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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtttcgtggtttcagtttctgctcttttatttaaatatccttgtctcgtgaagattgtgtttcatgaaaattttctgaactattctacagGTTAGACTTGTTAGAGTCACCAAAAGAGTTCACGAGGCATATTTTGCCCAGTTATTCCTTTCAAAG

Basic information

species Arabidopsis thaliana
transcript AT1G75380.2
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G75380.3 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA1784S00200.1 (Glycine max), 3'ss of exon 4
----------------gtatgtttcgtggtttcagtttctgctcttttatttaaatatcctt---gtctcgtga--agattgtgtttcatgaaaattttctgaactattctacagGTTAGACTTGTTAGAGTCACCAAAAGAGTTCACGAGGCATATTTTGCCCAGTTATTCCTTTCAAAG
                 | | |    |   | |   || || | |  |||||    ||| ||   ||  |  ||  | |||  |  |||    |  ||  |  |   ||| |||||| | |||||| ||||| ||||  |||||||| |||||||| |||||||||||             
gtaagattctgtttatctttatactcttactcctaattgtgttgtgatatttttccatcattcaggttccacgatgaaattaagaatcaaatcatgttgtttcatgcttccacagGTCAAACTTGTCAGAGTAACCAGGAGAGTTCATGAGGCATACTTTGCCCAGTT-------------

upper sequence: AT1G75380.3 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv18s0001g12960.t01 (Vitis vinifera), 3'ss of exon 6
gtatgtttcgtggtttcagtttctgctcttttatttaaatatccttgtctcgtgaagattgtgtttcatgaaaat--tttctgaa--ctattctacagGTTAGACTTGTTAGAGTCACCAAAAGAGTTCACGAGGCATATTTTGCCCAGTTATTCCTTTCAAAG
||| ||||    | ||    |||| | |  |    | |  ||| | || |    |    | | ||| |||| | |   |||  ||  || |||| ||||| |  |||||| |||||||||| || || ||||||||||||||||| ||||||| |||  |||||
gtaagtttga--gcttg---ttctaccccctgccctcatgatcatggtttta-aatttctctttttgatgacattgacttcaaaatcctcttctgcagGTGAAGCTTGTTCGAGTCACCAAGAGGGTACACGAGGCATATTTTGCTCAGTTATACCTCACAAAG
















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|124775721|gb|EH865850.1|EH865850
EST:     ATCAAGTGGTGAAGGAAATGGTGGACAAGATGGGTTACGAA                         GTTAGACTTGTTAGAGTCACCAAAAGAGTTCACGAGGCATATTTTGCCCAG
genomic: ATCAAGTGGTGAAGGAAATGGTGGACAAGATGGGTTACGAAgtatgtttcg ... tattctacagGTTAGACTTGTTAGAGTCACCAAAAGAGTTCACGAGGCATATTTTGCCCAG
EST: gi|124996261|gb|EL068530.1|EL068530
EST:     CCATGTATCAAGTGGTGAAGGAAATGGTGGACAAGATGGGTTACGAA                         GTTAGACTTGTTAGAGTCACCAAAAGAGTTCACGAGGCATATTTTGCCCAG
genomic: CCATGTATCAAGTGGTGAAGGAAATGGTGGACAAGATGGGTTACGAAgtatgtttcg ... tattctacagGTTAGACTTGTTAGAGTCACCAAAAGAGTTCACGAGGCATATTTTGCCCAG
EST: gi|125046952|gb|EL119221.1|EL119221
EST:     ACCATGTATCAAGTGGTGAAGGAAATGGTGGAACAAAGATGGGTTACGAA                         GTTAGACTTGTTAGAGTCACC
genomic: ACCATGTATCAAGTGGTGAAGGAAATGGTGGA-CAA-GATGGGTTACGAAgtatgtttcg ... tattctacagGTTAGACTTGTTAGAGTCACC
EST: gi|124864013|gb|EH948450.1|EH948450
EST:     CAACCATGTATCAAGTGGTGAAGGAAATGGTGGACAAGATGGGTTACGAA                         GTTAGACTTGTTAGAGTCACCAAAAGAGTTCACGAGGCATATTT
genomic: CAACCATGTATCAAGTGGTGAAGGAAATGGTGGACAAGATGGGTTACGAAgtatgtttcg ... tattctacagGTTAGACTTGTTAGAGTCACCAAAAGAGTTCACGAGGCATATTT
EST: gi|124955850|gb|EL030827.1|EL030827
EST:     GGTGGACAAGATGGGTTACGAA                         GTTAGACTTGTTAGAGTCACCAAAAGAGTTCACGAGGCATATTTTGCCCAG
genomic: GGTGGACAAGATGGGTTACGAAgtatgtttcg ... tattctacagGTTAGACTTGTTAGAGTCACCAAAAGAGTTCACGAGGCATATTTTGCCCAG
EST: gi|47829045|gb|CK118729.1|CK118729
EST:     CAACCATGTATCAAGTGGTGAAGGAAATGGTGGACAAGATGGGTTACGAA                         GTTAGACTTGTTAGAGTCACCAAAAGAGTTCACGAGGCATATTTTGCCCAG
genomic: CAACCATGTATCAAGTGGTGAAGGAAATGGTGGACAAGATGGGTTACGAAgtatgtttcg ... tattctacagGTTAGACTTGTTAGAGTCACCAAAAGAGTTCACGAGGCATATTTTGCCCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatccttgtctcgtgaagattgtgtttcatgaaaattttctgaactattctacagGTTAGACTTGTTAGAGTCACCAAAAGAGTTCACGAGGCATATTTTGCCCAGTTATTCCTTTCAAAG
                                            ctattct  CT-rich tract
                        tttcatgaaaatttt  TA-rich tract