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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCGGCCCACTTGCTGCCTATTATAAACTGCCACTTAATCGTGTCCTAGTGgtaggtgtttgtttcttttttcatgaacacacaggaggactgtgtatcttttatatattagagagaaagaaagaggaccaatcccaagtacacagagaac...

Basic information

species Zea mays
transcript GRMZM5G896731_T02
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G896731_T02 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os05g51800.1 (Oryza sativa), 5'ss of exon 3
GTCGGCCCACTTGCTGCCTATTATAAACTGCCACTTAATCGTGTCCTAGTGgtaggtgtt--tgtttctt-ttttcatgaacacacaggaggactgtgtatcttttatatattagagagaaagaaagaggaccaatcccaagtacacagagaac
|| || ||||||||||||||||||||||| ||||||||||||||||| |||||| || ||    | |||  | || ||||   |  ||    |  |   ||||    | |  | | | |||    ||                           
GTTGGGCCACTTGCTGCCTATTATAAACTACCACTTAATCGTGTCCTTGTGgtaagtattgtaatatctaatctttatgagtgctaagttacatagca-atctgactttt-ctggtgtgaatttcag---------------------------

upper sequence: GRMZM5G896731_T02 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os03g22610.1 (Oryza sativa), 5'ss of exon 5
GTCGGCCCACTTGCTGCCTATTATAAACTGCCACTTAATCGTGTCCTAGTGgtaggtgtt--tgtttctt-ttttcatgaacacacaggaggactgtg-tatcttttatatatta-gagagaaagaaagaggaccaatcccaagtacacagagaac
|| || ||||||||||||||||||||| | ||||||||||| ||||| |||||  || ||    | |||  | || |||| | |  ||    |  |   | |  ||| | ||||  |||    ||                               
GTTGGGCCACTTGCTGCCTATTATAAATTACCACTTAATCGCGTCCTTGTGgttagtattgtaatatctaatctttatgagcgctaagttacatggcaatctgatttctctattgtgagttttag-------------------------------
















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|89248113|gb|DY619899.1|DY619899
EST:     TCGGCCCACTTGCTGCCTATTATAAACTGCCACTTAATCGTGTCCTAGTG                         GCGTTTGATGACATGGACTTGCCATGTGGAGTTCTCCGTCTACAGCCAAAA
genomic: TCGGCCCACTTGCTGCCTATTATAAACTGCCACTTAATCGTGTCCTAGTGgtaggtgttt ... tgagtttcagGCGTTTGATGACATGGACTTGCCATGTGGAGTTCTCCGTCTACAGCCAAAA
EST: gi|78109136|gb|DV527553.1|DV527553
EST:     TCGGCCCACTTGCTGCCTATTATAAACTGCCACTTAATCGTGTCCTAGTG                         GCGTTTGATGACATGGACTTGCCATGTGGAGTTCTCCGTCTACAGCCAAAA
genomic: TCGGCCCACTTGCTGCCTATTATAAACTGCCACTTAATCGTGTCCTAGTGgtaggtgttt ... tgagtttcagGCGTTTGATGACATGGACTTGCCATGTGGAGTTCTCCGTCTACAGCCAAAA
EST: gi|88756830|gb|DY540971.1|DY540971
EST:     TCGGCCCACTTGCTGCCTATTATAAACTGCCACTTAATCGTGTCCTAGTG                         GCGTTTGATGACATGGACTTGCCAT
genomic: TCGGCCCACTTGCTGCCTATTATAAACTGCCACTTAATCGTGTCCTAGTGgtaggtgttt ... tgagtttcagGCGTTTGATGACATGGACTTGCCAT
EST: gi|86468848|gb|DY235218.1|DY235218
EST:     CTGCCACTTAATCGTGTCCTAGTG                         GCGTTTGATGACATGGACTTGCCATGTGGAGTTCTCCGTCTACAGCCAAAA
genomic: CTGCCACTTAATCGTGTCCTAGTGgtaggtgttt ... tgagtttcagGCGTTTGATGACATGGACTTGCCATGTGGAGTTCTCCGTCTACAGCCAAAA
EST: gi|71438321|gb|DR819371.1|DR819371
EST:     TCGGCCCACTTGCTGCCTATTATAAACTGCCACTTAATCGTGTCCTAGTG                         GCGTTTGATGACATGGACTTGCCATGTGGAGTTCTCCGTCTACAGCCAAAA
genomic: TCGGCCCACTTGCTGCCTATTATAAACTGCCACTTAATCGTGTCCTAGTGgtaggtgttt ... tgagtttcagGCGTTTGATGACATGGACTTGCCATGTGGAGTTCTCCGTCTACAGCCAAAA
EST: gi|76293027|gb|DV032595.1|DV032595
EST:     TCGGCCCACTTGCTGTCTATTATAAACTGCCACTTAATCGTGTCCTAGTG                         GCGTTTGATGACATGGACTTGCCATGTGGAGTTCTCCGTCTACAGCCAAAA
genomic: TCGGCCCACTTGCTGCCTATTATAAACTGCCACTTAATCGTGTCCTAGTGgtaggtgttt ... tgagtttcagGCGTTTGATGACATGGACTTGCCATGTGGAGTTCTCCGTCTACAGCCAAAA
EST: gi|89250808|gb|DY622594.1|DY622594
EST:     TCGGCCCACTTGCTGCCTATTATAAACTGCCACTTAATCGTGTCCTAGTG                         GCGTTTGATGACATGGACTTGCCATGTGGAGTTCTCCGTCTACAGCCAAAA
genomic: TCGGCCCACTTGCTGCCTATTATAAACTGCCACTTAATCGTGTCCTAGTGgtaggtgttt ... tgagtttcagGCGTTTGATGACATGGACTTGCCATGTGGAGTTCTCCGTCTACAGCCAAAA
EST: gi|78109135|gb|DV527552.1|DV527552
EST:     TCGGCCCACTTGCTGCCTATTATAAACTGCCACTTAATCGTGTCCTAGTG                         GCGTTTGATGACATGGACTTGCCATGTGGAGTTCTCCGTCTACAGCCAAAA
genomic: TCGGCCCACTTGCTGCCTATTATAAACTGCCACTTAATCGTGTCCTAGTGgtaggtgttt ... tgagtttcagGCGTTTGATGACATGGACTTGCCATGTGGAGTTCTCCGTCTACAGCCAAAA
EST: gi|60358732|gb|DN225705.1|DN225705
EST:     TCGGCCCACTTGCTGCCTATTATAAACTGCCACTTAATCGTGTCCTAGTG                         GCGTTTGATGACATGGACTTGCCATGTGGAGTTCTCCGTCTACAGCCAAAA
genomic: TCGGCCCACTTGCTGCCTATTATAAACTGCCACTTAATCGTGTCCTAGTGgtaggtgttt ... tgagtttcagGCGTTTGATGACATGGACTTGCCATGTGGAGTTCTCCGTCTACAGCCAAAA
EST: gi|91050003|gb|EB160421.1|EB160421
EST:     TCGGCCCACTTGCTGCCTATTATAAACTGCCACTTAATCGTGTCCTAGTG                         GCGTTTGATGACATGGACTTGCCATGTGGAGTTCTCCGTCTACAGCCAAAA
genomic: TCGGCCCACTTGCTGCCTATTATAAACTGCCACTTAATCGTGTCCTAGTGgtaggtgttt ... tgagtttcagGCGTTTGATGACATGGACTTGCCATGTGGAGTTCTCCGTCTACAGCCAAAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTCGGCCCACTTGCTGCCTATTATAAACTGCCACTTAATCGTGTCCTAGTGgtaggtgtttgtttcttttttcatgaacacacaggaggactgtgtatcttttatatattagagagaaagaaagaggaccaatcccaagtacacagagaac

- - - - -  TGCTGC