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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaatactcttactccattgacataaacctcagttttcgtcactccctcttcaatctctggtcactaggatactcattggttttattcttgtatggccatacactttgtgattgattgaattttcttgaagGTTATGAGGATTATATAGGGTTCTTGTGCACCACACCTGGTATCGATGCTCACGAGATAAAAAACTTCACAAACACTCCATGCAATTTCAAAATGGTTCA

Basic information

species Arabidopsis thaliana
transcript AT4G30020.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G30020.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA09G06640.1 (Glycine max), 3'ss of exon 10
gtaaatactcttactccattgacataaacctcagttttcgtcactccctcttcaatctctggtcactaggatactcattggttttattcttgtatggccatacactttgtgattgattgaattttcttgaagGTTATGAGGATTATATAGGGTTCTTGTGCACCACACCTGGTATCGATGCTCACGAGATAAAAAACTTCACAAACACTCCATGCAATTTCAAAATGGTTCA
                       | ||||   | ||| |   | ||  |      |||    ||| ||  | |   |   |    |       |     ||    ||  | | |     |||  |  || ||| || ||||||||| |||||||||||||||| |||||||| || |||| | |||||||||| |||| ||||||| | ||||| ||   ||  ||||  ||
---------------------ctaaaaacaatattttcctgtaatcaat------tctagtatcaatacaacaagaaaaagcaaca-----acaaaaaaatctgtttgattaatttgctaatcattatgcagGATACGAGGATTATCTAGGGTTCTTGTGCACAACACCTGGCATTGATGTTAACGAGATAAAGAACTACACAAACTCGCCATGTAACAACACCATGGGCCA

upper sequence: AT4G30020.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA15G17830.1 (Glycine max), 3'ss of exon 9
gtaaatactcttactccattgacataaacctcagttttcgtcactccctcttcaatctctggtcactaggatactcattggttttattcttgtatggccatacactttgtgattgattgaattttcttgaagGTTATGAGGATTATATAGGGTTCTTGTGCACCACACCTGGTATCGATGCTCACGAGATAAAAAACTTCACAAACACTCCATGCAATTTCAAAATGGTTCA
                        |  ||   |      |||   |  |  ||||| ||| | ||  |  | |       |    |       |     ||   ||| || | |     |||  | ||| ||| || ||||||||| |||||||||||||||| |||||||| || |||| ||| |||||||| |||| ||||||| | ||||| ||   ||  ||||  ||
------------------------tgtactaaaagcaatgtcttcctgtaatcaat-tctag-catcaaaaca------agaaaaaccaacaaaaaagaatctgcttagttaatttgctaatcattttgcagGATACGAGGATTATCTAGGGTTCTTGTGCACAACACCTGGCATTGATGTTCATGAGATAAAGAACTACACAAACTCCCCATGTAACAACACCATGGGCCA

upper sequence: AT4G30020.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA17G06740.1 (Glycine max), 3'ss of exon 9
gtaaatactcttactccattgacataaacctcagttttcgtcactccctcttcaatctctggtcactaggatactcattggttttattcttgtatggccatacactttgtgattgattgaattttcttgaagGTTATGAGGATTATATAGGGTTCTTGTGCACCACACCTGGTATCGATGCTCACGAGATAAAAAACTTCACAAACACTCCATGCAATTTCAAAATGGTTCA
               | ||| ||  ||||   ||| |  | || ||| || |  ||| | |   |  |  |   | |||     |||| |  ||             | ||| | ||  |    | ||| ||| || |||||||||||||| ||||||||||| |||||| | || |||| ||| |||||||  |||| |||  |||| ||||| ||   |   ||||   |
-------------tgctatttactcaaac---agtatatgacaatccatcatggatcacagtgtaa-aaaacctttattcagcatattttaataaa-----------tttgaatcatcaa----ttttgcagGGTACGAGGATTATATAGGCTTCTTGTGCACAACACCTAGCATTGATGTTCATGAGATAAGGAACTACACTCACACCCCATGTAACACCTCCATGGGCAA

upper sequence: AT4G30020.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: Vv11s0103g00550.t01 (Vitis vinifera), 3'ss of exon 10
gtaaatactcttactccattgacataaacctcagttttcgtcactccctcttcaatctctggtcactaggatactcattggttttattcttgtatggccatacactttgtgattgattgaattttcttgaagGTTATGAGGATTATATAGGGTTCTTGTGCACCACACCTGGTATCGATGCTCACGAGATAAAAAACTTCACAAACACTCCATGCAATTTCAAAATGGTTCA
              |  ||||    |||  |   ||||    |  |  | ||  ||        ||| |   | ||||||     | |||   ||      |||||     |||   |    ||| ||| || ||||||||| || ||||||||||||||||| ||||| || || |||||||| |||||||| |||| ||||| |   |||||||||| ||  ||||  | 
------------gatatattgg---aaatatatatttta---agacatttttggattat-----actggagca-tcattgagcacaatctcaaatcattg-acactc----attccct---cttttttgtagCTTATGAGGACTACATAGGGTTCTTGTGCACAACACCAGGAATTGATGCTCATGAGATAAAGAACTACACAAGCTTACCATGCAATTACACCATGGGCCG

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|116427755|gb|EG470347.1|EG470347
EST:     TCATGTCAATCCAAGCGCTGCTCTAGACCCTGGTCTCATCTTTGATGCAG                         GTTATGAGGATTATATAGGGTTCTTGTGCACCACACCTGGTATCGATGCTC
genomic: TCATGTCAATCCAAGCGCTGCTCTAGACCCTGGTCTCATCTTTGATGCAGgtaaatactc ... tttcttgaagGTTATGAGGATTATATAGGGTTCTTGTGCACCACACCTGGTATCGATGCTC






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttggttttattcttgtatggccatacactttgtgattgattgaattttcttgaagGTTATGAGGATTATATAGGGTTCTTGTGCACCACACCTGGTATCGATGCTCACGAGATAAAAAACTTCACAAACACTCCATGCAATTTCAAAATGGTTCA
                                 gattgat  putative branch site (score: 4)
                                            ttttctt  putative PPT
                                  attgattgaatttt  TA-rich tract