCTCAACAGCTATCGATGGCAAGATAAAAGCCTGGCTCTATGATCTTCTTGGTTCTAGAGTTGACTATGATGCACCAGGGCATTGGTGCACTA

upper sequence: AT3G16830.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: EFJ30926 (Selaginella moellendorffii), 3'ss of exon 13
gtgcaggcatctcttgtttaaaaagacctgaaaaactttccctttcgctgtcttgtaatttatttttctcttttt-ttactatgcagTTTATATTCTCAACCGCTCTTGATGGAAAGATCAAGGCGTGGCTCTATGATAATGTTGGTTCTCGGGTTGATTATGACGCACCGGGACAGTGGTGTACAA
                                   || |  |  | || || || |   ||||   | | |  || || || ||||||||||||| || ||||| |||||||| || ||||| || ||||| || |||||| | |||||||| || |||||||| || || || |  ||||| ||||
---------------------------------gtctgtgtccattgccgttttctttattatgggtttatggttattgctctgcagTTTATATTTTCCACCGCACTTGATGGGAAAATCAAAGCTTGGCTTTACGATAATCTCGGTTCTCGAGTAGATTATGATGCTCCTGGTCGCTGGTGCACAA

upper sequence: AT3G16830.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: EFJ17248 (Selaginella moellendorffii), 3'ss of exon 13
gtgcaggcatctcttgtttaaaaagacctgaaaaactttccctttcgctgtcttgtaatttatttttctcttttt-ttactatgcagTTTATATTCTCAACCGCTCTTGATGGAAAGATCAAGGCGTGGCTCTATGATAATGTTGGTTCTCGGGTTGATTATGACGCACCGGGACAGTGGTGTACAA
                                   || |  |  | || || || |   ||||   | | |  || || || ||||||||||||| || ||||| |||||||| || ||||| || ||||| || |||||| | |||||||| || |||||||| || || || |  ||||| ||||
---------------------------------gtctgtatccattgccgttttctttattatgggtttatggttattgctctgcagTTTATATTTTCCACCGCACTTGATGGTAAAATCAAAGCTTGGCTTTACGATAATCTCGGTTCTCGAGTAGATTATGATGCTCCTGGTCGCTGGTGCACAA

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|47831151|gb|CK120835.1|CK120835
EST:     ACGAGGCACCAGTTTATTCCATTTGCCCTCACCAGAAGGAAAATATTCAG                         TTTATATTCTCAACCGCTCTTGATGGAAAGATCAAGGCGTGGCTCTATGAT
genomic: ACGAGGCACCAGTTTATTCCATTTGCCCTCACCAGAAGGAAAATATTCAGgtgcaggcat ... tactatgcagTTTATATTCTCAACCGCTCTTGATGGAAAGATCAAGGCGTGGCTCTATGAT
EST: gi|86059274|gb|DR355031.1|DR355031
EST:     ACGAGGCACCAGTTTATTCCATTTGCCCTCACCAGAAGGAAAATATTCAG                         TTTATTTTCTCAACCGCTCTTGATGGAAAGATCAAGGCGTGGCTCTATGAT
genomic: ACGAGGCACCAGTTTATTCCATTTGCCCTCACCAGAAGGAAAATATTCAGgtgcaggcat ... tactatgcagTTTATATTCTCAACCGCTCTTGATGGAAAGATCAAGGCGTGGCTCTATGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaactttccctttcgctgtcttgtaatttatttttctctttttttactatgcagTTTATATTCTCAACCGCTCTTGATGGAAAGATCAAGGCGTGGCTCTATGATAATGTTGGTTCTCGGGTTGATTATGACGCACCGGGACAGTGGTGTACAA
                   tcttgtaatttatttt  CT-rich tract
                     ttgtaatttatttttc  TA-rich tract