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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaactatttcctacatttgaaccttttttaatcttttttgtagtttttgcttcataatatttgtaaatgcatgccagattgataatccgctgggttttcttcaaacatttttgataagtttctgttaatggtgacagATTTGCAGGGCGCTTGCTTACATCCATAATTCCTTTGGTCTTTGTCACCGTGATATCAAGCCTCAAAACCTGCTG

Basic information

species Arabidopsis thaliana
transcript AT1G09840.2
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G09840.6 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA12G28730.2 (Glycine max), 3'ss of exon 5
gtaactatttcctacatttgaaccttttttaatcttttttgtagtttttgcttcataatatttgtaaatgcatgccagattgataatccgctgggttttcttcaaacatttttgataagtttctgttaatggtgacagATTTGCAGGGCGCTTGCTTACATCCATAATTCCTTTGGTCTTTGTCACCGTGATATCAAGCCTCAAAACCTGCTG
                              ||      |      || ||     || |  || ||||| | |   | |||  |  | |  ||  | ||  |    | | |||      | |||| |  |||   |||||||||||||| |||||||| || ||||| | | ||||| | ||||| ||||| ||||| ||||| ||||| || 
-----------------------------gaaggaaagtaaggtattgtgtgatttactcattttaaatccctatta-atttcttgttcattgattatttattt--cttcttt------tctctgattttggctgcagATTTGCAGGGCCCTTGCTTATATACATAACTGCATTGGTATATGTCATCGTGACATCAAACCTCAGAACCTACTT

upper sequence: AT1G09840.6 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA16G00400.1 (Glycine max), 3'ss of exon 4
gtaactatttcctacatttgaaccttttttaatcttttttgtagtttttgcttcataatatttgtaaatgcatgccagattgataatccgctgggttttcttcaaacatttttgataagtttctgttaatggtgacagATTTGCAGGGCGCTTGCTTACATCCATAATTCCTTTGGTCTTTGTCACCGTGATATCAAGCCTCAAAACCTGCTG
                    ||       |||  | || |||  |||   |        |||| ||||| | |   | |||  || |||  ||  | ||  |    | | |||      |||||| |  |||   |||||||||||||| |||||||| || ||||| | | ||||| | ||||| ||||| ||||| ||||| ||||| || 
--------------------aaaggaaagtaaagtattgtgtgatttacac--------attt-taaatccctatta-atttctagtccattgattatttattt--cttcttt------tttctgattttggctgcagATTTGCAGGGCCCTTGCTTATATACATAACTGCATTGGTATATGTCATCGTGACATCAAACCTCAGAACCTACTT

upper sequence: AT1G09840.6 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv12s0035g01060.t01 (Vitis vinifera), 3'ss of exon 4
gtaactatttcctacatttgaaccttttttaatcttttttgtagtttttgcttcataatatttgtaaatgcatgccaga-ttgataatccgctgggttttcttcaaacatttttgataagtttctgttaatggtgacagATTTGCAGGGCGCTTGCTTACATCCATAATTCCTTTGGTCTTTGTCACCGTGATATCAAGCCTCAAAACCTGCTG
                              ||     | ||||| || |  || || |   |      |   | |  || ||||||||          ||  |||  ||||  | || | | |||     ||||   |||| ||||| |||||||| || || ||||||| | ||||| ||||||||||||| ||||||||||| ||| | || 
------------------------------aaaaacatatgtagcttat--tttatcactgtaagggttatgtactggagttgataattga-------tttatcatgcattactaattattctcttactctggttgtagATCTGCAGAGCGCTTGCGTATATACATAATTGCATTGGTATTTGTCACCGTGACATCAAGCCTCAGAACTTACTT

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|125259881|gb|EL273966.1|EL273966
EST:     ATTGATATATGTTAAACTCTACACCTATTCAG                         ATTTGCAGGGCGCTTGCTTACATCCATAATTCCTTTGGTCTTTGTCACCG
genomic: ATTGATATATGTTAAACTCTACACCTA-TCAGgtaactattt ... atggtgacagATTTGCAGGGCGCTTGCTTACATCCATAATTCCTTTGGTCTTTGTCACCG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taatccgctgggttttcttcaaacatttttgataagtttctgttaatggtgacagATTTGCAGGGCGCTTGCTTACATCCATAATTCCTTTGGTCTTTGTCACCGTGATATCAAGCCTCAAAACCTGCTG
                                        tgttaat  putative branch site (score: 3)
                    aaacatttttgataa  TA-rich tract