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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatgcccttgtgttcaacaaatcatgtgtttattttctctctcaatcagcaaatgggggattcttctttacatattctcttttttctcgcttgaagGGTGCTTCAATGCTACTCCTAGCATTGTCCTTCACCTGGAAAGCTCTGGCACCTTATTCTGGTACTCTTGCTGTTGTTGGCACTGTTCT

Basic information

species Zea mays
transcript GRMZM2G153704_T07
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G153704_T02 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os01g04190.1 (Oryza sativa), 3'ss of exon 11
gtaatgcccttgtgttcaacaaatcatgtgtttattttctctctcaatcagcaaatgggggattcttctttacatattctct-tttttctcgcttgaagGGTGCTTCAATGCTACTCCTAGCATTGTCCTTCACCTGGAAAGCTCTGGCACCTTATTCTGGTACTCTTGCTGTTGTTGGCACTGTTCT
||| | || || | |   | ||| ||||| ||| | ||   || ||||    ||| |   |    ||  ||| |  ||| ||  || || |  ||||||| ||| |||||| |||| ||| ||||||||||||| ||||| ||| ||||||||||||| ||  |||||||||||| |||||||||| |
gta-taccattatctaggataaaccatgtttttgtctt---tcacaatattgaaacgaaag---tttgcttaaaagttcactgcttctcccttttgaagGCTGCCTCAATGTTACTTCTATCATTGTCCTTCACGTGGAAGGCTTTGGCACCTTATTCAGGCCCTCTTGCTGTTGCTGGCACTGTTTT

upper sequence: GRMZM2G153704_T02 (Zea mays), 3'ss of exon 11
lower sequence: AT5G16150.1 (Arabidopsis thaliana), 3'ss of exon 11
gtaatgcccttgtgttcaacaaatcatgtgtttattttctc---tctcaatcagca-----aatgggggattcttctttacat--attctcttttttctcgcttgaagGGTGCT-TCAATGCTACTCCTAGCATTGTCCTTCACCTGGAAAGCTCTGGCACCTTATTCTGGTACTCTTGCTGTTGTTGGCACTGTTCT
     |  | ||| || |  |||     |    || |||     |||||| |  ||     | |     |       | || |  ||| | |  |||     |  || ||   | ||||||||  | ||  | ||||||||||| ||||| ||||| ||  | |||||||| || ||||| |||||||| ||||||||
-----gtacatgtttttattaaaattcttagccatattcgaaaatctcaaccctcattagtattaccacaacaggactaacttggattttatggttttgtattgaaaagGCTTTGTCAATGCTGTTACTCTCCTTGTCCTTCACATGGAAGGCTCTTGCTGCCTATTCTGGAACCCTTGCCGTTGTTGGAACTGTTCT
















