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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGGACAGAGCAACCTCCGATCTTAAGAACACCAATGTTAGACTTAAAGATACCGTGAACCAGgtaatttaagtttggaatctatttcttggactctcagccacataggtctgttcttgatacctaatataaaagcattgtcttttgtttacag

Basic information

species Arabidopsis thaliana
transcript AT3G09740.1
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G09740.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: GLYMA13G20220.1 (Glycine max), 5'ss of exon 7
GTGGACAGAGCAACCTCCGATCTTAAGAACACCAATGTTAGACTTAAAGATACCGTGAACCAGgtaatttaagtttggaatctatttct-tggactctcagccacataggtctgttcttgata--cctaatataaaa----gcattgtcttttgtttacag
|||||||  ||| |||| || |||||||| || ||||||||||||||||| || ||||||||||| |  | | |    | ||| | | | |  | |  || | |  ||    | |   |||||    |  |    ||      ||  | ||||   | |||
GTGGACAAGGCATCCTCTGACCTTAAGAATACAAATGTTAGACTTAAAGACACTGTGAACCAGgttagctgactaca-attctgtctgtatacatttccatcaatttaaagttttatctgatagatttcttgctgaatcttatatgatttttttcatccag

upper sequence: AT3G09740.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: GLYMA03G33680.1 (Glycine max), 5'ss of exon 7
GTGGACAGAGCAACCTCCGATCTTAAGAACACCAATGTTAGACTTAAAGATACCGTGAACCAGgtaatttaagtttggaatctatttcttggactctcagccacat--aggtctgttcttgat--acctaatataaaagc----attgtcttttgtttacag-----
|||||||| ||| | || || ||||| || |||||||||||||||| |||||| |||||||||||  ||||  |    | |||   |||| || ||||| | |  |  || |   |   |||   |  | ||||  || |    || || ||||| ||   |     
GTGGACAGGGCATCTTCTGACCTTAAAAATACCAATGTTAGACTTAGAGATACAGTGAACCAGgttttttatctgct-actcttagtcttagattctcatcaattttcagttgcatcagtgacagattttatattgaatcttatatggttttttggttctcgtccag

upper sequence: AT3G09740.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: GLYMA10G05870.1 (Glycine max), 5'ss of exon 8
GTGGACAGAGCAACCTCCGATCTTAAGAACACCAATGTTAGACTTAAAGATACCGTGAACCAGgtaatttaagtttggaatctatttct-tggactctcagccacatagg------tctgttcttgatacctaat--ataaaagcattgtcttttgtttacag
|||||||  ||| |||| || |||||||| || ||||||||||||||||| || ||||||||||| |  | | |    | | ||| | | | || |  || | |  ||        |||||  | |||  ||     |       ||  | ||||   | |||
GTGGACAAGGCATCCTCTGACCTTAAGAATACAAATGTTAGACTTAAAGACACAGTGAACCAGgttagctgactaca-attgtatctgtatagatttccatcaatttaaagttgtatctgtgatagatttcttgctgactcttatatgatttttttcatccag

upper sequence: AT3G09740.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: GLYMA19G36410.1 (Glycine max), 5'ss of exon 7
GTGGACAGAGCAACCTCCGATCTTAAGAACACCAATGTTAGACTTAAAGATACCGTGAACCAGgtaatttaagtttggaatctatttcttggactctcagccacataggtctgttcttgatacctaatataaaagc-----attgtcttttgtttacag----
|||||||| ||| | || || ||||| || |||||||||||||||| ||| || |||||||||||  ||||| |    | |||   |||| || | ||| | |  |     ||     |  ||  | | | | ||      || || |||||||   |     
GTGGACAGGGCATCTTCTGACCTTAAAAATACCAATGTTAGACTTAGAGACACAGTGAACCAGgttttttaactgca-actcttagtcttagattttcatcaatttccagttgcatcagtgacagattttgagagtcttatatggttttttgttctgatccag

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|86081762|gb|DR377521.1|DR377521
EST:     CCTCCGATCTTAAGAACACCAATGTTAGACTTAAAGATACCGTGAACCAG                         CTGAGATCTAGCCGGAACTTCTGTATCGATATTGTTTTGTTGTGTATTGTT
genomic: CCTCCGATCTTAAGAACACCAATGTTAGACTTAAAGATACCGTGAACCAGgtaatttaag ... ttgtttacagCTGAGATCTAGCCGGAACTTCTGTATCGATATTGTTTTGTTGTGTATTGTT
EST: gi|116431994|gb|EG474586.1|EG474586
EST:     CCTCCGATCTTAAGAACACCAATGTTAGACTTAAAGATACCGTGAACCAG                         CTGAGATCTAGCCGGAACTTCTGTATCGATATTGTTTTGTTGTGTATTGTT
genomic: CCTCCGATCTTAAGAACACCAATGTTAGACTTAAAGATACCGTGAACCAGgtaatttaag ... ttgtttacagCTGAGATCTAGCCGGAACTTCTGTATCGATATTGTTTTGTTGTGTATTGTT
EST: gi|86084593|gb|DR380352.1|DR380352
EST:     CCTCCGATCTTAAGAACACCAATGTTAGACTTAAAGATACCGTGAACCAG                         CTGAGATCTAGCCGGAACTTCTGTATCSMTATTGTYYTGTTGTGTATTGTT
genomic: CCTCCGATCTTAAGAACACCAATGTTAGACTTAAAGATACCGTGAACCAGgtaatttaag ... ttgtttacagCTGAGATCTAGCCGGAACTTCTGTATCGATATTGTTTTGTTGTGTATTGTT
EST: gi|125279763|gb|EL293848.1|EL293848
EST:     CCAATGTTAGACTTAAAGATACCGTGAACCAG                         CTGAGATCTAGCCGGAACTTCTGTATCGATATTGTTTTGTTGTGTATTGTT
genomic: CCAATGTTAGACTTAAAGATACCGTGAACCAGgtaatttaag ... ttgtttacagCTGAGATCTAGCCGGAACTTCTGTATCGATATTGTTTTGTTGTGTATTGTT
EST: gi|116435937|gb|EG478529.1|EG478529
EST:     CCTCCGATCTTAAGAACACCAATGTTAGACTTAAAGATACCGTGAACCAG                         CTGAGATCTAGCCGGAACTTCTGTATCGATATTGTTTTGTTGTGTATTGTT
genomic: CCTCCGATCTTAAGAACACCAATGTTAGACTTAAAGATACCGTGAACCAGgtaatttaag ... ttgtttacagCTGAGATCTAGCCGGAACTTCTGTATCGATATTGTTTTGTTGTGTATTGTT
EST: gi|124982167|gb|EL054992.1|EL054992
EST:     CCTCCGATCTTAAGAACACCAATGTTAGACTTAAAGATACCGTGAACCAG                         CTGAGATCTAGCCGGAACTTCTGTATCG
genomic: CCTCCGATCTTAAGAACACCAATGTTAGACTTAAAGATACCGTGAACCAGgtaatttaag ... ttgtttacagCTGAGATCTAGCCGGAACTTCTGTATCG
EST: gi|125284447|gb|EL298532.1|EL298532
EST:     CCTCCGATCTTAAGAACACCAATGTTAGACTTAAAGATACCGTGAACCAG                         CTGAGATCTAGCCGGAACT
genomic: CCTCCGATCTTAAGAACACCAATGTTAGACTTAAAGATACCGTGAACCAGgtaatttaag ... ttgtttacagCTGAGATCTAGCCGGAACT
EST: gi|125253861|gb|EL267946.1|EL267946
EST:     TTAAGAACACCAATGTTAGACTTAAAGATACCGTGAACCAG                         CTGAGATCTAGCCGGAACTTCTGTATCGATATTGTTTTGTTGTGTATCGTT
genomic: TTAAGAACACCAATGTTAGACTTAAAGATACCGTGAACCAGgtaatttaag ... ttgtttacagCTGAGATCTAGCCGGAACTTCTGTATCGATATTGTTTTGTTGTGTATTGTT

Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGGACAGAGCAACCTCCGATCTTAAGAACACCAATGTTAGACTTAAAGATACCGTGAACCAGgtaatttaagtttggaatctatttcttggactctcagccacataggtctgttcttgatacctaatataaaagcattgtcttttgtttacag

- - - - - - - - - - - - AAGAAC