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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtgtatatagttttcttgctttattttcagatgattgcttaattcatgctgattattcaaactagcaagcactttttttaccaaaaagggtctggtagtgacactgttgttaattacccagTTCTACACAAAATTAGAGGAGAAACATAAAGCTTTGGAAGCAGAGAAGGACGAGGCTGAGGCCAGGAAAAAG

Basic information

species Zea mays
transcript GRMZM2G163912_T03
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G163912_T03 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os03g58480.1 (Oryza sativa), 3'ss of exon 4
gtgtgtatatagttttcttgctttattttcagatgattgcttaattcatgctgattattca-aactagcaa--gcacttt-ttttaccaaaaagggtctggtagtgacactg-ttgttaattacccagTTCTACACAAAATTAGAGGAGAAACATAAAGCTTTGGAAGCAGAGAAGGACGAGGCTGAGGCCAGGAAAAAG
|||  ||| ||||||  |||| ||||||  |||||    ||||| |  || |  ||||| | || |||| |  ||| ||| ||||  | ||||    |||||  | | | || ||| |  ||   |||||||||||||||||||| |||||||| || || |||||||| |||||| | ||||| |||||| ||||||||
gtgaatatgtagtttgattgcattatttcaagatggcctcttaaat-gtgtttgttatttacaaatagcgatggcattttcttttctctaaaaatagctggtgctcatagtgattgctgtttcttcagTTCTACACAAAATTAGAAGAGAAACACAAGGCCTTGGAAGCTGAGAAGAATGAGGCCGAGGCCCGGAAAAAG
















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|211431804|gb|FL298785.1|FL298785
EST:     CTGTTGCCCCATCATTTGTGTGTGCTAACCGTGCTGACAAGAGGAAGGAG                         TTCTACACAAAATTAGAGGAGAAACATAAAGCTTTGGAAGCAGAGAAGGAC
genomic: CTGTTGCCCCATCATTTGTGTGTGCTAACCGTGCTGACAAGAGGAAGGAGgtgtgtatat ... aattacccagTTCTACACAAAATTAGAGGAGAAACATAAAGCTTTGGAAGCAGAGAAGGAC
EST: gi|31350916|gb|CD435273.1|CD435273
EST:     CTGTTGCCCCATCATTTGTGTGTGCTAACCGTGCTGACAAGAGGAAGGAG                         TTCTACACAAAATTAGAGGAGAAACATAAAGCTTTGGAAGCAGAGAAGGAC
genomic: CTGTTGCCCCATCATTTGTGTGTGCTAACCGTGCTGACAAGAGGAAGGAGgtgtgtatat ... aattacccagTTCTACACAAAATTAGAGGAGAAACATAAAGCTTTGGAAGCAGAGAAGGAC
EST: gi|211431802|gb|FL298783.1|FL298783
EST:     CTGTTGCCCCATCATTTGTGTGTGCTAACCGTGCTGACAAGAGGAAGGAG                         TTCTACACAAAATTAGAGGAGAAACATAAAGCTTTGGAAGCAGAGAAGGAC
genomic: CTGTTGCCCCATCATTTGTGTGTGCTAACCGTGCTGACAAGAGGAAGGAGgtgtgtatat ... aattacccagTTCTACACAAAATTAGAGGAGAAACATAAAGCTTTGGAAGCAGAGAAGGAC
EST: gi|32833725|gb|CD973403.1|CD973403
EST:     CTGTTGCCCCATCATTTGTGTGTGCTAACCGTGCTGACAAGAGGAAGGAG                         TTCTACACAAAATTAGAGGAGAAACATAAAGCTTTGGAAGCAGAGAAGGAC
genomic: CTGTTGCCCCATCATTTGTGTGTGCTAACCGTGCTGACAAGAGGAAGGAGgtgtgtatat ... aattacccagTTCTACACAAAATTAGAGGAGAAACATAAAGCTTTGGAAGCAGAGAAGGAC
EST: gi|211431805|gb|FL298786.1|FL298786
EST:     CTGTTGCCCCATCATTTGTGTGTGCTAACCGTGCTGACAAGAGGAAGGAG                         TTCTACACAAAATTAGAGGAGAAACATAAAGCTTTGGAAGCAGAGAAGGAC
genomic: CTGTTGCCCCATCATTTGTGTGTGCTAACCGTGCTGACAAGAGGAAGGAGgtgtgtatat ... aattacccagTTCTACACAAAATTAGAGGAGAAACATAAAGCTTTGGAAGCAGAGAAGGAC
EST: gi|89757168|gb|DY686883.1|DY686883
EST:     CTGTTGCCCCATCATTTGTGTGTGCTAACCGTGCTGACAAGAGGAAGGAG                         TTCTACACAAAATTAGAGGAGAAACATAAAGCTTTGGAAGCAGAGAAGGAC
genomic: CTGTTGCCCCATCATTTGTGTGTGCTAACCGTGCTGACAAGAGGAAGGAGgtgtgtatat ... aattacccagTTCTACACAAAATTAGAGGAGAAACATAAAGCTTTGGAAGCAGAGAAGGAC
EST: gi|211431800|gb|FL298781.1|FL298781
EST:     CTGTTGCCCCATCATTTGTGTGTGCTAACCGTGCTGACAAGAGGAAGGAG                         TTCTACACAAAATTAGAGGAGAAACATAAAGCTTTGGAAGCAGAGAATGAC
genomic: CTGTTGCCCCATCATTTGTGTGTGCTAACCGTGCTGACAAGAGGAAGGAGgtgtgtatat ... aattacccagTTCTACACAAAATTAGAGGAGAAACATAAAGCTTTGGAAGCAGAGAAGGAC
EST: gi|211431801|gb|FL298782.1|FL298782
EST:     CTGTTGCCCCATCATTTGTGTGTGCTAACCGTGCTGACAAGAGGAAGGAG                         TTCTACACAAAATTAGAGGAGAAACATAAAGCTTTGGAAGCAGAGAAGGAC
genomic: CTGTTGCCCCATCATTTGTGTGTGCTAACCGTGCTGACAAGAGGAAGGAGgtgtgtatat ... aattacccagTTCTACACAAAATTAGAGGAGAAACATAAAGCTTTGGAAGCAGAGAAGGAC
EST: gi|211431803|gb|FL298784.1|FL298784
EST:     CTGTTGCCCCATCATTTGTGTGTGCTAACCGTGCTGACAAGAGGAAGGAG                         TTCTACACAAAATTAGAGGAGAAACATAAAGCTTTGGAAGCAGAGAAGGAC
genomic: CTGTTGCCCCATCATTTGTGTGTGCTAACCGTGCTGACAAGAGGAAGGAGgtgtgtatat ... aattacccagTTCTACACAAAATTAGAGGAGAAACATAAAGCTTTGGAAGCAGAGAAGGAC
EST: gi|32910548|gb|CF015360.1|CF015360
EST:     CTGTTGCCCCATCATTTGTGTGTGCTAACCGTGCTGACAAGAGGAAGGAG                         TTCTACACAAAATTAGAGGAGAAACATAAAGCTTTGGAAGCAGAGAAGGAC
genomic: CTGTTGCCCCATCATTTGTGTGTGCTAACCGTGCTGACAAGAGGAAGGAGgtgtgtatat ... aattacccagTTCTACACAAAATTAGAGGAGAAACATAAAGCTTTGGAAGCAGAGAAGGAC
EST: gi|87156202|gb|DY400991.1|DY400991
EST:     CTGTTGCCCCATCATTTGTGTGTGCTAACCGTGCTGACAAGAGGAAGGAG                         TTCTACACAAAATTAGAGGAGAAACATAAAGCTTTGGAAGCAGAGAAGGAC
genomic: CTGTTGCCCCATCATTTGTGTGTGCTAACCGTGCTGACAAGAGGAAGGAGgtgtgtatat ... aattacccagTTCTACACAAAATTAGAGGAGAAACATAAAGCTTTGGAAGCAGAGAAGGAC
EST: gi|148993804|gb|EE033889.2|EE033889
EST:     CTGTTGCCCCATCATTTGTGTGTGCTAACCGTGCTGACAAGAGGAAGGAG                         TTCTACACAAAATTAGAGGAGAAACATAAAGCTTTGGAAGCAGAGAAGGAC
genomic: CTGTTGCCCCATCATTTGTGTGTGCTAACCGTGCTGACAAGAGGAAGGAGgtgtgtatat ... aattacccagTTCTACACAAAATTAGAGGAGAAACATAAAGCTTTGGAAGCAGAGAAGGAC
EST: gi|22521109|gb|BU079920.1|BU079920
EST:     CTGTTGCCCCATCATTTGTGTGTGCTAACCGTGCTGACAAGAGGAAGGAG                         TTCTACACAAAATTAGAGGAGAAACATAAAGCTTTGGAAGCAGAGAAGGAC
genomic: CTGTTGCCCCATCATTTGTGTGTGCTAACCGTGCTGACAAGAGGAAGGAGgtgtgtatat ... aattacccagTTCTACACAAAATTAGAGGAGAAACATAAAGCTTTGGAAGCAGAGAAGGAC
EST: gi|149099628|gb|EE185673.2|EE185673
EST:     CTGTTGCCCCATCATTTGTGTGTGCTAACCGTGCTGACAAGAGGAAGGAG                         TTCTACACAAAATTAGAGGAGAAACATAAAGCTTTGGAAGC
genomic: CTGTTGCCCCATCATTTGTGTGTGCTAACCGTGCTGACAAGAGGAAGGAGgtgtgtatat ... aattacccagTTCTACACAAAATTAGAGGAGAAACATAAAGCTTTGGAAGC
EST: gi|87156913|gb|DY401702.1|DY401702
EST:     CTGTTGCCCCATCATTTGTGTGTGCTAACCGTGCTGACAAGAGGAAGGAG                         TTCTACACAAAATTAGAGGAGAAACATAAAGCTTTGGAAGCAGAGAAGGAC
genomic: CTGTTGCCCCATCATTTGTGTGTGCTAACCGTGCTGACAAGAGGAAGGAGgtgtgtatat ... aattacccagTTCTACACAAAATTAGAGGAGAAACATAAAGCTTTGGAAGCAGAGAAGGAC
EST: gi|32836136|gb|CD975814.1|CD975814
EST:     CTGTTGCNCCATCATTTGTGTGTGCTAACCGTGCTGACAAGAGGAAGGAG                         TTCTACACAAAATTAGAGGAGAAACATAAAGCTTTGGAAGCAGAGAAGGAC
genomic: CTGTTGCCCCATCATTTGTGTGTGCTAACCGTGCTGACAAGAGGAAGGAGgtgtgtatat ... aattacccagTTCTACACAAAATTAGAGGAGAAACATAAAGCTTTGGAAGCAGAGAAGGAC
EST: gi|32867073|gb|CF006755.1|CF006755
EST:     CTGTTGCCCCATCATTTGTGTGTGCTAACCGTGCTGACAAGAGGAAGGAG                         TTCTACACAAAATTAGAGGAGAAACATAAAGCTTTGGAAGCAGAGAAGGAC
genomic: CTGTTGCCCCATCATTTGTGTGTGCTAACCGTGCTGACAAGAGGAAGGAGgtgtgtatat ... aattacccagTTCTACACAAAATTAGAGGAGAAACATAAAGCTTTGGAAGCAGAGAAGGAC
EST: gi|22473217|gb|BU037697.1|BU037697
EST:     CTGTTGCCCCATCATTTGTGTGTGCTAACCGTGCTGACAAGAGGAAGGAG                         TTCTACACAAAATTAGAGGAGAAACATAAAGCTTTGGAAGCAGAGAAGGAC
genomic: CTGTTGCCCCATCATTTGTGTGTGCTAACCGTGCTGACAAGAGGAAGGAGgtgtgtatat ... aattacccagTTCTACACAAAATTAGAGGAGAAACATAAAGCTTTGGAAGCAGAGAAGGAC
EST: gi|22520704|gb|BU079515.1|BU079515
EST:     CTGTTGCCCCATCATTTGTGTGTGCTAACCGTGCTGACAAGAGGAAGGAG                         TTCTACACAAAATTAGAGGAGAAACATAAAGCTTTGGAAGCAGAGAAGGAC
genomic: CTGTTGCCCCATCATTTGTGTGTGCTAACCGTGCTGACAAGAGGAAGGAGgtgtgtatat ... aattacccagTTCTACACAAAATTAGAGGAGAAACATAAAGCTTTGGAAGCAGAGAAGGAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagcactttttttaccaaaaagggtctggtagtgacactgttgttaattacccagTTCTACACAAAATTAGAGGAGAAACATAAAGCTTTGGAAGCAGAGAAGGACGAGGCTGAGGCCAGGAAAAAG
                                         tgttaat  putative branch site (score: 3)
      tttttttaccaaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgtgtatatagttttcttgctttattttcagatgattgcttaattcatgctgattattcaaactagcaagcactttttttaccaaaaagggtctggtagtgacactgttgttaattacccagTTCTACACAAAATTAGAGGAGAAACATAAAGCTTTGGAAGCAGAGAAGGACGAGGCTGAGGCCAGGAAAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG