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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTAAACTGTGGGGTGAAAAGCGGTTTTCTACGCCTGGTCTGAAGCTGAAAAACCATGTGGATCTTGTTGAGCTTCTCGGTATTGCAGATACCAAAAGAGgtagtattgacttgcactttgccgacctccttgctctgtgttaaagggtttttgtgctatagggtttcaattgtaatgctattttggcctcag

Basic information

species Arabidopsis thaliana
transcript AT5G27470.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G27470.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA10G29600.1 (Glycine max), 5'ss of exon 4
---------ATTAAACTGTGGGGTGAAAAGCGGTTTTCTACGCCTGGTCTGAAGCTGAAAAACCATGTGGATCTTGTTGAGCTTCTCGGTATTGCAGATACCAAAAGAGgtagtattgacttgcac-tttgccgacctccttgctctgtgttaaagggtttttgtgctatagggtttcaattgtaatgctattttggcctcag-----------
          ||| |  |||||| || ||  |  |          |  |  |||||||| || ||||||||||| |||||||||||||||||||||||||| || | ||||    |  | |||  | | |   ||     |     | | || |    ||||||||   |  ||     |||   |||   |||  |  |              
AATGTTGTTGTTAGATCGTGGGGAGAGAAAAGAGTG---------GAGCCTAAGCTGAAGAATCATGTGGATCTAGTTGAGCTTCTCGGTATTGCAGATACAAAGAAAGgtt---tgaatttgttcatctagtgattgagtgataatttatttattcatttttgtggggtgcggggc--atttggatgacttttaagtttggaattttgtgttg

upper sequence: AT5G27470.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA20G37700.1 (Glycine max), 5'ss of exon 4
---------ATTAAACTGTGGGGTGAAAAGCGGTTTTCTACGCCTGGTCTGAAGCTGAAAAACCATGTGGATCTTGTTGAGCTTCTCGGTATTGCAGATACCAAAAGAGgtagtattgacttgcac-tttgccgacctccttgctctgtgttaaagggtttttgtgctataggg---tttcaattgtaatgctattttggcctcag------
          ||| |  |||||| || ||| |  |          |  |  |||||||| || ||||||||||| |||||||||||||| || |||||||| || | ||||    |  | |||  | | |  ||  |   |     | | || |    |||| |||   |   |    ||    ||   |   |||||||  ||        
AATGTTGTCGTTAGATCGTGGGGAGAGAAGAGAGTG---------GAGCCTAAGCTGAAGAATCATGTGGATCTAGTTGAGCTTCTCGGGATAGCAGATACAAAGAAAGgtt---tgaatttgttcatctagcgttcgagtgatgatttatttattaattttcgtggggtgaagagcctttggatgacttttaattttggaatcttgtgttg
















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|86070371|gb|DR366128.1|DR366128
EST:     AAACCATGTGGATCTTGTTGAGCTTCTCGGTATTGCAGATACCAAAAGAG                         GTGCTGAAATCGCTGGAGCAAGAGGCTTTTTCTTGAAAGGAGATGGNTTGA
genomic: AAACCATGTGGATCTTGTTGAGCTTCTCGGTATTGCAGATACCAAAAGAGgtagtattga ... ttggcctcagGTGCTGAAATCGCTGGAGCAAGAGGCTTTTTCTTGAAAGGAGATGGTTTGA
EST: gi|125259641|gb|EL273726.1|EL273726
EST:     AAACCATGTGGATCTTGTTGAGCTTCTCGGTATTGCAGATACCAAAAGAG                         GTGCTGAAATCGCTGGAGCAAGAG
genomic: AAACCATGTGGATCTTGTTGAGCTTCTCGGTATTGCAGATACCAAAAGAGgtagtattga ... ttggcctcagGTGCTGAAATCGCTGGAGCAAGAG
EST: gi|124866045|gb|EH950482.1|EH950482
EST:     TTGAGCTTCTCGGTATTGCAGATACCAAAAGAG                         GTGCTGAAATCGCTGGAGCAAGAGGCTTTTTCTTGAAAGGAGATGGTTTGA
genomic: TTGAGCTTCTCGGTATTGCAGATACCAAAAGAGgtagtattga ... ttggcctcagGTGCTGAAATCGCTGGAGCAAGAGGCTTTTTCTTGAAAGGAGATGGTTTGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATTAAACTGTGGGGTGAAAAGCGGTTTTCTACGCCTGGTCTGAAGCTGAAAAACCATGTGGATCTTGTTGAGCTTCTCGGTATTGCAGATACCAAAAGAGgtagtattgacttgcactttgccgacctccttgctctgtgttaaagggtttttgtgctatagggtttcaattgtaatgctattttggcctcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT