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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacttaattctcatctgttacacatttcttttgaaacgttggcgtttgttaattttctttaatttggttctgtttggtgcagTTGCTGCTTAAGGGTTTTGCAGAACGTGGTGCTAAGAGAATCCGCGTCCATATTCTTACTGATGGTCGTGATGTTTTGGATGGTTCTAGTGTCGGATTTG

Basic information

species Arabidopsis thaliana
transcript AT3G08590.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G08590.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os05g40420.1 (Oryza sativa), 3'ss of exon 4
--------------------gtacttaattctcatctgttac--------------acatttcttttgaa-acgttggcgtttgt------taattttctttaa-tttggttctgtttggt-gcagTTGCTGCTTAAGGGTTTTGCAGAACGTGGTGCTAAGAGAATCCGCGTCCATATTCTTACTGATGGTCGTGATGTTTTGGATGGTTCTAGTGTCGGATTTG
                     || ||   | ||||||  ||               |  |||||||  || | ||||   | |        ||||| | |||   ||| ||  |   || |   ||||||| || || |||      |    ||| || || | |||||| || || |||||||||||||| |||||||||||||||||  | || || || ||||
gtataaaagtactcttttctatagtttgctatcatcttgtatagtatgaggcactaatgtttctttacaacatgttgatctgtccagtatctaattctttttgtcttttgtcattcctgtttatagTTGCTCCTGAATGGTGCAAGTGCGAATGGAGCGAAAAAAATCCGTGTTCACATTCTTACTGATGGACGTGATGTTTTGGATGGCACAAGCGTTGGTTTTG

upper sequence: AT3G08590.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM5G833389_T02 (Zea mays), 3'ss of exon 4
gtacttaattctcatctgttacacatttcttttgaaac-gttggcgtttgttaattttctttaatttggttctg-tttggtgcagTTGCTGCTTAAGGGTTTTGCAGAACGTGGTGCTAAGAGAATCCGCGTCCATATTCTTACTGATGGTCGTGATGTTTTGGATGGTTCTAGTGTCGGATTTG
    ||  |  |  ||| |     ||||    ||   | |||   |       |||| || ||||||  ||  |  |   | ||||| || || || ||| |    ||  | || || || | |||||| || || || ||||||||||| |||||||||||||||||    ||| | || || |
--gtttgctaatattctttcttcaatttagcctggttcagttactgccacaagatttactataatttttttggggctctatccagTTACTTCTGAAAGGTGTCAGTGAGAGAGGGGCGAAAAAAATCCGTGTGCACATCCTTACTGATGGACGTGATGTTTTGGATGGAAGCAGTATTGGTTTCG

upper sequence: AT3G08590.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM5G833389_T01 (Zea mays), 3'ss of exon 4
gtacttaattctcatctgttacacatttcttttgaaac-gttggcgtttgttaattttctttaatttggttctg-tttggtgcagTTGCTGCTTAAGGGTTTTGCAGAACGTGGTGCTAAGAGAATCCGCGTCCATATTCTTACTGATGGTCGTGATGTTTTGGATGGTTCTAGTGTCGGATTTG-----------------------------------------------------------------------------------------
    ||  |  |  ||| |     ||||    ||   | |||   |       |||| || ||||||  ||  |  |   | ||||| || || || ||| |    ||  | || || || | |||||| || || || ||||||||||| |||||||||||||||||    ||| | || || |                                                                                         
--gtttgctaatattctttcttcaatttagcctggttcagttactgccacaagatttactataatttttttggggctctatccagttacttctgaaaggtgtcagtgagagaggggcgaaaaaaatccgtgtgcacatccttactgatggacgtgatgttttggatggaagcagTATTGGTTTCGTGGAGACCCTAGAGAATGATCTTTTGGAGCTTAGAGCGAAGGGTGTTGATGCACAAATTGCATCTGGTGGTGGAAGGATGTATGTTACG

