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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgattcataaatgcctctcaataagttccatgggtctatttcattcttttgttccattgtccttaaaagtagaaatccattcctctgttttactaacccttaagatgaagtccttatagtttcatattaatgatctatgctttaatattttttgatggacagTTGATGCCCATCCTGGAGACGCTGTATAACGCTTCAAAGAGAACATCATCTAATCAAATATACATGATGCTAATTGTACTTCTCATACTTAGTCAGGATT

Basic information

species Arabidopsis thaliana
transcript AT1G04200.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G04200.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA20G28880.1 (Glycine max), 3'ss of exon 7
gtatgattcataaatgcctctcaataagttccatgggtctatttcattcttttgttccattgtccttaaaagtagaaatccattcctctgttttactaacccttaagatgaagtccttatagtttcatattaatgatctatgctttaatattttttga--tggacagTTGATGCCCATCCTGGAGACGCTGTATAACGCTTCAAAGAGAACATCATCTAATCAAATATACATGATGCTAATTGTACTTCTCATACTTAGTCAGGATT---
                                                       |  |||||| |   |  ||   | | |  |  ||| |      ||   ||  ||||    || ||| ||     ||| |     || | |  | || || |||  |  |||||| ||||| || |||||  | || || || ||| |||  || ||  |   ||||||||| |||||| |||||||| ||||||||||||| ||||| ||||   
------------------------------------------------------cttgattgtcatgtgatatatgtaactac-ctgctgat------acatgtagaatga----ctaataattaagccttatt--ctgatacctggacatcttatgaaattaacagTTAATGCCAATTCTGGAAGCTCTATACAATGCTCCAAGTAGGACTGC---TAATCAAATTTACATGTTGCTAATTATACTTCTCATACTCAGTCAAGATTCTT

upper sequence: AT1G04200.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA10G38920.2 (Glycine max), 3'ss of exon 8
gtatgattcataaatgcctctcaataagttccatgggtctatttcattcttttgttccattgtccttaaaagtagaaatccattcctctgttttactaacccttaagatgaagtccttatagtttcatattaatgatctatgctttaatattttttgatggacagTTGATGCCCATCCTGGAGACGCTGTATAACGCTTCAAAGAGAACATCATCTAATCAAATATACATGATGCTAATTGTACTTCTCATACTTAGTCAGGATT---
                                                  |||  |  |||||| |   |  ||   | | |  |  ||| | ||  |      |  || ||| ||||||  | | |||   |     |||  | | | |||         |||||| ||||| || |||||  | || || || ||| |||  || ||| |   ||||||||| |||||| |||||||| ||||||||||||| ||||| ||||   
--------------------------------------------------tttacttgattgtcatgtgatatatgtaactac-ctgctgatgtagaatgatggacaattaag-ccttat--tctgatacctaca---tatcttatgaaatt--------aacagTTAATGCCAATTCTGGAAGCTCTATACAATGCTCCAAGTAGGACAGC---TAATCAAATTTACATGTTGCTAATTATACTTCTCATACTCAGTCAAGATTCTT

upper sequence: AT1G04200.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA10G00550.1 (Glycine max), 3'ss of exon 8
gtatgattcataaatgcctctcaataagttccatgggtctatttcattcttttgttccattgtccttaaaagtagaaatccattcctctgttttactaacccttaagatgaagtccttatagtttcatattaatgatctatgctttaatattttttgatggacagTTGATGCCCATCCTGGAGACGCTGTATAACGCTTCAAAGAGAACATCATCTAATCAAATATACATGATGCTAATTGTACTTCTCATACTTAGTCAGGATT---
                                                   |  |||   | || ||||   || |  ||  | |   ||  |    ||    | ||           || || |||| ||  |||||  || ||  || || |   ||  |||||| ||||| || || ||  |  | ||| | |||  || ||  ||| | |   ||||||| |||||| || ||||| ||||||||||||||||||| |||    
--------------------------------------------------ctcattcttatatc-ttaatcatacaggtct-tactagtgcatctacaatgactgagg----------attgtatcatgttt-tgatccttgttt--attttgtgaaattaacagTTAATGCCAATTCTAGAAGCATTATATGATGCTCGAAGGATGACAGCTT---ATCAAATTTACATGTTGTTAATTATACTTCTCATACTTAGTCAAGATACTT

upper sequence: AT1G04200.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA15G24080.1 (Glycine max), 3'ss of exon 9
gtatgattcataaatgcctctcaataagttccatgggtctatttcattcttttgttccattgtccttaaaagtagaaatccattcctctgttttactaacccttaagatgaagtccttatagtttcatattaatgatctatgctttaatattttttgatggacagTTGATGCCCATCCTGGAGACGCTGTATAACGCTTCAAAGAGAACATCATCTAATCAAATATACATGATGCTAATTGTACTTCTCATACTTAGTCAGGATT---
                                           |||||||| | |   | |     |     ||  | | |||        || | | ||        ||| |     || || |||| ||  |||||  || ||   | || |   ||  |||||| ||||| || || ||  |  | ||| | |||  || ||| ||| |   ||||||||| |||||  || ||||| ||||||||||||||||||| ||||   
------------------------------------------ctcattcttatatcttaatcatactggtcttactagtgcatc-------ttcattgac--------tgagg-----attgtgtcatgttc-tgatccttgttt--gttttgtgaaattaacagTTAATGCCAATTCTAGAAGCATTATATGATGCTCGAAGGAGGACAGC---TAATCAAATTTACATTTTGTTAATTATACTTCTCATACTTAGTCAAGATTCTT

upper sequence: AT1G04200.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: Vv05s0020g04100.t01 (Vitis vinifera), 3'ss of exon 8
gtatgattcataaatgcctctcaataagttccatgggtctatttcattcttttgttccattgtccttaaaagtagaaatccattcctctgttttactaacccttaagatgaagtccttatagtttcatattaatgatctatgctttaatattttttgatggacagTTGATGCCCATCCTGGAGACGCTGTATAACGCTTCAAAGAGAACATCATCTAATCAAATATACATGATGCTAATTGTACTTCTCATACTTAGTCAGGATT---
                                                          |   | |||||   ||  |         ||   ||||||    ||  | ||     |   | || |   |     |||  | || ||   ||   |   ||  |||||||||||||||  |||||||  ||||||| || |||| ||| ||||   |||||||||| |||||| || | ||| | ||||| ||||||||||||||||   
----------------------------------------------------------accattcttaattatatgaggaggcatttcatatttacttgatct-gacatagctgcagcacagctgagt----ttgacatgtgtttc--taccctgaaatcaacagTTGATGCCCATTTTGGAGACCTTGTATAATGCGTCAAGGAGGACAT---CTAATCAAATCTACATGTTGTTGATTATCCTTCTTATACTTAGTCAGGATTCCT

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|86088183|gb|DR383942.1|DR383942
EST:     ATTCCGACTTTAAGGAGTATGTGTTGGTGCGAACTGATTTGGATACTTTG                         TTGATGCCCATCCTGGAGACGCTGTATAACGCTTCAAAGAGAACATCATCT
genomic: ATTCCGACTTTAAGGAGTATGTGTTGGTGCGAACTGATTTGGATACTTTGgtatgattca ... tgatggacagTTGATGCCCATCCTGGAGACGCTGTATAACGCTTCAAAGAGAACATCATCT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagtccttatagtttcatattaatgatctatgctttaatattttttgatggacagTTGATGCCCATCCTGGAGACGCTGTATAACGCTTCAAAGAGAACATCATCTAATCAAATATACATGATGCTAATTGTACTTCTCATACTTAGTCAGGATT
                                      tatttttt  CT-rich tract
            tttcatattaatgatc  TA-rich tract