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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgtcatacctgcccataccagtacttttgcaactatttaattattcttaatctataatgcaatagctttggtattcaaaaagatgcattcttttaccagGGGCACACTGCCATCAATGAACTCATTAGGGCGCTGGTTTGGGGAGCCTGTAAGGGCTGCTATTCTGCAAACCAAT

Basic information

species Zea mays
transcript GRMZM2G011456_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G011456_T03 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os02g04660.1 (Oryza sativa), 3'ss of exon 5
gtaagtgtcatacctgc----ccatacca-gtactttt------gcaactat-ttaattattcttaatctataatgcaatagctttggtattca----aaaagatg--cattcttttaccagGGGCACACTGCCATCAATGAACTCATTAGGGCGCTGGTTTGGGGAGCCTGTAAGGGCTGCTATTCTGCAAACCAAT
|||||||   | | |||        |||| || ||||       |  |  || | | | ||  | ||||||| |||  |||| |||||| ||||    ||| | ||   ||||  ||| |||| ||||||||||||| ||||| ||| ||||||| |||||||||||||||||||| ||||| ||||| ||||| |||
gtaagtgatgttcttgcattgttgcaccaagtgctttcttccaagtgaagatgtcactgataataaatctatcatgttatagttttggttttcattacaaaggttggctattcacttatcagGAGCACACTGCCATCTATGAATTCACTAGGGCGGTGGTTTGGGGAGCCTGTAAGAGCTGCAATTCTTCAAACAAAT
















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|211230912|gb|FL222481.1|FL222481
EST:     AGAT-GCTATGTGACCATAGTAGCCCACTATGCGTGGCACTTGATATTTC                         GGGCACACTGCCATCAATGAACTCATTTAAGGCGCTGGTTTGGGGAGCCTG
genomic: AGATTGCTATGTGACCATAGTAGCCAACTATGCGTGGCACTTGATATTTCgtaagtgtca ... cttttaccagGGGCACACTGCCATCAATGAACTCATT-AGGGCGCTGGTTTGGGGAGCCTG
EST: gi|71311078|gb|DR791853.1|DR791853
EST:     AGATTGCTATGTGACCATAGTAGCCAACTATGCGTGGCACTTGATATTTC                         GGGCACACTGCCATCAATGAACTCATTAGGGCGCTGGTTTGGGGAGCCTGT
genomic: AGATTGCTATGTGACCATAGTAGCCAACTATGCGTGGCACTTGATATTTCgtaagtgtca ... cttttaccagGGGCACACTGCCATCAATGAACTCATTAGGGCGCTGGTTTGGGGAGCCTGT
EST: gi|71300983|gb|DR786520.1|DR786520
EST:     AGATTGCTATGTGACCATAGTAGCCAACTATGCGTGGCACTTGATATTTC                         GGGCACACTGCCATCAATGAACTCATTAGGGCGCTGGTTTGGGGAGCCTGT
genomic: AGATTGCTATGTGACCATAGTAGCCAACTATGCGTGGCACTTGATATTTCgtaagtgtca ... cttttaccagGGGCACACTGCCATCAATGAACTCATTAGGGCGCTGGTTTGGGGAGCCTGT
EST: gi|89762829|gb|DY690269.1|DY690269
EST:     AGATTGCTATGTGACCATAGTAGCCAACTATGCGTGGCACTTGATATTTC                         GGGCACACTGCCATCAATGAACTCATT
genomic: AGATTGCTATGTGACCATAGTAGCCAACTATGCGTGGCACTTGATATTTCgtaagtgtca ... cttttaccagGGGCACACTGCCATCAATGAACTCATT
EST: gi|91876145|gb|EB406102.1|EB406102
EST:     AGATTGCTATGTGACCATAGTAGCCAACTATGCGTGGCACTTGATATTTC                         GGGCACACTGCCATCAATGAAC
genomic: AGATTGCTATGTGACCATAGTAGCCAACTATGCGTGGCACTTGATATTTCgtaagtgtca ... cttttaccagGGGCACACTGCCATCAATGAAC
EST: gi|74233408|gb|DT641322.1|DT641322
EST:     AGATTGCTATGTGACCATAGTAGCCAACTATGCGTGGCACTTGATATTTC                         GGGCACACTGCCATCAATGAACTCATTAGGGCGCTGGTTTGGGGAGCCTGT
genomic: AGATTGCTATGTGACCATAGTAGCCAACTATGCGTGGCACTTGATATTTCgtaagtgtca ... cttttaccagGGGCACACTGCCATCAATGAACTCATTAGGGCGCTGGTTTGGGGAGCCTGT
EST: gi|78117239|gb|DV535626.1|DV535626
EST:     AGATTGCTATGTGACCATAGTAGCCAACTATGCGTGGCACTTGATATTTC                         GGGCACACTGCCATCAATGAACTCATTANGGCGCTGGTTTGGGGAGCCTGT
genomic: AGATTGCTATGTGACCATAGTAGCCAACTATGCGTGGCACTTGATATTTCgtaagtgtca ... cttttaccagGGGCACACTGCCATCAATGAACTCATTAGGGCGCTGGTTTGGGGAGCCTGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttaatctataatgcaatagctttggtattcaaaaagatgcattcttttaccagGGGCACACTGCCATCAATGAACTCATTAGGGCGCTGGTTTGGGGAGCCTGTAAGGGCTGCTATTCTGCAAACCAAT
 tcttaat  putative branch site (score: 3)
                                           ttcttttacc  putative PPT
                           tattcaaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtgtcatacctgcccataccagtacttttgcaactatttaattattcttaatctataatgcaatagctttggtattcaaaaagatgcattcttttaccagGGGCACACTGCCATCAATGAACTCATTAGGGCGCTGGTTTGGGGAGCCTGTAAGGGCTGCTATTCTGCAAACCAAT

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