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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTGGTATTTGTGAGCTTCCATTTCACCCTATTAGCTCTGAGGAGATTGGAGGCGTTGGTGGAACgtaagttccttgttgatgcattatcaaacgttggaatcttacacgatcttatacctttatttgtttccactttttttggctttcag

Basic information

species Arabidopsis thaliana
transcript AT3G24170.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G24170.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA02G08180.1 (Glycine max), 5'ss of exon 2
GTTGGTATTTGTGAGCTTCCATTTCACCCTATTAGCTCTGAGGAGATTGGAGGCGTTGGTGGAACgtaagttc----cttg-------ttgatgcattatcaaacgttggaatcttacacga--tcttatacctttatttgtttccactttttttggctttcag-
|| || |||||||||||||||||||| || |||||||| ||    |||||||| || |||||||||||||||     ||||       ||  | | ||  || |  ||    |||| |      |||    | ||||| |  | |     ||  |||||      
GTGGGGATTTGTGAGCTTCCATTTCATCCAATTAGCTCAGAAACAATTGGAGGAGTCGGTGGAACgtaagttataaacttgaaaacatttctttcctttccatagattattttctttcgtctcttctctctcttttatctaatgcatacattcctggctaattac

upper sequence: AT3G24170.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA16G27210.1 (Glycine max), 5'ss of exon 3
GTTGGTATTTGTGAGCTTCCATTTCACCCTATTAGCTCTGAGGAGATTGGAGGCGTTGGTGGAACgtaagttccttgttgatgcattatcaaacgttggaatcttacacg--atcttatacctttatttgtttccactttttttggctttcag-------------
|| || |||||||||||||||||||| || ||||| || ||    |||||||| || |||||||||||||||  | |||     |||   |    ||    |   | |    || || | ||     || | ||   ||| |||       |              
GTGGGGATTTGTGAGCTTCCATTTCATCCAATTAGTTCAGAAACAATTGGAGGAGTCGGTGGAACgtaagtta-tagttatgaaattgatatctctttcctttccatagattattttcttccgcctcttctctctcttttatttaatgcatacattccttgctaat
















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|116480237|gb|EG522829.1|EG522829
EST:     CTTCCATTTCACCCTATTAGCTCTGAGGAGATTGGAGGCGTTGGTGGAAC                         CTGTGTTATCCGTGGTTGTGTTCCTAAAAAGATTCTCGTCTATGGAGCTAC
genomic: CTTCCATTTCACCCTATTAGCTCTGAGGAGATTGGAGGCGTTGGTGGAACgtaagttcct ... tggctttcagCTGTGTTATCCGTGGTTGTGTTCCTAAAAAGATTCTCGTCTATGGAGCTAC
EST: gi|164086636|gb|EL972184.1|EL972184
EST:     CGTTGGTGGAAC                         CTGTGTTATCCGTTGGTTGTGTTCCTAAAAAAGATTCTCGTCTATGGAGCT
genomic: CGTTGGTGGAACgtaagttcct ... tggctttcagCTGTGTTATCCG-TGGTTGTGTTCCT-AAAAAGATTCTCGTCTATGGAGCT
EST: gi|125125374|gb|EL170860.1|EL170860
EST:     CCCTATTAGCTCTGAGGAGATTGGAGGCGTTGGTGGAAC                         CTGTGTTATCCGTGGTTGTGTTCCTAAAAAGATTCTCGTCTATGGAGCTAC
genomic: CCCTATTAGCTCTGAGGAGATTGGAGGCGTTGGTGGAACgtaagttcct ... tggctttcagCTGTGTTATCCGTGGTTGTGTTCCTAAAAAGATTCTCGTCTATGGAGCTAC
EST: gi|116428975|gb|EG471567.1|EG471567
EST:     CTTCCATTTCACCCTATTAGCTCTGAGGAGATTGGAGGCGTTGGTGGAAC                         CTGTGTTATCCGTGGTTGTGTTCCTAAAAAGATTCTCGTCTATGGAGCTAC
genomic: CTTCCATTTCACCCTATTAGCTCTGAGGAGATTGGAGGCGTTGGTGGAACgtaagttcct ... tggctttcagCTGTGTTATCCGTGGTTGTGTTCCTAAAAAGATTCTCGTCTATGGAGCTAC
EST: gi|125319978|gb|EL334063.1|EL334063
EST:     TCCATTTCACCCTATTAGCTCTGAGGAGATTGGAAGGACGTTGGTGGAAC                         CTGTGTTATCCGTGGTTGTGTTC
genomic: TCCATTTCACCCTATTAGCTCTGAGGAGATTGGA-GG-CGTTGGTGGAACgtaagttcct ... tggctttcagCTGTGTTATCCGTGGTTGTGTTC
EST: gi|116462895|gb|EG505487.1|EG505487
EST:     CTTCCATTTCACCCTATTAGCTCTGAGGAGATTGGAGGCGTTGGTGGAAC                         CTGTGTTATCCGTGGTTGTGTACCTAAAAAGATTCTCGTCTATGGAGCTAC
genomic: CTTCCATTTCACCCTATTAGCTCTGAGGAGATTGGAGGCGTTGGTGGAACgtaagttcct ... tggctttcagCTGTGTTATCCGTGGTTGTGTTCCTAAAAAGATTCTCGTCTATGGAGCTAC
EST: gi|164226499|gb|EL972258.1|EL972258
EST:     GTTGGTGGAAC                         CTGTGTTATCCGTTGGTTTGTGTTCCTAAAAAGATTCTCGTCTATGGAGCT
genomic: GTTGGTGGAACgtaagttcct ... tggctttcagCTGTGTTATCCG-TGG-TTGTGTTCCTAAAAAGATTCTCGTCTATGGAGCT
EST: gi|116422003|gb|EG464595.1|EG464595
EST:     CTTCCATTTCACCCTATTAGCTCTGAGGAGATTGGAGGCGTTGGTGGAAC                         CTGTGTTATCCGTGGTTGTGTTCCTAAAAAGATTCTCGTCTATGGAGCTAC
genomic: CTTCCATTTCACCCTATTAGCTCTGAGGAGATTGGAGGCGTTGGTGGAACgtaagttcct ... tggctttcagCTGTGTTATCCGTGGTTGTGTTCCTAAAAAGATTCTCGTCTATGGAGCTAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTGGTATTTGTGAGCTTCCATTTCACCCTATTAGCTCTGAGGAGATTGGAGGCGTTGGTGGAACgtaagttccttgttgatgcattatcaaacgttggaatcttacacgatcttatacctttatttgtttccactttttttggctttcag

- - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA