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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATAAATGTAATGTGGTTGGACTTTGTGACTTACCTGCATCACCATGGTCATGAAGATAAGCTTCCTTGGTACCGTGGCAAGgtaaaatacatattctctgcttccactgttctttgactacatcgctctttcttttaaggttaaagccaactggtgtgtaaatctcatgattctcccaaaacag

Basic information

species Arabidopsis thaliana
transcript AT3G11170.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G11170.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: LOC_Os03g18070.1 (Oryza sativa), 5'ss of exon 6
ATAAATGTAATGTGGTTGGACTTTGTGACTTACCTGCATCACCATGGTCATGAAGATAAGCTTCCTTGGTACCGTGGCAAGgtaaaatacat-----attctctgcttccactgttctttgactacatcgctctt-tcttttaaggttaaagccaactggtgtgtaaatctcatgattctcccaaaacag
|||  ||| |||||| | || ||||| || ||  |||| || ||||| ||||| || |||||||||||||||||||| ||||||||  | ||     ||| | ||  |   || ||  |  |  |        |   |  |||| ||| ||   |||| |    ||   |   |   | |          
ATATTTGTTATGTGGCTTGATTTTGTCACATATTTGCACCATCATGGCCATGAGGACAAGCTTCCTTGGTACCGTGGAAAGgtaaataatattattaattgtatgggtttgctatttgtaaatgattcaaggatggccacttaatgttgaaa--aactaggagatagtccatttttgtttgtt-------

upper sequence: AT3G11170.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: Vv13s0067g01120.t01 (Vitis vinifera), 5'ss of exon 6
ATAAATGTAATGTGGTTGGACTTTGTGACTTACCTGCATCACCATGGTCATGAAGATAAGCTTCCTTGGTACCGTGGCAAGgta--aaatacatattctctgcttccactgttctttgactacatcgctctttcttttaa-------ggttaaagccaactggtg-tgtaaatctcatgattctcccaaaacag--------------------------
||    || ||||||||||| || ||||||||| ||||||||||||| |||||||| |||||||||||||| ||||| ||||||  |||| ||  ||||||   |      | ||     ||  ||  ||||   |  ||       ||  |||    | || |  |  | |  |||  ||| |  |  || |                           
ATTTTCGTCATGTGGTTGGATTTAGTGACTTACTTGCATCACCATGGCCATGAAGAGAAGCTTCCTTGGTATCGTGGAAAGgtatcaaattcagtttctctagattaggcctgctgattatatttcattcttcgctgcaacaaagagggaaaaaagagaatgctaataaacaattcagcattttaactgaaaacccgacttctggctctgtttttcacag
















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|125241998|gb|EL256083.1|EL256083
EST:     CACCATGGTCATGAAGATAAGCTTCCTTGGTACCGTGGCAAG                         GAGTGGAGTTACCTGAGAGGAGGACTTACAACATTGGATCGTGACTACGGA
genomic: CACCATGGTCATGAAGATAAGCTTCCTTGGTACCGTGGCAAGgtaaaataca ... cccaaaacagGAGTGGAGTTACCTGAGAGGAGGACTTACAACATTGGATCGTGACTACGGA
EST: gi|124754906|gb|EH845036.1|EH845036
EST:     CTTCCTTGGTACCGTGGCAAG                         GAGTGGAGTTACCTGAGAGGAGGACTTACAACATTGGGTCGTGACTACGGA
genomic: CTTCCTTGGTACCGTGGCAAGgtaaaataca ... cccaaaacagGAGTGGAGTTACCTGAGAGGAGGACTTACAACATTGGATCGTGACTACGGA
EST: gi|125207205|gb|EL222159.1|EL222159
EST:     ACCTGCATCACCATGGTCATGAAGATAAGCTTCCTTGGTACCGTGGCAAG                         GAGTGGAGTTACCTGAGAGGAGGA
genomic: ACCTGCATCACCATGGTCATGAAGATAAGCTTCCTTGGTACCGTGGCAAGgtaaaataca ... cccaaaacagGAGTGGAGTTACCTGAGAGGAGGA
EST: gi|125086049|gb|EL145659.1|EL145659
EST:     CCATGGTCATGAAGATAAGCTTCCTTGGTACCGTGGCAAG                         GAGTGGAGTTACCTGAGAGGAGGACTTACAACATTGGATCGTGACTACGGA
genomic: CCATGGTCATGAAGATAAGCTTCCTTGGTACCGTGGCAAGgtaaaataca ... cccaaaacagGAGTGGAGTTACCTGAGAGGAGGACTTACAACATTGGATCGTGACTACGGA
EST: gi|125086240|gb|EL145779.1|EL145779
EST:     CCTGCATCACCATGGTCATGAAGATAAGCTTCCTTGGTACCGTGGCAAG                         GAGTGGAGTTACCTGAGAGGAGGACTTACAACATTGGATCGTGACTACGGA
genomic: CCTGCATCACCATGGTCATGAAGATAAGCTTCCTTGGTACCGTGGCAAGgtaaaataca ... cccaaaacagGAGTGGAGTTACCTGAGAGGAGGACTTACAACATTGGATCGTGACTACGGA
EST: gi|124770625|gb|EH860755.1|EH860755
EST:     ACCTGCATCACCATGGTCATGAAGATAAGCTTCCTTGGTACCGTGGCAAG                         GAGTGGAGTTA
genomic: ACCTGCATCACCATGGTCATGAAGATAAGCTTCCTTGGTACCGTGGCAAGgtaaaataca ... cccaaaacagGAGTGGAGTTA
EST: gi|116378423|gb|EG421015.1|EG421015
EST:     ACCTGCATCACCATGGTCATGAAGATAAGCTTCCTTGGTACCGTGGCAAG                         GAGTGGAGTTACCTGAGAGGAGGACTTACAACATTGGATCGTGACTACGGA
genomic: ACCTGCATCACCATGGTCATGAAGATAAGCTTCCTTGGTACCGTGGCAAGgtaaaataca ... cccaaaacagGAGTGGAGTTACCTGAGAGGAGGACTTACAACATTGGATCGTGACTACGGA
EST: gi|124761279|gb|EH851409.1|EH851409
EST:     CTTCCTTGGTACCGTGGCAAG                         GAGTGGAGTTACCTTGAGAGGAGGACTTACAACATTGGATCGTGACTACGG
genomic: CTTCCTTGGTACCGTGGCAAGgtaaaataca ... cccaaaacagGAGTGGAGTTACC-TGAGAGGAGGACTTACAACATTGGATCGTGACTACGG

Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATAAATGTAATGTGGTTGGACTTTGTGACTTACCTGCATCACCATGGTCATGAAGATAAGCTTCCTTGGTACCGTGGCAAGgtaaaatacatattctctgcttccactgttctttgactacatcgctctttcttttaaggttaaagccaactggtgtgtaaatctcatgattctcccaaaacag

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