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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagctttttactgactctgcgatatgataagtagagtaatttggaactaaatatccattttaaattgctttgggatttaatatgcatttctatatttcagAAGTAAAGCTTGTGGATGTCCCAGAAATGAACTATACATCAGCGGATCAGCCCCATCCCCGTGGCGAAATATGTGTTAGGGGTCCTATCATTTTTACAGG

Basic information

species Arabidopsis thaliana
transcript AT3G05970.1
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G05970.1 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: LOC_Os11g04980.2 (Oryza sativa), 3'ss of exon 16
gtgagctttttactgactctgcgatatgataagtagagtaatttggaactaaatatccattttaaattgct-ttgggatttaatatgcatttctatatttcagAAGTAAAGCTTGTGGATGTCCCAGAAATGAACTATACATCAGCGGATCAGCCCCATCCCCGTGGCGAAATATGTGTTAGGGGTCCTATCATTTTTACAGG
 | | |     | | | |||  | | | ||    |    || |      |   | | | |  ||     || |    || |||      || | || |||||||  | ||||| |||||||||||||||||||| || || || | |||||| ||  |||| ||||| ||||| |||||||||||  |||  || |||   ||
-ttaaccccaaa-taagtcta-ggtttcatcttcaactaaaatattgtttttttttgcgtgctatcacactctcataatgtaaatcctgttgccatttttcagAGATTAAGCTAGTGGATGTCCCAGAAATGAATTACACCTCTGAGGATCAACCATATCCTCGTGGAGAAATTTGTGTTAGGGGAACTACGATATTTTTTGG

upper sequence: AT3G05970.1 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: LOC_Os12g04990.3 (Oryza sativa), 3'ss of exon 15
---------------------------------------------gtgagctttttactgactctgcgatatgataagtagagtaatttggaactaaatatc-cattttaaattgctttgggatttaatatgcatttctatatttcagAAGTAAAGCTTGTGGATGTCCCAGAAATGAACTATACATCAGCGGATCAGCCCCATCCCCGTGGCGAAATATGTGTTAGGGGTCCTATCATTTTTACAGG
                                              |   | ||||  | ||  |      | |    ||  ||  ||| | ||  | |||| | | | | | |  |     |   ||  |   ||||||| |||||||  | || || |||||||||||||||||||| || || || | |||| | ||  |||| ||||| ||||| ||||||||||| ||||  || ||    ||
gtaagatctgtgtttgggtttaactagacttggttggataaataacttgtccttttgttcacagtaattcctcactgttattgt--ttttgtac--attatcacttctcacactcttccataacgcaaattctgtttctatttttcagAGATTAAACTAGTGGATGTCCCAGAAATGAATTACACCTCTGAGGATGAACCATATCCTCGTGGAGAAATCTGTGTTAGGGGACCTACGATATTCTGTGG

upper sequence: AT3G05970.1 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: GRMZM2G176546_T01 (Zea mays), 3'ss of exon 7
gtgagctttttac-tgactctgcgatatgataagtagagtaatttggaactaaatatccattttaaattgctttgggatttaa---tatgcatttctatatttcagAAGTAAAGCTTGTGGATGTCCCAGAAATGAACTATACATCAGCGGATCAGCCCCATCCCCGTGGCGAAATATGTGTTAGGGGTCCTATCATTTTTACAGG
   | |   | || |   | | | | || ||  |  | |   ||||    |   |||   | | | |  | || |  || |     | ||  |||| || ||||||| || || ||||||||||||||||||||||| |||||||| |  ||||| ||  |||| ||||| ||||| |||||||| || ||||| || ||    ||
--aatcaaatgacatccatatccaaaataattgggtgtgcc-tttgtgcttttgtattattgtcaca--gtttcgtaatgtggatctttgtgtttccat-tttcagAGGTGAAACTTGTGGATGTCCCAGAAATGAATTATACATCTGATGATCAACCTTATCCTCGTGGAGAAATTTGTGTTAGAGGACCTATAATATTCCAGGG

upper sequence: AT3G05970.1 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: GRMZM2G059381_T03 (Zea mays), 3'ss of exon 3
gtgagctttttactgactctgcgatatgataagta-gagtaatttggaactaaatatccattttaaattgctttgggatttaatatgcatttctatatttcagAAGTAAAGCTTGTGGATGTCCCAGAAATGAACTATACATCAGCGGATCAGCCCCATCCCCGTGGCGAAATATGTGTTAGGGGTCCTATCATTTTTACAGG
 | | ||   | |  || || | | |||| |  |  |  | ||    | |||  |       |   | | || |   | |  | || |  || | |  |||||| || || |||||||| |||||||||||||| ||||| || | |||||| ||  |||| ||||| || || ||||||||||| ||||| || ||    ||
-taaactaggttc-aacacttcaagatgaaagatctgcatgatgctaagctatgtgcattggtcccagt-ctctaacaatgcacattctgttttcttcttcagAGGTTAAACTTGTGGACGTCCCAGAAATGAATTATACTTCGGAGGATCAACCGTATCCTCGTGGAGAGATTTGTGTTAGGGGACCTATAATATTCTGTGG

upper sequence: AT3G05970.1 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: GLYMA10G39540.1 (Glycine max), 3'ss of exon 16
gtgagctttttactgactctgcgatatgataagtagagtaatttggaactaaa--tatccat---tttaaattgctttgggatttaatatgcatttctatatttcagAAGTAAAGCTTGTGGATGTCCCAGAAATGAACTATACATCAGCGGATCAGCCCCATCCCCGTGGCGAAATATGTGTTAGGGGTCCTATCATTTTTACAGG
     |||||||  ||       || | | |  |  ||| || |  || | |    |||  |   |||    ||| | | |     |  |   ||  | | |||||||  |||| ||||||||||| |||||||||||||||||||| |  ||||||||| |||||||||| ||||| ||||| |||||||| ||  |||||   ||
---cactttttatgga----agaatttaaaagatgaagttatatttaatttatgtcatctgtagctttcttatgcctagtgccaagagttttgttcttttgtttcagAGATAAAACTTGTGGATGTTCCAGAAATGAACTATACATCTGATGATCAGCCCAATCCCCGTGGTGAAATTTGTGTCAGGGGTCCCATTGTTTTTCGGGG

upper sequence: AT3G05970.1 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: GLYMA20G28200.1 (Glycine max), 3'ss of exon 16
gtgagctttttactgactctgcgatatgataagtagagtaatttggaactaaatatccattttaaattgctttgggatttaatatgcatttctatatttcagAAGTAAAGCTTGTGGATGTCCCAGAAATGAACTATACATCAGCGGATCAGCCCCATCCCCGTGGCGAAATATGTGTTAGGGGTCCTATCATTTTTACAGG
 |    || | |  || | |   | |||| || ||   | | ||      |  | |    |||    ||| | | |     |  |   ||  | | |||||||  |||| || |||||||| |||||||||||||||||||| |  ||||||||| |||||||||| ||||| ||||| ||||||||  |  |||||  |||
ctccttttatgaaagaatttaaaagatga-aattatgtttaatttatgtcagctgta-gctttgttatgcctagtgccaacagttttgttcttttgtttcagAGATAAAACTAGTGGATGTTCCAGAAATGAACTATACATCTGATGATCAGCCCAATCCCCGTGGTGAAATTTGTGTCAGGGGTCCCCTTGTTTTTCGAGG

upper sequence: AT3G05970.1 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: GLYMA15G34650.1 (Glycine max), 3'ss of exon 4
-------------------gtgagctttttac-tgactctgcgatatgataagtagagtaatttggaactaaatatccattttaaattgctttgg--gatttaatatgcatttct-atatttcagAAGTA---AAGCTTGTGGATGTCCCAGAAATGAACTATAC--ATCAGCGGATCAGCCCCAT----CCCCGTGGCGAAATATGTGTTAGGGGTCCTATCATTTTTACAGG-------------------------
                      |||||       || |  | | ||||  |  |   ||   |   |  ||     | |||| |      |||||  |||||    ||  | ||  ||   | |    ||   ||    |  ||       |  || |  |  |   || ||     || ||   |     | | |   | |   |||| ||     | | |   | || |||                          
gttttcaacaagataaaaaagaagcttagaggacgagttcgagttatggca--ttaggtgcctcacatttatcacccgatttcatggaattttggaagatttgccttggttgtcggatgactgaaggatatgcaatgacggagagtcttgtgttataagTTGCATTGATGAGGATGACAACCTTGTTGGCTCTCCTAATGTAGCCTGTGATATAAAACTTGTGGATGTTCCAGAAATGAACTATACATCTGATGATCAG

upper sequence: AT3G05970.1 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: Vv05s0020g03080.t01 (Vitis vinifera), 3'ss of exon 16
gtgagctttttactgactctgcgatatgataagtagagtaatttggaactaaatat---ccattttaaattgctttgggat---ttaatatgcatttcta-tatttcagAAGTAAAGCTTGTGGATGTCCCAGAAATGAACTATACATCAGCGGATCAGCCCCATCCCCGTGGCGAAATATGTGTTAGGGGTCCTATCATTTTTACAGG
           |   |   || |   |  | |||| |  |||||       | | |   |  |  |    |  ||||||||   || || |  |||| |  | |||||||||| |||||||||||||| || ||||||||||| ||||| | |||||||||| |||| ||||| ||||| |||||| ||||||| ||  |||||  |||
--------aacaagaaaaatgtggc-tcctgagtacaacaattttctttccattgtggtctgtgctgctctattttgggataaatttatgttaatttgtcctctttcagAAGTGAAGCTTGTGGATGTTCCGGAAATGAACTACACATCTGAGGATCAGCCCTATCCTCGTGGTGAAATCTGTGTTCGGGGTCCCATTCTTTTTCTAGG

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|125212169|gb|EL227123.1|EL227123
EST:     CGAGGGTGATAACCTCACTGGACATGTTGGCTCTCCTAATCCAGCTTGTG                         AAGTAAAGCTTGTGGATGTCCCTGAAATGAACTAT
genomic: CGAGGGTGATAACCTCACTGGACATGTTGGCTCTCCTAATCCAGCTTGTGgtgagctttt ... tatatttcagAAGTAAAGCTTGTGGATGTCCCAGAAATGAACTAT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actaaatatccattttaaattgctttgggatttaatatgcatttctatatttcagAAGTAAAGCTTGTGGATGTCCCAGAAATGAACTATACATCAGCGGATCAGCCCCATCCCCGTGGCGAAATATGTGTTAGGGGTCCTATCATTTTTACAGG
                                       catttct  CT-rich tract
                             atttaatatgcatttc  TA-rich tract