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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgattttctttatccagctgatggggttataggtatcgtgctactcatgtatatcttaattatatgacctcattgagtttcagGCTGCTGTTGAGGAAGGTATTGTCGTTGGTGGTGGTTGCACTCTGCTCCGGCTTGCATCAAAGGTCGATGCCATCAAGGATACCCTTGAAAATGATGAAG

Basic information

species Arabidopsis thaliana
transcript AT3G13470.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G13470.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: LOC_Os06g02380.1 (Oryza sativa), 3'ss of exon 10
-------------------------------------------------------------------gtgattttctttatccagctgatggggttataggtatcgtgctactca-tgtatatcttaattatatgacctcattgagtttcagGCTGCTGTTGAGGAAGGTATTGTCGTTGGTGGTGGTTGCACTCTGCTCCGGCTTGCATCAAAGGTCGATGCCATCAAGGATACCCTTGAAAATGATGAAG
                                                                    | |  |  ||| |   ||| |  | |||      | ||| || ||   | |  ||||| |        |||| |||    ||||||||||||||||||||||||||| |||||||| || |||||||| ||  | || ||| | |  || || ||||||||||| | ||| || ||||||||  
gttagtctgttgttataactgctttgagatagaaatagattaatgtttgcttcttaaggaagaaaaattaaggtagtttgtt--gctcactgagttgatatcaacgttcttctggctttggatctttaaaccgcttcctctttg----tcagGCTGCTGTTGAGGAAGGTATTGTTGTTGGTGGAGGGTGCACTCTTCTGAGACTGGCAGCTAGAGTTGACGCCATCAAGGACAACCTGGAGAATGATGAGC

upper sequence: AT3G13470.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: LOC_Os02g01280.1 (Oryza sativa), 3'ss of exon 10
-----------------------------------gtgattttctttatccagctgatggggttataggtatcgtgctactcatgtatatcttaattatatgacctcattgagtttcagGCTGCTGTTGAGGAAGGTATTGTCGTTGGTGGTGGTTGCACTCTGCTCCGGCTTGCATCAAAGGTCGATGCCATCAAGGATACCCTTGAAAATGATGAAG
                                   | ||||   || |   |||     |    | |   |   |     |    | | | ||| ||| ||    |   |  ||  ||||| |||||||||||||||||||| ||||| ||||| || || ||  | |||||||||||||| || |||||||| |  || || ||||| ||||||||| 
gtgaatacttctctttgttaatataatttaattttgggattgcattcagagagccttctgatgcacatagagtatatgggtttgttgtttgttactta-atagttt-gctctgtggcagGCGGCTGTTGAGGAAGGTATTGTTGTTGGAGGTGGCTGTACGCTTTTGCGGCTTGCATCAAAAGTTGATGCCATTATAGAAACACTTGAGAATGATGAAC

upper sequence: AT3G13470.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GRMZM2G095252_T02 (Zea mays), 3'ss of exon 4
-----------------------------------------------------------gtgattttctttatccag--ctgatggggttata--ggtatcgtgctactcatgt-atatcttaattatatgacctcattgagttt-cagGCTGCTGTTGAGGAAGGTATTGTCGTTGGTGGTGGTTGCACTCTGCTCCGGCTTGCATCAAAGGTCGATGCCATCAAGGATACCCTTGAAAATGATGAAG
                                                              | || ||||   |||  |  || || || |    ||       || |   || |||| |   | | ||  |  | ||   |||  ||||||||||||||||||||||||| |||||||| || ||||| ||  | ||||||||| | || |||||||||||||||||||| || || || |||||  
gtaagttgtcggagtaattaaccattttgtgctgccagatttatatttgcttcatgaggaatacttcctttgatcagaacatataggtttgttctagttcaactttattttggttatatatcgctaaaattgctcctttttctttatagGCTGCTGTTGAGGAAGGTATTGTTGTTGGTGGAGGATGCACCCTTTTGCGGCTTGCAGCTAAAGTCGATGCCATCAAGGATACACTGGAGAACGATGAGC

upper sequence: AT3G13470.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GRMZM2G083716_T04 (Zea mays), 3'ss of exon 9
--------------gtgattttctttatccagctg-atggggttataggtatcgtgctactcatgtatatcttaattatatgacctcattgagttt-cagGCTGCTGTTGAGGAAGGTATTGTCGTTGGTGGTGGTTGCACTCTGCTCCGGCTTGCATCAAAGGTCGATGCCATCAAGGATACCCTTGAAAATGATGAAG
               |   ||  |  | |   ||| ||    |  |   |    | ||  | |  ||| | | | | |  |    || ||   ||  |||||||| ||||||||||||||||| |||||||| || ||||||||  | ||||||||| | || ||||| |||||||||||||| || || || || ||  
atcactccatactccttgcttcttgaaacattctgtattttctgctgaattctcttctggttacatatgtatcactaaagttgtttctttctcttcacagGCTGCCGTTGAGGAAGGTATTGTTGTTGGTGGAGGGTGCACTCTTTTGCGGCTTGCAGCTAAAGTCGACGCCATCAAGGATACACTGGAGAACGACGAGC

upper sequence: AT3G13470.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA08G18760.1 (Glycine max), 3'ss of exon 9
gtgattttctttatccagctgatggggttataggtatcgtgctactcatgtatatcttaattatatgacctcattgagtttcagGCTGCTGTTGAGGAAGGTATTGTCGTTGGTGGTGGTTGCACTCTGCTCCGGCTTGCATCAAAGGTCGATGCCATCAAGGATACCCTTGAAAATGATGAAG
|||   || | | |||         | || ||| | |  ||  | ||     | |||  |   ||  |  |  |||| |||||||| ||||| |||||||||||||| |||||||||||||||||||| ||  | |||||||||||||| ||||| |||||||||| |||||| ||||||||||
gtgtccttttctttccca-----aagtttttagattttttgggattc-----tgtctgtaagctaatagtttgttgactttcagGCAGCTGTAGAGGAAGGTATTGTTGTTGGTGGTGGTTGCACTCTTCTGAGACTTGCATCAAAGGTGGATGCAATCAAGGATAGCCTTGATAATGATGAAG

upper sequence: AT3G13470.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA15G40110.1 (Glycine max), 3'ss of exon 9
gtgattttctttatccagctgatggggttataggtatcgtgctactcatgtatatcttaattatatgacctcattgagtttcagGCTGCTGTTGAGGAAGGTATTGTCGTTGGTGGTGGTTGCACTCTGCTCCGGCTTGCATCAAAGGTCGATGCCATCAAGGATACCCTTGAAAATGATGAAG
    | | ||||      |  |   | || ||| | || |   | |  ||| | | | |  || ||    |  |||| |||||||| ||||| ||||| |||||||| |||||||||||||||||||| ||  | |||||||||||||| ||  | |||||||||| |||||| ||||||||||
---gtatccttttctttcccaa--agtttttagatttcttttgaattctgtttctgtaagcta-atagttt-gttgactttcagGCAGCTGTAGAGGAGGGTATTGTAGTTGGTGGTGGTTGCACTCTTCTGAGACTTGCATCAAAGGTGGACACAATCAAGGATAGCCTTGATAATGATGAAG

upper sequence: AT3G13470.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: Vv06s0004g00240.t01 (Vitis vinifera), 3'ss of exon 10
--------------------gtgattttctttatccagctgatggggtt--ataggtatcgtgctactcatgtatatcttaattatatgac---ctcattgagtttcagGCTGCTGTTGAGGAAGGTATTGTCGTTGGTGGTGGTTGCACTCTGCTCCGGCTTGCATCAAAGGTCGATGCCATCAAGGATACCCTTGAAAATGATGAAG
                     ||    |   |  | || || |    ||  | ||  || |  |  |      |    | | |  |||| |    ||| ||| |||||||| |||||||||||||| ||||| || |||||||| |||||||| ||  | ||||| |||||||| |||||||||||||| || ||||| |||||||| |
gtaatttctttcatgaaattatggcactgaattgctagttgctaatattcaagagtgatggcacagccagaacagtattaagtagtatggcattttcaatgattttcagGCAGCTGTTGAGGAAGGGATTGTTGTAGGTGGTGGGTGCACTCTCCTGAGACTTGCCTCAAAGGTGGATGCCATCAAGGACACGCTTGATAATGATGAGG

upper sequence: AT3G13470.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: EFJ36935 (Selaginella moellendorffii), 3'ss of exon 9
gtgattttctttatccagctgatggggttataggtatcgtgctactcatgtatatcttaattatatgacctcattgagtttcagGCTGCTGTTGAGGAAGGTATTGTCGTTGGTGGTGGTTGCACTCTGCTCCGGCTTGCATCAAAGGTCGATGCCATCAAGGATACCCTTGAAAATGATGAAG
                              ||  ||   |   | ||  | ||||  |  |  || |   |  || | || |||||||||||||| ||||| || || || ||||| ||     |||| ||  | ||  |    ||||| ||||||||||||||||||||||| ||||| ||  
-----------------------------gtaaatag-atcggattctggaatattgtggt-gtaag---tgtttaaattgcagGCTGCTGTTGAAGAAGGCATCGTTGTCGGTGGGGGAATTGCTCTTCTAAGACTGTCTAGCAAGGTTGATGCCATCAAGGATACCCTTGAGAATGACGAGC

upper sequence: AT3G13470.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: EFJ33580 (Selaginella moellendorffii), 3'ss of exon 9
gtgattttctttatccagctgatggggttataggtatcgtgctactcatgtatatcttaattatatgacctcattgagtttcagGCTGCTGTTGAGGAAGGTATTGTCGTTGGTGGTGGTTGCACTCTGCTCCGGCTTGCATCAAAGGTCGATGCCATCAAGGATACCCTTGAAAATGATGAAG
                              ||  ||   ||  | ||  | ||||  |  |  || |   |  || | || |||||||||||||| ||||| || || || ||||| ||     |||| ||  | ||  |    ||||| ||||||||||||||||||||||| ||||| ||  
-----------------------------gtaaatagattgg-attctggaatattgtggt-gtaag---tgtttaaattgcagGCTGCTGTTGAAGAAGGCATCGTTGTCGGTGGGGGAATTGCTCTTCTAAGACTGTCTAGCAAGGTTGATGCCATCAAGGATACCCTTGAGAATGACGAGC

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|124710247|gb|EH801649.1|EH801649
EST:     CTCTTAATGCTACAAAG                         GCTGCTGTTGAGGAAGGTATTGTCGTTGGTGGTGGTTGCACTCTGCTCCGG
genomic: CTCTTAATGCTACAAAGgtgattttct ... tgagtttcagGCTGCTGTTGAGGAAGGTATTGTCGTTGGTGGTGGTTGCACTCTGCTCCGG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ataggtatcgtgctactcatgtatatcttaattatatgacctcattgagtttcagGCTGCTGTTGAGGAAGGTATTGTCGTTGGTGGTGGTTGCACTCTGCTCCGGCTTGCATCAAAGGTCGATGCCATCAAGGATACCCTTGAAAATGATGAAG
                         tcttaat  putative branch site (score: 3)
                                       cctcatt  putative PPT
                tcatgtatatcttaat  TA-rich tract