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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagcaatcatttcgcttcatagcctgtcccatattatttagctgaatagtattgagagaggactgatctttcttttgactcgtacagTCAGCAATTATATCATTGGGACTGATTGGCGCTGGAACTAATAACGCAAGGATAGCCGGGATGCTTCGGAACCTCTCCAGCTATTATTACAAAGACATGA

Basic information

species Arabidopsis thaliana
transcript AT2G20580.1
intron # 18
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G20580.1 (Arabidopsis thaliana), 3'ss of exon 18
lower sequence: LOC_Os09g15750.1 (Oryza sativa), 3'ss of exon 20
gttagcaatcatttcgctt-catagcctgtcccatattatttagctgaat-agtattgagagaggactgatctttcttttgactcgtacagTCAGCAATTATATCATTGGGACTGATTGGCGCTGGAACTAATAACGCAAGGATAGCCGGGATGCTTCGGAACCTCTCCAGCTATTATTACAAAGACATGA
||||| || |   || ||  || | |||   ||||||||   || |  || || ||||| |        |||      |||   | | ||| | ||||| || ||  ||||  |||| || ||||| || || || ||  | ||||| |||||||||||||||||||| || ||||||||||||||     
gttagtaacc---tcactaacaaaaccta--ccatatta---agttctatgagcattgatatttattcaatcaaa---ttggtacatgcagGCTGCAATAATCTCCCTGGGCTTGATAGGGGCTGGTACAAACAATGCCCGAATAGCTGGGATGCTTCGGAACCTCTCAAGTTATTATTACAAAGAAGCAG

upper sequence: AT2G20580.1 (Arabidopsis thaliana), 3'ss of exon 18
lower sequence: LOC_Os06g48640.2 (Oryza sativa), 3'ss of exon 20
gttagcaatcatttcgcttcatagcctgtcccatattatttagctgaatagtattgagagaggactgatctttcttttgactcgtacagTCAGCAATTATATCATTGGGACTGATTGGCGCTGGAACTAATAACGCAAGGATAGCCGGGATGCTTCGGAACCTCTCCAGCTATTATTACAAAGACATGA
||||| || |    |    || | |||   |||||||| ||     |  || |||||        |||||   ||   |   | | ||| | ||||| || ||  ||||  |||| || ||||| || || || ||  | ||||| |||||||||||||||||||| || ||||||||||||||     
gttagtaacctcaccag--caaaaccta--ccatattaatt--tctatgagcattgattttaatttgatcaaact---ggtacatgcagGCTGCAATCATCTCCCTGGGCTTGATAGGGGCTGGTACAAACAATGCCCGTATAGCTGGGATGCTTCGGAACCTCTCAAGTTATTATTACAAAGAAGCAG
















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|86050680|gb|DR346435.1|DR346435
EST:     TGGACACCTTGAGCCGGCTTAGCCATGACACAGATTCGGAAGTTGCCATG                         TCAGCAATTATATCATTGGGACTGA
genomic: TGGACACCTTGAGCCGGCTTAGCCATGACACAGATTCGGAAGTTGCCATGgttagcaatc ... actcgtacagTCAGCAATTATATCATTGGGACTGA
EST: gi|164051982|gb|ES204782.1|ES204782
EST:     TGGACACCTTGAGCCGGCTTAGCCATGACACAGATTCGGAAGTTGCCATG                         TCAGCAATTATATCA
genomic: TGGACACCTTGAGCCGGCTTAGCCATGACACAGATTCGGAAGTTGCCATGgttagcaatc ... actcgtacagTCAGCAATTATATCA
EST: gi|116466338|gb|EG508930.1|EG508930
EST:     CCTTGAGCCGGCTTAGCCATGACACAGATTCGGAAGTTGCCATG                         TCAGCAATTATATCATTGGGACTGATTGGCGCTGGAACTAATAACGCAAGG
genomic: CCTTGAGCCGGCTTAGCCATGACACAGATTCGGAAGTTGCCATGgttagcaatc ... actcgtacagTCAGCAATTATATCATTGGGACTGATTGGCGCTGGAACTAATAACGCAAGG
EST: gi|125290286|gb|EL304371.1|EL304371
EST:     TGGACACCTTGAGCCGGCTTAGCCATGACACAGATTCGGAAGTTGCCATG                         TCAGCAATTATATCATTGGGACTGATTGGCGCTGGAACTAA
genomic: TGGACACCTTGAGCCGGCTTAGCCATGACACAGATTCGGAAGTTGCCATGgttagcaatc ... actcgtacagTCAGCAATTATATCATTGGGACTGATTGGCGCTGGAACTAA
EST: gi|86050679|gb|DR346434.1|DR346434
EST:     TGGACACCTTGAGCCGGCTTAGCCATGACACAGATTCGGAAGTTGCCATG                         TCAGCAATTATATCATTGGGACTGATTGGCGCTGGAACTAATAACGCAAGG
genomic: TGGACACCTTGAGCCGGCTTAGCCATGACACAGATTCGGAAGTTGCCATGgttagcaatc ... actcgtacagTCAGCAATTATATCATTGGGACTGATTGGCGCTGGAACTAATAACGCAAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attatttagctgaatagtattgagagaggactgatctttcttttgactcgtacagTCAGCAATTATATCATTGGGACTGATTGGCGCTGGAACTAATAACGCAAGGATAGCCGGGATGCTTCGGAACCTCTCCAGCTATTATTACAAAGACATGA
                                        ttttgac  putative branch site (score: 3)
                                  tctttcttttgactc  CT-rich tract
            aatagtatt  TA-rich tract