upper sequence: AT3G08590.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA09G40690.1 (Glycine max), 3'ss of exon 3
gtacttaattctcatctgttacacatttcttttgaaacgttggcgtttgttaattttctttaatttggttctgtttggtgcagTTGCTGCTTAAGGGTTTTGCAGAACGTGGTGCTAAGAGAATCCGCGTCCATATTCTTACTGATGGTCGTGATGTTTTGGATGGTTCTAGTGTCGGATTTG
     | ||| |     |||  |  | | |||        ||      ||| ||| | | ||| |  ||  | ||  || |||||| ||||||| ||  ||   || || |||| ||| ||| |||| |||||||||||||| ||||| |||||||||||||||||||| ||||| || ||||
----gtgattatttggggttggagttgtttttccttcttgtgtatacagtttattctttctaactaagtattttt--gtacagTTGTTGCTTAAAGGAGTTAGCGAGCGAGGTGTTAAAAGAGTCCGTGTCCATATTCTTACAGATGGCCGTGATGTTTTGGATGGTTCAAGTGTGGGGTTTG

upper sequence: AT3G08590.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA18G45120.1 (Glycine max), 3'ss of exon 4
gtacttaattctcatctgttacacatttcttttgaaacgttggcgtttgttaattttctttaatttggttctgtttggtgcagTTGCTGCTTAAGGGTTTTGCAGAACGTGGTGCTAAGAGAATCCGCGTCCATATTCTTACTGATGGTCGTGATGTTTTGGATGGTTCTAGTGTCGGATTTG
||  ||| ||    |  |       |||| ||        ||   |  ||| ||| | | ||| |   | || ||  || |||||| ||||||| ||  ||   || || |||| ||| ||| |||| |||||||||||||| ||||| ||||||||||||||||                  
gtgattatttggggttggagctgtttttccttcatg----tgtattcagtttattctttctaactaactactttt--gtacagTTGTTGCTTAAAGGAGTTAGTGAGCGAGGTGTTAAAAGAGTCCGTGTCCATATTCTTACAGATGGCCGTGATGTTTTGGATG------------------

upper sequence: AT3G08590.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv08s0056g00200.t01 (Vitis vinifera), 3'ss of exon 3
---------------gtacttaattctcatctgttacacatttcttttgaaacgttggcgtttgttaattttctttaatttggttctgtttggtg-cagTTGCTGCTTAAGGGTTTTGCAGAACGTGGTGCTAAGAGAATCCGCGTCCATATTCTTACTGATGGTCGTGATGTTTTGGATGGTTCTAGTGTCGGATTTG
               | | |  |||  | | || |      |  ||||| |        |   | | ||  || |   ||||| | | | |  || ||||| ||  | || ||   |   ||   |||||| || |||||||| |||||||| ||||||||||| |||||||||||||||||||| ||||| || ||||
gtatgttttgttgttgaattctattaccttgtgattggatatagttttgtatttcccaggggagatcatgatcctc--tttggctttttctcttggcagTTACTTTTAAAAGGAGCTAGTGAGAATGGTGCAAAAAGAATCCGTGTCCATATCCTTACTGATGGGCGTGATGTTTTGGATGGTTCCAGTGTTGGGTTTG

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|164097053|gb|ES174327.1|ES174327
EST:     TTGGTCTTCTAAGCGATGGTGGAGTTCACTCTCGTTTGGATCAAGTCCAG                         TTGCTGCTTAAGGGTTTTGCAGAACGTGGTGCTAAGAGAATCCGCGTCCAT
genomic: TTGGTCTTCTAAGCGATGGTGGAGTTCACTCTCGTTTGGATCAAGTCCAGgtacttaatt ... tttggtgcagTTGCTGCTTAAGGGTTTTGCAGAACGTGGTGCTAAGAGAATCCGCGTCCAT
EST: gi|164103797|gb|ES172660.1|ES172660
EST:     GTGGAGTTCACTCTCGTTTGGATCAAGTCCAG                         TTGCTGCTTAAGGGTTTTGCAGAACGTGGTGCTAAGAGAATCCG
genomic: GTGGAGTTCACTCTCGTTTGGATCAAGTCCAGgtacttaatt ... tttggtgcagTTGCTGCTTAAGGGTTTTGCAGAACGTGGTGCTAAGAGAATCCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttttgaaacgttggcgtttgttaattttctttaatttggttctgtttggtgcagTTGCTGCTTAAGGGTTTTGCAGAACGTGGTGCTAAGAGAATCCGCGTCCATATTCTTACTGATGGTCGTGATGTTTTGGATGGTTCTAGTGTCGGATTTG
                                        ttctgttt  CT-rich tract
                 tttgttaattttcttt  TA-rich tract