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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACTCTAATGGAGAGAGGATATGAACTTGTTTCTGGTGGAACTGACAACCATCTGGTTCTAGTGAATCTAAAGCCCAAGgtcacttgatctttttttgtatataatcttcttttatatttcttagttaaaactcattttttattcgattttgtttgcag

Basic information

species Arabidopsis thaliana
transcript AT4G37930.1
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G37930.1 (Arabidopsis thaliana), 5'ss of exon 12
lower sequence: GRMZM2G135283_T02 (Zea mays), 5'ss of exon 11
ACTCTAATGGAGAGAGGATATGAACTTGTTTCTGGTGGAACTGACAACCATCTGGTTCTAGTGAATCTAAAGCCCAAGgtcacttga--tctttttttgtatataatc-ttcttttatatttcttagttaaaactcattttttattcgat-tttgtttgcag----------------------------------------------------------------------------------------------------
|  || ||    | |||||||||||| || |||||||| |||||||||||| | ||||| |||||||| |||   |||||    | |     | |||    | |  || || |||||||  | |||| ||   ||   |   || | | |  || |||| |                                                                                                     
AGCCTGATTTCAAAAGGATATGAACTCGTCTCTGGTGGGACTGACAACCATTTAGTTCTGGTGAATCTCAAGAATAAGgtaggataaaagtgtgtttcacgttttgtcatttttttatagatattagctattgctttatacatactagctacttttttgtacgtattatctaaatgtgctaaatagacaaaacctacttgtttccagttctaatgccatgtctgaacaatattgtatttttaaaaaaaatttatgtatatag
















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|116411252|gb|EG453844.1|EG453844
EST:     TTTCTGGTGGAACTGACAACCATCTGGTTCTAGTGAATCTAAAGCCCAAG                         GGAATTGATGGATCTAGAGTTGAGAAAGTGTTGGAAGCTGTTCACATTGCA
genomic: TTTCTGGTGGAACTGACAACCATCTGGTTCTAGTGAATCTAAAGCCCAAGgtcacttgat ... ttgtttgcagGGAATTGATGGATCTAGAGTTGAGAAAGTGTTGGAAGCTGTTCACATTGCA
EST: gi|124812402|gb|EH897268.1|EH897268
EST:     TGAATCTAAAGCCCAAG                         GGAATTGATGGATCTAGAGTTGAGAAAGTGTTGGAAGCTGTTCACATTGCA
genomic: TGAATCTAAAGCCCAAGgtcacttgat ... ttgtttgcagGGAATTGATGGATCTAGAGTTGAGAAAGTGTTGGAAGCTGTTCACATTGCA
EST: gi|125311199|gb|EL325284.1|EL325284
EST:     CAACCATCTGGTTCTAGTGAATCTAAAGCCCAAG                         GGAATTGATGGATCTAGAGTTGAGAAAGTGTTGGAAGCTGTTCACATTGCA
genomic: CAACCATCTGGTTCTAGTGAATCTAAAGCCCAAGgtcacttgat ... ttgtttgcagGGAATTGATGGATCTAGAGTTGAGAAAGTGTTGGAAGCTGTTCACATTGCA
EST: gi|86059292|gb|DR355049.1|DR355049
EST:     TTTCTGGTGGAACTGACAACCATCTGGTTCTAGTGAATCTAAAGCCCAAG                         GGAATTGATGGATCTAGAGTTGAGAAAGTGTTGGAAGCTGTTCACATTGCA
genomic: TTTCTGGTGGAACTGACAACCATCTGGTTCTAGTGAATCTAAAGCCCAAGgtcacttgat ... ttgtttgcagGGAATTGATGGATCTAGAGTTGAGAAAGTGTTGGAAGCTGTTCACATTGCA
EST: gi|125232196|gb|EL246281.1|EL246281
EST:     TTTCTGGTGGAACTGACAACCATCTGGTTCTAGTGAATCTAAAGCCCAAG                         GGAATTGATGGATCTAGAGTTGAGAAAGTGTTGGAAGCTGTTCACATTG
genomic: TTTCTGGTGGAACTGACAACCATCTGGTTCTAGTGAATCTAAAGCCCAAGgtcacttgat ... ttgtttgcagGGAATTGATGGATCTAGAGTTGAGAAAGTGTTGGAAGCTGTTCACATTG
EST: gi|152034927|gb|BP840236.2|BP840236
EST:     TTTCTGGTGGAACTGACAACCATCTGGTTCTAGTGAATCTAAAGCCCAAG                         GGAATTGATGGATCTAGAGTTGAGAAAGTGTTGGGAAAGCTGT-CACA
genomic: TTTCTGGTGGAACTGACAACCATCTGGTTCTAGTGAATCTAAAGCCCAAGgtcacttgat ... ttgtttgcagGGAATTGATGGATCTAGAGTTGAGAAAGTGTTGG-AA-GCTGTTCACA
EST: gi|125250198|gb|EL264283.1|EL264283
EST:     GTGAATCTAAAGACCCAAG                         GGAATTGATGGATCTAGAGTTGAGAAAGTGTTGGAAGCTGTTCACATTGC
genomic: GTGAATCTAAAG-CCCAAGgtcacttgat ... ttgtttgcagGGAATTGATGGATCTAGAGTTGAGAAAGTGTTGGAAGCTGTTCACATTGC
EST: gi|125069291|gb|EL135118.1|EL135118
EST:     TTTCTGGTGGAACTGACAACCATCTGGTTCTAGTGAATCTAAAGCCCAAG                         GGAATTGATGGATCTAGAGTTGAGAAAGTG
genomic: TTTCTGGTGGAACTGACAACCATCTGGTTCTAGTGAATCTAAAGCCCAAGgtcacttgat ... ttgtttgcagGGAATTGATGGATCTAGAGTTGAGAAAGTG
EST: gi|124833736|gb|EH918175.1|EH918175
EST:     AACCATCTGGTTCTAGTGAATCTAAAGCCCAAG                         GGAATTGATGGATCTAGAGTTGAGAAAGTAGTTGGAAGCTGTTCACATTGC
genomic: AACCATCTGGTTCTAGTGAATCTAAAGCCCAAGgtcacttgat ... ttgtttgcagGGAATTGATGGATCTAGAGTTGAGAAAGT-GTTGGAAGCTGTTCACATTGC
EST: gi|125034577|gb|EL106846.1|EL106846
EST:     CAACCATCTGGTTCTAGTGAATCTAAAGCCCAAG                         GGAATTGATGGATCTAGAGTTGAGAAAGTGTTGGAAG
genomic: CAACCATCTGGTTCTAGTGAATCTAAAGCCCAAGgtcacttgat ... ttgtttgcagGGAATTGATGGATCTAGAGTTGAGAAAGTGTTGGAAG
EST: gi|116443767|gb|EG486359.1|EG486359
EST:     TTTCTGGTGGAACTGACAACCATCTGGTTCTAGTGAATCTAAAGCCCAAG                         GGAATTGATGGATCTAGAGTTGAGAAAGTGTTGGAAGCTGTTCACATTGCA
genomic: TTTCTGGTGGAACTGACAACCATCTGGTTCTAGTGAATCTAAAGCCCAAGgtcacttgat ... ttgtttgcagGGAATTGATGGATCTAGAGTTGAGAAAGTGTTGGAAGCTGTTCACATTGCA
EST: gi|116484717|gb|EG527309.1|EG527309
EST:     TTTCTGGTGGAACTGACAACCATCTGGTTCTAGTGAATCTAAAGCCCAAG                         GGAATTGATGGATCTAGAGTTGAGAAAGTGTTGGAAGCTGTTCACATTGCA
genomic: TTTCTGGTGGAACTGACAACCATCTGGTTCTAGTGAATCTAAAGCCCAAGgtcacttgat ... ttgtttgcagGGAATTGATGGATCTAGAGTTGAGAAAGTGTTGGAAGCTGTTCACATTGCA
EST: gi|125023824|gb|EL096093.1|EL096093
EST:     TTTCTGGTGGAACTGACAACCATCTGGTTCTAGTGAATCTAAAGCCCAAG                         GGAATTGATGGATCTAGAGTTGAGAAAGTGTTGGAAGCTGTTCAC
genomic: TTTCTGGTGGAACTGACAACCATCTGGTTCTAGTGAATCTAAAGCCCAAGgtcacttgat ... ttgtttgcagGGAATTGATGGATCTAGAGTTGAGAAAGTGTTGGAAGCTGTTCAC
EST: gi|125014906|gb|EL087175.1|EL087175
EST:     TTTCTGGTGGAACTGACAACCATCTGGTTCTAGTGAATCTAAAGCCCAAG                         GGAATTGATGGAT
genomic: TTTCTGGTGGAACTGACAACCATCTGGTTCTAGTGAATCTAAAGCCCAAGgtcacttgat ... ttgtttgcagGGAATTGATGGAT
EST: gi|125093473|gb|EL151040.1|EL151040
EST:     CTGACAACCATCTGGTTCTAGTGAATCTAAAGCCCAAG                         GGAATTGATGGATCTAGAGTTGAGAAAGTGTTGGAAGCTGTTCACATTGCA
genomic: CTGACAACCATCTGGTTCTAGTGAATCTAAAGCCCAAGgtcacttgat ... ttgtttgcagGGAATTGATGGATCTAGAGTTGAGAAAGTGTTGGAAGCTGTTCACATTGCA
EST: gi|86079465|gb|DR375222.1|DR375222
EST:     TTTCTGGTGGAACTGACAACCATCTGGTTCTAGTGAATCTAAAGCCCAAG                         GGAATTGATGGATCTAGAGTTGAGAAAGTGTTGGAAGCTGTTCACATTGCA
genomic: TTTCTGGTGGAACTGACAACCATCTGGTTCTAGTGAATCTAAAGCCCAAGgtcacttgat ... ttgtttgcagGGAATTGATGGATCTAGAGTTGAGAAAGTGTTGGAAGCTGTTCACATTGCA
EST: gi|125221567|gb|EL235652.1|EL235652
EST:     TTTCTGGTGGAACTGACAACCATCTGGTTCTAGTGAATCTAAAGCCCAAG                         GGAATTGATGGATCTAGAGTTGAGAAAGTGTTGGAAGCTGTTCACATTGCA
genomic: TTTCTGGTGGAACTGACAACCATCTGGTTCTAGTGAATCTAAAGCCCAAGgtcacttgat ... ttgtttgcagGGAATTGATGGATCTAGAGTTGAGAAAGTGTTGGAAGCTGTTCACATTGCA
EST: gi|124921623|gb|EH995222.1|EH995222
EST:     TTTCTGGTGGAACTGACAACCATCTGGTTCTAGTGAATCTAAAGCCCAAG                         GGAATTGATGGATCTAGAGTTGAG
genomic: TTTCTGGTGGAACTGACAACCATCTGGTTCTAGTGAATCTAAAGCCCAAGgtcacttgat ... ttgtttgcagGGAATTGATGGATCTAGAGTTGAG
EST: gi|116484716|gb|EG527308.1|EG527308
EST:     TTTCTGGTGGAACTGACAACCATCTGGTTCTAGTGAATCTAAAGCCCAAG                         GGAATTGATGGATCTAGAGTTGAGAAAGTGTTGGAAGCTGTTCACATTGCA
genomic: TTTCTGGTGGAACTGACAACCATCTGGTTCTAGTGAATCTAAAGCCCAAGgtcacttgat ... ttgtttgcagGGAATTGATGGATCTAGAGTTGAGAAAGTGTTGGAAGCTGTTCACATTGCA
EST: gi|116484726|gb|EG527318.1|EG527318
EST:     TTTCTGGTGGAACTGACAACCATCTGGTTTTAGTGAATTTAAAGCCCAAG                         GGAATTGATGGATCTAGAGTTGAGAAAGTGTTGGAAGCTGTTCACATTGCA
genomic: TTTCTGGTGGAACTGACAACCATCTGGTTCTAGTGAATCTAAAGCCCAAGgtcacttgat ... ttgtttgcagGGAATTGATGGATCTAGAGTTGAGAAAGTGTTGGAAGCTGTTCACATTGCA
EST: gi|125037437|gb|EL109706.1|EL109706
EST:     CTTCTGGTGGAACTGACAACCATCTGGTTCTAGTGAATCTAAAGCCCAAG                         GGAATTGATGGATCTAGAGTTGAGAAAG
genomic: TTTCTGGTGGAACTGACAACCATCTGGTTCTAGTGAATCTAAAGCCCAAGgtcacttgat ... ttgtttgcagGGAATTGATGGATCTAGAGTTGAGAAAG
EST: gi|125269651|gb|EL283736.1|EL283736
EST:     AACCATCTGGTTCTAGTGAATCTAAAGCCCAAG                         GGAATTGATGGATCTAGAGTTGAGAAAGTGTTGGAAGCTGTTCACATTGCA
genomic: AACCATCTGGTTCTAGTGAATCTAAAGCCCAAGgtcacttgat ... ttgtttgcagGGAATTGATGGATCTAGAGTTGAGAAAGTGTTGGAAGCTGTTCACATTGCA
EST: gi|124776422|gb|EH866549.1|EH866549
EST:     GTGAATCTAAAGCCCAAG                         GGAATTGATGGATCTAGAGTTGAGAAAGTGTTGGAAGCTGTTCACATTGCA
genomic: GTGAATCTAAAGCCCAAGgtcacttgat ... ttgtttgcagGGAATTGATGGATCTAGAGTTGAGAAAGTGTTGGAAGCTGTTCACATTGCA
EST: gi|124714652|gb|EH806054.1|EH806054
EST:     CTAGTGAATCTAAAGCCCAAG                         GGAATTGATGGATCTAGAGTTGAGAAAGCGTTGGAAGCTGTTCACATTGCA
genomic: CTAGTGAATCTAAAGCCCAAGgtcacttgat ... ttgtttgcagGGAATTGATGGATCTAGAGTTGAGAAAGTGTTGGAAGCTGTTCACATTGCA
EST: gi|124931415|gb|EL008774.1|EL008774
EST:     TTTCTGGTGGAACTGACAACCATCTGGTTCTAGTGAATCTAAAGCCCAAG                         GGAATTGATGGATCTAGAGTTG
genomic: TTTCTGGTGGAACTGACAACCATCTGGTTCTAGTGAATCTAAAGCCCAAGgtcacttgat ... ttgtttgcagGGAATTGATGGATCTAGAGTTG
EST: gi|116484725|gb|EG527317.1|EG527317
EST:     TTTCTGGTGGAACTGACAACCATCTGGTTCTAGTGAATCTAAAGCCCAAG                         GGAATTGATGGATCTAGAGTTGAGAAAGTGTTGGAAGCTGTTCACATTGCA
genomic: TTTCTGGTGGAACTGACAACCATCTGGTTCTAGTGAATCTAAAGCCCAAGgtcacttgat ... ttgtttgcagGGAATTGATGGATCTAGAGTTGAGAAAGTGTTGGAAGCTGTTCACATTGCA
EST: gi|125301983|gb|EL316068.1|EL316068
EST:     GGTTCTAGTGAATCTAAAGCCCAAG                         GGAATTGATGGATCTAGAGTTGAGAAAGTGTTGGAAGCTGTTCACATTGCA
genomic: GGTTCTAGTGAATCTAAAGCCCAAGgtcacttgat ... ttgtttgcagGGAATTGATGGATCTAGAGTTGAGAAAGTGTTGGAAGCTGTTCACATTGCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACTCTAATGGAGAGAGGATATGAACTTGTTTCTGGTGGAACTGACAACCATCTGGTTCTAGTGAATCTAAAGCCCAAGgtcacttgatctttttttgtatataatcttcttttatatttcttagttaaaactcattttttattcgattttgtttgcag

- - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - -  GGTGGA