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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTGCTTGCATATTCTCTATAGTTGCTTGCATTGTTGGTAGTGATGAACTTTCCGAGGCTTCTCAGATACTCTCTTGCTGTGCTGATATGGTCTACTGCACgtctgtatttacttcttgtgatttttagattctccctctaatctattcatgttcacgaattgctaatattttgcggtcttgattttcttgcag

Basic information

species Arabidopsis thaliana
transcript AT1G63830.2
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G63830.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: LOC_Os03g03180.1 (Oryza sativa), 5'ss of exon 6
TTGCTTGCATATTCTCTATAGTTGCTTGCATTGTTGGTAGTGATGAACTTTCCGAGGCTTCTCAGATACTCTCTTGCTGTGCTGATATGGTCTACTGCACgtctgtatttacttct-tgtgatttttagattctccc--tctaatctattcatgttcacgaattgctaatattttgcggtcttgattttcttgcag
||||||| || |||||||||||||| |||||||||||||| || ||||| |||||||| || || || || |||| ||||||||||||||||| ||| | | | || ||| ||||| | | | | || ||||| | | | | | | ||| || |||| ||||||
TTGCTTGTATCTTCTCTATAGTTGCCGCTATTGTTGGTAGTGAAGAGCTTTCAGAGGCTTCCCAAATCCTTTCCTGCTTGTCTGATATGGTCTACTGCTCgtaagctctcataactctgttattttctcttctccatagttaagtcccccaatgttgataatcttgtgac-ctgtgcaccattt-tttttttgcag

upper sequence: AT1G63830.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: GRMZM2G060564_T04 (Zea mays), 5'ss of exon 5
TTGCTTGCATATTCTCTATAGTTGCTTGCATTGTTGGTAGTGATGAACTTTCCGAGGCTTCTCAGATACTCTCTTGCTGTGCTGATATGGTCTACTGCACgtctgtatttacttc-ttgtgatttttagattctccctctaatctattcatgttcacgaattgctaatattttgcggtcttgattttcttgcag
|||||||||| |||||||||||||| ||||||||||| || || ||||| |||||||| ||||| || ||| ||||| |||||||||| |||| | ||| ||| |||| | ||||| | | | | |||| || |||| | ||| ||| | ||||||
TTGCTTGCATCTTCTCTATAGTTGCAGCTATTGTTGGTAGCGAGGAGCTTTCAGAGGCTTCCCAGATCCTTAATTGTCTGTCTGATTTGGTCTACTGGACgtaaggccgcccttaactgtctttttgcaaatctccatagcaaatgtctcagttc------tgataatcctatgccac----attcttttgcag

upper sequence: AT1G63830.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: GRMZM2G060564_T02 (Zea mays), 5'ss of exon 6
TTGCTTGCATATTCTCTATAGTTGCTTGCATTGTTGGTAGTGATGAACTTTCCGAGGCTTCTCAGATACTCTCTTGCTGTGCTGATATGGTCTACTGCACgtctgtatttacttc-ttgtgatttttagattctccct--ctaatctattcatgttcacgaat---tgcta--atattttgcggtcttgattttcttgcag
|||||||||| |||||||||||||| ||||||||||| || || ||||| |||||||| ||||| || ||| ||||| |||||||||| |||| | ||| ||| |||| | ||||| | | ||| | | | | | | ||| | | |||||| | || | |
TTGCTTGCATCTTCTCTATAGTTGCAGCTATTGTTGGTAGCGAGGAGCTTTCAGAGGCTTCCCAGATCCTTAATTGTCTGTCTGATTTGGTCTACTGGACgtaaggccgcccttaactgtctttttgcaaatctccatagcaaatgtctcagttctgataatcctatgccacattcttttgcagggtttgtgcatgtatg-

upper sequence: AT1G63830.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: GRMZM2G060564_T01 (Zea mays), 5'ss of exon 6
TTGCTTGCATATTCTCTATAGTTGCTTGCATTGTTGGTAGTGATGAACTTTCCGAGGCTTCTCAGATACTCTCTTGCTGTGCTGATATGGTCTACTGCACgtctgtatttacttc-ttgtgatttttagattctccct--ctaatctattcatgttcacgaat---tgcta--atattttgc--ggtcttgattttcttgcag----------------------------------------------------------------------------------------
||||||||| |||||||||||||| ||||||||||| || || ||||| |||||||| ||||| || ||| ||||| |||||||||| |||| | ||| ||| |||| | ||||| | | ||| | | | | | | ||| | | |||||| ||| | | |||||
-TGCTTGCATCTTCTCTATAGTTGCAGCTATTGTTGGTAGCGAGGAGCTTTCAGAGGCTTCCCAGATCCTTAATTGTCTGTCTGATTTGGTCTACTGGACGtaaggccgcccttaactgtctttttgcaaatctccatagcaaatgtctcagttctgataatcctatgccacattcttttgcagggtttgtgcatgtatgcaggtatataactcattcttttcttctcgcaaccttactgatcagggctcttgtgaaccaaaccctcacatatccttcttgtggcattgaa

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|125256993|gb|EL271078.1|EL271078
EST:     CTCTTGCTGTGCTGATATGGTCTACTGCAC                         GGTCTGCGCATGTATGCAG
genomic: CTCTTGCTGTGCTGATATGGTCTACTGCACgtctgtattt ... tttcttgcagGGTCTGCGCATGTATGCAG
EST: gi|125185229|gb|EL200183.1|EL200183
EST:     TTCTCAGATACTCTCTTGCTGTGCTGATATGGTCTACTGCAC                         GGTCTGCGCATGTATGCAG
genomic: TTCTCAGATACTCTCTTGCTGTGCTGATATGGTCTACTGCACgtctgtattt ... tttcttgcagGGTCTGCGCATGTATGCAG
EST: gi|164227380|gb|EL976397.1|EL976397
EST:     TCCGAGGCTTCTCAGATACTCTCTTGCTGTGCTGATATGGTCTACTGCAC                         GGTCTGCGCATGTATGCAGACACA
genomic: TCCGAGGCTTCTCAGATACTCTCTTGCTGTGCTGATATGGTCTACTGCACgtctgtattt ... tttcttgcagGGTCTGCGCATGTATGCAGACACA
EST: gi|164133434|gb|ES055671.1|ES055671
EST:     GATACTCTCTTGCTGTGCTGATATGGTCTACTGCAC                         GGTCTGCGCATGTATGCAG
genomic: GATACTCTCTTGCTGTGCTGATATGGTCTACTGCACgtctgtattt ... tttcttgcagGGTCTGCGCATGTATGCAG
EST: gi|116478578|gb|EG521170.1|EG521170
EST:     GCTGTGCTGATATGGTCTACTGCAC                         GGTCTGCGCATGTATGCAG
genomic: GCTGTGCTGATATGGTCTACTGCACgtctgtattt ... tttcttgcagGGTCTGCGCATGTATGCAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTGCTTGCATATTCTCTATAGTTGCTTGCATTGTTGGTAGTGATGAACTTTCCGAGGCTTCTCAGATACTCTCTTGCTGTGCTGATATGGTCTACTGCACgtctgtatttacttcttgtgatttttagattctccctctaatctattcatgttcacgaattgctaatattttgcggtcttgattttcttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT