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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agtaatgtttgttcaaaagacataattcagcgaaataatccgccaaacactccttatattacagtgttgtgctgctgtttataatgttattctttgtcagGTGTTGGAAACAAATAGAGCTGAGCAATCTCAGAGTCATGTGCATAGAATGTATTTTATGGGTCCTAATACATTCAGTGAACCGTGGCATCTCTCACACA

Basic information

species Arabidopsis thaliana
transcript AT5G11700.1
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G11700.1 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: LOC_Os05g09360.1 (Oryza sativa), 3'ss of exon 12
agtaatgtttgttcaaaagacataattcagcgaaataatccgccaaacactccttatattacagtgttgtgctgctgtttataatgttattctt-tgtcagGTGTTGGAAACAAATAGAGCTGAGCAATCTCAGAGTCATGTGCATAGAATGTATTTTATGGGTCCTAATACATTCAGTGAACCGTGGCATCTCTCACACA
            |   |  ||||  | ||     |   |    |    |    |  | | |  ||  ||   |   ||| | |    |  || | ||  ||||  ||||||| ||||| || ||  |||||||  |||||||||| || |||||||| |||||||| || || ||||||||||| ||||||||  ||||||
-----------gtagcagaacattctgcattcctaatttgtttctttaagctgtggtgtgattgttctggtttttcgttgaaatctctcctcatgtggtagGTACTGGAAACCAATAGGGCCGAAGAATCTCACTGTCATGTGCACAGGATGTATTTCATGGGTCCCAACACCTTCAGTGAACCTTGGCATCTACCACACA

upper sequence: AT5G11700.1 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: LOC_Os01g09246.1 (Oryza sativa), 3'ss of exon 14
agtaatgtttgttcaaaagacataattcagcgaaataatccgccaaacact-ccttatattacagtgttgtgctgctgtttataatgttattctttgt--cagGTGTTGGAAACAAATAGAGCTGAGCAATCTCAGAGTCATGTGCATAGAATGTATTTTATGGGTCCTAATACATTCAGTGAACCGTGGCATCTCTCACACA
                      || || |   |     |||| ||     |     |||| ||  |  || | |    |  |   | || || |||||  ||||| |||||||| ||||| |||||| |||| ||  | ||||| || || |||||||| ||||| || || || ||||||||||| ||||||||| ||||||
---------------------gtattttatacaccgcttccgtcatgttgtgtgccatatgaccatcatgggttctcatagaagttttttttgtttgttgcagGTCTTGGAAACTAATAGGGCTGAGGAATCGCATGGGCATGTACACAGGATGTATTTCATGGGCCCCAACACCTTCAGTGAACCTTGGCATCTCCCACACA

upper sequence: AT5G11700.1 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: GRMZM2G350818_T02 (Zea mays), 3'ss of exon 7
agtaatgtttgttcaaaagacataattcagcgaaataatccgccaaacactccttatattacagtgttgtgctgctgtttataatgttattctttgtcagGTGTTGGAAACAAATAGAGCTGAGCAATCTCAGAGTCATGTGCATAGAATGTATTTTATGGGTCCTAATACATTCAGTGAACCGTGGCATCTCTCACACA
 || |  |   |||    |   | ||||  |  ||||| |||        || ||    |  | ||||   |||   ||| |  | || |     | ||||| ||||||||||| || || ||  |||||||  |||||||||| || |||||||| ||||| || || || ||||||||||| ||||||||| ||||||
-gtgaaatccattctgttgtgctgattcc-cttaataagccgtggtgtggtcatt----tctaatgtta--ctgaaatttctgctattgt-----ggcagGTATTGGAAACAAACAGGGCAGAAGAATCTCACTGTCATGTGCACAGGATGTATTTCATGGGCCCAAACACCTTCAGTGAACCTTGGCATCTCCCACACA

upper sequence: AT5G11700.1 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: GRMZM2G412234_T01 (Zea mays), 3'ss of exon 4
agtaatgtttgttcaaaagacataattcagcgaaataatccgccaaacactccttatattacagtgttgtgctgctgtttataatgttattctttgtcagGTGTTGGAAACAAATAGAGCTGAGCAATCTCAGAGTCATGTGCATAGAATGTATTTTATGGGTCCTAATACATTCAGTGAACCGTGGCATCTCTCACACA
          || |   | || |  |      | ||||       ||  |     |  |  |||  ||      ||| | | ||  | ||  ||   |||||  | ||||| ||||| |||||  | || ||  ||||||| || || |||||||| |||||||| || || ||||||||||| ||||||||| ||||||
----------gtacttcataccttttctgcatagataacatcttgaatgccatgcacctc-cagaatt------ctgataaaaaaatgataattacacagGTCATTGAAACTAATAGGGCTGAAGAGTCACAAGGTCATGTACACAGGATGTATTTCATGGGTCCCAACACCTTCAGTGAACCTTGGCATCTCCCACACA

upper sequence: AT5G11700.1 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: GLYMA06G09360.1 (Glycine max), 3'ss of exon 14
agtaatgtttgttcaaaagacat--aattcagcgaaataatccgccaaa--cactccttatattacagtgttgtgctgctgttt-----ataatgttattctttgtcagGTGTTGGAAACAAATAGAGCTGAGCAATCTCAGAGTCATGTGCATAGAATGTATTTTATGGGTCCTAATACATTCAGTGAACCGTGGCATCTCTCACACA
        || |||  |     |  |||| ||  |||||  || |  |      |  ||   || || | || |  |  |  |      || |||  || ||   | |||||||||||||||| ||||  ||| | || ||||||||||| || |||||||| |||||||| |||||||| |||||||| || ||||||||  |||| |
--------ttattctgatatttttgaattaagataaatatgccccttattttgtttttttatttgcaatatttttttattaatggcatgatgatgacatgctgcat-agGTGTTGGAAACAAACAGAGTCGAGGAGTCCCAGAGTCATGTTCACAGAATGTACTTTATGGGACCTAATACTTTCAGTGAGCCCTGGCATCTGCCACATA

upper sequence: AT5G11700.1 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: GLYMA04G09230.1 (Glycine max), 3'ss of exon 14
----------------------------------------agtaatgtttgttcaaaagacataat-tcagcgaaataatccgccaaacactccttatatt----acagtgttgtgctgctgt--ttataatgttattctttgtcagGTGTTGGAAACAAATAGAGCTGAGCAATCTCAGAGTCATGTGCATAGAATGTATTTTATGGGTCCTAATACATTCAGTGAACCGTGGCATCTCTCACACA
                                          | || |||||  | ||    |||| |   |   |  | | || |     |  || ||||    | | | || |  |  |    | || ||| | |  | ||| |||||||||| ||||| |||| |||| | || ||||||||||| || |||||||| |||||||| |||||||| |||||||| || ||||||||  |||| |
gtttttctcaaatcatgtggttcctcttctgtttctttattctgatatttgtgaataaagattaatatgccccttaacagcagctattttgtttttttatttgcaataattttttattaatagcatgatgatgatgtgttatgt-agGTGTTGGAGACAAACAGAGTTGAGGAGTCCCAGAGTCATGTTCACAGAATGTACTTTATGGGACCTAATACTTTCAGTGAGCCCTGGCATCTGCCACATA

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|86068464|gb|DR364221.1|DR364221
EST:     AGATCATTCGTTCCCTTTCCTGGAATCACTTAATGAG                         GTGTTGGAAACAAATAGAGCTGAGCAATCTCAGAGTCATGTGCATAGAATG
genomic: AGATCATTCGTTCCCTTTCCTGGAATCACTTAATGAGgttagatgat ... tctttgtcagGTGTTGGAAACAAATAGAGCTGAGCAATCTCAGAGTCATGTGCATAGAATG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aacactccttatattacagtgttgtgctgctgtttataatgttattctttgtcagGTGTTGGAAACAAATAGAGCTGAGCAATCTCAGAGTCATGTGCATAGAATGTATTTTATGGGTCCTAATACATTCAGTGAACCGTGGCATCTCTCACACA
                                         ttattcttt  CT-rich tract
                                tttataatgttattct  TA-rich tract