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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagaattcataacttctgttttgtactttccagaaattttttattgtgataaataatgttaaatctactcttgtgcagGTATGAGGGTCAACGTTCTGTGGAAGCCCTTGCAGAATTTGTTAACAGCGAAGCAG

Basic information

species Zea mays
transcript GRMZM2G159369_T02
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G159369_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os05g06430.1 (Oryza sativa), 3'ss of exon 3
gtgagaattcataact-tctgttttgtactt--tccagaaattttttattgtgataaataatg---ttaaatcta---ctcttgtgcagGTATGAGGGTCAACGTTCTGTGGAAGCCCTTGCAGAATTTGTTAACAGCGAAGCAG
|||||||| |||   | | ||||   ||||   ||   | ||||| | | || |  || ||||    |||   ||    |  |||  |||||||| ||||||||| | | ||||||||||||||||| |||||||   |||||||
gtgagaatacatgcttctttgttgattactcaatcactacattttctgtcgtaaagaacaatgaccctaatgttaaacttactgtttagGTATGAAGGTCAACGTACCGCGGAAGCCCTTGCAGAATATGTTAACTCTGAAGCAG
















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|211332792|gb|FK966335.1|FK966335
EST:     GGGTACCCCACAATTCAATGGTTTCCCAAAGGTTCCCTGGAGCCAAAGAA                         GTATGAGGGTCAACGTTCTGTGGAAGCCCTTGCAGAATTTGTTAACAGCGA
genomic: GGGTACCCCACAATTCAATGGTTTCCCAAAGGTTCCCTGGAGCCAAAGAAgtgagaattc ... tcttgtgcagGTATGAGGGTCAACGTTCTGTGGAAGCCCTTGCAGAATTTGTTAACAGCGA
EST: gi|22819386|gb|BU499476.1|BU499476
EST:     GGGTACCCCACAATTCAATGGTTTCCCAAAGGTTCCCTGGAGCCAAAGAA                         GTATGAGGGTCAACGTTCTGTGGAAGCCCTTGCAGAATTTGTTAACAGCGA
genomic: GGGTACCCCACAATTCAATGGTTTCCCAAAGGTTCCCTGGAGCCAAAGAAgtgagaattc ... tcttgtgcagGTATGAGGGTCAACGTTCTGTGGAAGCCCTTGCAGAATTTGTTAACAGCGA
EST: gi|211334956|gb|FK966345.1|FK966345
EST:     GGGTACCCCACAATTCAATGGTTTCCCAAAGGTTCCCTGGAGCCAAAGAA                         GTATGAGGGTCAACGTTCTGTGGAAGCCCTTGCAGAATTTGTTAACAGCGA
genomic: GGGTACCCCACAATTCAATGGTTTCCCAAAGGTTCCCTGGAGCCAAAGAAgtgagaattc ... tcttgtgcagGTATGAGGGTCAACGTTCTGTGGAAGCCCTTGCAGAATTTGTTAACAGCGA
EST: gi|211332783|gb|FK966326.1|FK966326
EST:     GGGTACCCCACAATTCAATGGTTTCCCAAAGGTTCCCTGGAGCCAAAGAA                         GTATGAGGGTCAACGTTCTGTGGAAGCCCTTGCAGAATTTGTTAACAGCGA
genomic: GGGTACCCCACAATTCAATGGTTTCCCAAAGGTTCCCTGGAGCCAAAGAAgtgagaattc ... tcttgtgcagGTATGAGGGTCAACGTTCTGTGGAAGCCCTTGCAGAATTTGTTAACAGCGA
EST: gi|13388613|gb|BG462252.1|BG462252
EST:     GGGTACCCCACAATTCAATGGTTTCCCAAAGGTTCCCTGGAGCCAAAGAA                         GTATGAGGGTCAACGTT
genomic: GGGTACCCCACAATTCAATGGTTTCCCAAAGGTTCCCTGGAGCCAAAGAAgtgagaattc ... tcttgtgcagGTATGAGGGTCAACGTT
EST: gi|148935523|gb|EC879564.2|EC879564
EST:     GGGTACCCCACAATTCAATGGTTTCCCAAAGGTTCCCTGGAGCCAAAGAA                         GTATGAGGGTCAACGTTCTGTGGAAGCCCTTGCAGAATTTGTTAACAGCGA
genomic: GGGTACCCCACAATTCAATGGTTTCCCAAAGGTTCCCTGGAGCCAAAGAAgtgagaattc ... tcttgtgcagGTATGAGGGTCAACGTTCTGTGGAAGCCCTTGCAGAATTTGTTAACAGCGA
EST: gi|13178109|gb|BG349367.1|BG349367
EST:     GGGTACCCCACAATTCAATGGTTTCCCAAAGGTTCCCTGGAGCCAAAGAA                         GTATGAGGGTCAACGTTCTGTGGAAGCCCTTGCAGAATTTGTTAACAGCGA
genomic: GGGTACCCCACAATTCAATGGTTTCCCAAAGGTTCCCTGGAGCCAAAGAAgtgagaattc ... tcttgtgcagGTATGAGGGTCAACGTTCTGTGGAAGCCCTTGCAGAATTTGTTAACAGCGA
EST: gi|24763723|gb|CA398894.1|CA398894
EST:     GGGTACCCCACAATTCAATGGTTTCCCAAAGGTTCCCTGGAGCCAAAGAA                         GTATGAGGGTCAACGTTCTGTGGAAGCCCTTGCAGAATTTGTTAACAGCGA
genomic: GGGTACCCCACAATTCAATGGTTTCCCAAAGGTTCCCTGGAGCCAAAGAAgtgagaattc ... tcttgtgcagGTATGAGGGTCAACGTTCTGTGGAAGCCCTTGCAGAATTTGTTAACAGCGA
EST: gi|32837026|gb|CD976704.1|CD976704
EST:     ACCCCACAATTCAATGGTTTCCCAAAGGTTCCCTGGAGCCAAAGAA                         GTATGAGGGTCAACGTTCTGTGGAAGCCCTTGCAGAATTTGTTAACAGCGA
genomic: ACCCCACAATTCAATGGTTTCCCAAAGGTTCCCTGGAGCCAAAGAAgtgagaattc ... tcttgtgcagGTATGAGGGTCAACGTTCTGTGGAAGCCCTTGCAGAATTTGTTAACAGCGA
EST: gi|21891538|gb|BQ744751.1|BQ744751
EST:     GGGTACCCCACAATTCAATGGTTTCCCAAAGGTTCCCTGGAGCCAAAGAA                         GTATGAGGGTCAACGTTCTGTGGAAGCCCTTGCAGAATTTGTTAACAGCGA
genomic: GGGTACCCCACAATTCAATGGTTTCCCAAAGGTTCCCTGGAGCCAAAGAAgtgagaattc ... tcttgtgcagGTATGAGGGTCAACGTTCTGTGGAAGCCCTTGCAGAATTTGTTAACAGCGA
EST: gi|211332787|gb|FK966330.1|FK966330
EST:     GGGTACCCCACAATTCAATGGTTTCCCAAAGGTTCCCTGGAGCCAAAGAA                         GTATGAGGGTCAACGTTCTGTGGAAGCCCTTGCAGAATTTGTTAACAGCGA
genomic: GGGTACCCCACAATTCAATGGTTTCCCAAAGGTTCCCTGGAGCCAAAGAAgtgagaattc ... tcttgtgcagGTATGAGGGTCAACGTTCTGTGGAAGCCCTTGCAGAATTTGTTAACAGCGA
EST: gi|211334959|gb|FK966348.1|FK966348
EST:     GGGTACCCCACAATTCAATGGTTTCCCAAAGGTTCCCTGGAGCCAAAGAA                         GTATGAGGGTCAACGTTCTGTGGAAGCCCTTGCAGAATTTGTTAACAGCGA
genomic: GGGTACCCCACAATTCAATGGTTTCCCAAAGGTTCCCTGGAGCCAAAGAAgtgagaattc ... tcttgtgcagGTATGAGGGTCAACGTTCTGTGGAAGCCCTTGCAGAATTTGTTAACAGCGA
EST: gi|32858375|gb|CD998056.1|CD998056
EST:     GGGTACCCCACAATTCAATGGTTTCCCAAAGGTTCCCTGGAGCCAAAGAA                         GTATGAGGGTCAACGTTCTGTGGAAGCCCTTGCAGAATTTGTTAACAGCGA
genomic: GGGTACCCCACAATTCAATGGTTTCCCAAAGGTTCCCTGGAGCCAAAGAAgtgagaattc ... tcttgtgcagGTATGAGGGTCAACGTTCTGTGGAAGCCCTTGCAGAATTTGTTAACAGCGA
EST: gi|9254368|gb|BE344836.1|BE344836
EST:     GGGTACCCCACAATTCAATGGTTTCCCAAAGGTTCCCTGGAGCCAAAGAA                         GTATGAGGGTCAACGTTCTGTGGAAGCCCTTGCAGAATTTGTTAACAGCGA
genomic: GGGTACCCCACAATTCAATGGTTTCCCAAAGGTTCCCTGGAGCCAAAGAAgtgagaattc ... tcttgtgcagGTATGAGGGTCAACGTTCTGTGGAAGCCCTTGCAGAATTTGTTAACAGCGA
EST: gi|88755206|gb|DY539347.1|DY539347
EST:     GGGTACCCCACAATTCAATGGTTTCCCAAAGGTTCCCTGGAGCCAAAGAA                         GTATGAGGGTCAACGTTCTGTGGAAGCCCTTGCAGAATTTGTTAACAGCGA
genomic: GGGTACCCCACAATTCAATGGTTTCCCAAAGGTTCCCTGGAGCCAAAGAAgtgagaattc ... tcttgtgcagGTATGAGGGTCAACGTTCTGTGGAAGCCCTTGCAGAATTTGTTAACAGCGA
EST: gi|211332782|gb|FK966325.1|FK966325
EST:     GGGTACCCCACAATTCAATGGTTTCCCAAAGGTTCCCTGGAGCCAAAGAA                         GTATGAGGGTCAACGTTCTGTGGAAGCCCTTGCAGAATTTGTTAACAGCGA
genomic: GGGTACCCCACAATTCAATGGTTTCCCAAAGGTTCCCTGGAGCCAAAGAAgtgagaattc ... tcttgtgcagGTATGAGGGTCAACGTTCTGTGGAAGCCCTTGCAGAATTTGTTAACAGCGA
EST: gi|111145784|gb|EE258169.1|EE258169
EST:     GGGTACCCCACAATTCAATGGTTTCCCAAAGGTTCCCTGGAGCCAAAGAA                         GTATGAGGGTCAACGTTCTGTGGAAGCCCTTGCAGAATTTGTTAACAGCGA
genomic: GGGTACCCCACAATTCAATGGTTTCCCAAAGGTTCCCTGGAGCCAAAGAAgtgagaattc ... tcttgtgcagGTATGAGGGTCAACGTTCTGTGGAAGCCCTTGCAGAATTTGTTAACAGCGA
EST: gi|211334948|gb|FK966337.1|FK966337
EST:     GGGTACCCCACAATTCAATGGTTTCCCAAAGGTTCCCTGGAGCCAAAGAA                         GTATGAGGGTCAACGTTCTGTGGAAGCCCTTGCAGAATTTGTTAACAGCGA
genomic: GGGTACCCCACAATTCAATGGTTTCCCAAAGGTTCCCTGGAGCCAAAGAAgtgagaattc ... tcttgtgcagGTATGAGGGTCAACGTTCTGTGGAAGCCCTTGCAGAATTTGTTAACAGCGA
EST: gi|33285626|gb|CF075421.1|CF075421
EST:     GGGTACCCCACAATTCAATGGTTTCCCAAAGGTTCCCTGGAGCCAAAGAA                         GTATGAGGGTCAACGTTCTGTGGAAGCCCTTGCAGAATTTGTTAACAGCGA
genomic: GGGTACCCCACAATTCAATGGTTTCCCAAAGGTTCCCTGGAGCCAAAGAAgtgagaattc ... tcttgtgcagGTATGAGGGTCAACGTTCTGTGGAAGCCCTTGCAGAATTTGTTAACAGCGA
EST: gi|211334955|gb|FK966344.1|FK966344
EST:     GGGTACCCCACAATTCAATGGTTTCCCAAAGGTTCCCTGGAGCCAAAGAA                         GTATGAGGGTCAACGTTCTGTGGAAGCCCTTGCAGAATTTGTTAACAGCGA
genomic: GGGTACCCCACAATTCAATGGTTTCCCAAAGGTTCCCTGGAGCCAAAGAAgtgagaattc ... tcttgtgcagGTATGAGGGTCAACGTTCTGTGGAAGCCCTTGCAGAATTTGTTAACAGCGA
EST: gi|31360143|gb|CD444500.1|CD444500
EST:     GGGTACCCCACAATTCAATGGTTTCCCAAAGGTTCCCTGGAGCCAAAGAA                         GTATGAGGGTCAACGTTCTGTGGAAGCCCTTGCAGAATTTGTTAACAGCGA
genomic: GGGTACCCCACAATTCAATGGTTTCCCAAAGGTTCCCTGGAGCCAAAGAAgtgagaattc ... tcttgtgcagGTATGAGGGTCAACGTTCTGTGGAAGCCCTTGCAGAATTTGTTAACAGCGA
EST: gi|20507142|gb|BQ279504.1|BQ279504
EST:     GGGTACCCCACAATTCAATGGTTTCCCAAAGGTTCCCTGGAGCCAAAGAA                         GTATGAGGGTCAACGTTCTGTGGAAGCCCTTGCAGAATTTGTTAACAGCGA
genomic: GGGTACCCCACAATTCAATGGTTTCCCAAAGGTTCCCTGGAGCCAAAGAAgtgagaattc ... tcttgtgcagGTATGAGGGTCAACGTTCTGTGGAAGCCCTTGCAGAATTTGTTAACAGCGA
EST: gi|26457090|gb|CA828673.1|CA828673
EST:     GGGTACCCCACAATTCAATGGTTTCCCAAAGGTTCCCTGGAGCCAAAGAA                         GTATGAGGGTCAACGTTCTGTGGAAGCCCTTGCAGAATTTGTTAACAGCGA
genomic: GGGTACCCCACAATTCAATGGTTTCCCAAAGGTTCCCTGGAGCCAAAGAAgtgagaattc ... tcttgtgcagGTATGAGGGTCAACGTTCTGTGGAAGCCCTTGCAGAATTTGTTAACAGCGA
EST: gi|211332789|gb|FK966332.1|FK966332
EST:     GGGTACCCCACAATTCAATGGTTTCCCAAAGGTTCCCTGGAGCCAAAGAA                         GTATGAGGGTCAACGTTCTGTGGAAGCCCTTGCAGAATTTGTTAACAGCGA
genomic: GGGTACCCCACAATTCAATGGTTTCCCAAAGGTTCCCTGGAGCCAAAGAAgtgagaattc ... tcttgtgcagGTATGAGGGTCAACGTTCTGTGGAAGCCCTTGCAGAATTTGTTAACAGCGA
EST: gi|6994161|gb|AW453375.1|AW453375
EST:     GGGTACCCCACAATTCAATGGTTTCCCAAAGGTTCCCTGGAGCCAAAGAA                         GTATGAGGGTCAACGTTCTGTGGAAGCCCTTGCAGAATTTGTTAACAGCGA
genomic: GGGTACCCCACAATTCAATGGTTTCCCAAAGGTTCCCTGGAGCCAAAGAAgtgagaattc ... tcttgtgcagGTATGAGGGTCAACGTTCTGTGGAAGCCCTTGCAGAATTTGTTAACAGCGA
EST: gi|211332788|gb|FK966331.1|FK966331
EST:     GGGTACCCCACAATTCAATGGTTTCCCAAAGGTTCCCTGGAGCCAAAGAA                         GTATGAGGGTCAACGTTCTGTGGAAGCCCTTGCAGAATTTGTTAACAGCGA
genomic: GGGTACCCCACAATTCAATGGTTTCCCAAAGGTTCCCTGGAGCCAAAGAAgtgagaattc ... tcttgtgcagGTATGAGGGTCAACGTTCTGTGGAAGCCCTTGCAGAATTTGTTAACAGCGA
EST: gi|211332781|gb|FK966324.1|FK966324
EST:     GGGTACCCCACAATTCAATGGTTTCCCAAAGGTTCCCTGGAGCCAAAGAA                         GTATGAGGGTCAACGTTCTGTGGAAGCCCTTGCAGAATTTGTTAACAGCGA
genomic: GGGTACCCCACAATTCAATGGTTTCCCAAAGGTTCCCTGGAGCCAAAGAAgtgagaattc ... tcttgtgcagGTATGAGGGTCAACGTTCTGTGGAAGCCCTTGCAGAATTTGTTAACAGCGA
EST: gi|32864543|gb|CF004225.1|CF004225
EST:     GGGTACCCCACAATTCAATGGTTTCCCAAAGGTTCCCTGGAGCCAAAGAA                         GTATGAGGGTCAACGTTCTGTGGAAGCCCTTGCAGAATTTGTTAACAGCGA
genomic: GGGTACCCCACAATTCAATGGTTTCCCAAAGGTTCCCTGGAGCCAAAGAAgtgagaattc ... tcttgtgcagGTATGAGGGTCAACGTTCTGTGGAAGCCCTTGCAGAATTTGTTAACAGCGA
EST: gi|211332785|gb|FK966328.1|FK966328
EST:     GGGTACCCCACAATTCAATGGTTTCCCAAAGGTTCCCTGGAGCCAAAGAA                         GTATGAGGGTCAACGTTCTGTGGAAGCCCTTGCAGAATTTGTTAAC
genomic: GGGTACCCCACAATTCAATGGTTTCCCAAAGGTTCCCTGGAGCCAAAGAAgtgagaattc ... tcttgtgcagGTATGAGGGTCAACGTTCTGTGGAAGCCCTTGCAGAATTTGTTAAC
EST: gi|211334949|gb|FK966338.1|FK966338
EST:     GGGTACCC-ACAATTCAATGGTTTCCCAAAGGTTCCCTGGAGCCAAAGAA                         GTATGAGGGTCAACGTTCTGTGGAAGCCCTTGCAGAATTTGTTAACAGCGA
genomic: GGGTACCCCACAATTCAATGGTTTCCCAAAGGTTCCCTGGAGCCAAAGAAgtgagaattc ... tcttgtgcagGTATGAGGGTCAACGTTCTGTGGAAGCCCTTGCAGAATTTGTTAACAGCGA
EST: gi|22935460|gb|BU571735.1|BU571735
EST:     GGGTACCCCACAATTCAATGGTTTCCCAAAGGTTCCCTGGAGCCAAAGAA                         GTATGAGGGTCAACGTTCTGTGGAAGCCCTTGCAGAATTTGTTAACAGCGA
genomic: GGGTACCCCACAATTCAATGGTTTCCCAAAGGTTCCCTGGAGCCAAAGAAgtgagaattc ... tcttgtgcagGTATGAGGGTCAACGTTCTGTGGAAGCCCTTGCAGAATTTGTTAACAGCGA
EST: gi|211334953|gb|FK966342.1|FK966342
EST:     GGGTACCCCACAATTCAATGGTTTCCCAAAGGTTCCCTGGAGCCAAAGAA                         GTATGAGGGTCAACGTTCTGTGGAAGCCCTTGCAGAATTTGTTAAC
genomic: GGGTACCCCACAATTCAATGGTTTCCCAAAGGTTCCCTGGAGCCAAAGAAgtgagaattc ... tcttgtgcagGTATGAGGGTCAACGTTCTGTGGAAGCCCTTGCAGAATTTGTTAAC
EST: gi|211334954|gb|FK966343.1|FK966343
EST:     GGGTACCCCACAATTCAATGGTTTCCCAAAGGTTCCCTGGAGCCAAAGAA                         GTATGAGGGTCAACGTTCTGTGGAAGCCCTTGCAGAATT
genomic: GGGTACCCCACAATTCAATGGTTTCCCAAAGGTTCCCTGGAGCCAAAGAAgtgagaattc ... tcttgtgcagGTATGAGGGTCAACGTTCTGTGGAAGCCCTTGCAGAATT
EST: gi|211332790|gb|FK966333.1|FK966333
EST:     GGGTACCCCACAATTCAATGGTTTCCCAAAGGTTCCCTGGAGCCAAAGAA                         GTATGAGGGTCAACGTTCTGTGGAAGCCCTTGCAGAA
genomic: GGGTACCCCACAATTCAATGGTTTCCCAAAGGTTCCCTGGAGCCAAAGAAgtgagaattc ... tcttgtgcagGTATGAGGGTCAACGTTCTGTGGAAGCCCTTGCAGAA
EST: gi|211334957|gb|FK966346.1|FK966346
EST:     GGGTACCCCACAATTCAATGGTTTCCCAAAGGTTCCCTGGAGCCAAAGAA                         GTATGAGGGTCAACGTTCTGTGGAAGCCCTTGCAGAATTTGTTAACAGCGA
genomic: GGGTACCCCACAATTCAATGGTTTCCCAAAGGTTCCCTGGAGCCAAAGAAgtgagaattc ... tcttgtgcagGTATGAGGGTCAACGTTCTGTGGAAGCCCTTGCAGAATTTGTTAACAGCGA
EST: gi|211001445|gb|FL439450.1|FL439450
EST:     -GGTACCCCACAATTCAATGGTTTCCCAAAGGTTCCCTGGAGCCAAAGAA                         GTATGAGGGTCAACGTTCTGTGGAAGCCCTTGCAGAATTTGTTAACAGCGA
genomic: GGGTACCCCACAATTCAATGGTTTCCCAAAGGTTCCCTGGAGCCAAAGAAgtgagaattc ... tcttgtgcagGTATGAGGGTCAACGTTCTGTGGAAGCCCTTGCAGAATTTGTTAACAGCGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tactttccagaaattttttattgtgataaataatgttaaatctactcttgtgcagGTATGAGGGTCAACGTTCTGTGGAAGCCCTTGCAGAATTTGTTAACAGCGAAGCAG
                                        tctactctt  CT-rich tract
        agaaattttttattgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagaattcataacttctgttttgtactttccagaaattttttattgtgataaataatgttaaatctactcttgtgcagGTATGAGGGTCAACGTTCTGTGGAAGCCCTTGCAGAATTTGTTAACAGCGAAGCAG

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