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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgacttgatcaaatccgtatatgtaatgtaaaaaagtgttactagcagctatcccctcgtagaacagaaaataaactctcagacttctctacctcatcttgtggtgcatatgactgcagATCTCGAAAAAAGGACAAATTACGATACCGATACCCTCGTGGAGAGTCCTACCTTGATGTAATCCAACG

Basic information

species Arabidopsis thaliana
transcript AT1G07110.1
intron # 19
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G07110.1 (Arabidopsis thaliana), 3'ss of exon 19
lower sequence: LOC_Os05g07130.2 (Oryza sativa), 3'ss of exon 19
gtaagtgacttgatcaaatccgtatatgtaatgtaaaaaagtgttactagcagctatcccctcgtagaacagaaaataaactctcagacttctctacctcatcttgtggtgcatatgactgc-agATCTCGAAAAAAGGACAAATTACGATACCGATACCCTCGTGGAGAGTCCTACCTTGATGTAATCCAACG
                        | |||||       |  | | ||| || | |   |     |  |    |   |    | | | ||   | |    | | ||    | | | |  |  | ||||| || || |||||||||||| |||| |||||||| |||||||| || ||||||||||| || ||  |
------------------------tgtgtaagtcttgcacttatcactggctggtccacttgtatttattgaatgcttgcatatgaaacacttatgatgc-ttttccaatacttgttgcaaccagATCACGCAAGAAGGACAAATTAAGATATCGATACCCCCGTGGAGAATCTTACCTTGATGTGATTCAGAG
















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|124886394|gb|EH965296.1|EH965296
EST:     TGCCAGAAGAATACGA                         ATCTCGAAAAAAGGACAAATTACGATACCGATACCCTCGTGGAGAGTCCTA
genomic: TGCCAGAAGAATACGAgtaagtgact ... atgactgcagATCTCGAAAAAAGGACAAATTACGATACCGATACCCTCGTGGAGAGTCCTA
EST: gi|124956129|gb|EL031083.1|EL031083
EST:     GATGGGATGACATATGAAGAGGTAAAGAAGAACATGCCAGAAGAATACGA                         ATCTCGAAAAAAGGACAAATTACGATACCGATACCCTCGTGGAGAGTCCTA
genomic: GATGGGATGACATATGAAGAGGTAAAGAAGAACATGCCAGAAGAATACGAgtaagtgact ... atgactgcagATCTCGAAAAAAGGACAAATTACGATACCGATACCCTCGTGGAGAGTCCTA
EST: gi|116416224|gb|EG458816.1|EG458816
EST:     GATGGGATGACATATGAAGAGGTAAAGAAGAACATGCCAGAAGAATACGA                         ATCTCGAAAAAAGGACAAATTACGATACCGATACCCTCGTGGAGAGTCCTA
genomic: GATGGGATGACATATGAAGAGGTAAAGAAGAACATGCCAGAAGAATACGAgtaagtgact ... atgactgcagATCTCGAAAAAAGGACAAATTACGATACCGATACCCTCGTGGAGAGTCCTA
EST: gi|124761435|gb|EH851565.1|EH851565
EST:     TATGAAGAGGTAAAGAAGAACATGCCAGAAGAATACGA                         ATCTCGAAAAAAGGACAAATTACGATACCGATACCCT
genomic: TATGAAGAGGTAAAGAAGAACATGCCAGAAGAATACGAgtaagtgact ... atgactgcagATCTCGAAAAAAGGACAAATTACGATACCGATACCCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cagaaaataaactctcagacttctctacctcatcttgtggtgcatatgactgcagATCTCGAAAAAAGGACAAATTACGATACCGATACCCTCGTGGAGAGTCCTACCTTGATGTAATCCAACG
     aataaact  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtgacttgatcaaatccgtatatgtaatgtaaaaaagtgttactagcagctatcccctcgtagaacagaaaataaactctcagacttctctacctcatcttgtggtgcatatgactgcagATCTCGAAAAAAGGACAAATTACGATACCGATACCCTCGTGGAGAGTCCTACCTTGATGTAATCCAACG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA