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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcatttcttatcgtcaacattgacttaattactcctgcaacagtatcaattattttgttcacgcagccatcaccgacctattctattacagGTGGAGAAAATCAAGGCGTTGATGCTAATGGGAATTCACTCGACTTCTCAACGAAGCTGCTCCACCTCGCATGGCACCCGACCGAGAATTCTATTGCATG

Basic information

species Zea mays
transcript GRMZM2G165418_T02
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G165418_T01 (Zea mays), 3'ss of exon 13
lower sequence: LOC_Os06g36770.2 (Oryza sativa), 3'ss of exon 13
----gtcatttcttatcgtcaacattgacttaattactcctgcaacagtatca-att---attttgttcacgcagccatcaccgacctattctattacagGTGGAGAAAATCAAGGCGTTGATGCTAATGGGAATTCACTCGACTTCTCAACGAAGCTGCTCCACCTCGCATGGCACCCGACCGAGAATTCTATTGCATG
    || | || |  |   || ||   | ||  | | | |||  | | ||| | |||   | |    |    || ||||   | |  || | |  || |||||| |||||||||||||||||||| ||||| |||||| | ||||| || || ||| ||||||| || ||||||||||| || ||||||||||| |||||
gtatgttacttttctttcacatcaagaattt--tcagtactgagataatatgatattggcaatcaccttgtccaaccattttc-atataatatgctatagGTGGGGAAAATCAAGGCGTTGATGCCAATGGAAATTCATTTGACTTTTCGACAAAGTTGCTCCATCTTGCATGGCACCCAACTGAGAATTCTATCGCATG
















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|8273151|gb|BE012242.1|BE012242
EST:     AGCAAGGCCCACACGGACACTAACTTCTTTTGCCCGTGGTGTTCGNAGAG                         GTGGAGAAAATCAAGGCGTTGATGCTAATGGGAATTCACTCGACTTCTCAA
genomic: AGCAAGGCCCACACGGACACTAACTTCTTTTGCCCGTGGTGTTCGGAGAGgtcatttctt ... tctattacagGTGGAGAAAATCAAGGCGTTGATGCTAATGGGAATTCACTCGACTTCTCAA
EST: gi|78180163|gb|DV550536.1|DV550536
EST:     AGCAAGGCCCACACGGACACTAACTTCTTTTGCCCGTGGTGTTCGGAGAG                         GTGGAGAAAATCAAGGCGTTGATGCTAATGGGAATTCACTCGACTTCTCAA
genomic: AGCAAGGCCCACACGGACACTAACTTCTTTTGCCCGTGGTGTTCGGAGAGgtcatttctt ... tctattacagGTGGAGAAAATCAAGGCGTTGATGCTAATGGGAATTCACTCGACTTCTCAA
EST: gi|33090978|gb|CF050972.1|CF050972
EST:     AGCAAGGCCCACACGGACACTAACTTCTTTTGCCCGTGGTGTTCGGAGAG                         GTGGAGAAAATCAAGGCGTTGATGCTAATGGGAATTCACTCGACTTCTCAA
genomic: AGCAAGGCCCACACGGACACTAACTTCTTTTGCCCGTGGTGTTCGGAGAGgtcatttctt ... tctattacagGTGGAGAAAATCAAGGCGTTGATGCTAATGGGAATTCACTCGACTTCTCAA
EST: gi|37397098|gb|CF635844.1|CF635844
EST:     AGCAAGGCCCACACGGACACTAACTTCTTTTGCCCGTGGTGTTCGGAGAG                         GTGGAGAAAATCAAGGCGTTGATGCTAATGGGAATTCACTCGACTTCTCAA
genomic: AGCAAGGCCCACACGGACACTAACTTCTTTTGCCCGTGGTGTTCGGAGAGgtcatttctt ... tctattacagGTGGAGAAAATCAAGGCGTTGATGCTAATGGGAATTCACTCGACTTCTCAA
EST: gi|211538557|gb|FL475991.1|FL475991
EST:     CCACAGGGACACTAACTTCTTTTGCCCGTGGTGTTCGGAGAG                         GTGGAGAAAATCAAGGCGTTGATGCTAATGGGAATTCACTCGACTTCTCAA
genomic: CCACACGGACACTAACTTCTTTTGCCCGTGGTGTTCGGAGAGgtcatttctt ... tctattacagGTGGAGAAAATCAAGGCGTTGATGCTAATGGGAATTCACTCGACTTCTCAA
EST: gi|71419453|gb|DR804773.1|DR804773
EST:     AGCAAGGCCCACACGGACACTAACTTCTTTTGCCCGTGGTGTTCGGAGAG                         GTGGAGAAAATCAAGGCGTTGATGCTAATGGGAATTCACTCGACTTCTCAA
genomic: AGCAAGGCCCACACGGACACTAACTTCTTTTGCCCGTGGTGTTCGGAGAGgtcatttctt ... tctattacagGTGGAGAAAATCAAGGCGTTGATGCTAATGGGAATTCACTCGACTTCTCAA
EST: gi|18166015|gb|BM335854.1|BM335854
EST:     AGCAAGGCCCACACGGACACTAACTTCTTTTGCCCGTGGTGTTCGGAGAG                         GTGGAGAAAATCAAGGCGTTGATGCTAATGGGAATTCACTCGACTTCTCAA
genomic: AGCAAGGCCCACACGGACACTAACTTCTTTTGCCCGTGGTGTTCGGAGAGgtcatttctt ... tctattacagGTGGAGAAAATCAAGGCGTTGATGCTAATGGGAATTCACTCGACTTCTCAA
EST: gi|83278851|gb|DV942859.1|DV942859
EST:     AGCAAGGCCCACACGGACACTAACTTCTTTTGCCCGTGGTGTTCGGAGAG                         GTGGAGAAAATCAAGGCGTTGATGCTAATGGGAATTCACTCGACTTCTCAA
genomic: AGCAAGGCCCACACGGACACTAACTTCTTTTGCCCGTGGTGTTCGGAGAGgtcatttctt ... tctattacagGTGGAGAAAATCAAGGCGTTGATGCTAATGGGAATTCACTCGACTTCTCAA
EST: gi|24934367|gb|CA452585.1|CA452585
EST:     AGCAAGGCCCACACGGACACTAACTTCTTTTGCCCGTGGTGTTCGGAGAG                         GTGGAGAAAATCAAGGCGTTGATGCTAATGGGAATTCACTCGACTTCTCAA
genomic: AGCAAGGCCCACACGGACACTAACTTCTTTTGCCCGTGGTGTTCGGAGAGgtcatttctt ... tctattacagGTGGAGAAAATCAAGGCGTTGATGCTAATGGGAATTCACTCGACTTCTCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcaacagtatcaattattttgttcacgcagccatcaccgacctattctattacagGTGGAGAAAATCAAGGCGTTGATGCTAATGGGAATTCACTCGACTTCTCAACGAAGCTGCTCCACCTCGCATGGCACCCGACCGAGAATTCTATTGCATG
                                        cctattct  CT-rich tract
       tatcaattattttgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcatttcttatcgtcaacattgacttaattactcctgcaacagtatcaattattttgttcacgcagccatcaccgacctattctattacagGTGGAGAAAATCAAGGCGTTGATGCTAATGGGAATTCACTCGACTTCTCAACGAAGCTGCTCCACCTCGCATGGCACCCGACCGAGAATTCTATTGCATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT