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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tactggcatcttctctaatttaatcaatcattccacacaatcactatctcttttagttttttatgttctttgagttaatgtctcctctgtccctcctcagTCTAAACATCCAAGATATTCTGGGGAAAACTTGGAGAAGAATAAAGTTCTGTATACACGACTTGAAATGTTGTCCAAGAAGTATGGGTGCACACCTGCTC

Basic information

species Zea mays
transcript GRMZM5G813143_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G813143_T02 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os10g28320.1 (Oryza sativa), 3'ss of exon 5
------------------tactggcatcttctctaatttaatcaatcattccacacaatcactatctcttttagttttttatgttctttgagttaatgtctcctctgtccctcctcagTCTAAACATCCAAGATATTCTGGGGAAAACTTGGAGAAGAATAAAGTTCTGTATACACGACTTGAAATGTTGTCCAAGAAGTATGGGTGCACACCTGCTC
                  ||||   |||||||   |   |   ||   ||    | | ||  | | |  |  ||||   ||  | || | | ||| | ||| || ||   || | ||| ||| ||||||||| ||   |||||||||||||||||||||||||||| | || |||||| |||||  | |  |||  |||||||| ||| | |||||||
gtaaaattaaattcacactactataatcttcttctacacagggaagt-ttgggtatagtc-ttctattctgcagttgagtacatcctataacttagtatcttctttgctacttcacagACTAGACATCCAAGGTACAATGGGGAAAACTTGGAGAAGAATAAAGTTTTCTACACACGAATTGAAGAGCTTGCCACCAAGTATGGCTGCTCCCCTGCTC
















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|91877298|gb|EB407255.1|EB407255
EST:     TCTTTGCTGGCAGGGCAGCTGTAGAACGTGTTCCATCAGAAAGTCTATTG                         TCTAAACATCCAAGATATTCTGGGGAAAACTTGGAGAAGAATAAAGTTCTG
genomic: TCTTTGCTGGCAGGGCAGCTGTAGAACGTGTTCCATCAGAAAGTCTATTGgtaaatgaaa ... ccctcctcagTCTAAACATCCAAGATATTCTGGGGAAAACTTGGAGAAGAATAAAGTTCTG
EST: gi|74244513|gb|DT652427.1|DT652427
EST:     TCTTTGCTGGCAGGGCAGCTGTAGAACGTGTTCCATCAGAAAGTCTATTG                         TCTAAACATCCAAGATATTCTGGGGAAAACTTGGAGAAGAATAAAGTTCTG
genomic: TCTTTGCTGGCAGGGCAGCTGTAGAACGTGTTCCATCAGAAAGTCTATTGgtaaatgaaa ... ccctcctcagTCTAAACATCCAAGATATTCTGGGGAAAACTTGGAGAAGAATAAAGTTCTG
EST: gi|76292810|gb|DV032378.1|DV032378
EST:     TGTAGAACGTGTTCCATCAGAAAGTCTATTG                         TCTAAACATCCAAGATATTCTGGGGAAAACTTGGAGAAGAATAAAGTTCTG
genomic: TGTAGAACGTGTTCCATCAGAAAGTCTATTGgtaaatgaaa ... ccctcctcagTCTAAACATCCAAGATATTCTGGGGAAAACTTGGAGAAGAATAAAGTTCTG
EST: gi|88756482|gb|DY540623.1|DY540623
EST:     TCTTTGCTGGGAGGGCAGCTGTAGAACGTGTTCCATCAGAAAGTCTATTG                         TCTAAACATCCAAGATATTCTGGG
genomic: TCTTTGCTGGCAGGGCAGCTGTAGAACGTGTTCCATCAGAAAGTCTATTGgtaaatgaaa ... ccctcctcagTCTAAACATCCAAGATATTCTGGG
EST: gi|91873437|gb|EB403394.1|EB403394
EST:     TCTTTGCTGGCAGGGCAGCTGTAGAACGTGTTCCATCAGAAAGTCTATTG                         TCTAAACATCCAAGATACTTCTGGGGAAAACTTGGAGAAGAATAAAG
genomic: TCTTTGCTGGCAGGGCAGCTGTAGAACGTGTTCCATCAGAAAGTCTATTGgtaaatgaaa ... ccctcctcagTCTAAACATCCAAGATA-TTCTGGGGAAAACTTGGAGAAGAATAAAG
EST: gi|88757821|gb|DY541962.1|DY541962
EST:     TCTTTGCTGGCAGGGCAGCTGTAGAACGTGTTCCATCAGAAAGTCTATTG                         TCTAAACATCCA
genomic: TCTTTGCTGGCAGGGCAGCTGTAGAACGTGTTCCATCAGAAAGTCTATTGgtaaatgaaa ... ccctcctcagTCTAAACATCCA
EST: gi|76021184|gb|DT948354.1|DT948354
EST:     TCTTTGCTGGCAGGGCAGCTGTAGAACGTGTTCCATCAGAAAGTCTATTG                         TCTAAACATCCAAGATATTCTGGGGAAAACTTGGAGAAGAATAAAGTTCTG
genomic: TCTTTGCTGGCAGGGCAGCTGTAGAACGTGTTCCATCAGAAAGTCTATTGgtaaatgaaa ... ccctcctcagTCTAAACATCCAAGATATTCTGGGGAAAACTTGGAGAAGAATAAAGTTCTG
EST: gi|76021183|gb|DT948353.1|DT948353
EST:     TCTTTGCTGGCAGGGCAGCTGTAGAACGTGTTCCATCAGAAAGTCTATTG                         TCTAAACATCCAAGATATTCTGGGGAAAACTTGGAGAAGAATAAAGTTCTG
genomic: TCTTTGCTGGCAGGGCAGCTGTAGAACGTGTTCCATCAGAAAGTCTATTGgtaaatgaaa ... ccctcctcagTCTAAACATCCAAGATATTCTGGGGAAAACTTGGAGAAGAATAAAGTTCTG
EST: gi|91875442|gb|EB405399.1|EB405399
EST:     TCTTTGCTGGCAGGGCAGCTGTAGAACGTGTTCCATCAGAAAGTCTATTG                         TCTAAACATCCAAGATATTCTAGGGAAAACTTGGAGAAGAATAAAGTTCTG
genomic: TCTTTGCTGGCAGGGCAGCTGTAGAACGTGTTCCATCAGAAAGTCTATTGgtaaatgaaa ... ccctcctcagTCTAAACATCCAAGATATTCTGGGGAAAACTTGGAGAAGAATAAAGTTCTG
EST: gi|78114482|gb|DV532871.1|DV532871
EST:     TCTTTGCTGGCAGGGCAGCTGTAGAACGTGTTCCATCAGAAAGTCTATTG                         TCTAAACATCCAAGATATTCTGGGGAAAACTTGGAGAAGAATAAAGTTCTG
genomic: TCTTTGCTGGCAGGGCAGCTGTAGAACGTGTTCCATCAGAAAGTCTATTGgtaaatgaaa ... ccctcctcagTCTAAACATCCAAGATATTCTGGGGAAAACTTGGAGAAGAATAAAGTTCTG
EST: gi|89761100|gb|DY689250.1|DY689250
EST:     TCTTTGCTGGCAGGGCAGCTGTAGAACGTGTTCCATCAGAAAGTCTATTG                         TCTAAACATCCAAGATATTTTGGGGAAAACTTGGAGAAGAATAAAGTTCTG
genomic: TCTTTGCTGGCAGGGCAGCTGTAGAACGTGTTCCATCAGAAAGTCTATTGgtaaatgaaa ... ccctcctcagTCTAAACATCCAAGATATTCTGGGGAAAACTTGGAGAAGAATAAAGTTCTG
EST: gi|76288052|gb|DV027620.1|DV027620
EST:     TCTTTGCTGGCAGGGCAGCTGTAGAACGTGTTCCATCAGAAAGTCTATTG                         TCTAAACATCCAAGATATTCTGGGGAAAACTTGGAGAAGAATAAAAGT-CT
genomic: TCTTTGCTGGCAGGGCAGCTGTAGAACGTGTTCCATCAGAAAGTCTATTGgtaaatgaaa ... ccctcctcagTCTAAACATCCAAGATATTCTGGGGAAAACTTGGAGAAGAATAAA-GTTCT
EST: gi|91055988|gb|EB166406.1|EB166406
EST:     TCTTTGCTGGCAGGGCAGCTGTAGAACGTGTTCCATCAGAAAGTCTATTG                         TCTAAACATCCAAGATATTCTGGGGAAAACTTGGAGAAGA-TAAAGTTCTG
genomic: TCTTTGCTGGCAGGGCAGCTGTAGAACGTGTTCCATCAGAAAGTCTATTGgtaaatgaaa ... ccctcctcagTCTAAACATCCAAGATATTCTGGGGAAAACTTGGAGAAGAATAAAGTTCTG
EST: gi|76288051|gb|DV027619.1|DV027619
EST:     TCTTTGCTGGCAGGGCAGCTGTAGAACGTGTTCCATCAGAAAGTCTATTG                         TCTAAACATCCAAGATATTCTGGGGAAAACTTGGAGAAGAATAAAGTTCTG
genomic: TCTTTGCTGGCAGGGCAGCTGTAGAACGTGTTCCATCAGAAAGTCTATTGgtaaatgaaa ... ccctcctcagTCTAAACATCCAAGATATTCTGGGGAAAACTTGGAGAAGAATAAAGTTCTG
EST: gi|91877299|gb|EB407256.1|EB407256
EST:     TCTTTGCTGGCAGGGCAGCTGTAGAACGTGTTCCATCAGAAAGTCTATTG                         TCTAAACATCCAAGATATTCTGGGGAAAACTTGGAGAAGAATAAAGTTCTG
genomic: TCTTTGCTGGCAGGGCAGCTGTAGAACGTGTTCCATCAGAAAGTCTATTGgtaaatgaaa ... ccctcctcagTCTAAACATCCAAGATATTCTGGGGAAAACTTGGAGAAGAATAAAGTTCTG
EST: gi|101392432|gb|EB818145.1|EB818145
EST:     TCTTTGTTGGCAGGGCAGCTGTAGAACGTGTTCCATCAGAAAGTCTATTG                         TCTAAACATCCAAGATATTCTGGGGAAAACTTGGAGAGGAATAAAGTTCTG
genomic: TCTTTGCTGGCAGGGCAGCTGTAGAACGTGTTCCATCAGAAAGTCTATTGgtaaatgaaa ... ccctcctcagTCTAAACATCCAAGATATTCTGGGGAAAACTTGGAGAAGAATAAAGTTCTG
EST: gi|89755224|gb|DY685733.1|DY685733
EST:     TCTTTGCTGGCAGGGCAGCTGTAGAACGTGTTCCATCAGAAAGTCTATTG                         TCTAAACATCCAAGATATTCTGGGGAAAACTTGGAGAAGAATAAAGTTCTG
genomic: TCTTTGCTGGCAGGGCAGCTGTAGAACGTGTTCCATCAGAAAGTCTATTGgtaaatgaaa ... ccctcctcagTCTAAACATCCAAGATATTCTGGGGAAAACTTGGAGAAGAATAAAGTTCTG
EST: gi|76011255|gb|DT938425.1|DT938425
EST:     TCTTTGCTGGCAGGGCAGCTGTAGAACGTGTTCCATCAGAAAGTCTATTG                         TCTAAACATCCAAGATATTCTGGGGAAAACTTGGAGAAGAATAAAGTTCTG
genomic: TCTTTGCTGGCAGGGCAGCTGTAGAACGTGTTCCATCAGAAAGTCTATTGgtaaatgaaa ... ccctcctcagTCTAAACATCCAAGATATTCTGGGGAAAACTTGGAGAAGAATAAAGTTCTG
EST: gi|60355056|gb|DN222029.1|DN222029
EST:     TCTTTGCTGGCAGGGCAGCTGTAGAACGTGTTCCATCAGAAAGTCTATTG                         TCTAAACATCCAAGATATTCTGGGGAAAACTTGGAGAAGAATAAAGTTCTG
genomic: TCTTTGCTGGCAGGGCAGCTGTAGAACGTGTTCCATCAGAAAGTCTATTGgtaaatgaaa ... ccctcctcagTCTAAACATCCAAGATATTCTGGGGAAAACTTGGAGAAGAATAAAGTTCTG
EST: gi|91873436|gb|EB403393.1|EB403393
EST:     TCTTTGCTGGCAGGGCAGCTGTAGAACGTGTTCCATCAGAAAGTCTATTG                         TCTAAACATCCAAGATATTCTGGGGAAAACTTGGAGAAGAATAAAGTTCTG
genomic: TCTTTGCTGGCAGGGCAGCTGTAGAACGTGTTCCATCAGAAAGTCTATTGgtaaatgaaa ... ccctcctcagTCTAAACATCCAAGATATTCTGGGGAAAACTTGGAGAAGAATAAAGTTCTG
EST: gi|74244046|gb|DT651960.1|DT651960
EST:     TCTTTGCTGGCAGGGCAGCTGTAGAACGTGTTCCATCAGAAAGTCTATTG                         TCTAAACATCCAAGATATTCTGGGGAAAACTTGGAGAAGAATAAAGTTCTG
genomic: TCTTTGCTGGCAGGGCAGCTGTAGAACGTGTTCCATCAGAAAGTCTATTGgtaaatgaaa ... ccctcctcagTCTAAACATCCAAGATATTCTGGGGAAAACTTGGAGAAGAATAAAGTTCTG
EST: gi|78112031|gb|DV530427.1|DV530427
EST:     TCTTTGCTGGCAGGGCAGCTGTAGAACGTGTTCCATCAGAAAGTCTATTG                         TCTAAACATCCAAGATATTCTGGGGAAAACTTGGAGAAGAATAAAGTTCTG
genomic: TCTTTGCTGGCAGGGCAGCTGTAGAACGTGTTCCATCAGAAAGTCTATTGgtaaatgaaa ... ccctcctcagTCTAAACATCCAAGATATTCTGGGGAAAACTTGGAGAAGAATAAAGTTCTG
EST: gi|89762828|gb|DY690268.1|DY690268
EST:     TCTTTGCTGGCAGGGCAGCTGTAGAACGTGTTCCATCAGAAAGTCTATTG                         TCTAAACATCCA-GATATT
genomic: TCTTTGCTGGCAGGGCAGCTGTAGAACGTGTTCCATCAGAAAGTCTATTGgtaaatgaaa ... ccctcctcagTCTAAACATCCAAGATATT
EST: gi|89761102|gb|DY689251.1|DY689251
EST:     TCTTTGCTGGCAGGGCAGCTGTAGAACGTGTTCCATCAGAAAGTCTATTG                         TCTAAACATCCAAGATATTCTGGGGAAAACTTGG
genomic: TCTTTGCTGGCAGGGCAGCTGTAGAACGTGTTCCATCAGAAAGTCTATTGgtaaatgaaa ... ccctcctcagTCTAAACATCCAAGATATTCTGGGGAAAACTTGG
EST: gi|78087084|gb|DV515477.1|DV515477
EST:     TCTTTGCTGGCAGGGCAGCTGTAGAACGTGTTCCATCAGAAAGTCTATTG                         TCTAAACATCCAAGATATTCTGGGGAAAACTTGGAGAAGAATAAAGTTCTG
genomic: TCTTTGCTGGCAGGGCAGCTGTAGAACGTGTTCCATCAGAAAGTCTATTGgtaaatgaaa ... ccctcctcagTCTAAACATCCAAGATATTCTGGGGAAAACTTGGAGAAGAATAAAGTTCTG
EST: gi|60341512|gb|DN208485.1|DN208485
EST:     TCTTTGCTGGCAGGGCAGCTGTAGAACGTGTTCCATCAGAAAGTCTATTG                         TCTAAACATCCAAGATATTCTGGGGAAAACTTGGAGAAGAATAAAGTTCTG
genomic: TCTTTGCTGGCAGGGCAGCTGTAGAACGTGTTCCATCAGAAAGTCTATTGgtaaatgaaa ... ccctcctcagTCTAAACATCCAAGATATTCTGGGGAAAACTTGGAGAAGAATAAAGTTCTG
EST: gi|101392434|gb|EB818146.1|EB818146
EST:     TCTTTGCTGGCAGGGCAGCTGTAGAACGTGTTCCATCAGAAAGTCTATTG                         TCTAAACATCCAAGATATTCTGGGGAAAACTTGGAGAAGAATAAAGTTCTG
genomic: TCTTTGCTGGCAGGGCAGCTGTAGAACGTGTTCCATCAGAAAGTCTATTGgtaaatgaaa ... ccctcctcagTCTAAACATCCAAGATATTCTGGGGAAAACTTGGAGAAGAATAAAGTTCTG
EST: gi|91875443|gb|EB405400.1|EB405400
EST:     TCTTTGCTGGCAGGGCAGCTGTAGAACGTGTTCCATCAGAAAGTCTATTG                         TCTAAACATCCAAGATATTCTAGGGAAAACTTGGAGAAGAATAAAGTTCTG
genomic: TCTTTGCTGGCAGGGCAGCTGTAGAACGTGTTCCATCAGAAAGTCTATTGgtaaatgaaa ... ccctcctcagTCTAAACATCCAAGATATTCTGGGGAAAACTTGGAGAAGAATAAAGTTCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atctcttttagttttttatgttctttgagttaatgtctcctctgtccctcctcagTCTAAACATCCAAGATATTCTGGGGAAAACTTGGAGAAGAATAAAGTTCTGTATACACGACTTGAAATGTTGTCCAAGAAGTATGGGTGCACACCTGCTC
                           agttaat  putative branch site (score: 4)
                                 tgtctcctctgtccct  CT-rich tract
     ttttagttttttatgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tactggcatcttctctaatttaatcaatcattccacacaatcactatctcttttagttttttatgttctttgagttaatgtctcctctgtccctcctcagTCTAAACATCCAAGATATTCTGGGGAAAACTTGGAGAAGAATAAAGTTCTGTATACACGACTTGAAATGTTGTCCAAGAAGTATGGGTGCACACCTGCTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT