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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGAGGAAAGAGTTCATAGCTGGACTTCACAAGCAGAAGACTGAGCTTTTCATGGTTCTTATCGAGAAAAAGCTGCTTCCGCTTCGACCCGGTGTTGCAAAgttagtgtcacttctaatgttctattctatattctcgatgctattacttgaatgtcccttttgagtttgatttttttaaagtctaaaacttttaacccaa...

Basic information

species Arabidopsis thaliana
transcript AT3G48420.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G48420.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: Vv17s0000g09910.t01 (Vitis vinifera), 5'ss of exon 3
AGAGGAAAGAGTTCATAGCTGGACTTCACAAGCAGAAGACTGAGCTTTTCATGGTTCTTATCGAGAAAAAGCTGCTTCCGCTTCGACCCGGTGTTGCAAAgttagtgtcacttctaatgttctattcta-tattctcgatgctattacttgaatgtcccttttgagt-ttgatttttttaaagtctaaaacttttaacccaa
| ||||| || ||||| |||   ||||||||||  || |||||  | |||||||| || || |||||||| ||||| || |||||||||||||||||||||| |||     ||   || ||||  | || | | ||  ||  ||||  |   ||        ||| | |||   ||  |  |   |  | |||||   |  |
AAAGGAAGGAATTCATTGCTTCTCTTCACAAGCGAAAAACTGAATTGTTCATGGTCCTGATTGAGAAAAAACTGCTGCCTCTTCGACCCGGTGTTGCAAAgtcagttctgttt--gatcttctgctttaatgtgctatattttattgttattattattaacatgattgttgcaattagtccaccttgcatcttttggtcgta
















