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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatatatacttcttcctttactattgttgttgttgacataactgttgatctaatcatctgagaaatatacacaattcttagGATCGAGATGGCTATTGGAAGATGATGCAGAAGTACATAGGATCTGATGTTACATCAATGGTGACCCTTCCTGTGATTATTTTTGAACCAATGACAATGC

Basic information

species Arabidopsis thaliana
transcript AT3G09300.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G09300.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os03g16690.1 (Oryza sativa), 3'ss of exon 2
-----------------gtatatatacttcttcctttactattgttgttgttgacataactgttgatcta-atcatctgagaaatatacacaattcttagGATCGAGATGGCTATTGGAAGATGATGCAGAAGTACATAGGATCTGATGTTACATCAATGGTGACCCTTCCTGTGATTATTTTTGAACCAATGACAATGC
                  |    | || | |   |||    |      ||||  | |   | |   |  | ||  |||    | |  |   |||    ||||||| ||| | ||||||||||||||||| |||||||||||  | |||||||||||| | ||||| ||||| || || |||||||| |||||||||||||
gatctttctagaggatgattggaacacctttgtatttcagctgcacagtgttctcgtgtatatcccttcatatgctcttgacattccaattaatctgcagGATCGTGATAGTTATTGGAAGATGATGCACAAGTACATAGGGGCAGATGTTACATCACTTGTGACACTTCCGGTCATCATTTTTGAGCCAATGACAATGC

upper sequence: AT3G09300.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G114126_T02 (Zea mays), 3'ss of exon 2
-------------gtatatatacttcttcctttactattgttgttgtt--gacataactgttgatctaatcatctgagaa----atatacacaattcttagGATCGAGATGGCTATTGGAAGATGATGCAGAAGTACATAGGATCTGATGTTACATCAATGGTGACCCTTCCTGTGATTATTTTTGAACCAATGACAATGC
             |   |||    | || |  |  |||  |||  |||  |   | | |   |||| | |  | | | ||     | |    ||||   ||||||| ||| ||||||||||||||||||| |||||||||||||| |||||||||||| | ||||| ||||| || || |||||||| |||||||||||||
tctatggttttaaggtcatagtagttttacgatcgtatacttgaagttctggtctgattcaggatc-actattttaacaaccttgtgtggttaatttgcagGATCGTGATAGCTATTGGAAGATGATGCACAAGTACATAGGATCAGATGTTACATCACTTGTGACACTTCCAGTCATAATTTTTGAGCCAATGACAATGC

upper sequence: AT3G09300.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G174644_T01 (Zea mays), 3'ss of exon 2
---------------gtatatatacttcttcctttactattgttgttgttgacataactgttgatctaatcatctgagaaatatacac----aattcttagGATCGAGATGGCTATTGGAAGATGATGCAGAAGTACATAGGATCTGATGTTACATCAATGGTGACCCTTCCTGTGATTATTTTTGAACCAATGACAATGC
                |  |  || ||  |    |||  |||  |||  |||| | | |   ||||      | | | ||  ||        ||||   |||| || ||| |||| |||||||||||||| || ||||||||||| |||||||||||| | ||||| ||||| || || |||||||| |||||||||||||
atcgtagtagttatgatccaactatttactatcctacacttggagtt-ctgacctgattcaggatcacgatctttaacaatcatgtgtggttaatttgcagGACCGTGATAGCTACTGGAAGATGATGCACAAATACATAGGATCAGATGTTACATCACTTGTGACACTTCCAGTCATAATTTTTGAGCCAATGACAATGC

upper sequence: AT3G09300.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: PP1S148_87V6.1 (Physcomitrella patens), 3'ss of exon 2
---------------------------------------------------------------------------------------------------gtatatatacttcttcctttactat----tgttgttgttgacataactgttgatcta--atcatctgagaaatatacacaattcttagGATCGAGATGGCTATTGGAAGATGATGCAGAAGTACATAGGATCTGATGTTACATCAATGGTGACCCTTCCTGTGATTATTTTTGAACCAATGACAATGC
                                                                                                    |  || ||  || || |  | | |    ||      |    | | | | ||   ||   |    |      |||     |     ||||| ||||  | |||||||| |||||||| ||||||||||| |||||  |||| ||||||||||| ||||| || || || ||||| || ||||| | ||
gtgaccttcatcttcatgccttaagcatcgagatcagtaatcatttttaatgtatgttgtggtgtggcattagtgccaatttcggcgaactggattggaattaatttaactcctcttgaattttaatgtgaaagaatcagtacatcggctgccttaccgttgggtttttgttatgtggcaagtgcagGATAGAGAAAGTTATTGGAAAATGATGCACAAGTACATAGGTTCTGACATTACTTCAATGGTGACACTTCCAGTCATCATATTTGAGCCCATGACTACGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgttgttgacataactgttgatctaatcatctgagaaatatacacaattcttagGATCGAGATGGCTATTGGAAGATGATGCAGAAGTACATAGGATCTGATGTTACATCAATGGTGACCCTTCCTGTGATTATTTTTGAACCAATGACAATGC
                     atctaat  putative branch site (score: 3)
                                                ttctt  putative PPT
                                    aaatatacacaatt  TA-rich tract