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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcaggatttcatcttatgattatcgtggtgtgtgttattacagtgttctttgatgatgtttccacttagcgttttagtcatatttttttctttccagAATGAACAATTGAATAAGATTTATGAGCTTTGTGGATCACCTGATGAAAGCAACTGGCCTGGAGTTTCCAAGATGCCTTGGTATAACCAAATGAAATCAT

Basic information

species Arabidopsis thaliana
transcript AT5G64960.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G64960.2 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv00s0805g00020.t01 (Vitis vinifera), 3'ss of exon 6
---gtcaggatttcatcttatgattatcgtggtgtgtgtta--ttacagtgttctttgatgatgtttccacttagcgttttagtcatatttttttctttccagAATGAACAATTGAATAAGATTTATGAGCTTTGTGGATCACCTGATGAAAGCAACTGGCCTGGAGTTTCCAAGATGCCTTGGTATAACCAAATGAAATCAT
    |  |    |||| |||  |||    |  |   ||  |  |  |     | ||  || |  | |  |   ||    ||  |  | |||   || || |||  |||||||||||| ||||| | ||||||||||||||| |||||||| | |||||||||||| ||||||||||| |||||||||||| |  | ||| || 
actcttggtggatcatttta--attcatataattgatgacaagtatctactatattcaataacttctataag-agaaaattgattttgtttacatcattgcagCCTGAACAATTGAAAAAGATATTTGAGCTTTGTGGATCTCCTGATGAGAACAACTGGCCTGGTGTTTCCAAGATCCCTTGGTATAACAATTTCAAACCAG
















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|86059280|gb|DR355037.1|DR355037
EST:     TATTTGCTGAACTTTTGAATGGAAAACCAATCTTGCCTGGGAAAACTGAG                         AATGAACAATTGAATAAGATTTATGAGCTTTGTGGATCACCTGATGAAAGC
genomic: TATTTGCTGAACTTTTGAATGGAAAACCAATCTTGCCTGGGAAAACTGAGgtcaggattt ... ttctttccagAATGAACAATTGAATAAGATTTATGAGCTTTGTGGATCACCTGATGAAAGC
EST: gi|124884820|gb|EH963722.1|EH963722
EST:     GGAAAACCAATCTTGCCTGGGAAAACTGAG                         AATGAACAATTGAATAAGATTTATGAGCTTTGTGGATCACCTGATGAAAGC
genomic: GGAAAACCAATCTTGCCTGGGAAAACTGAGgtcaggattt ... ttctttccagAATGAACAATTGAATAAGATTTATGAGCTTTGTGGATCACCTGATGAAAGC
EST: gi|164227882|gb|ES119663.1|ES119663
EST:     TATTTGCTGAACTTTTGAATGGAAAACCAATCTTGCCTGGGAAAACTGAG                         AATGAACAATTGAATAAGATTTATGAGCTTTGTGGATCACCTGATGAAAGC
genomic: TATTTGCTGAACTTTTGAATGGAAAACCAATCTTGCCTGGGAAAACTGAGgtcaggattt ... ttctttccagAATGAACAATTGAATAAGATTTATGAGCTTTGTGGATCACCTGATGAAAGC
EST: gi|86059279|gb|DR355036.1|DR355036
EST:     TATTTGCTGAACTTTTGAATGGAAAACCAATCTTGCCTGGGAAAGCTGAG                         AATGAACAATAGAATAAGATTTATGAGCTTTGTGGATCACCTGATGAAAGC
genomic: TATTTGCTGAACTTTTGAATGGAAAACCAATCTTGCCTGGGAAAACTGAGgtcaggattt ... ttctttccagAATGAACAATTGAATAAGATTTATGAGCTTTGTGGATCACCTGATGAAAGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgttctttgatgatgtttccacttagcgttttagtcatatttttttctttccagAATGAACAATTGAATAAGATTTATGAGCTTTGTGGATCACCTGATGAAAGCAACTGGCCTGGAGTTTCCAAGATGCCTTGGTATAACCAAATGAAATCAT
     ctttgat  putative branch site (score: 5)
                                   tcatatttttttcttt  putative PPT
                             ttttagtcatattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcaggatttcatcttatgattatcgtggtgtgtgttattacagtgttctttgatgatgtttccacttagcgttttagtcatatttttttctttccagAATGAACAATTGAATAAGATTTATGAGCTTTGTGGATCACCTGATGAAAGCAACTGGCCTGGAGTTTCCAAGATGCCTTGGTATAACCAAATGAAATCAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG