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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACATTTGATGCGGTTGATGGGAAGCAAGCAAGAAGGACAAATTCCTCTAGCCCCCTAGGAGAGCTCTTCGATCATGgtgatttatttttcccatgttcctcctttgattatctgttttcagtttgtttctagatttttctgacatgtgttccaatattgcag

Basic information

species Arabidopsis thaliana
transcript AT1G13560.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G13560.2 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GLYMA12G08720.1 (Glycine max), 5'ss of exon 6
ACATTTGATGCGGTTGATGGGAAGCAAGCAAGAAGGACAAATTCCTCTAGCCCCCTAGGAGAGCTCTTCGATCATGgtgatttatttttcccatgttcctcctttgattatctgttttca-gtttgtttctagattttt--ctgacatgtgttccaata---ttgcag
||||||||||| ||||||||||||||||| ||| | ||||||||||| |||||  | || |||||||| ||||||||||||||   |      | ||  || ||  ||| | | |  | | |  |   | |   || ||     | |||| ||| | |    ||||||
ACATTTGATGCTGTTGATGGGAAGCAAGCTAGACGAACAAATTCCTCAAGCCCATTGGGGGAGCTCTTTGATCATGgtgattttcctgcattgtttttttcattctattgtttttcattatgcatacctgtttgttattaatgaagatgttttcaactgtatttgcag

upper sequence: AT1G13560.2 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GLYMA02G14210.1 (Glycine max), 5'ss of exon 6
ACATTTGATGCGGTTGATGGGAAGCAAGCAAGAAGGACAAATTCCTCTAGCCCCCTAGGAGAGCTCTTCGATCATGgtgatttatttttcccatgttcctcctttgattatctgttttca-gtttgtttctagattttt--ctgacatgtgttccaata---ttgcag
||||||||||| ||||| ||||||||||| ||| | ||||||||||| |||||  | || |||||||| ||||||||||||||   |      ||||  || ||  ||||| | |  | | | ||   | |  ||| ||     | |||| ||| | |    ||||||
ACATTTGATGCTGTTGACGGGAAGCAAGCTAGACGAACAAATTCCTCAAGCCCATTGGGGGAGCTCTTTGATCATGgtgattttcctgcattgtgtttttcattctattatttttcattatgcttacctgtttattattaatgaagatgttttcaactgtatttgcag

upper sequence: AT1G13560.2 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: Vv01s0010g00950.t01 (Vitis vinifera), 5'ss of exon 6
ACATTTGATGCGGTTGATGGGAAGCAAGCAAGAAGGACAAATTCCTCTAGCCCCCTAGGAGAGCTCTTCGATCATGgtgatttatttttcccatgttcctcctttgattatct----gttttcagttt-gtttctagattttt-ctgacatgtgttccaatattgcag
|| |||||||| ||||||||||||||||||||  |||||||||||||||| ||  | ||||| || || || |||||||||||    ||  ||| |  ||  |||    || |    ||| | | |||       |||| | |  |||||  || |    ||||||||
ACTTTTGATGCTGTTGATGGGAAGCAAGCAAGGCGGACAAATTCCTCTAGTCCATTGGGAGAACTTTTTGACCATGgtgatttccccttgtcatatatcttattttggcattttgaagttctgaatttcaaagggagatatatattgacacatgatt---tattgcag

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|86070079|gb|DR365836.1|DR365836
EST:     AGCAAGAAGGACAAATTCCTCTAGCCCCCTAGGAGAGCNCTTCCATCATG                         TTTGTGACGCGCTTGCTTGTGCGTTTGAAGCC
genomic: AGCAAGAAGGACAAATTCCTCTAGCCCCCTAGGAGAGCTCTTCGATCATGgtgatttatt ... aatattgcagGTTGTGACGCGCTTGCTTGTGCGTTTGAAGCC
EST: gi|86070078|gb|DR365835.1|DR365835
EST:     AGCAAGAAGGACAAATTCCTCTAGCCCCCTAGGAGAGCTCTTCGATCATG                         GTTGTGACGCGCTT
genomic: AGCAAGAAGGACAAATTCCTCTAGCCCCCTAGGAGAGCTCTTCGATCATGgtgatttatt ... aatattgcagGTTGTGACGCGCTT
EST: gi|86070080|gb|DR365837.1|DR365837
EST:     AGCAAGAAGGACAAATTCCTCTAGCCCCCTAGGAGAGCTCTTCGATCATG                         GTTGTGACGCGCTTGCTTGTGCG
genomic: AGCAAGAAGGACAAATTCCTCTAGCCCCCTAGGAGAGCTCTTCGATCATGgtgatttatt ... aatattgcagGTTGTGACGCGCTTGCTTGTGCG
EST: gi|86070077|gb|DR365834.1|DR365834
EST:     AGCAAGAAGGACAAATTCCTCTAGCCCCCTAGGAGAGCTCTTCGATCATG                         GTTGTGACGCGCTTGCTTGTGCG
genomic: AGCAAGAAGGACAAATTCCTCTAGCCCCCTAGGAGAGCTCTTCGATCATGgtgatttatt ... aatattgcagGTTGTGACGCGCTTGCTTGTGCG
EST: gi|86070081|gb|DR365838.1|DR365838
EST:     AGCAAGAAGGACAAATTCCTCTAGCCCCCTAGGAGAGCTCTTCGATCATG                         GTTGTGACGCGCTTGCTTGTGCG
genomic: AGCAAGAAGGACAAATTCCTCTAGCCCCCTAGGAGAGCTCTTCGATCATGgtgatttatt ... aatattgcagGTTGTGACGCGCTTGCTTGTGCG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACATTTGATGCGGTTGATGGGAAGCAAGCAAGAAGGACAAATTCCTCTAGCCCCCTAGGAGAGCTCTTCGATCATGgtgatttatttttcccatgttcctcctttgattatctgttttcagtttgtttctagatttttctgacatgtgttccaatattgcag

- - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT