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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTCTAGCCAACAAGCTCTTCCTCCTCACTCATCCAGATGTTCCAGACATCGAGAAAGTCCAGCTCAAGTCTGAGGTTTTGGATTTCATCAGATCCCATGgttaagcagctccttttctctaatcagtgagaattagcttaatatttcttcgagattttatgttcctgatgtttcgttggtgtttttatttattttag

Basic information

species Arabidopsis thaliana
transcript AT4G24820.2
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G24820.2 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: EFJ29963 (Selaginella moellendorffii), 5'ss of exon 1
ATTCTAGCCAACAAGCTCTTCCTCCTCACTCATCCAGATGTTCCAGACATCGAGAAAGTCCAGCTCAAGTCTGAGGTTTTGGATTTCATCAGATCCCATGgttaagcagctccttttctctaatcagtgagaattagcttaatatttcttcgagattttatgttcctgatgtttcgttggtgtttttatttattttag
   || ||    ||||||||| | ||| |   ||| ||  |||||||||||||||| ||||||||||||   |||| | || ||| |  |||    |  |   |  | |           |||     |||| || | | |    || |  | ||||  |   || ||  | |  || |                   
GAGCTCGCACGTAAGCTCTTCTTGCTCTCAGCTCCGGAGATTCCAGACATCGAGAAGGTCCAGCTCAAG---GAGGATGTG-ATTGCGGCAG----CGAGAGAAGACGg-----------taa-----gagatttcggtgag--gttttgagggattccagcctcatggcggtgtgtag-------------------

upper sequence: AT4G24820.2 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: EFJ25080 (Selaginella moellendorffii), 5'ss of exon 1
ATTCTAGCCAACAAGCTCTTCCTCCTCACTCATCCAGATGTTCCAGACATCGAGAAAGTCCAGCTCAAGTCTGAGGTTTTGGATTTCATCAGATCCCATGgttaagcagctccttttctctaatcagtgagaattagcttaatatttcttcgagattttatgttcctgatgtttcgttggtgtttttatttattttag
   || ||    ||||||||| | ||| |   ||| ||  |||||||||||||||| ||||||||||||   |||| | || ||| |  |||    |  |   |  | |       |      || |||||  ||     | |    | ||  |    | |||                                   
GAGCTCGCACGTAAGCTCTTCTTGCTCTCAGCTCCGGAGATTCCAGACATCGAGAAGGTCCAGCTCAAG---GAGGATGTG-ATTGCGGCAG----CGAGAGAAGACGgtaagagatt-----tcggtgaggtttgagggattccagcctcatggcggtgtgtag---------------------------------
















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|47828397|gb|CK118081.1|CK118081
EST:     CGAGAAAGTCCAGCTCAAGTCTGAGGTTTTGGATTTCATCAGATCCCATG                         GTATGGCTCCTTTGTACGAAACCCTAATTGCCTCTTCGGTGCTGGATTTGG
genomic: CGAGAAAGTCCAGCTCAAGTCTGAGGTTTTGGATTTCATCAGATCCCATGgttaagcagc ... tttattttagGTATGGCTCCTTTGTACGAAACCCTAATTGCCTCTTCGGTGCTGGATTTGG
EST: gi|164190569|gb|ES023568.1|ES023568
EST:     AAAGTCCAGCTCAAGTCTGAGGTTTTGGATTTCATCAGATCCCATG                         GTATGGCTCCTTTGTACGAAACCCTAATTGCCTCTTCGGTGCTGGATTTGG
genomic: AAAGTCCAGCTCAAGTCTGAGGTTTTGGATTTCATCAGATCCCATGgttaagcagc ... tttattttagGTATGGCTCCTTTGTACGAAACCCTAATTGCCTCTTCGGTGCTGGATTTGG
EST: gi|116470488|gb|EG513080.1|EG513080
EST:     AGGTTTTGGATTTCATCAGATCCCATG                         GTATGGCTCCTTTGTACGAAACCCTAATTGCCTCTTCGGTGCTGGATTTGG
genomic: AGGTTTTGGATTTCATCAGATCCCATGgttaagcagc ... tttattttagGTATGGCTCCTTTGTACGAAACCCTAATTGCCTCTTCGGTGCTGGATTTGG
EST: gi|152037891|gb|BP801755.2|BP801755
EST:     CGAGAAAGTCCAGCTCAAGTCTGAGGTTTTGGATTTCATCAGATCCCATG                         GTATGGCTCCTTTGTACGAAACCCTAATTGCCTCTTCGGTGCTGGATTTGG
genomic: CGAGAAAGTCCAGCTCAAGTCTGAGGTTTTGGATTTCATCAGATCCCATGgttaagcagc ... tttattttagGTATGGCTCCTTTGTACGAAACCCTAATTGCCTCTTCGGTGCTGGATTTGG
EST: gi|116431061|gb|EG473653.1|EG473653
EST:     CGAGAAAGTCCAGCTCAAGTCTGAGGTTTTGGATTTCATCAGATCCCATG                         GTATGGCTCCTTTGTACGAAACCCTAATTGCCTCTTCGGTGCTGGATTTGG
genomic: CGAGAAAGTCCAGCTCAAGTCTGAGGTTTTGGATTTCATCAGATCCCATGgttaagcagc ... tttattttagGTATGGCTCCTTTGTACGAAACCCTAATTGCCTCTTCGGTGCTGGATTTGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATTCTAGCCAACAAGCTCTTCCTCCTCACTCATCCAGATGTTCCAGACATCGAGAAAGTCCAGCTCAAGTCTGAGGTTTTGGATTTCATCAGATCCCATGgttaagcagctccttttctctaatcagtgagaattagcttaatatttcttcgagattttatgttcctgatgtttcgttggtgtttttatttattttag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA