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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagaatagactactcccttgtgttattcaatatgtatttgatttccttaacgagaaggtattgcgtgcttacagGTTTAAAGTTGTCCAGTGAGTATACACTACCTGAAGAAGTAAGAAAAGCAGGGTTTGAGATTTGTCCTGATGAGTTGGGATCAATTGTAGAAGGTCATGA

Basic information

species Arabidopsis thaliana
transcript AT1G27770.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G27770.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA06G04900.1 (Glycine max), 3'ss of exon 2
gtgagaatagactactcccttgtgttat----tcaatatgta--tttgatttcctta--acgagaaggtattgcgtgcttacagGTTTAAAGTTGTCCAGTGAGTATACACTACCTGAAGAAGTAAGAAAAGCAGGGTTTGAGATTTGTCCTGATGAGTTGGGATCAATTGTAGAAGGTCATGA
|| |||| || | ||   | |||  | |    |   | || |  ||| | ||   ||  |  || | || ||  |  | | ||||| |||| ||||| |||||||| ||  |||| |||||||| | |  |||||| ||||| |||||| |||||||| ||||||||||||| || || | |||
gtaagaa-agtcaacctgcatgtactttaatattgttgtgaagttttcacttttatacaataagcaagtctt-tgctcctccagGTCTAAATTTGTCGAGTGAGTACACTGTACCAGAAGAAGTTAAAGCAGCAGGCTTTGAAATTTGTGCTGATGAGCTGGGATCAATTGTTGAGGGACGTGA

upper sequence: AT1G27770.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA04G04810.1 (Glycine max), 3'ss of exon 2
gtgagaatagactactcccttgtgttattcaat-------atgtatttgatttc-cttaacgagaaggtattgcgtgcttacagGTTTAAAGTTGTCCAGTGAGTATACACTACCTGAAGAAGTAAGAAAAGCAGGGTTTGAGATTTGTCCTGATGAGTTGGGATCAATTGTAGAAGGTCATGA
|| |||| || | ||   | || | | |   ||       | || ||   |||  |  ||  || | || ||  |  | | ||||| |||| ||||| | |||||| ||  |||| |||||||| | ||  ||||| ||||| |||||| |||||||| ||||||||||||| || || | |||
gtaagaa-agtcaacctgcatgagctttgatattattgtgacgttttcacttttacacaataagcaagtctt-tgctcctccagGTCTAAATTTGTCAACTGAGTACACTGTACCAGAAGAAGTTAAAACTGCAGGCTTTGAAATTTGTGCTGATGAGCTGGGATCAATTGTTGAGGGACGTGA

upper sequence: AT1G27770.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv18s0001g09150.t01 (Vitis vinifera), 3'ss of exon 2
gtgagaatagactactcccttgtgttattcaa----tatg-tatttgatttccttaacgagaaggtattgcgtgcttacagGTTTAAAGTTGTCCAGTGAGTATACACTACCTGAAGAAGTAAGAAAAGCAGGGTTTGAGATTTGTCCTGATGAGTTGGGATCAATTGTAGAAGGTCATGA------
|| |||| |  || |   ||| |   | ||||    | || || |    |           |  | ||| |      |    || |   ||||||||||| ||      |||||| ||||||| |   ||||| ||| | |||||| |||||||||||||||||||||| ||||| |||||      
gtaagaacat-cttcagtcttctccaactcaaaggttctgatagtgaggtgtgccttttttattggatttcccttcaatgccttcagGTTTGTCCAGTGACTACGTTGCACCTGAGGAAGTAACAGCTGCAGGTTTTCAAATTTGTGCTGATGAGTTGGGATCAATTGTGGAAGGCCATGACTTAAA

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|116441410|gb|EG484002.1|EG484002
EST:     ATTTCGAGTGGCGGTCTTAGTTTCACAAGCTGCACTTCAGTTCATTAATA                         GTTTAAAGTTGTCCAGTGAGTATACACTACCTGAAGAAGTAAGAAAAGCAG
genomic: ATTTCGAGTGGCGGTCTTAGTTTCACAAGCTGCACTTCAGTTCATTAATAgtgagaatag ... gtgcttacagGTTTAAAGTTGTCCAGTGAGTATACACTACCTGAAGAAGTAAGAAAAGCAG
EST: gi|116432621|gb|EG475213.1|EG475213
EST:     ATTTCGAGTGGCGGTCTTAGTTTCACAAGCTGCACTTCAGTTCATTAATA                         GTTTAAAGTTGTCCAGTGAGTATACACTACCTGAAGAAGTAAGAAAAGCAG
genomic: ATTTCGAGTGGCGGTCTTAGTTTCACAAGCTGCACTTCAGTTCATTAATAgtgagaatag ... gtgcttacagGTTTAAAGTTGTCCAGTGAGTATACACTACCTGAAGAAGTAAGAAAAGCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgttattcaatatgtatttgatttccttaacgagaaggtattgcgtgcttacagGTTTAAAGTTGTCCAGTGAGTATACACTACCTGAAGAAGTAAGAAAAGCAGGGTTTGAGATTTGTCCTGATGAGTTGGGATCAATTGTAGAAGGTCATGA
                         ccttaac  putative branch site (score: 3)
         aatatgtatttgattt  TA-rich tract