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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TAGCGACGATTTACTTTATCTGAAAGAACAGATGGAAGCAGAGGAAGATGCAGAACGTCTTCTGAGACGAACTGAGAAACGGGCTTTTGCTGCCTTTAAAatatcctttcttaaatgctcagatatcatgattttgagcactaagttatttgatatatacttgcctagatgtttttttgtaatctttcttgaccatatatcac

Basic information

species Arabidopsis thaliana
transcript AT1G73350.2
intron # 4
splice site 5'
intron type U12 (go to U12 genes for details)

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G73350.2 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GRMZM2G146786_T01 (Zea mays), 5'ss of exon 4
TAGCGACGATTTACTTTATCTGAAAGAACAGATGGAAGCAGAGGAAGATGCAGAACGTCTTCTGAGACGAACTGAGAAACGGGCTTTTGCTGCCTTTAAAatatcctttcttaaatgctcagatatcatgattttgagcactaagttatttgatatatacttgcctagatgtttttttgtaatctttcttgaccatatatcac-------------------------------------------------------------------------------------------
 ||||| ||||| ||||| |||||||| || |||||||| || ||||||||||| || |||||  | |  |||||||| ||||| |||||||| ||||| ||||||||| ||||        | | | |   |||      ||     ||    |||   |    |  || |  ||  || | ||||  ||   |  | || |                                                                                           
CAGCGATGATTTGCTTTACCTGAAAGAGCAAATGGAAGCTGAAGAAGATGCAGAGCGCCTTCTTCGTCATACTGAGAAGCGGGCATTTGCTGCTTTTAAGatatcctttattaatcatc--aacaactttgcttttcctgttatacagttaatgatacggtctgattaatatggttcagttagcttttctggaaacttttcgcacctttacaattcagtttccttccgttcaaatagtgcaatagaaacatgtggtctaagctatctctttgctatctttaactctgacattac

upper sequence: AT1G73350.2 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA09G28980.2 (Glycine max), 5'ss of exon 4
TAGCGACGATTTACTTTATCTGAAAGAACAGATGGAAGCAGAGGAAGATGCAGAACGTCTTCTGAGACGAACTGAGAAACGGGCTTTTGCTGCCTTTAAAatatcctttcttaaatgctcagatatcatgattttgagcactaagttatttgatatatacttg-cctagatgtttttttgtaatctttcttgaccat-atatcac-
 || || ||| |||||||||| ||||| || |||||||| ||||| ||||||||||| || ||| | || ||||| |||||||| |||||||| ||||| |||||||||  |      |  || | ||| |   |     | | |||  || || |    |||   | ||    ||||| |   ||      || || |  |  | 
CAGTGATGATCTACTTTATCTCAAAGAGCAAATGGAAGCCGAGGAGGATGCAGAACGCCTCCTGCGTCGCACTGAAAAACGGGCATTTGCTGCATTTAAGatatccttttgtggtcattgcgaca-cataacaat-----ccatgtttcttcatcttgggttgattttgactgatttttatgtcctactactacaattaccttgct

upper sequence: AT1G73350.2 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: PP1S402_46V6.1 (Physcomitrella patens), 5'ss of exon 4
-------TAGCGACGATTTACTTTATCTGAAAGAACAGATGGAAGCAGAGGAAGATGCAGAACGTCTTCTGAGACGAACTGAGAAACGGGCTTTTGCTGCCTTTAAAatatcctttcttaaatgctcagatatcatgattttg----agcactaagttatttgatatatacttgcctagatgtttttttgtaatctttcttgaccatatatcac
       ||| || ||||| |||||  | ||||| || |||||||| ||||| ||||| || ||  | | | ||||||||||||||||||| || || || ||||||||||||||      |   | |  ||| ||  ||||     ||  |||   |||   | ||    ||  ||| |  | |    | | |  |  | ||           
CATTGGATAGTGATGATTTGCTTTACTTAAAAGAGCAAATGGAAGCTGAGGAGGATGCGGAGCGGTTGCGGCGACGAACTGAGAAACGGGCGTTCGCAgcttttaaaatatccttat---gacatttatttattatatttttctatcagtgctacaatatc-aaaattggattatctaaaaatgtc--agaagtgatggtagag----------

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|86078871|gb|DR374628.1|DR374628
EST:     CAGAACGTCTTCTGAGACGAACTGAGAAACGGGCTTTTGCTGCCTTTAAA                         AAAGCTGCAACCCAAGCTGATTCATCTCCAGCATCTATTCCCTTGNC-MTT
genomic: CAGAACGTCTTCTGAGACGAACTGAGAAACGGGCTTTTGCTGCCTTTAAAatatcctttc ... catatatcacAAAGCTGCAACCCAAGCTGATTCATCTCCAGCATCTATTCCCTTGCCACTT
EST: gi|116453295|gb|EG495887.1|EG495887
EST:     CAGAACGTCTTCTGAGACGAACTGAGAAACGGGCTTTTGCTGCCTTTAAA                         AAAGCTGCAACCCAAGCTGATTCATCTCCAGCATCTATTCCCTTGCCACTT
genomic: CAGAACGTCTTCTGAGACGAACTGAGAAACGGGCTTTTGCTGCCTTTAAAatatcctttc ... catatatcacAAAGCTGCAACCCAAGCTGATTCATCTCCAGCATCTATTCCCTTGCCACTT
EST: gi|116453294|gb|EG495886.1|EG495886
EST:     CAGAACGTCTTCTGAGACGAACTGAGAAACGGGCTTTTGCTGCCTTTAAA                         AAAGCTGCAACCCAAGCTGATTCATCTCCAGCATCTATTCCCTTGCCACTT
genomic: CAGAACGTCTTCTGAGACGAACTGAGAAACGGGCTTTTGCTGCCTTTAAAatatcctttc ... catatatcacAAAGCTGCAACCCAAGCTGATTCATCTCCAGCATCTATTCCCTTGCCACTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TAGCGACGATTTACTTTATCTGAAAGAACAGATGGAAGCAGAGGAAGATGCAGAACGTCTTCTGAGACGAACTGAGAAACGGGCTTTTGCTGCCTTTAAAatatcctttcttaaatgctcagatatcatgattttgagcactaagttatttgatatatacttgcctagatgtttttttgtaatctttcttgaccatatatcac

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC