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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaattaacaacatttggattttgattgattgacacaatcctcacatgatgaggttttgagtgtgtgttttggctctctcactgagtttgtggaatgtatatttcagTTTCTCTAGTGGAGGTGAAGACGGTTACGTGAGGCTGCATCATTTTGACTCCGACTACTTCAACATCAAGATTTAGATTCCGACTACTTGAACGTCAACC

Basic information

species Arabidopsis thaliana
transcript AT2G46280.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G46280.3 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os05g16660.1 (Oryza sativa), 3'ss of exon 6
gtaaattaacaacatttggattttgattgattgacacaatcctcacatgatgaggttttgagtgtgt---gttttg-gctctctcactgagtttgtggaatgtatatttcagTTTCTCTAGTGGAGGTGAAGACGGTTACGTGAGGCTGCATCATTTTGACTCCGACTACTTCAACATCAAGATTTAGATTCCGACTACTTGAACGTCAACC
              ||      |   ||     |    ||  | |  | |||  |||  ||  ||||   | |||| |||      ||   | | |   | |    |  ||| ||||| ||||| |||||||| || || || |||||||| |||||||| || ||||||||||||||||||||||| |    ||     ||||  ||    
------------tcttcaagcatattttctcacatgtcatggttaatttatgttgttcagaaagtgttttgctttgagcttcagttcttcatgtataatacggtgttaacagCTTCTCGAGTGGTGGTGAAGATGGATATGTAAGGCTGCACCATTTTGATTCTGACTACTTCAACATCAAGATTTAAAGCAAGAAGTTGTGAAACTCTGAG

upper sequence: AT2G46280.3 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os08g21660.1 (Oryza sativa), 3'ss of exon 6
gtaaattaacaacatttggattttgattgattgacacaatcctcacatgatgaggttttgagtgtgtgttttggctctctcactgagtttgtggaatgtatatttcagTTTCTCTAGTGGAGGTGAAGACGGTTACGTGAGGCTGCATCATTTTGACTCCGACTACTTCAACATCAAGATTTAGATTCCGACTACTTGAACGTCAACC
     ||  |  ||      ||||  ||   | |    ||  | |  | | | | |||||  | || | ||  | | | |||      |  ||  ||||  |   ||| || || ||||| |||||||| || || || |||||||| |||||||| || ||||||||||||||||||||||| |    ||     ||||  ||    
----gttctcttcaagcatgttttttttctctcatgtgatggttaattaaagtgtttttgctt-tgagcttcagttat-tcatatctatgatgcgatgttaaa--cagCTTTTCGAGTGGTGGTGAAGATGGATATGTAAGGCTGCACCATTTTGATTCTGACTACTTCAACATCAAGATTTAAACCTAGAAGTTCTGAAACTCTGAG

upper sequence: AT2G46280.3 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G028834_T03 (Zea mays), 3'ss of exon 6
gtaaattaacaacatttggattttgattgattgacacaatcctcacatgatgaggttttgagtgtgtgttttggctctctcactgagtttgtggaatgtatatttcagTTTCTCTAGTGGAGGTGAAGACGGTTACGTGAGGCTGCATCATTTTGACTCCGACTACTTCAACATCAAGATTTAGATTCCGACTACTTGAACGTCAACC---
 |   |  | | | |||    || | ||   |||   | |      |  || | ||||   || | | || |   | | ||  ||  ||| |    ||    | | ||||| || ||||| |||||||| ||||| || ||||||||||||||||| ||||||||||||| ||||||||| |||||   ||  ||  ||     ||||   
ctttgtagaaacctttttctcttaggtt--ctgaagtagtttatctagtataaagttt---gttttt-ttctaattatgtccatg--ttttttctctgatcttattagTTTTTCAAGTGGCGGTGAAGATGGTTATGTAAGGCTGCATCATTTTGATTCCGACTACTTCAGCATCAAGATGTAGATAAAGAACACCAGA---CTAACCCGA

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|124838828|gb|EH923267.1|EH923267
EST:     GGTCATTTTGGACCTATAAATGCTTTGGCATTCAATCCTGATGGGAAGAG                         TTTCTCTAGTGG
genomic: GGTCATTTTGGACCTATAAATGCTTTGGCATTCAATCCTGATGGGAAGAGgtaaattaac ... tatatttcagTTTCTCTAGTGG
EST: gi|125081411|gb|EL142644.1|EL142644
EST:     GACCTATAAATGCTTTGGCATTCAATCCTGATGGGAAGAG                         TTTCTCTAGTGGAGGTGAAGACGGTTACGTGAGGCTGCATCATTTTGACTC
genomic: GACCTATAAATGCTTTGGCATTCAATCCTGATGGGAAGAGgtaaattaac ... tatatttcagTTTCTCTAGTGGAGGTGAAGACGGTTACGTGAGGCTGCATCATTTTGACTC
EST: gi|164037758|gb|ES148773.1|ES148773
EST:     GTCATTTTGGACCTATAAATGCTTTGGCATTCAATCCTGATGGGGAAGAG                         TTTCTCTAGTGGAGGTGAAGACGGTTACGTGAGGC
genomic: GTCATTTTGGACCTATAAATGCTTTGGCATTCAATCCTGATGGG-AAGAGgtaaattaac ... tatatttcagTTTCTCTAGTGGAGGTGAAGACGGTTACGTGAGGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggttttgagtgtgtgttttggctctctcactgagtttgtggaatgtatatttcagTTTCTCTAGTGGAGGTGAAGACGGTTACGTGAGGCTGCATCATTTTGACTCCGACTACTTCAACATCAAGATTTAGATTCCGACTACTTGAACGTCAACC
                       ctctcac  putative branch site (score: 3)
                                         aatgtatattt  TA-rich tract