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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATCTATATTGGGCTGACAGTGGTGATTTAGTAGCCATTGCTAGTGACACATCATTCTACATCTTGAAATTCAACgtgaggatcctgtccaacaaacactcttatgctgtgaatttctatatgcgattcatggattgtccaagtgctaacatggtgttcttgttatacag

Basic information

species Arabidopsis thaliana
transcript AT1G52360.2
intron # 14
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G52360.2 (Arabidopsis thaliana), 5'ss of exon 14
lower sequence: LOC_Os02g11840.2 (Oryza sativa), 5'ss of exon 5
AATCTATATTGGGCTGACAGTGGTGATTTAGTAGCCATTGCTAGTGACACATCATTCTACATCTTGAAATTCAACgtgaggatcctgtccaacaaacactcttatgctgtgaatttctat-atgcgattcatggattgtccaagtgctaacatggtgttcttgttatacag
||||| |||||||| || ||||||||||||||  | ||||| |||||||| ||||||||||| ||||| | ||| || ||     | | |  ||     |  |  ||| || | ||| || |||  |    |   |  |  || |  |||||      |  |    | |||
AATCTCTATTGGGCCGATAGTGGTGATTTAGTGACAATTGCAAGTGACACCTCATTCTACATTTTGAAGTACAATgtaag----tttttctgcat---tttgttggctctgtagttcaatgatgtaacatctacttgatgtaacta-taacacaacaattataccttccag

upper sequence: AT1G52360.2 (Arabidopsis thaliana), 5'ss of exon 14
lower sequence: GRMZM2G124886_T01 (Zea mays), 5'ss of exon 14
AATCTATATTGGGCTGACAGTGGTGATTTAGTAGCCATTGCTAGTGACACATCATTCTACATCTTGAAATTCAACgtgaggatcctgtccaac--aaacactcttatgctgtgaatttct-------atatgcgattcatggattgtccaagtgctaa--catggtgttcttgttatacag----------------------------------------------
||||| || |||||||||||||||||||||||| | ||||| ||||| || ||||||||||| |||||||  || |||||     |  |   |  ||   |   | | | ||  |  | |       ||   | |||  | |    |   | ||  ||   | |  |   || || | | |                                              
AATCTTTACTGGGCTGACAGTGGTGATTTAGTAACAATTGCAAGTGATACGTCATTCTACATTTTGAAATATAATgtgagttctgtcactgtcttaattgcctatgttcagttgacctttcagttacatccactattttttgtcctttttaatgtcaaattaagaagaaattatttttctggtcaaattgaaatgtattaatacaaaagtttccttttatcttgtag

upper sequence: AT1G52360.2 (Arabidopsis thaliana), 5'ss of exon 14
lower sequence: GRMZM2G141587_T02 (Zea mays), 5'ss of exon 14
AATCTATATTGGGCTGACAGTGGTGATTTAGTAGCCATTGCTAGTGACACATCATTCTACATCTTGAAATTCAACgtgaggatcctgtc-------caacaaacactcttatgctgtgaatttctatatgcgattcatggatt------------gtccaagtgctaacatggtgttcttgttatacag-----------------------------------------
||||| || |||||||||||||||||||||||| | ||||| ||||| || ||||||||||| |||||||  || |||||  | |||||        |  ||   |   | | | ||  |  | | | |   || ||  ||||            ||| || |   ||       || ||  |   ||                                          
AATCTTTACTGGGCTGACAGTGGTGATTTAGTAACAATTGCAAGTGATACGTCATTCTACATTTTGAAATATAATgtgag--ttctgtcattaccttattaattgcctatgttcagtcgacctttctgttacatccactgatttgtgtcttttatgtcaaattaagaagcaatcattttttctggtcaaatggacatgtactaacacaaaagtttccttttatcttgtag

upper sequence: AT1G52360.2 (Arabidopsis thaliana), 5'ss of exon 14
lower sequence: GRMZM2G443953_T03 (Zea mays), 5'ss of exon 15
AATCTATATTGGGCTGACAGTGGTGATTTAGTAGCCATTGCTAGTGACACATCATTCTACATCTTGAAATTCAACgtgag--gatcct---gtccaacaaacactcttatgctgtgaatttctat-atgc-gatt---catggattgt--ccaagtgctaaca-tggtgttcttgttatacag----------------------------------
||| ||||||||||||||||||||||||| ||  | || || || ||  | ||||||||||| ||||| | ||| |||||   ||  |    |     | | ||| | |         ||| |||  ||| | ||   ||   |||||   |     || ||| |||| | | |  | ||                                     
AATGTATATTGGGCTGACAGTGGTGATTTGGTGACAATAGCAAGCGATTCGTCATTCTACATTTTGAAGTACAATgtgagttaattttcacatattgtagatactgt-agatcacagttttttattgtgctggttaagcacatattgtattctgcaactgacaatggtatgccttgtctattatttactaacgcaactctaacttgataacatctag

upper sequence: AT1G52360.2 (Arabidopsis thaliana), 5'ss of exon 14
lower sequence: GLYMA15G01680.1 (Glycine max), 5'ss of exon 14
AATCTATATTGGGCTGACAGTGGTGATTTAGTAGCCATTGCTAGTGACACATCATTCTACATCTTGAAATTCAACgtgaggatcctgtccaacaaacact----cttat-gctgt-gaatttctatatgcgat-tcatggattgtccaagtgcta-acatggtgttcttgttatacag-----------------------------------------------------------
|| || || |||||||||||||||||| ||||| | ||||||||||| ||||||||||||||  |||| | ||| ||||||||  |    |||     ||    ||||| | ||| |  || || |     |  ||        |||       | |||     ||  || |  |                                                              
AACCTCTACTGGGCTGACAGTGGTGATCTAGTAACAATTGCTAGTGATACATCATTCTACATTCTGAAGTACAATgtgaggattttcgtgaacttcatcttttccttatagttgttggcttgctttgaagaacatcccaccccctccccccaacacacacacaatttctgctgaatgtatattttgtagatctttactggtagtgcccttgaaacatattgacttccattattgcag

upper sequence: AT1G52360.2 (Arabidopsis thaliana), 5'ss of exon 14
lower sequence: GLYMA13G43680.2 (Glycine max), 5'ss of exon 14
AATCTATATTGGGCTGACAGTGGTGATTTAGTAGCCATTGCTAGTGACACATCATTCTACATCTTGAAATTCAACgtgaggatcctgtccaacaaacactcttatgctgtgaatttctatatgcgattcatggat----tgtcca--agtgctaacatggtgttcttgttatacag------------------------------------------------
|| || || |||||||||||||||||| ||||| | |||||||| || ||||||||||||||  |||| | ||| |||||||  ||    |||   ||   ||    | |  || |     |||  |||| | ||    || ||   | |  |      |  |   | ||  ||||                                                
AACCTCTACTGGGCTGACAGTGGTGATCTAGTAACAATTGCTAGCGATACATCATTCTACATTCTGAAGTACAATgtgaggactctcatgaactt-catcttttccttatagatgttggcttgct-ttcaagaatattttgccccttactatttctgccgaatgtatatttgacagatctttactggtagtgccctttaaacattttgacttccactattgcag

upper sequence: AT1G52360.2 (Arabidopsis thaliana), 5'ss of exon 14
lower sequence: GLYMA07G03890.2 (Glycine max), 5'ss of exon 3
AATCTATATTGGGCTGACAGTGGTGATTTAGTAGCCATTGCTAGTGACACATCATTCTACATCTTGAAATTCAACgtgaggatcctg--------tccaacaaacactcttatgctgtgaatt---tctatatgcgatt-catggattgtccaagtgct---aacatggtg--ttcttgttatacag
|| || || |||||||| ||||||||| ||||  | ||||||||||| ||||||||||| ||| |||| | ||| |||||||| ||          ||  |   | |||||||| | |   ||   |  ||||  |||  ||   | |    |||  ||   |||||  |   |||   |  | |||
AACCTCTACTGGGCTGATAGTGGTGATCTAGTGACGATTGCTAGTGATACATCATTCTATATCCTGAAGTACAATgtgaggattctaaattgtcccccccccccctctcttatgtttttggttaaatgaatatctgatggcacttactagtgaagcactgtaaacattttaacttccactgttgcag

