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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgatttttttgaccctttgagttttaacttattgtatttttttatgtctgttatagacttgaattggctcacaggcctgtctttcattttgcactcatttttcatcagGTACGAAATTGTCTGAGGATAGCAGGAAATATGGTTCAGAGAATACATGTACGAATGGTAACGTATTAACACGGGCTGCACTGAACTATGGGCGTGCTCG

Basic information

species Arabidopsis thaliana
transcript AT4G34660.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G34660.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA12G04210.1 (Glycine max), 3'ss of exon 3
gtgatttttttgaccctttgagttttaacttattgtatttttttat--gtctgttatagacttgaattggctcacaggcctgtctttcattttgcactcatttttcatcagGTACGAAATTGTCTGAGGATAGCAGGAAATATGGTTCAGAGAATACATGTACGAATGGTAACGTATTAACACGGGCTGCACTGAACTATGGGCGTGCTCG
                    | | ||   ||||     || | |||  || ||||  |||    |||    | |  |   | |  |  |   |   || ||||   | |||| || || ||||| || |||||||||||||||||| |||| ||||||||||| |  |||||   | |  |  | |||||||| |  | || ||| || | 
--------------gtaagtaatattggtttataaagcttctatataagtttgttgcaga---aaatgttattattgaattcttctataccattatcttattt---aacagGAACAAAGTTGTCAGAAGATAGCAGGAAATATGGTGCAGAAAATACATGTACCAGCGGTAATACACTGTCTAGAGCTGCACTAAGTTTTGCGCGAGCCCA

upper sequence: AT4G34660.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA06G01120.2 (Glycine max), 3'ss of exon 3
gtgatttttttgaccctttgagttttaacttattgtatttttttatgtctgttatagacttga-attggctca---caggcctgtctttcattttgcactcatttttcatcagGTACGAAATTGTCTGAGGATAGCAGGAAATATGGTTCAGAGAATACATGTACGAATGGTAACGTATTAACACGGGCTGCACTGAACTATGGGCGTGCTCG
             ||| |  | |    | ||  |  ||   |||     |  | ||  ||| | |  |||||    |||   |||  || | ||  ||  | || || | |||| || || || || || |||||||||||||||||| |||| ||||||||||| | |||||     ||| || | ||||| || || ||||  ||||| ||
------------ccccctgtaatagagattttctccatgagtttgatcttagtttaatcttaataccggctcttatcagtattgttattgaattgccatac-ttgtttaacagGAACAAAGTTATCAGAAGATAGCAGGAAATATGGTGCAGATAATACATGTACCAGTGGTAGTACTTTATCAAGAGCTGCGCTAAATTATGCACGTGCCCG

upper sequence: AT4G34660.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA11G11950.3 (Glycine max), 3'ss of exon 3
gtgatttttttgaccctttgagttttaacttattgtatttttttatgtctgttatagacttgaattggctcacaggcctgtctttca--ttttgcactcatttttcatcagGTACGAAATTGTCTGAGGATAGCAGGAAATATGGTTCAGAGAATACATGTACGAATGGTAACGTATTAACACGGGCTGCACTGAACTATGGGCGTGCTCG
                                  |||   || |    ||  |||| |  |   ||| |  | |   || |  || |  |  |  |    || || | |||| || || ||||| || || ||||||||||||||| |||| ||||||||||| | ||||||   | |  |  | |||||||| |  | || ||  || | 
----------------------------------gtaaggttatgaagcttctatataactttgttg-cagaaaacactattattgaactcctctatatcttatttaacagGAACAAAGTTGTCAGAAGACAGCAGGAAATATGGTGCAGAAAATACATGTACCAGTGGTAATACACTGTCGAGAGCTGCACTAAGTTTTGCGCAAGCCCA

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|47831064|gb|CK120748.1|CK120748
EST:     TCGTGGTGTGGAAGGTTATATAGTTACAGGGTCAAAACAAGTTGAAATAG                         GTACGAAATTGTCTGAGGATAGCAGGAAATATGGTTCAGAGAATACATGTA
genomic: TCGTGGTGTGGAAGGTTATATAGTTACAGGGTCAAAACAAGTTGAAATAGgtgatttttt ... ttttcatcagGTACGAAATTGTCTGAGGATAGCAGGAAATATGGTTCAGAGAATACATGTA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagacttgaattggctcacaggcctgtctttcattttgcactcatttttcatcagGTACGAAATTGTCTGAGGATAGCAGGAAATATGGTTCAGAGAATACATGTACGAATGGTAACGTATTAACACGGGCTGCACTGAACTATGGGCGTGCTCG
            ggctcac  putative branch site (score: 3)
                                        ctcatttttc  putative PPT
                            tttcatttt  TA-rich tract