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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttcttcttcttcagcatatttacatgttctttgcttttaaagcttcttctaattcgaatctgttataatttgtagACTAATAACAGTGAAGAAGCGAATTCAAAGCAGCAAGCAGATGTAAAAACCCTAATTAGGTCATATAAACAAGCTCTTCTCAACGGAGACGAAACCTCAG

Basic information

species Arabidopsis thaliana
transcript AT1G36390.1
intron # 1
splice site 3'
intron type U2

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|86049257|gb|DR345012.1|DR345012
EST:     CACTCATTTCAAAACCCAGTCGAAAATTCCCAATCTTCTCTGCTCACCAA                         ACTAATAACAATGAAGAAGCGAATTCAAAGCAGCAAGCAGATGTAAAAACC
genomic: CACTCATTTCAAAACCCAGTCGAAAATTCCCAATCTTCTCTGCTCACCAAgtaagttctt ... taatttgtagACTAATAACAGTGAAGAAGCGAATTCAAAGCAGCAAGCAGATGTAAAAACC
EST: gi|86049255|gb|DR345010.1|DR345010
EST:     CACTCATTTCAAAACCCAGTCGAAAATTCCCAATCTTCTCTGCTCACCAA                         ACTAATAACAATGAAGAAGCGAATTCAAAGCAGCAAGCAGATGTAAAAACC
genomic: CACTCATTTCAAAACCCAGTCGAAAATTCCCAATCTTCTCTGCTCACCAAgtaagttctt ... taatttgtagACTAATAACAGTGAAGAAGCGAATTCAAAGCAGCAAGCAGATGTAAAAACC
EST: gi|86049254|gb|DR345009.1|DR345009
EST:     CACTCATTTCAAAACCCAGTCGAAAATTCCCAATCTTCTCTGCTCACCAA                         ACTAATAACAATGAAGAAGCGAATTCAAAGCAGCAAGCAGATGTRAAAACC
genomic: CACTCATTTCAAAACCCAGTCGAAAATTCCCAATCTTCTCTGCTCACCAAgtaagttctt ... taatttgtagACTAATAACAGTGAAGAAGCGAATTCAAAGCAGCAAGCAGATGTAAAAACC
EST: gi|86049252|gb|DR345007.1|DR345007
EST:     CACTCATTTCAAAACCCAGTCGAAAATTCCCAATCTTCTCTGCTCACCAA                         ACTAATAACAATGAAGAAGCGAATTCAAAGCAGCAAGCAGATGTAAAAACC
genomic: CACTCATTTCAAAACCCAGTCGAAAATTCCCAATCTTCTCTGCTCACCAAgtaagttctt ... taatttgtagACTAATAACAGTGAAGAAGCGAATTCAAAGCAGCAAGCAGATGTAAAAACC
EST: gi|86049256|gb|DR345011.1|DR345011
EST:     CACTCATTTCAAAACCCAGTCGAAAATTCCCAATCTTCTCTGCTCACCAA                         ACTAATAACAATGAAGAAGCGAATTCAAAGCAGCAAGCAGATGTAAAAACC
genomic: CACTCATTTCAAAACCCAGTCGAAAATTCCCAATCTTCTCTGCTCACCAAgtaagttctt ... taatttgtagACTAATAACAGTGAAGAAGCGAATTCAAAGCAGCAAGCAGATGTAAAAACC
EST: gi|86049253|gb|DR345008.1|DR345008
EST:     CACTCATTTCAAAACCCAGTCGAAAATTCCCAATCTTCTCTGCTCACCAA                         ACTAATAACAATGAAGAAGCGAATTCAAAGCAGCAAGCAGATGTAAAAAAC
genomic: CACTCATTTCAAAACCCAGTCGAAAATTCCCAATCTTCTCTGCTCACCAAgtaagttctt ... taatttgtagACTAATAACAGTGAAGAAGCGAATTCAAAGCAGCAAGCAGATGTAAAAA-C
EST: gi|86049249|gb|DR345004.1|DR345004
EST:     ACTCATTTCAAAACCCAGTCGAAAATTCCCAATCTTCTCTGCATCACCAA                         ACTAATAACAATGAAGAAGCGAATTCAAAGCAGCAAGCAGATGTAAAAAC
genomic: ACTCATTTCAAAACCCAGTCGAAAATTCCCAATCTTCTCTGC-TCACCAAgtaagttctt ... taatttgtagACTAATAACAGTGAAGAAGCGAATTCAAAGCAGCAAGCAGATGTAAAAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tacatgttctttgcttttaaagcttcttctaattcgaatctgttataatttgtagACTAATAACAGTGAAGAAGCGAATTCAAAGCAGCAAGCAGATGTAAAAACCCTAATTAGGTCATATAAACAAGCTCTTCTCAACGGAGACGAAACCTCAG
                          ttctaat  putative branch site (score: 2)
                                    aatctgttataattt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagttcttcttcttcagcatatttacatgttctttgcttttaaagcttcttctaattcgaatctgttataatttgtagACTAATAACAGTGAAGAAGCGAATTCAAAGCAGCAAGCAGATGTAAAAACCCTAATTAGGTCATATAAACAAGCTCTTCTCAACGGAGACGAAACCTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT