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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ccatatcatttgcaatcgtacctgtgagaagttttgaattccgatttctcgtctgatatatctattgttctgtgtcctttgttgtatccatgttctaaagATGGATGGGAGAAGAGATGGGTAAAATCTGACTGGAAGAAAGATGATAATACTGCTGGGGAATGGAAACACACAGCTGGAAATTGGTCTGGTGATGCTAA

Basic information

species Arabidopsis thaliana
transcript AT1G56340.2
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G56340.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv14s0060g01290.t01 (Vitis vinifera), 3'ss of exon 1
ccatatcatttgcaatc-gtacctgtgagaagttttgaattccgatttctcgtctgatatatctattgttctgtgtcctttgttgtatccatgttctaa-------agATGGATGGGAGAAGAGATGGGTAAAATCTGACTGGAAGAAAGATGATAATACTGCTGGGGAATGGAAACACACAGCTGGAAATTGGTCTGGTGATGCTAA
         |   ||||  | | |||   || |  | |||    ||||    ||| ||   | |  ||   || |||   | |   || ||| ||  ||       ||||||||||||||| |  ||||| ||||| || |||||||||||||| || |  ||||||||||||||  ||||  |||| || |||  ||| ||  | ||
--------ctgataatccatgcttgtttcaattaataaatcagtatttgctttcttatgactttcctgcattgggtctaatatgtaattcatttttgaatactttaagATGGATGGGAGAATAAGTGGGTTAAATCCGAATGGAAGAAAGATGAGAACATGGCTGGGGAATGGAACTACACCTCTGGTAAATGGCATGGAGACCCGAA
















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|164062952|gb|ES037421.1|ES037421
EST:     TCTCGTGGTGACCGTCTCTGCTGAAGTTATCTTCGAGGAGAAATTCGAAG                         ATGGATGGGAGAAGAGATGGGTAAAATCTGACTGGAAGAAAGA
genomic: TCTCGTGGTGATCGTCTCTGCTGAAGTTATCTTCGAGGAGAAATTCGAAGgtatctacat ... tgttctaaagATGGATGGGAGAAGAGATGGGTAAAATCTGACTGGAAGAAAGA
EST: gi|86070958|gb|DR366715.1|DR366715
EST:     TCTCGTGGTGATCGTCTCTGCTGAAGTTATCTTCGAGGAGAAATTCGAAG                         ATGGATGGGAGAAGAGATGGGTAAAATCTGACTGGAAGAAAGATGATAATA
genomic: TCTCGTGGTGATCGTCTCTGCTGAAGTTATCTTCGAGGAGAAATTCGAAGgtatctacat ... tgttctaaagATGGATGGGAGAAGAGATGGGTAAAATCTGACTGGAAGAAAGATGATAATA
EST: gi|86070961|gb|DR366718.1|DR366718
EST:     TCTCGTGGTGATCGTCTCTGCTGAAGTTATCTTCGAGGAGAAATTCGAAG                         ATGGATGGGAGAAGAGATGGGTAAAATCTGACTGGAAGAAAGATGATAATA
genomic: TCTCGTGGTGATCGTCTCTGCTGAAGTTATCTTCGAGGAGAAATTCGAAGgtatctacat ... tgttctaaagATGGATGGGAGAAGAGATGGGTAAAATCTGACTGGAAGAAAGATGATAATA
EST: gi|86070960|gb|DR366717.1|DR366717
EST:     TCTCGTGGTGATCGTCTCTGCTGAAGTTATCTTCGAGGAGAAATTCGAAG                         ATGGATGGGAGAAGAGATGGGTAAAATCTGACTGGAAGGAAGATGATAATA
genomic: TCTCGTGGTGATCGTCTCTGCTGAAGTTATCTTCGAGGAGAAATTCGAAGgtatctacat ... tgttctaaagATGGATGGGAGAAGAGATGGGTAAAATCTGACTGGAAGAAAGATGATAATA
EST: gi|164222756|gb|ES128919.1|ES128919
EST:     GAAATTCGAAG                         ATGGATGGGAGAAGAGATGGGTAAAATCTGACTGGAAGAAAGATGATAATA
genomic: GAAATTCGAAGgtatctacat ... tgttctaaagATGGATGGGAGAAGAGATGGGTAAAATCTGACTGGAAGAAAGATGATAATA
EST: gi|116465698|gb|EG508290.1|EG508290
EST:     TCTCGTGGTGATCGTCTCTGCTGAAGTTATCTTCGAGGAGAAATTCGAAG                         ATGGATGGGAGAAGAGATGGGTAAAATCTGACTGGAAGAAAGATGATAATA
genomic: TCTCGTGGTGATCGTCTCTGCTGAAGTTATCTTCGAGGAGAAATTCGAAGgtatctacat ... tgttctaaagATGGATGGGAGAAGAGATGGGTAAAATCTGACTGGAAGAAAGATGATAATA
EST: gi|86070962|gb|DR366719.1|DR366719
EST:     GATCGTCTCTGCTGAAGTTATCTTCGAGGAGAAATTCGAAG                         ATGGATGGGAGAAGAGATGGGTAAAATCTGACTGGAAGAAAGATGATAATA
genomic: GATCGTCTCTGCTGAAGTTATCTTCGAGGAGAAATTCGAAGgtatctacat ... tgttctaaagATGGATGGGAGAAGAGATGGGTAAAATCTGACTGGAAGAAAGATGATAATA
EST: gi|86070954|gb|DR366711.1|DR366711
EST:     TCTCGTGGTGATCGTCTCTGCTGAAGTTATCTTCGAGGAGAAATTCGAAG                         ATGGATGGGAGAAGAGATGGGTAAAATCTGACTGGAAGAAAGATGATAATA
genomic: TCTCGTGGTGATCGTCTCTGCTGAAGTTATCTTCGAGGAGAAATTCGAAGgtatctacat ... tgttctaaagATGGATGGGAGAAGAGATGGGTAAAATCTGACTGGAAGAAAGATGATAATA
EST: gi|86070959|gb|DR366716.1|DR366716
EST:     TCTCGTGGTGATCGTCTCTGCTGAAGTTATCTTCGAGGAGAAATTCGAAG                         ATGGATGGGAGAAGAGATGGGTAAAATCTGACTGGAAGAAAGATGATAATA
genomic: TCTCGTGGTGATCGTCTCTGCTGAAGTTATCTTCGAGGAGAAATTCGAAGgtatctacat ... tgttctaaagATGGATGGGAGAAGAGATGGGTAAAATCTGACTGGAAGAAAGATGATAATA
EST: gi|86070953|gb|DR366710.1|DR366710
EST:     TCTCGTGGTGATCGTCTCTGCTGAAGTTATCTTCGAGGAGAAATTCGAAG                         ATGGATGGGAGAAGAGATGGGTAAAATCTGACTGGAAGAAAGATGATAATA
genomic: TCTCGTGGTGATCGTCTCTGCTGAAGTTATCTTCGAGGAGAAATTCGAAGgtatctacat ... tgttctaaagATGGATGGGAGAAGAGATGGGTAAAATCTGACTGGAAGAAAGATGATAATA
EST: gi|86070957|gb|DR366714.1|DR366714
EST:     TCTCGTGGTGATCGTCTCTGCTGAAGTTATCTTCGAGGAGAAATTCGAAG                         ATGGATGGGAGAAGAGATGGGTAAAATCTGACTGGAAGAAAGATGATAATA
genomic: TCTCGTGGTGATCGTCTCTGCTGAAGTTATCTTCGAGGAGAAATTCGAAGgtatctacat ... tgttctaaagATGGATGGGAGAAGAGATGGGTAAAATCTGACTGGAAGAAAGATGATAATA
EST: gi|86070956|gb|DR366713.1|DR366713
EST:     AAGTTATCTTCGAGGAGAAATTCGAAG                         ATGGATGGGAGAAGAGATGGGTAAAATCTGACTGGAAGAAAGATGATAATA
genomic: AAGTTATCTTCGAGGAGAAATTCGAAGgtatctacat ... tgttctaaagATGGATGGGAGAAGAGATGGGTAAAATCTGACTGGAAGAAAGATGATAATA
EST: gi|116482409|gb|EG525001.1|EG525001
EST:     TCTCGTGGTGATCGTCTCTGCTGAAGTTATCTTCGAGGAGAAATTCGAAG                         ATGGATGGGAGAAGAGATGGGTAAAATCTGACTGGAAGAAAGATGATAATA
genomic: TCTCGTGGTGATCGTCTCTGCTGAAGTTATCTTCGAGGAGAAATTCGAAGgtatctacat ... tgttctaaagATGGATGGGAGAAGAGATGGGTAAAATCTGACTGGAAGAAAGATGATAATA
EST: gi|116465734|gb|EG508326.1|EG508326
EST:     TCTCGTGGTGATCGTCTCTGCTGAAGTTATCTTCGAGGAGAAATTCGAAG                         ATGGATGGGAGAAGAGATGGGTAAAATCTGACTGGAAGAAAGATGATAATA
genomic: TCTCGTGGTGATCGTCTCTGCTGAAGTTATCTTCGAGGAGAAATTCGAAGgtatctacat ... tgttctaaagATGGATGGGAGAAGAGATGGGTAAAATCTGACTGGAAGAAAGATGATAATA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctcgtctgatatatctattgttctgtgtcctttgttgtatccatgttctaaagATGGATGGGAGAAGAGATGGGTAAAATCTGACTGGAAGAAAGATGATAATACTGCTGGGGAATGGAAACACACAGCTGGAAATTGGTCTGGTGATGCTAA
     gtctgat  putative branch site (score: 4)
          atatatctattgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ccatatcatttgcaatcgtacctgtgagaagttttgaattccgatttctcgtctgatatatctattgttctgtgtcctttgttgtatccatgttctaaagATGGATGGGAGAAGAGATGGGTAAAATCTGACTGGAAGAAAGATGATAATACTGCTGGGGAATGGAAACACACAGCTGGAAATTGGTCTGGTGATGCTAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
ccatatc
- - - - - - - - - - - - - - - gttttga