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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtagtagtctaaattgaaatatttttgttttgtggttgttcttgatggaaaaggtttgatcttgttttgttagtattgatgttaggattcatactctagtctctggatttgatttgttgatacgtatatatttgcagTCTCTGGGGAGGCTCTGTGATCAATTTAGGGACTAAGAAGCATAGAGACAAGTATTTTGATGGCATTGACAATCTTGATTACACCGGTTGCTTTGCCATG

Basic information

species Arabidopsis thaliana
transcript AT5G65110.2
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G65110.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G445791_T01 (Zea mays), 3'ss of exon 1
gttagtagtagtctaaattgaaatatttttgttttgtggttgttcttgatggaaaaggtttg-atcttgttttgttagtattgatgttaggattcatactctagtctctggatttgatttgttgatacgtatatatt--tgcagTCTCTGGGGAGGCTCTGTGATCAATTTAGGGACTAAGAAGCATAGAGACAAGTATTTTGATGGCATTGACAATCTTGATTACACCGGTTGCTTTGCCATG
                                        ||| |||   |   ||  |||| | |  | | ||| | | |  || |   |||  |     ||||||||    | |  ||     ||| |   |  |  |||||||||||||| || ||||| || ||| |||| || || ||||| ||||| ||||| |||||||| ||||||||| | |||||  | |              
----------------------------------------tgtccttctggattaaattttgtagccagctatgt-actctctatct---gatagaagtcttagtctctcatatagtattaactttacctccttgctaatgcagTCTCTGGGGTGGTTCTGTCATAAATCTAGGAACCAAAAAGCACAGAGATAAGTACTTTGATGGAATTGACAATTTGGATTATCCAG--------------

upper sequence: AT5G65110.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G099666_T01 (Zea mays), 3'ss of exon 1
gttagtagtagtctaaattgaaatatttttgttttgtggttgttcttgatggaaaaggtttg-atcttgttttgttagtattgatgttaggattcatactctagtctctggatttgatttgttgatacgtatatatt--tgcagTCTCTGGGGAGGCTCTGTGATCAATTTAGGGACTAAGAAGCATAGAGACAAGTATTTTGATGGCATTGACAATCTTGATTACACCGGTTGCTTTGCCATG
                                        ||| |||   |   ||  |||| | |  | | ||| | | |  || |   |||        ||||||||    | |   |     ||| |   |  |  |||||||||||||| || ||||| || ||| |||| || || ||||| ||||| ||||| |||||||| ||||||||| | |||||  | || || || || |||
----------------------------------------tgtccttctagattaaattttgtagccagctatgt-actctctatct---gatagcagtcttagtctctcatatagtactaactttacctccttgctaatgcagTCTCTGGGGTGGTTCTGTCATAAATCTAGGAACCAAAAAGCACAGAGATAAGTACTTTGATGGAATTGACAATTTGGATTATCCAGGCTGTTTCGCAATG

upper sequence: AT5G65110.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G045376_T01 (Zea mays), 3'ss of exon 1
gttagtagtagtctaaattgaaatatttttgttttgtggttgttcttgatggaaaaggtttg-atcttgttttgttagtattgatgttaggattcatactctagtctctggatttgatttgttgatacgtatatatt--tgcagTCTCTGGGGAGGCTCTGTGATCAATTTAGGGACTAAGAAGCATAGAGACAAGTATTTTGATGGCATTGACAATCTTGATTACACCGGTTGCTTTGCCATG
                                        ||| |||   |   ||  |||| | |  | | ||| | | |  || |   |||  |     ||||||||    | |  ||     ||| |   |  |  |||||||||||||| || ||||| || ||| |||| || || ||||| ||||| ||||| |||||||| ||||||||| | |||||  | || || ||||| |||
----------------------------------------tgtccttctggattaaattttgtagccagctatgt-actctctatct---gatagaagtcttagtctctcatatagtattaactttacctccttgctaatgcagTCTCTGGGGTGGTTCTGTCATAAATCTAGGAACCAAAAAGCACAGAGATAAGTACTTTGATGGAATTGACAATTTGGATTATCCAGGCTGTTTTGCAATG

upper sequence: AT5G65110.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G419782_T02 (Zea mays), 3'ss of exon 1
gttagtagtagtctaaattgaaatatttttgttttgtggttgttcttgatggaaaaggtttg-atcttgttttgttagtattgatgttaggattcatactctagtctctggatttgatttgttgatacgtatatatt--tgcagTCTCTGGGGAGGCTCTGTGATCAATTTAGGGACTAAGAAGCATAGAGACAAGTATTTTGATGGCATTGACAATCTTGATTACACCGGTTGCTTTGCCATG
                                        ||| |||   |   ||  |||| | |  | | ||| | | |  || |   |||  |     ||||||||    | |  ||     ||| |   |  |  |||||||||||||| || ||||| || ||| |||| || || ||||| ||||| ||||| |||||||| ||||||||| | |||||  | ||||| ||||| |||
----------------------------------------tgtccttctggattaaattttgtagccagctatgt-actctctatct---gatagaagtcttagtctctcatatagtattaactttacctccttgctaatgcagTCTCTGGGGTGGTTCTGTCATAAATCTAGGAACCAAAAAGCACAGAGATAAGTACTTTGATGGAATTGACAATTTGGATTATCCAGGTTGTTTTGCAATG

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|116424484|gb|EG467076.1|EG467076
EST:     GTTGGAAGTGTTGATATGTCCCTTGGGATTAAGATGGGCGTTCAATACAG                         TCTCTGGGGAGGCTCTGTGATCAATTTAGGGACTAAGAAGCATAGAGACAA
genomic: GTTGGAAGTGTTGATATGTCCCTTGGGATTAAGATGGGCGTTCAATACAGgttagtagta ... atatttgcagTCTCTGGGGAGGCTCTGTGATCAATTTAGGGACTAAGAAGCATAGAGACAA
EST: gi|116403249|gb|EG445841.1|EG445841
EST:     GTTGGAAGTGTTGATATGTCCCTTGGGATTAAGATGGGCGTTCAATACAG                         TCTCTGGGGAGGCTCTGTGATCAATTTAGGGACTAAGAAGCATAGAGACAA
genomic: GTTGGAAGTGTTGATATGTCCCTTGGGATTAAGATGGGCGTTCAATACAGgttagtagta ... atatttgcagTCTCTGGGGAGGCTCTGTGATCAATTTAGGGACTAAGAAGCATAGAGACAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taggattcatactctagtctctggatttgatttgttgatacgtatatatttgcagTCTCTGGGGAGGCTCTGTGATCAATTTAGGGACTAAGAAGCATAGAGACAAGTATTTTGATGGCATTGACAATCTTGATTACACCGGTTGCTTTGCCATG
                                tgttgat  putative branch site (score: 4)
                                     atacgtatatattt  TA-rich tract