upper sequence: AT1G52360.2 (Arabidopsis thaliana), 5'ss of exon 14
lower sequence: GLYMA08G22140.1 (Glycine max), 5'ss of exon 14
AATCTATATTGGGCTGACAGTGGTGATTTAGTAGCCATTGCTAGTGACACATCATTCTACATCTTGAAATTCAACgtgaggatcctgtccaacaaacactcttatgctg-------tgaatttctatatgcgattcatggattgtccaagtgctaacatggtgttcttgttatacag--------------------------------------------------
|| || || |||||||| || |||||||||||  | ||||||||||| ||||||||||| ||| | || | ||| |||||||| ||    |    || || ||||  |        ||| ||| |||     |  ||| | ||  ||   |       ||||    |   |||                                                      
AACCTGTACTGGGCTGATAGCGGTGATTTAGTGACGATTGCTAGTGATACATCATTCTATATCCTTAAGTACAATgtgaggattctaaatacttgacccttttattttacacttgttgactttttatgaaaaag-catcgttttcccccctatgtttttggttaaatgaatatctgatggcacttactagtgaagcacagtaaacattttaacttccattgttgcag

upper sequence: AT1G52360.2 (Arabidopsis thaliana), 5'ss of exon 14
lower sequence: Vv11s0016g04180.t01 (Vitis vinifera), 5'ss of exon 14
AATCTATATTGGGCTGACAGTGGTGATTTAGTAGCCATTGCTAGTGACACATCATTCTACATCTTGAAATTCAACgtgaggatcctgtccaacaaacactcttatgctgtgaatttctatatgcgat--tcatggattgtccaagtgctaacatggtgttcttgttatacag-------------------------------------------
||||| ||||||||||| |||||||||||||| || ||||| |||||  ||||||| |||||||| || | ||| || ||  | ||  |         ||||||| |     | || |||  |  ||  |||| ||||   ||     |    | || ||    | ||                                               
AATCTTTATTGGGCTGATAGTGGTGATTTAGTGGCAATTGCAAGTGATTCATCATTTTACATCTTAAAGTACAATgtaagctttctccctttttggttctcttatccc----acttttatgagaaatcatcatagatttgtcataaaatctattcgttttacaatcatttgagattaagtacctcacttaacaaccaaatatgtttatttggcag

upper sequence: AT1G52360.2 (Arabidopsis thaliana), 5'ss of exon 14
lower sequence: Vv09s0002g04810.t01 (Vitis vinifera), 5'ss of exon 14
AATCTATATTGGGCTGACAGTGGTGATTTAGTAGCCATTGCTAGTGACACATCATTCTACATCTTGAAATTCAACgtgaggatcct-gtccaacaaacactcttatg---ctgtgaatttctatatgcgattcatggattgtccaagtgc-taacatggtgttct-tgttatacag---------------------------
|| || ||||||||||| ||||| ||||| || |||||||| ||||| |||||||| |||||| |||| | ||| ||  |||||||      |  ||  ||||| |     |||| | ||||   | |   |   | |||| |||| ||| | |  ||| |  ||   ||  | |                            
AACCTCTATTGGGCTGATAGTGGGGATTTGGTGGCCATTGCCAGTGATACATCATTTTACATCCTGAAGTACAATgtatggatcctcaaattattaatcctctttttaacttgtgtaattctcctttcctctatagaattggccaaatgcatgatttggagcactgcattccaaattgaactttttttaatttaattttgcag

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|19878420|gb|AU239251.1|AU239251
EST:     ATTTAGTAGCCATTGCTAGTGACACATCATTCTACATCTTGAAATTCAAC                         CGCGACTTAGTTACCTCACATTTTGATAGCGGAAGACCTACTGAGGAAGAA
genomic: ATTTAGTAGCCATTGCTAGTGACACATCATTCTACATCTTGAAATTCAACgtgaggatcc ... tgttatacagCGCGACTTAGTTACCTCACATTTTGATAGCGGAAGACCTACTGAGGAAGAA