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|125043323|gb|EL115592.1|EL115592
EST:     ATGGTTCTTATCGAGAAAAAGCTGCTTCCGCTTCGACCCGGTGTTGCAAA                         GTTGGTTGATCAAGCTTTAACAAACGGAGTCAAA
genomic: ATGGTTCTTATCGAGAAAAAGCTGCTTCCGCTTCGACCCGGTGTTGCAAAgttagtgtca ... aactttgcagGTTGGTTGATCAAGCTTTAACAAACGGAGTCAAA
EST: gi|86078346|gb|DR374103.1|DR374103
EST:     ATGGTTCTTATCGAGAAAAAGCTGCTTCCGCTTCGACCCGGTGTTGCAAA                         GTTGGTTGATCAAGCTTTAACAAACGGAGTCAAAGTAGCTGTGTGCAGTAC
genomic: ATGGTTCTTATCGAGAAAAAGCTGCTTCCGCTTCGACCCGGTGTTGCAAAgttagtgtca ... aactttgcagGTTGGTTGATCAAGCTTTAACAAACGGAGTCAAAGTAGCTGTGTGCAGTAC
EST: gi|124749747|gb|EH839877.1|EH839877
EST:     GACCCGGTGTTGCAAA                         GTTGGTTGATCAAGCTTTAACAAACGGAGTCAAAGTAGCTGTGTGCAGTAC
genomic: GACCCGGTGTTGCAAAgttagtgtca ... aactttgcagGTTGGTTGATCAAGCTTTAACAAACGGAGTCAAAGTAGCTGTGTGCAGTAC
EST: gi|125159047|gb|EL187350.1|EL187350
EST:     ATGGTTCTTATCGAGAAAAAGCTGCTTCCGCTTCGACCCGGTGTTGCAAA                         GTTGGTTGATCAAGCTTTAACAAACGGA
genomic: ATGGTTCTTATCGAGAAAAAGCTGCTTCCGCTTCGACCCGGTGTTGCAAAgttagtgtca ... aactttgcagGTTGGTTGATCAAGCTTTAACAAACGGA
EST: gi|125314296|gb|EL328381.1|EL328381
EST:     TATCGAGAAAAAAGCTGCTTCCGCTTCGACCCGGTGTTGCAAA                         GTTGGTTGATCAAGCTTTAACAAACGGAGTCAAAGTAG
genomic: TATCGAG-AAAAAGCTGCTTCCGCTTCGACCCGGTGTTGCAAAgttagtgtca ... aactttgcagGTTGGTTGATCAAGCTTTAACAAACGGAGTCAAAGTAG
EST: gi|124921503|gb|EH995114.1|EH995114
EST:     TTCTTATCGAGAAAAAGCTGCTTCCGCTTCGACCCGGTGTTGCAAA                         GTTGGTTGATCAAGCTTTAACAAACGGAGTCAAAGTAGCTGTGTGCAGTAC
genomic: TTCTTATCGAGAAAAAGCTGCTTCCGCTTCGACCCGGTGTTGCAAAgttagtgtca ... aactttgcagGTTGGTTGATCAAGCTTTAACAAACGGAGTCAAAGTAGCTGTGTGCAGTAC
EST: gi|124715225|gb|EH806627.1|EH806627
EST:     GTTCTTATCGAGAAAGAGCTGCTTCCGCTTCGACCCGGTGTTGCAAA                         GTTGGTTGATCAAGCTTTAACAAACGGAGTCAAAAGTAGCTGTGTGCAGTA
genomic: GTTCTTATCGAGAAAAAGCTGCTTCCGCTTCGACCCGGTGTTGCAAAgttagtgtca ... aactttgcagGTTGGTTGATCAAGCTTTAACAAACGGAGTCAAA-GTAGCTGTGTGCAGTA
EST: gi|47832151|gb|CK121835.1|CK121835
EST:     ATGGTTCTTATCGAGAAAAAGCTGCTTCCGCTTCGACCCGGTGTTGCAAA                         GTTGGTTGATCAAGCTTTAACAAACGGAGTCAAAGTAGCTGTGTGCAGTAC
genomic: ATGGTTCTTATCGAGAAAAAGCTGCTTCCGCTTCGACCCGGTGTTGCAAAgttagtgtca ... aactttgcagGTTGGTTGATCAAGCTTTAACAAACGGAGTCAAAGTAGCTGTGTGCAGTAC
EST: gi|124940081|gb|EL016564.1|EL016564
EST:     ATGGTTCTTATCGAGAAAAAGCTGCTTCCGCTTCGACCCGGTGTTGCAAA                         GTTGGTTGATCAAGCTTTAACAAACGGAGT
genomic: ATGGTTCTTATCGAGAAAAAGCTGCTTCCGCTTCGACCCGGTGTTGCAAAgttagtgtca ... aactttgcagGTTGGTTGATCAAGCTTTAACAAACGGAGT
EST: gi|125121623|gb|EL168703.1|EL168703
EST:     GACCCGGTGTTGCAAA                         GTTGGTTGATCAAGCTTTAACAAACGGAGTCAAAGTAGCTGTGTGCAGTAC
genomic: GACCCGGTGTTGCAAAgttagtgtca ... aactttgcagGTTGGTTGATCAAGCTTTAACAAACGGAGTCAAAGTAGCTGTGTGCAGTAC
EST: gi|125075727|gb|EL139160.1|EL139160
EST:     GACCCGGTGTTGCAAA                         GTTGGTTGATCAAGCTTTAACAAACGGAGTCAAAGTAGCTGTGTGCAGTAC
genomic: GACCCGGTGTTGCAAAgttagtgtca ... aactttgcagGTTGGTTGATCAAGCTTTAACAAACGGAGTCAAAGTAGCTGTGTGCAGTAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGAGGAAAGAGTTCATAGCTGGACTTCACAAGCAGAAGACTGAGCTTTTCATGGTTCTTATCGAGAAAAAGCTGCTTCCGCTTCGACCCGGTGTTGCAAAgttagtgtcacttctaatgttctattctatattctcgatgctattacttgaatgtcccttttgagtttgatttttttaaagtctaaaacttttaacccaa

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tccctttt