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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgttttgttctttgatttcattatatcacctcaaagattgttgattttagcttactgaatcttagattttgtttgtttttggaagGTATCAAGAAATTTTAACTGATCCTAGTTATGCTGGGCAGTTTGTGCTAATGACAAACCCACAAATTGGTAATACTGGTGTCAATCCTG

Basic information

species Arabidopsis thaliana
transcript AT3G27740.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G27740.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os02g47850.3 (Oryza sativa), 3'ss of exon 3
------------------------------------------------------gtatgttttgttctt--tgatttcattatatc--acctcaa-agattgttgattttagcttactgaatctta-------gattttgtttgtttt------tgga----agGTATCAAGAAATTTTAACTGATCCTAGTTATGCTGGGCAGTTTGTGCTAATGACAAACCCACAAATTGGTAATACTGGTGTCAATCCTG
                                                      ||   | ||||||||  ||||      | | |  ||||||  | || |||||     || |||||  | ||        ||      |    |       |||     ||||||||||| ||||| |||||||| || |||||||| || ||||| || ||||| |||||||| ||||| || |||||||| |||||||
gtaaatcaactaaccgtttgagtgatggcatttgtttcctgttgtggttgagatgtgcttattgttcttcctgatagagaaacaactaacctcatcaaatagttgagacgcgcgtactgcttattgacaacaggaaacaactaacctcatcaaatgggctgcagGTATCAAGAGATTTTGACTGATCCAAGCTATGCTGGTCAATTTGTCCTCATGACCAACCCACATATTGGAAACACTGGTGTTAATCCTG

upper sequence: AT3G27740.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G029573_T01 (Zea mays), 3'ss of exon 3
-----gtatgttttgttc-----tttgatttcattatatcacctcaaagatt---gttgattttagcttactgaatcttagattttgtttgtttttggaagGTATCAAGAAATTTTAACTGATCCTAGTTATGCTGGGCAGTTTGTGCTAATGACAAACCCACAAATTGGTAATACTGGTGTCAATCCTG
       |||  ||||        ||   || || ||    |  || |  |    || |   | ||  |  | | |   |       |||||  ||| | | ||||| || ||||| || ||||| ||||||||||| |||||||| |||||||| || || || ||||| || ||||| || |||||||
attgaacatgacttgtcgatgcagttatgttgatgattatgcaccataattctaggtaggactaagaattgttacttacatggcacatttgtggttgca-gCTATCAGGAGATTTTGACCGATCCAAGTTATGCTGGTCAGTTTGTCCTAATGACCAATCCTCATATTGGGAACACTGGCGTTAATCCTG

upper sequence: AT3G27740.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA04G39390.1 (Glycine max), 3'ss of exon 2
------------------gtatgttttgttctttgatttcattatatcacctcaaagattgttgatt--ttagcttactgaatcttagattttgtttgtttttggaagGTATCAAGAAATTTTAACTGATCCTAGTTATGCTGGGCAGTTTGTGCTAATGACAAACCCACAAATTGGTAATACTGGTGTCAATCCTG
                   |  | | |||  ||   ||||||    |  | |  | | |   |   |   | | || ||   | ||   || ||| |||  ||   ||||||||||||||||| |||||||||||||||||||| ||||||||||| |||||||||||||| ||||| ||||||||  | |||  ||
gtgaggaaactatgaatcttgggatgtgtgtttctttttcatggctttgcttgcatgctgaatatgtggctggttttctt--tgttgtgttgtgtgtgtgattatcagGTATCAAGAAATTTTGACTGATCCTAGTTATGCTGGCCAGTTTGTGCTCATGACAAACCCACATATTGGGAATACTGGCATAAATTTTG

upper sequence: AT3G27740.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA05G32190.1 (Glycine max), 3'ss of exon 2
---------gtatgttttgttctttgat-----ttcattatatcacctcaaagat-tgttgattttagcttactgaatcttagattttgtttgtttttggaagGTATCAAGAAATTTTAACTGATCCTAGTTATGCTGGGCAGTTTGTGCTAATGACAAACCCACAAATTGGTAATACTGGTGTCAATCCTG
               ||| |   |  |      ||||||  |||    ||  ||| |   ||| ||   ||  ||  | ||  ||  | | ||||    | ||||||||||||||| |||| ||||||||||||||||| |||||||| || |||||||| ||||| |||||||| |||||||| |||  ||
gtgagatgaactaactttatatataaaccggcattcattcaatctgagcatggatataccgatgtttcatt--tgtttatttaataatatctgttaactgcagGTATCAAGAAATTCTAACAGATCCTAGTTATGCTGGTCAGTTTGTACTGATGACAAATCCACATATTGGTAACACTGGTGTAAATTTTG

upper sequence: AT3G27740.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA06G15510.3 (Glycine max), 3'ss of exon 2
-------------------------gtatgttttgttctttgatttcattatatcacctcaaagattgttgattttagcttactgaatcttagattttgtttgtttttggaagGTATCAAGAAATTTTAACTGATCCTAGTTATGCTGGGCAGTTTGTGCTAATGACAAACCCACAAATTGGTAATACTGGTGTCAATCCTG
                         |  |||| | || || | |||  ||  ||  |   |    | |||| ||||  |||      | ||   || ||| |||  ||   ||||||||||||||||| || ||||||||||||||||| ||||||||||| |||||||| ||||| ||||| || |||||  | |||  ||
gtgaggatactatgaatcttgggatgcgtgttctttttttggttttgcttgcat-gctaaatgagtggttggtttt--ctt------tgttgtgttgtgtgtgtgattctcagGTATCAAGAAATTTTGACAGATCCTAGTTATGCTGGCCAGTTTGTGCTCATGACAAATCCACATATTGGGAACACTGGCATAAATTTTG

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|125211314|gb|EL226268.1|EL226268
EST:     ATTGGTGTTTAACACTTCCTTGACAGG                         GTATCAAGAAATTTTAACTGATCCTAGTTATGCTGGGCAGTTTGTGCTAAT
genomic: ATTGGTGTTTAACACTTCCTTGACAGGgtatgttttg ... tttttggaagGTATCAAGAAATTTTAACTGATCCTAGTTATGCTGGGCAGTTTGTGCTAAT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcaaagattgttgattttagcttactgaatcttagattttgtttgtttttggaagGTATCAAGAAATTTTAACTGATCCTAGTTATGCTGGGCAGTTTGTGCTAATGACAAACCCACAAATTGGTAATACTGGTGTCAATCCTG
                  agcttac  putative branch site (score: 3)
                                    ttttgtttgttttt  putative PPT
                                   attttgtttgttttt  TA-rich tract