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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGCTGGACCTCCTTCACCAGCTGATCATTTGAGAGATGTTTTCTACAGAATGGGACTTGATGACAAGgttattttgattttgttctcttttgtgttattcatgtcaaacgtgaatatttttgttattctgaatattctttttgacaaacag

Basic information

species Arabidopsis thaliana
transcript AT1G77490.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G77490.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GRMZM2G120517_T03 (Zea mays), 5'ss of exon 6
ATGCTGGACCTCCTTCACCAGCTGATCATTTGAGAGATGTTTTCTACAGAATGGGACTTGATGACAAGgttattttgattttgttctcttttgtgttattcatgtcaaacgtgaatatttttgttattctgaatattctttttga-caaacag
||||||| ||   |||||| ||||| || ||||| || || |||||||||||||| ||| ||||||||||  |   |||   |  | |||      |||   |||| ||      |  ||  | | ||   |||  |  |  ||| |   |||
ATGCTGGCCCAAGTTCACCTGCTGACCACTTGAGGGAGGTATTCTACAGAATGGGCCTTAATGACAAGgt-gtgcagatcacga-cacttaaccagtatgtgtgtctaattgactttgttgagctgtttgaaattctaatcatgagcttgcag

upper sequence: AT1G77490.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: Vv18s0001g02470.t01 (Vitis vinifera), 5'ss of exon 6
ATGCTGGACCTCCTTCACCAGCTGATCATTTGAGAGATGTTTTCTACAGAATGGGACTTGATGACAAGgttattttgattttgttctcttttgtgttattcatgtcaaacgtgaatatt--tttgttattctgaatatt---ctttttgacaaacag
||||||| || |||||||| ||||||||| |  | |||||||||||||||||||| ||  ||||||||||||| || ||   |||| | ||    |||||| |        |   ||||  | | | ||  | | | ||   ||||||||     ||
ATGCTGGCCCCCCTTCACCTGCTGATCATCTACGTGATGTTTTCTACAGAATGGGGCTAAATGACAAGgttatattcatcaagttcacatt-actttattcttaagtgttatctctattgatatatgatgtttactgttgaactttttgatctttag
















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|125262954|gb|EL277039.1|EL277039
EST:     CAGCTGATCATTTGAGAGATGTTTTCTACAGAATGGGACTTGATGACAAG                         GAAATAGTTGCCTTGTCTGGTGCACATACCTTAGGGAGAGCC
genomic: CAGCTGATCATTTGAGAGATGTTTTCTACAGAATGGGACTTGATGACAAGgttattttga ... tgacaaacagGAAATAGTTGCCTTGTCTGGTGCACATACCTTAGGGAGAGCC
EST: gi|124856631|gb|EH941068.1|EH941068
EST:     GCTGATCATTTGAGAGATGTTTTCTACAGAATGGGACTTGATGACAAG                         GAAATAGTTGCCTTGTCTGGTGCACATACCTTAGGGAGAGCCAGA
genomic: GCTGATCATTTGAGAGATGTTTTCTACAGAATGGGACTTGATGACAAGgttattttga ... tgacaaacagGAAATAGTTGCCTTGTCTGGTGCACATACCTTAGGGAGAGCCAGA
EST: gi|125162625|gb|EL189395.1|EL189395
EST:     CAGCTGATCATTTGAGAGATGTTTTCTACAGAATGGGACTTGATGACAAG                         GAAATAGTTGCCTTGTCTGGTGCACATACCTT
genomic: CAGCTGATCATTTGAGAGATGTTTTCTACAGAATGGGACTTGATGACAAGgttattttga ... tgacaaacagGAAATAGTTGCCTTGTCTGGTGCACATACCTT
EST: gi|125292455|gb|EL306540.1|EL306540
EST:     CAGCTGATCATTTGAGAGATGTTTTCTACAGAATGGGACTTGATGACAAG                         GAAATAGTTGCCTTGTCTGGTGCACATA
genomic: CAGCTGATCATTTGAGAGATGTTTTCTACAGAATGGGACTTGATGACAAGgttattttga ... tgacaaacagGAAATAGTTGCCTTGTCTGGTGCACATA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATGCTGGACCTCCTTCACCAGCTGATCATTTGAGAGATGTTTTCTACAGAATGGGACTTGATGACAAGgttattttgattttgttctcttttgtgttattcatgtcaaacgtgaatatttttgttattctgaatattctttttgacaaacag

- - - - - - - - - CAGCTG
- - - - - - - - -  AGCTGA
- - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - -  GAGATG