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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGATGCGAGAGTTATGTGGGACCAAAAAACTGGGCGCTCGAGAGGCTTTGGGTTTGTTTCCTTCCGCAATCAACAGgtaatgtacattctttaaatcatgcagtgagtttttgttttagctcaaggattgttcgtggtttacattaatgttaaatgttgatttcatttgcag

Basic information

species Arabidopsis thaliana
transcript AT3G14100.1
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G14100.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: LOC_Os07g42380.1 (Oryza sativa), 5'ss of exon 7
GGATGCGAGAGTTATGTGGGACCAAAAAACTGGGCGCTCGAGAGGCTTTGGGTTTGTTTCCTTCCGCAATCAACAGgtaatgtacattctttaaatcatgcagtgagtttttgttttagctcaaggattgttcgtggtttacattaatgttaaatgttgatttcatttgcag
 |||||  ||||||||||||| ||||| |||||  | || ||||| | ||| |||||||||||| | ||||||||||||  ||| |||||  ||| || |      |  ||||| |  | ||   | ||  || ||  | || | ||    |  | ||   |    || |||
TGATGCCCGAGTTATGTGGGATCAAAAGACTGGAAGATCTAGAGGTTATGGCTTTGTTTCCTTCAGGAATCAACAGgtatggta-attcta-aaagcacgt-----gcatttgtatgggttctttgtttactcctg--tcacttaaaaaaaagttttttggtgagcttacag

upper sequence: AT3G14100.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: GLYMA16G01230.1 (Glycine max), 5'ss of exon 7
GGATGCGAGAGTTATGTGGGACCAAAAAACTGGGCGCTCGAGAGGCTTTGGGTTTGTTTCCTTCCGCAATCAACAGgtaatgtacattctttaaatcatgcagtgagtttttgttttagctcaaggattgttcgtggtttacattaatgttaaatgttgatttcatttgcag
 ||||| || ||||||||||| || || |||||||| || || || ||||| |||||||| ||||| |||||||||||      ||   ||    | ||    | | |||||| | |  |       ||  |  ||||||  | | |  ||   | |||| ||  |||| ||
AGATGCTAGGGTTATGTGGGATCAGAAGACTGGGCGTTCAAGGGGATTTGGATTTGTTTCATTCCGTAATCAACAGgtc-----caaatttggttttataatcttaatttttggtgtgacaaggctctttattatggttttgacttagatttt-tcttgaatt--tttgtag

upper sequence: AT3G14100.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: GLYMA07G04640.1 (Glycine max), 5'ss of exon 7
GGATGCGAGAGTTATGTGGGACCAAAAAACTGGGCGCTCGAGAGGCTTTGGGTTTGTTTCCTTCCGCAATCAACAGgtaatgtacattctttaaatcatgcagtgagtttttgttttagctcaaggattgttcgtggtttacattaatgttaaatgttgatttcatt--tgcag
 ||||| || ||||||||||| || || |||||||| || || || ||||| |||||||| ||||| || ||||||||  |        ||  |||| |      | ||||   | || |   |||  | ||  || | |   || |  | |||| ||  ||  |||  || ||
AGATGCAAGGGTTATGTGGGATCAGAAGACTGGGCGTTCAAGGGGATTTGGATTTGTTTCATTCCGTAACCAACAGgtggt-------tttagaatctt------aattttctgtgtaac---agggctctttatgatgttt-ttgacttaaaatttttcttgaatttttgtag

upper sequence: AT3G14100.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: Vv09s0002g00880.t01 (Vitis vinifera), 5'ss of exon 7
GGATGCGAGAGTTATGTGGGACCAAAAAACTGGGCGCTCGAGAGGCTTTGGGTTTGTTTCCTTCCGCAATCAACAGgtaatgtacattctttaaatcatgcagtgagtttttgttttagctcaaggattgttcgtggtttacattaatgttaaatgttgatttcatttg--cag
 |||||||| ||||||||||| || || |||||||| || ||||| ||||| |||||||| |||||||||||||||||  | |   ||||||  ||  | || |   ||||| ||  ||  ||   ||||||  |  |    |||      ||   || ||||| ||||  |||
AGATGCGAGGGTTATGTGGGATCAGAAGACTGGGCGTTCAAGAGGGTTTGGATTTGTTTCTTTCCGCAATCAACAGgt--tcttttttcttttgatttttcaat---ttttttttccaga-cagatattgtttcttctaataattttctacaatattttatttcttttgttcag

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|125049053|gb|EL121322.1|EL121322
EST:     AAACTGGGCGCTCGAGAGGCTTTGGGTTTGTTTCCTTCCGCAATCAACAG                         GATTGCTCAAACTG
genomic: AAACTGGGCGCTCGAGAGGCTTTGGGTTTGTTTCCTTCCGCAATCAACAGgtaatgtaca ... tcatttgcagGAT-GCTCAAACTG
EST: gi|116378429|gb|EG421021.1|EG421021
EST:     TTTGGGTTTGTTTCCTTCCGCAATCAACAG                         GATGCTCAAACCGCCATTAATGAGATGAATG
genomic: TTTGGGTTTGTTTCCTTCCGCAATCAACAGgtaatgtaca ... tcatttgcagGATGCTCAAACTGCCATTAATGAGATGAATG
EST: gi|124946125|gb|EL022074.1|EL022074
EST:     AAACTGGGCGCTCGAGAGGCTTTGGGTTTGTTTCCTTCTGCAATCAACAG                         GATGCTCAAACTGCCATTAA
genomic: AAACTGGGCGCTCGAGAGGCTTTGGGTTTGTTTCCTTCCGCAATCAACAGgtaatgtaca ... tcatttgcagGATGCTCAAACTGCCATTAA
EST: gi|164012874|gb|ES123181.1|ES123181
EST:     AAACTGGGCGCTCGAGAGGCTTTGGGTTTGTTTCCTTCCGCAATCAACAG                         GATGCTCAAACTGCC
genomic: AAACTGGGCGCTCGAGAGGCTTTGGGTTTGTTTCCTTCCGCAATCAACAGgtaatgtaca ... tcatttgcagGATGCTCAAACTGCC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGATGCGAGAGTTATGTGGGACCAAAAAACTGGGCGCTCGAGAGGCTTTGGGTTTGTTTCCTTCCGCAATCAACAGgtaatgtacattctttaaatcatgcagtgagtttttgttttagctcaaggattgttcgtggtttacattaatgttaaatgttgatttcatttgcag

- - - - - - - - - - - - - - - - - - -  GAGAGG