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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGCTTGCATATTCTCCATAGTTGCATGTATTGTCGGTATGGATGAGCTTTCAGAAGCTTCTCAGATACTCACATGTTGCTCTGACATGGTGTACTGCACgtaagaatcccccatccaaagtgccattcttataagtttcgatcaaaacccaattttaacctattgtcctgatatatcgtactttgcttggtctgcag

Basic information

species Arabidopsis thaliana
transcript AT4G23470.3
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G23470.3 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GRMZM2G060564_T04 (Zea mays), 5'ss of exon 5
TGGCTTGCATATTCTCCATAGTTGCATGTATTGTCGGTATGGATGAGCTTTCAGAAGCTTCTCAGATACTCACATGTTGCTCTGACATGGTGTACTGCACgtaagaatcccccatccaaagtgccattcttataagtttcgatcaaaacccaattttaacctattgtcctgatatatcgtactttgc-ttggtctgcag
| |||||||| ||||| |||||||||  |||||| ||||  || ||||||||||| ||||| ||||| || |  |||   |||||  |||| ||||| |||||||    |||      || || | || ||  || | || ||   ||     | | |       || |||||| ||| ||     | ||  | |||||
TTGCTTGCATCTTCTCTATAGTTGCAGCTATTGTTGGTAGCGAGGAGCTTTCAGAGGCTTCCCAGATCCTTAATTGTCTGTCTGATTTGGTCTACTGGACgtaaggccgccctt----aactgtc-tttttgcaaatctccatagcaaat--gtctca-------gttctgata-atcctatgccacattcttttgcag

upper sequence: AT4G23470.3 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GRMZM2G060564_T01 (Zea mays), 5'ss of exon 6
TGGCTTGCATATTCTCCATAGTTGCATGTATTGTCGGTATGGATGAGCTTTCAGAAGCTTCTCAGATACTCACATGTTGCTCTGACATGGTGTACTGCACgtaagaatcccccatccaaagtgccattcttataagtttcgatcaaaacccaattttaacctattgtcctgatatatcgtactttgcttggtctgcag--------------------------------------------------------------------------------------------------
  |||||||| ||||| |||||||||  |||||| ||||  || ||||||||||| ||||| ||||| || |  |||   |||||  |||| ||||| |||||||    |||      || || | || ||  || | || ||   ||     |     |  ||  ||||     |   |  |||||  ||| ||                                                                                                     
-TGCTTGCATCTTCTCTATAGTTGCAGCTATTGTTGGTAGCGAGGAGCTTTCAGAGGCTTCCCAGATCCTTAATTGTCTGTCTGATTTGGTCTACTGGACGtaaggccgccctt----aactgtc-tttttgcaaatctccatagcaaatgtctcagttctgataatcctatgccacattcttttgcagggtttgtgcatgtatgcaggtatataactcattcttttcttctcgcaaccttactgatcagggctcttgtgaaccaaaccctcacatatccttcttgtggcattgaa

upper sequence: AT4G23470.3 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GRMZM2G060564_T02 (Zea mays), 5'ss of exon 6
TGGCTTGCATATTCTCCATAGTTGCATGTATTGTCGGTATGGATGAGCTTTCAGAAGCTTCTCAGATACTCACATGTTGCTCTGACATGGTGTACTGCACgtaagaatcccccatccaaagtgccattcttataagtttcgatcaaaacccaattttaacctattgtcctgatatatcgtactttgcttggtctgcag-------
| |||||||| ||||| |||||||||  |||||| ||||  || ||||||||||| ||||| ||||| || |  |||   |||||  |||| ||||| |||||||    |||      || || | || ||  || | || ||   ||     |     |  ||  ||||     |   |  |||||  ||| ||          
TTGCTTGCATCTTCTCTATAGTTGCAGCTATTGTTGGTAGCGAGGAGCTTTCAGAGGCTTCCCAGATCCTTAATTGTCTGTCTGATTTGGTCTACTGGACgtaaggccgccctt----aactgtc-tttttgcaaatctccatagcaaatgtctcagttctgataatcctatgccacattcttttgcagggtttgtgcatgtatg

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|125015062|gb|EL087331.1|EL087331
EST:     AAGCTTCTCAGGTACTCACATGTTGCTCTGACATGGTGTACTGCAC                         GGTTTGCGCATGTATGCAG
genomic: AAGCTTCTCAGATACTCACATGTTGCTCTGACATGGTGTACTGCACgtaagaatcc ... tggtctgcagGGTTTGCGCATGTATGCAG
EST: gi|116434599|gb|EG477191.1|EG477191
EST:     TCAGAAGCTTTTCAGATACTCACATGTTGCTCTGACATGGTGTACTGCAC                         GGTTTGCGCATGTATGCAG
genomic: TCAGAAGCTTCTCAGATACTCACATGTTGCTCTGACATGGTGTACTGCACgtaagaatcc ... tggtctgcagGGTTTGCGCATGTATGCAG
EST: gi|124733258|gb|EH824660.1|EH824660
EST:     CAGAAGCTTCTCAGATACTCACATGTTGCTCTGACATGGTGTACTGCAC                         GGTTTGCGCATGTA
genomic: CAGAAGCTTCTCAGATACTCACATGTTGCTCTGACATGGTGTACTGCACgtaagaatcc ... tggtctgcagGGTTTGCGCATGTA
EST: gi|125304293|gb|EL318378.1|EL318378
EST:     TCAGAAGCTTCTCAGATACTCACATGTTGCTCTGACATGGTGTACTGCAC                         GGTTTGCGCATGTATGCAG
genomic: TCAGAAGCTTCTCAGATACTCACATGTTGCTCTGACATGGTGTACTGCACgtaagaatcc ... tggtctgcagGGTTTGCGCATGTATGCAG
EST: gi|301501098|gb|HO206638.1|HO206638
EST:     TCAAAAGCTTCTCAAATACTCACATGTTGCTCTGACATGGTGTACTGCAC                         GGTTTGCGCATGTATGCAG
genomic: TCAGAAGCTTCTCAGATACTCACATGTTGCTCTGACATGGTGTACTGCACgtaagaatcc ... tggtctgcagGGTTTGCGCATGTATGCAG
EST: gi|124720550|gb|EH811952.1|EH811952
EST:     AAGCTTCTCAGATACTCACATGTTGCTCTGACATGGTGTACTGCAC                         GGTTTGCGCATGTATGCAG
genomic: AAGCTTCTCAGATACTCACATGTTGCTCTGACATGGTGTACTGCACgtaagaatcc ... tggtctgcagGGTTTGCGCATGTATGCAG
EST: gi|125134662|gb|EL175419.1|EL175419
EST:     TGGTGTACTGCAC                         GGTTTGCGCATGTATGCAG
genomic: TGGTGTACTGCACgtaagaatcc ... tggtctgcagGGTTTGCGCATGTATGCAG
EST: gi|124993508|gb|EL065777.1|EL065777
EST:     CTCACATGTTGCTCTGACATGGTGTACTGCAC                         GGTTTGCGCATGTATGCAG
genomic: CTCACATGTTGCTCTGACATGGTGTACTGCACgtaagaatcc ... tggtctgcagGGTTTGCGCATGTATGCAG
EST: gi|125044209|gb|EL116478.1|EL116478
EST:     TCAGAAGCTTCTCAGATACTCACATGTTGCTCTGACATGGTGTACTGCAC                         GGTTTGCGCATGTATGC
genomic: TCAGAAGCTTCTCAGATACTCACATGTTGCTCTGACATGGTGTACTGCACgtaagaatcc ... tggtctgcagGGTTTGCGCATGTATGC
EST: gi|86038882|gb|DR334637.1|DR334637
EST:     TCAGAAGCTTCTCAGATACTCACATGTTGCTCTGACATGGTGTACTGCAC                         GGTTTGCGCATGTATGCAG
genomic: TCAGAAGCTTCTCAGATACTCACATGTTGCTCTGACATGGTGTACTGCACgtaagaatcc ... tggtctgcagGGTTTGCGCATGTATGCAG
EST: gi|124929398|gb|EL006946.1|EL006946
EST:     TCTGACATGGTGTACTGCAC                         GGTTTGCGCATGTATGCAG
genomic: TCTGACATGGTGTACTGCACgtaagaatcc ... tggtctgcagGGTTTGCGCATGTATGCAG
EST: gi|116434598|gb|EG477190.1|EG477190
EST:     TCAGAAGCTTCTCAGATACTCACATGTTGCTCTGACATGGTGTACTGCAC                         GGTTTGCGCATGTATGCAG
genomic: TCAGAAGCTTCTCAGATACTCACATGTTGCTCTGACATGGTGTACTGCACgtaagaatcc ... tggtctgcagGGTTTGCGCATGTATGCAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGGCTTGCATATTCTCCATAGTTGCATGTATTGTCGGTATGGATGAGCTTTCAGAAGCTTCTCAGATACTCACATGTTGCTCTGACATGGTGTACTGCACgtaagaatcccccatccaaagtgccattcttataagtttcgatcaaaacccaattttaacctattgtcctgatatatcgtactttgcttggtctgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC