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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctttgtgaaatactttacactgcaaaataagccatgttgagaagaggcacagttagtaatttggttttatggctcattgttgttaaaatgttcattgcagGTCTTAGATTTCTTTGCTAAACTTATCCAGAGGGTATCTCCCAAGAGCTACCAACAAGCTCTTGCAGAAGTTCAAGTTTCTCAAAAGTTTTTGGAAAACT

Basic information

species Zea mays
transcript GRMZM2G090087_T02
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G090087_T02 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os05g45960.1 (Oryza sativa), 3'ss of exon 5
--------------------------------------------------------------------------------------ctttgtga-aatactttacactgcaaaataagccatgttgagaagaggcacagttagtaatttggttt------tatggctcattgttgttaa-------aatgttcattg-cagGTCTTAGATTTCTTTGCTAAACTTATCCAGAGGGTATCTCCCAAGAGCTACCAACAAGCTCTTGCAGAAGTTCAAGTTTCTCAAAAGTTTTTGGAAAACT
                                                                                      | || ||| | | || || |   |||| || | ||||||||||||  | | | | |   || || |||      ||| |||  | |||  | |       | || | |||| ||||| | |||||||||||||||||||||||||||||||||||| |||||||| || ||||||||||||||||||||||| |||||||| || ||||| ||||
gtatgttatcttaaaattaaatggtttgacttcctattactttcagtgagattttagatgactctagctgtgcatccattggcctgcattatgacactcctataaatgccaaattaggtcatgttgagaaggag-agaataaaggatatgcttttctatctattgcttttagtttctgattgtgtcattggtgattgacagGTTTCAGATTTCTTTGCTAAACTTATCCAGAGGGTATCTCCAAAGAGCTATCAGCAAGCTCTTGCAGAAGTTCAAGTCTCTCAAAAATTCTTGGAGAACT
















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|60339011|gb|DN205984.1|DN205984
EST:     TGTATGGAGATATATCTGCAAAAGCTGCGCATATGCTGGGCCAACCTGCA                         GTCTTAGATTTCTTTGCTAAACTTATCCAGAGGGTATCTCCCAAGAGCTAC
genomic: TGTATGGAGATATATCTGCAAAAGCTGCGCATATGCTGGGCCAACCTGCAgtatgccatc ... ttcattgcagGTCTTAGATTTCTTTGCTAAACTTATCCAGAGGGTATCTCCCAAGAGCTAC
EST: gi|211306987|gb|FL381273.1|FL381273
EST:     TGTATGGAGATATATCTGCAAAAGCTGCGCATATGCTGGGCCAACCTGCA                         GTCTTAGATTTCTTTGCTAAACTTATCCAGAGGGTATCTCC
genomic: TGTATGGAGATATATCTGCAAAAGCTGCGCATATGCTGGGCCAACCTGCAgtatgccatc ... ttcattgcagGTCTTAGATTTCTTTGCTAAACTTATCCAGAGGGTATCTCC
EST: gi|211108216|gb|FL373163.1|FL373163
EST:     TGTATGGAGATATATCTGCAAAAGCTGCGCATATGCTGGGCCAACCTGCA                         GTCTTAGATTTCTTTGCTAAACTTATCCAGAGGGTATCTCCCAAGAGCTAC
genomic: TGTATGGAGATATATCTGCAAAAGCTGCGCATATGCTGGGCCAACCTGCAgtatgccatc ... ttcattgcagGTCTTAGATTTCTTTGCTAAACTTATCCAGAGGGTATCTCCCAAGAGCTAC
EST: gi|28422609|gb|CB251943.1|CB251943
EST:     TGTATGGAGATATATCTGCAAAAGCTGCGCATATGCTGGGCCAACCTGCA                         GTCTTAGATTTCTTTGCTAAACTTATCCAGAGGGTATCTCCCAAGAGCTAC
genomic: TGTATGGAGATATATCTGCAAAAGCTGCGCATATGCTGGGCCAACCTGCAgtatgccatc ... ttcattgcagGTCTTAGATTTCTTTGCTAAACTTATCCAGAGGGTATCTCCCAAGAGCTAC
EST: gi|149071327|gb|EE159720.2|EE159720
EST:     TGTATGGAGATATATCTGCAAAAGCTGCGCATATGCTGGGCCAACCTGCA                         GTCTTAGATTTCTTTGCTAAACTTATCCAGAGGGTATCTCCCAAGAGCTAC
genomic: TGTATGGAGATATATCTGCAAAAGCTGCGCATATGCTGGGCCAACCTGCAgtatgccatc ... ttcattgcagGTCTTAGATTTCTTTGCTAAACTTATCCAGAGGGTATCTCCCAAGAGCTAC
EST: gi|211017676|gb|FL418607.1|FL418607
EST:     TGTATGGAGATATATCTGCAAAAGCTGCGCATATGCTGGGCCAACCTGCA                         GTCTTAGATTTCTTTGCTAAACTTATCCAGAGGGTATCTCCCAAGAGCTAC
genomic: TGTATGGAGATATATCTGCAAAAGCTGCGCATATGCTGGGCCAACCTGCAgtatgccatc ... ttcattgcagGTCTTAGATTTCTTTGCTAAACTTATCCAGAGGGTATCTCCCAAGAGCTAC
EST: gi|148958687|gb|EC904955.2|EC904955
EST:     TGTATGGAGATATATCTGCAAAAGCTGCGCATATGCTGGGCCAACCTGCA                         GTCTTAGATTTCTTTGCTAAACTTATCCAGAGGGTATCTCCCAAGAGCTAC
genomic: TGTATGGAGATATATCTGCAAAAGCTGCGCATATGCTGGGCCAACCTGCAgtatgccatc ... ttcattgcagGTCTTAGATTTCTTTGCTAAACTTATCCAGAGGGTATCTCCCAAGAGCTAC
EST: gi|60346857|gb|DN213830.1|DN213830
EST:     TGTATGGAGATATATCTGCAAAAGCTGCGCATATGCTGGGCCAACCTGCA                         GTCTTAGATTTCTTTGCTAAACTTATCCAGAGGGTATCTCCCAAGAGCTAC
genomic: TGTATGGAGATATATCTGCAAAAGCTGCGCATATGCTGGGCCAACCTGCAgtatgccatc ... ttcattgcagGTCTTAGATTTCTTTGCTAAACTTATCCAGAGGGTATCTCCCAAGAGCTAC
EST: gi|211451569|gb|FL371208.1|FL371208
EST:     TGTATGGAGATATATCTGCAAAAGCTGCGCATATGCTGGGCCAACCTGCA                         GTCTTAGATTTCTTTGCTAAACTTATCCAGAGGGTAT
genomic: TGTATGGAGATATATCTGCAAAAGCTGCGCATATGCTGGGCCAACCTGCAgtatgccatc ... ttcattgcagGTCTTAGATTTCTTTGCTAAACTTATCCAGAGGGTAT
EST: gi|211266997|gb|FL420589.1|FL420589
EST:     TGTATGGAGATATATCTGCAAAAGCTGCGCATATGCTGCGCCAACCTGCA                         GTCTTAGATTTCTTTGCTAAACTTATCCAGAGGGTATCTCCCCAGAGCTAC
genomic: TGTATGGAGATATATCTGCAAAAGCTGCGCATATGCTGGGCCAACCTGCAgtatgccatc ... ttcattgcagGTCTTAGATTTCTTTGCTAAACTTATCCAGAGGGTATCTCCCAAGAGCTAC
EST: gi|67026280|gb|CO455029.1|CO455029
EST:     TGTATGCAGATATATCTGCAAAAGCTGCGCATATGCTGGGCCAACCTGCA                         GTCTTAGATTTCTTTGCTAAACTTATCCAGAGGGTATCTCCCAAGAGCTAC
genomic: TGTATGGAGATATATCTGCAAAAGCTGCGCATATGCTGGGCCAACCTGCAgtatgccatc ... ttcattgcagGTCTTAGATTTCTTTGCTAAACTTATCCAGAGGGTATCTCCCAAGAGCTAC
EST: gi|211204247|gb|FL383416.1|FL383416
EST:     TGTATGGAGATATATCTGCAAAAGCTGCGCAT--GCTGGGCCAACCTGCA                         GTCTTAGATTTCT
genomic: TGTATGGAGATATATCTGCAAAAGCTGCGCATATGCTGGGCCAACCTGCAgtatgccatc ... ttcattgcagGTCTTAGATTTCT
EST: gi|211228711|gb|FL216929.1|FL216929
EST:     TGTATGGAGATATATCTGCAAAAGCTGCGCATATGCTGGGCCAACCTGCA                         GTCTTAGATTTCTTTGCTAAACTTATCCAGAGGGTATCTCCCAAGAGCTAC
genomic: TGTATGGAGATATATCTGCAAAAGCTGCGCATATGCTGGGCCAACCTGCAgtatgccatc ... ttcattgcagGTCTTAGATTTCTTTGCTAAACTTATCCAGAGGGTATCTCCCAAGAGCTAC
EST: gi|60399068|gb|DN231882.1|DN231882
EST:     TGTATGGAGATATATCTGCAAAAGCTGCGCATATGCTGGGCCAACCTGCA                         GTCTTAGATTTCTTTGCTAAACTTATCCAGAGGGTATCTCCCAAGAGCTAC
genomic: TGTATGGAGATATATCTGCAAAAGCTGCGCATATGCTGGGCCAACCTGCAgtatgccatc ... ttcattgcagGTCTTAGATTTCTTTGCTAAACTTATCCAGAGGGTATCTCCCAAGAGCTAC
EST: gi|211533298|gb|FL400243.1|FL400243
EST:     TGTATGGAGATATATCTGCAAAAGCTGCGCATATGCTGGGCCAACCTGCA                         GTCTTAGATTY-TTTGCTAAACTTATCCAGAGGGTATCT
genomic: TGTATGGAGATATATCTGCAAAAGCTGCGCATATGCTGGGCCAACCTGCAgtatgccatc ... ttcattgcagGTCTTAGATTTCTTTGCTAAACTTATCCAGAGGGTATCT
EST: gi|94472231|gb|EB701189.1|EB701189
EST:     TGTATGGAGATATATCTGCAAAAGCTGCGCATATGCTGGGCCAACCTGCA                         GTCTTAGATTTCTTTGCTAAACTTATCCAGAGGGTATCTCCCAAGAGCTAC
genomic: TGTATGGAGATATATCTGCAAAAGCTGCGCATATGCTGGGCCAACCTGCAgtatgccatc ... ttcattgcagGTCTTAGATTTCTTTGCTAAACTTATCCAGAGGGTATCTCCCAAGAGCTAC
EST: gi|211228709|gb|FL216927.1|FL216927
EST:     TGTATGGAGATATATCTGCAAAAGCTGCGCATATGCTGGGCCAACCTGCA                         GTCTTAGATTTCTTTGCTAAACTTATCCAGAGGGTATCTCCCAAGAGCTAC
genomic: TGTATGGAGATATATCTGCAAAAGCTGCGCATATGCTGGGCCAACCTGCAgtatgccatc ... ttcattgcagGTCTTAGATTTCTTTGCTAAACTTATCCAGAGGGTATCTCCCAAGAGCTAC
EST: gi|33102327|gb|CF062287.1|CF062287
EST:     TGTATGGAGATATATCTGCAAAAGCTGCGCATATGCTGGGCCAACCTGCA                         GTCTTAGATTTCTTTGCTAAACTTATCCAGAGGGTATCTCCCAAGAGCTAC
genomic: TGTATGGAGATATATCTGCAAAAGCTGCGCATATGCTGGGCCAACCTGCAgtatgccatc ... ttcattgcagGTCTTAGATTTCTTTGCTAAACTTATCCAGAGGGTATCTCCCAAGAGCTAC
EST: gi|211097512|gb|FL395914.1|FL395914
EST:     TGTATGGAGATATATCTGCAAAAGCTGCGCATATGCTGGGCCAACCTGCA                         GTCTTAGATTTCTTTGCTAAACTTATCCAGAGGGTATCTCCCAAGAGCTAC
genomic: TGTATGGAGATATATCTGCAAAAGCTGCGCATATGCTGGGCCAACCTGCAgtatgccatc ... ttcattgcagGTCTTAGATTTCTTTGCTAAACTTATCCAGAGGGTATCTCCCAAGAGCTAC
EST: gi|211410539|gb|FL375656.1|FL375656
EST:     TGTATGGAGATATATCTGCAAAAGCTGCGCATATGCTGGGCCAACCTGCA                         GTCTTANATTTCTTTTGCTAAACTTATCCAGAGGG
genomic: TGTATGGAGATATATCTGCAAAAGCTGCGCATATGCTGGGCCAACCTGCAgtatgccatc ... ttcattgcagGTCTTAGATTTCTTT-GCTAAACTTATCCAGAGGG
EST: gi|27522050|gb|CA989156.1|CA989156
EST:     TGTATGGAGATATATCTGCAAAAGCTGCGCATATGCTGGGCCAACCTGCA                         GTCTTAGATTTCTTTGCTAAACTTATCCAGAGGGTATCTCCCAAGAGCTAC
genomic: TGTATGGAGATATATCTGCAAAAGCTGCGCATATGCTGGGCCAACCTGCAgtatgccatc ... ttcattgcagGTCTTAGATTTCTTTGCTAAACTTATCCAGAGGGTATCTCCCAAGAGCTAC
EST: gi|211156670|gb|FL403860.1|FL403860
EST:     TGTATGGAGATATATCTGCAAAAGCTGCGCATATGCTGGGCCAACCTGCA                         GTCCTATATTTCTTTGC
genomic: TGTATGGAGATATATCTGCAAAAGCTGCGCATATGCTGGGCCAACCTGCAgtatgccatc ... ttcattgcagGTCTTAGATTTCTTTGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggcacagttagtaatttggttttatggctcattgttgttaaaatgttcattgcagGTCTTAGATTTCTTTGCTAAACTTATCCAGAGGGTATCTCCCAAGAGCTACCAACAAGCTCTTGCAGAAGTTCAAGTTTCTCAAAAGTTTTTGGAAAACT
           taatttggttttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctttgtgaaatactttacactgcaaaataagccatgttgagaagaggcacagttagtaatttggttttatggctcattgttgttaaaatgttcattgcagGTCTTAGATTTCTTTGCTAAACTTATCCAGAGGGTATCTCCCAAGAGCTACCAACAAGCTCTTGCAGAAGTTCAAGTTTCTCAAAAGTTTTTGGAAAACT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT