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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTGCAAGGCGAGAGGAGCCGATCTCAGGGTCCACTTCAAGgtaaatttcttgtactgattccggatctcaaaaatgaattagattaagtgattttcctatggggattaagcttgtagtttgaataaaacctgattaacaa...

Basic information

species Arabidopsis thaliana
transcript AT1G27400.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G27400.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: EFJ21308 (Selaginella moellendorffii), 5'ss of exon 2
CTTGCAAGGCGAGAGGAGCCGATCTCAGGGTCCACTTCAAGgtaaatttcttgtactgattc-cggatctcaaaaatgaattagattaagtgattttcctatggggattaagcttgtagtttgaataaaacctgattaacaa
||||||||||||||||  |||||||| ||||||||||||||||   | |  |  | |||||    ||||       |   || |  | |  ||| |      |||  ||   | ||| |                       
CTTGCAAGGCGAGAGGCTCCGATCTCCGGGTCCACTTCAAGgtgtgtgtgattgattgattgatcgatccttgtgtt--cttgggctgaaagatct------gggctttcttcgtgtcgcag--------------------

upper sequence: AT1G27400.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: EFJ26852 (Selaginella moellendorffii), 5'ss of exon 2
CTTGCAAGGCGAGAGGAGCCGATCTCAGGGTCCACTTCAAGgtaaatttcttgtactgattccggatctcaaaaatgaattagattaagtgattttcctatggggattaagcttgtagtttgaataaaacctgattaacaa
||||||||||||||||  |||||||| ||||||||||||||||   | |  |  | ||||      |        ||   |  |  |  ||   || ||  | |    |                                
CTTGCAAGGCGAGAGGCTCCGATCTCCGGGTCCACTTCAAGgtgtgtgtgattgattgatcgatccttgtgttcttgggctgaaagatctgggctttcttcgtgtcgcag-------------------------------
















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|164229631|gb|ES057186.1|ES057186
EST:     CTTGCAAGGCGAGAGGAGCCGATCTCAGGGTCCACTTCAAG                         AACACTAGAGAAACAGCGCACGCC
genomic: CTTGCAAGGCGAGAGGAGCCGATCTCAGGGTCCACTTCAAGgtaaatttct ... tatgaaacagAACACTAGAGAAACAGCGCACGCC
EST: gi|47827860|gb|CK117544.1|CK117544
EST:     CTTGCAAGGCGAGAGGAGCCGATCTCAGGGTCCACTTCAAG                         AACACTAGAGAAACAGCGCACGCCATAAGGAAGCTACCATTGAACAAGGCC
genomic: CTTGCAAGGCGAGAGGAGCCGATCTCAGGGTCCACTTCAAGgtaaatttct ... tatgaaacagAACACTAGAGAAACAGCGCACGCCATAAGGAAGCTACCATTGAACAAGGCC
EST: gi|124823160|gb|EH908026.1|EH908026
EST:     CTTGCAAGGCGAGAGGAGCCGATCTCAGGGTCCACTTCAAG                         AACACTAGAGAAACAGCGCACG
genomic: CTTGCAAGGCGAGAGGAGCCGATCTCAGGGTCCACTTCAAGgtaaatttct ... tatgaaacagAACACTAGAGAAACAGCGCACG
EST: gi|86074318|gb|DR370075.1|DR370075
EST:     CTTGCAAGGCGAGAGGAGCCGATCTCAGGGTCCACTTCAAG                         WACACTAGAGAAACWGCGCACGCCATAAGGAAGCTACCATTGAACAAGGCC
genomic: CTTGCAAGGCGAGAGGAGCCGATCTCAGGGTCCACTTCAAGgtaaatttct ... tatgaaacagAACACTAGAGAAACAGCGCACGCCATAAGGAAGCTACCATTGAACAAGGCC
EST: gi|163982884|gb|ES002582.1|ES002582
EST:     CTTGCAAGGCGAGAGGAGCCGATCTCAGGGTCCACTTCAAG                         AACACTAGAGAAACAGCGCACGC
genomic: CTTGCAAGGCGAGAGGAGCCGATCTCAGGGTCCACTTCAAGgtaaatttct ... tatgaaacagAACACTAGAGAAACAGCGCACGC
EST: gi|116444090|gb|EG486682.1|EG486682
EST:     CTTGCAAGGCGAGAGGAGCCGATCTCAGGGTCCACTTCAAG                         AACACTAGAGAAACAGCGCACGCCATAAGGAAGCTACCATTGAACAAGGCC
genomic: CTTGCAAGGCGAGAGGAGCCGATCTCAGGGTCCACTTCAAGgtaaatttct ... tatgaaacagAACACTAGAGAAACAGCGCACGCCATAAGGAAGCTACCATTGAACAAGGCC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTTGCAAGGCGAGAGGAGCCGATCTCAGGGTCCACTTCAAGgtaaatttcttgtactgattccggatctcaaaaatgaattagattaagtgattttcctatggggattaagcttgtagtttgaataaaacctgattaacaa

- - - - - GAGAGG
- - - - -  AGAGGA
- - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caaaaatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aataaaa