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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TAAACTCAGTGACCGGTTTCCTCAGCCATATGCAAATGAATCAGCTGCAAGGTTTGCTAATGGTGGAGCGTATCCTCCTGATCTAAGTCTTATAACTAAGgtctgctgctgctactttactttaactgaacatctgtagcaaacttgtgttttgtgttttaaatagttttaatgttctgccttccag

Basic information

species Arabidopsis thaliana
transcript AT3G27240.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G27240.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA16G06700.1 (Glycine max), 5'ss of exon 5
TAAACTCAGTGACCGGTTTCCTCAGCCATATGCAAATGAATCAGCTGCAAGGTTTGCTAATGGTGGAGCGTATCCTCCTGATCTAAGTCTTATAACTAAGgtctgctgctgctactttactttaactgaacatctgtagcaaacttgtgttttgtgttt--taaatagttttaatgttctg-ccttccag
|||||||||||| || |||||||||||||||||||||||| ||||||| |||||||||||||| ||||| |||||||| |||||||||||| | || || ||       ||||| || | || |    ||  ||| | | ||  || |  | | ||| |     | |  | ||   || ||   || |||
TAAACTCAGTGATCGTTTTCCTCAGCCATATGCAAATGAAGCAGCTGCTAGGTTTGCTAATGGAGGAGCTTATCCTCCAGATCTAAGTCTTGTTACCAAAgt-----aatgctaatt-atttgatagtaatgtctttgg-aattttctaatgtatgtctacctgaaatatatatccttgtgatttttcag

upper sequence: AT3G27240.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA19G24620.2 (Glycine max), 5'ss of exon 4
TAAACTCAGTGACCGGTTTCCTCAGCCATATGCAAATGAATCAGCTGCAAGGTTTGCTAATGGTGGAGCGTATCCTCCTGATCTAAGTCTTATAACTAAGgtctgctgctgctactttactttaactgaacatctgtagcaaacttgtgttttgtgttt---taaatagttttaatgttctg-ccttccag
||||||||| || || |||||||||||||||||||||||| ||||||| |||||||||||||| ||||| |||||||| |||||||||||||| || || ||       ||||| || | || |    || |||| |   ||  || |  | | ||| |   | || |  | ||   || ||   || |||
TAAACTCAGCGATCGTTTTCCTCAGCCATATGCAAATGAAGCAGCTGCTAGGTTTGCTAATGGAGGAGCTTATCCTCCAGATCTAAGTCTTATTACCAAAgt-----aatgctaatt-atttgatagtaatatctttga-aattttctaatgtatgtctacctgaaaatatatatccttttgatttttcag

upper sequence: AT3G27240.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA05G07020.1 (Glycine max), 5'ss of exon 4
TAAACTCAGTGACCGGTTTCCTCAGCCATATGCAAATGAATCAGCTGCAAGGTTTGCTAATGGTGGAGCGTATCCTCCTGATCTAAGTCTTATAACTAAGgtctgctgctgctactttactttaactgaacatctgtag-caaacttgtg-ttttgtgttttaaatagttttaatgttctgccttccag
|||||||||||| || ||||| |||||||||||||||||| |||| || |||||||||||||| ||||| |||||||| |||||||||||| | || || ||    ||    || | | ||  |    ||| ||| |||     ||| || |||| | |  |||||| |||||   ||     || |||
TAAACTCAGTGATCGCTTTCCCCAGCCATATGCAAATGAAGCAGCAGCTAGGTTTGCTAATGGAGGAGCCTATCCTCCAGATCTAAGTCTTGTTACCAAAgt--aatgagtgtagtctgct--agt--aacgtctttagattttcttttgcttttatatcataaataattttaccctta-atgtttcag

upper sequence: AT3G27240.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA19G22530.2 (Glycine max), 5'ss of exon 4
TAAACTCAGTGACCGGTTTCCTCAGCCATATGCAAATGAATCAGCTGCAAGGTTTGCTAATGGTGGAGCGTATCCTCCTGATCTAAGTCTTATAACTAAGgtctgctgctgctactttactttaactgaacatctgtagcaaacttgtgttttgtgttttaaatagttttaatgttctgccttccag
|||||||||||| || ||||| |||||||||||||||||| |||| || |||||||||||||| ||||| |||||||| |||||||||||| | || || ||    ||    || | | ||   | ||    | |  |       |   |||| | |   ||||| |||||   ||     || |||
TAAACTCAGTGATCGCTTTCCCCAGCCATATGCAAATGAAGCAGCAGCTAGGTTTGCTAATGGAGGAGCCTATCCTCCAGATCTAAGTCTTGTTACCAAAgt--aatgactgtagtctgctagtaatg--tttttagattttctattgcttttatatcggaaataattttaccctta-atatttcag

upper sequence: AT3G27240.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: Vv09s0002g05950.t01 (Vitis vinifera), 5'ss of exon 3
TAAACTCAGTGACCGGTTTCCTCAGCCATATGCAAATGAATCAGCTGCAAGGTTTGCTAATGGTGGAGCGTATCCTCCTGATCTAAGTCTTATAACTAAGgtctgctgctgctactttactttaactgaacatctgtagcaaacttgtgttttgtgttttaaatagttttaatgttctgccttccag
 || || ||||| || ||||||||||| ||||||||||||  ||| || || ||||||||||| ||||| |||||||| ||||||||||| || || ||||| |  |  |  |  | ||  |    |||      | ||  ||    |||        |  ||||  |  | | ||   |||  |||
AAAGCTAAGTGATCGTTTTCCTCAGCCTTATGCAAATGAACAAGCAGCTAGATTTGCTAATGGAGGAGCATATCCTCCAGATCTAAGTCTCATCACCAAGgtat--taattttgttatagatcccttga----tagaagtgaatggctgtcc-acccctacaataactg-actctttgtcctctcag

upper sequence: AT3G27240.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: Vv14s0171g00330.t01 (Vitis vinifera), 5'ss of exon 4
TAAACTCAGTGACCGGTTTCCTCAGCCATATGCAAATGAATCAGCTGCAAGGTTTGCTAATGGTGGAGCGTATCCTCCTGATCTAAGTCTTATAACTAAGgtctgctgctgctactttactttaactgaacatctgtagcaaacttgtgttttgtgttttaaatagttttaatgttctgccttccag
|||||||||||| || ||||||||||||||||||||||||  ||||||  ||||||||||||| ||||| |||||||| |||||||| ||||| || || ||    | ||  |  | |  |||  ||    ||    |  |    | |||| |     | | |   | ||  | || | | || |||
TAAACTCAGTGATCGTTTTCCTCAGCCATATGCAAATGAACAAGCTGCTCGGTTTGCTAATGGAGGAGCTTATCCTCCAGATCTAAGCCTTATCACCAAAgta-atttcta-tgttctggtttggcttcttatggagattatgtctatgttatccaagtgata---tcttgcttttgttcttttcag

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|124940266|gb|EL016732.1|EL016732
EST:     GGTTTGCTAATGGTGGAGCGTATCCTCCTGATCTAAGTCTTATAACTAAG                         GCACGTCACAATGGTCCAAA
genomic: GGTTTGCTAATGGTGGAGCGTATCCTCCTGATCTAAGTCTTATAACTAAGgtctgctgct ... tgccttccagGCACGTCACAATGGTCCAAA
EST: gi|125195190|gb|EL210144.1|EL210144
EST:     GTTTGCTAATTGGTGGAGCGTATCCTCCTGATCTAAGTCTTATAACTAAG                         GCACGTCACAATGGTCCAAACTATGTCTTTGCGCTT
genomic: GTTTGCTAA-TGGTGGAGCGTATCCTCCTGATCTAAGTCTTATAACTAAGgtctgctgct ... tgccttccagGCACGTCACAATGGTCCAAACTATGTCTTTGCGCTT
EST: gi|164101472|gb|ES113881.1|ES113881
EST:     CCTGATCTAAGTCTTATAACTAAG                         GCACGTCACAATGGTCCAAACTATGTCTTTGCGCTTCTGACTGGTTACCGT
genomic: CCTGATCTAAGTCTTATAACTAAGgtctgctgct ... tgccttccagGCACGTCACAATGGTCCAAACTATGTCTTTGCGCTTCTGACTGGTTACCGT
EST: gi|86050717|gb|DR346472.1|DR346472
EST:     GGTTTGCTAATGGTGGAGCGTATCCTCCTGATCTAAGTCTTATCACTAAG                         GCACGTCACAATGGTCCAAACTATGTCTTTGCGCTT
genomic: GGTTTGCTAATGGTGGAGCGTATCCTCCTGATCTAAGTCTTATAACTAAGgtctgctgct ... tgccttccagGCACGTCACAATGGTCCAAACTATGTCTTTGCGCTT
EST: gi|125185087|gb|EL200041.1|EL200041
EST:     CCTCCTGATCTAAGTCTTATGACTAAG                         GCACGTCACAATGGTCCAAACTATGTCTTTGCGCTTCTGACTGGTTACCGT
genomic: CCTCCTGATCTAAGTCTTATAACTAAGgtctgctgct ... tgccttccagGCACGTCACAATGGTCCAAACTATGTCTTTGCGCTTCTGACTGGTTACCGT
EST: gi|86050723|gb|DR346478.1|DR346478
EST:     GGTTTGCTAATGGTGGAGCGTATCCTCCTGATCTAAGTCTTATCACTAAG                         GCACGTCACAATGGTCCAAACTATGTCTTTGCGCTTCTGACTGGTTACCGT
genomic: GGTTTGCTAATGGTGGAGCGTATCCTCCTGATCTAAGTCTTATAACTAAGgtctgctgct ... tgccttccagGCACGTCACAATGGTCCAAACTATGTCTTTGCGCTTCTGACTGGTTACCGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TAAACTCAGTGACCGGTTTCCTCAGCCATATGCAAATGAATCAGCTGCAAGGTTTGCTAATGGTGGAGCGTATCCTCCTGATCTAAGTCTTATAACTAAGgtctgctgctgctactttactttaactgaacatctgtagcaaacttgtgttttgtgttttaaatagttttaatgttctgccttccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG