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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtctaattggcttaattggttggtttgagggtttaatagagaatgcaattgtttgttttgtcgaaatgtctaatggctggattaaagatgtaatgtgttattgtcttttctgcagAGTTAGCTGCTTCAGTACCTCGCACTGACGTAGTAGGAAAGAGTGAGTATTTCCGTTTTGGTATGAGGGATTCTCTTGCGATTGAGGCGTCTTTCTTGCA

Basic information

species Arabidopsis thaliana
transcript AT1G31480.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G31480.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA09G36920.1 (Glycine max), 3'ss of exon 1
gtgagtctaattggcttaattggttggtttgagggtttaatagagaat-gcaattgtttgttttgtcgaaatgtctaatggctggattaaagatgtaatgtgttattgtcttttctgcagAGTTAGCTGCTTCAGTACCTCGCACTGACGTAGTAGGAAAGAGTGAGTATTTCCGTTTTGGTATGAGGGATTCTCTTGCGATTGAGGCGTCTTTCTTGCA
                      ||  ||  |     |   ||| |  |  |||||   | || ||   | || | | ||   | ||||          | |||| |  |   |    ||||||| || || || || || |  || ||  | ||||| |||||||| ||||| |||||||| ||||| |||||||| || ||||| || |||||||||||
----------------------gtaagtacgtctcctagctagggttttacaattacgt-ttctgctaacatttattatttattgattg---------tttgtt-tcatacatctaacagAGTTGGCAGCCTCTGTCCCGCCAACAGAGATTGTAGGCAAGAGTGACTATTTTCGTTTTGGCATGAGAGATTCTCTCGCTATTGAAGCATCTTTCTTGCA
















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|116452414|gb|EG495006.1|EG495006
EST:     TGGGAGTGATGTTCGGTGGTACTTTTGTAAGGTTCCTTTGGCTGAAAATG                         AGTTAGCTGCTTCAGTACCTCGCACTGACGTAGTAGGAAAGAGTGAGTATT
genomic: TGGGAGTGATGTTCGGTGGTACTTTTGTAAGGTTCCTTTGGCTGAAAATGgtgagtctaa ... ttttctgcagAGTTAGCTGCTTCAGTACCTCGCACTGACGTAGTAGGAAAGAGTGAGTATT
EST: gi|116451033|gb|EG493625.1|EG493625
EST:     TGGGAGTGATGTTCGGTGGTACTTTTGTAAGGTTCCTTTGGCTGAAAATG                         AGTTAGCTGCTTCAGTACCTCGCACTGACGTAGTAGGAAAGAGTGAGTATT
genomic: TGGGAGTGATGTTCGGTGGTACTTTTGTAAGGTTCCTTTGGCTGAAAATGgtgagtctaa ... ttttctgcagAGTTAGCTGCTTCAGTACCTCGCACTGACGTAGTAGGAAAGAGTGAGTATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcgaaatgtctaatggctggattaaagatgtaatgtgttattgtcttttctgcagAGTTAGCTGCTTCAGTACCTCGCACTGACGTAGTAGGAAAGAGTGAGTATTTCCGTTTTGGTATGAGGGATTCTCTTGCGATTGAGGCGTCTTTCTTGCA
       gtctaat  putative branch site (score: 3)
                                     ttattgtcttttct  putative PPT
                    attaaagatgtaat  TA-rich tract