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|60339792|gb|DN206765.1|DN206765
EST:     TGGACAAACAAGGAAGGAAAAGCCTTCTGATAACAAGCTTTTCTGGAATG                         GGTGCTTCAATGCTACTCCTAGCATTGTCCTTCACCTGGAAAGCTCTGGCA
genomic: TGGACAAACAAGGAAGGAAAAGCCTTCTGATAACAAGCTTTTCTGGAATGgtaatgccct ... tcgcttgaagGGTGCTTCAATGCTACTCCTAGCATTGTCCTTCACCTGGAAAGCTCTGGCA
EST: gi|60400456|gb|DN233263.1|DN233263
EST:     TGGACAAACAAGGAAGGAAAAGCCTTCTGATAACAAGCTTTTCTGGAATG                         GGTGCTTCAATGCTACTCCTAGCATTGTCCTTCACCTGGAAAGCTCTGGCA
genomic: TGGACAAACAAGGAAGGAAAAGCCTTCTGATAACAAGCTTTTCTGGAATGgtaatgccct ... tcgcttgaagGGTGCTTCAATGCTACTCCTAGCATTGTCCTTCACCTGGAAAGCTCTGGCA
EST: gi|148981334|gb|EE027588.2|EE027588
EST:     TGGACAAACAAGGAAGGAAAAGCCTTCTGATAACAAGCTTTTCTGGAATG                         GGTGCTTCAATGCTACTCCTAGCATTGTCCTTCACCTGGAAAGCTCTGGCA
genomic: TGGACAAACAAGGAAGGAAAAGCCTTCTGATAACAAGCTTTTCTGGAATGgtaatgccct ... tcgcttgaagGGTGCTTCAATGCTACTCCTAGCATTGTCCTTCACCTGGAAAGCTCTGGCA
EST: gi|101389575|gb|EB816720.1|EB816720
EST:     TGGACAAACAAGGAAGGAAAAGCCTTCTGATAACAAGCTTTTCTGGAATG                         GGTGCTTCAATGCTACTCCTAGCATTGTCCTTCACCTGGAAAGCTCTGGCA
genomic: TGGACAAACAAGGAAGGAAAAGCCTTCTGATAACAAGCTTTTCTGGAATGgtaatgccct ... tcgcttgaagGGTGCTTCAATGCTACTCCTAGCATTGTCCTTCACCTGGAAAGCTCTGGCA
EST: gi|61119088|gb|DN560049.1|DN560049
EST:     TGGACAAACAAGGAAGGAAAAGCCTTCTGATAACAAGCTTTTCTGGAATG                         GGTGCTTCAATGCTACTCCTAGCATTGTCCTTCACCTGGAAAGCTCTGGCA
genomic: TGGACAAACAAGGAAGGAAAAGCCTTCTGATAACAAGCTTTTCTGGAATGgtaatgccct ... tcgcttgaagGGTGCTTCAATGCTACTCCTAGCATTGTCCTTCACCTGGAAAGCTCTGGCA
EST: gi|67035008|gb|CO463541.1|CO463541
EST:     TGGACAAACAAGGAAGGAAAAGCCTTCTGATAACAAGCTTTTCTGGAATG                         GGTGCTTNCA-TGCTACTCCTAGCATTGTCCTTCACCTGGAAAGCTCTGGC
genomic: TGGACAAACAAGGAAGGAAAAGCCTTCTGATAACAAGCTTTTCTGGAATGgtaatgccct ... tcgcttgaagGGTGCTT-CAATGCTACTCCTAGCATTGTCCTTCACCTGGAAAGCTCTGGC
EST: gi|60339583|gb|DN206556.1|DN206556
EST:     TGGACAAACAAGGAAGGAAAAGCCTTCTGATAACAAGCTTTTCTGGAATG                         GGTGCTTCAATGCTACTCCTAGCATTGTCCTTCACCTGGAAAGCTCTGGCA
genomic: TGGACAAACAAGGAAGGAAAAGCCTTCTGATAACAAGCTTTTCTGGAATGgtaatgccct ... tcgcttgaagGGTGCTTCAATGCTACTCCTAGCATTGTCCTTCACCTGGAAAGCTCTGGCA
EST: gi|211050165|gb|FL124866.1|FL124866
EST:     TGGACAAACAAGGAAGGAAAAGCCTTCTGATAACAAGCTTTTCTGGAATG                         GGTGCTTCAATGCTACTCCTAGCATTGTCCTTCACCTGGAAAGCTCTGGCA
genomic: TGGACAAACAAGGAAGGAAAAGCCTTCTGATAACAAGCTTTTCTGGAATGgtaatgccct ... tcgcttgaagGGTGCTTCAATGCTACTCCTAGCATTGTCCTTCACCTGGAAAGCTCTGGCA
EST: gi|211050168|gb|FL124869.1|FL124869
EST:     AACAAGGAAGGAAAAGCCTTCTGATAACAAGCTTTTCTGGAATG                         GGTGCTTCAATGCTACTCCTAGCATTGTCCTTCACCTGGAAAGCTCTGGCA
genomic: AACAAGGAAGGAAAAGCCTTCTGATAACAAGCTTTTCTGGAATGgtaatgccct ... tcgcttgaagGGTGCTTCAATGCTACTCCTAGCATTGTCCTTCACCTGGAAAGCTCTGGCA
EST: gi|67037358|gb|CO464198.1|CO464198
EST:     TGGACAAACAAGGAAGGAAAAGCCTTCTGATAACAAGCTTTTCTGGAATG                         GGTGCTTCAATGCTACTCCTAGCATTGTCCTTCACCTGGAAAGCTCTGGCA
genomic: TGGACAAACAAGGAAGGAAAAGCCTTCTGATAACAAGCTTTTCTGGAATGgtaatgccct ... tcgcttgaagGGTGCTTCAATGCTACTCCTAGCATTGTCCTTCACCTGGAAAGCTCTGGCA
EST: gi|149071544|gb|EE159937.2|EE159937
EST:     TGGACAAACAAGGAAGGAAAAGCCTTCTGATAACAAGCTTTTCTGGAATG                         GGTGCTTCAATGCTACTCCTAGCATTTTCCTTCACCTGGAAAGCTCTGGCA
genomic: TGGACAAACAAGGAAGGAAAAGCCTTCTGATAACAAGCTTTTCTGGAATGgtaatgccct ... tcgcttgaagGGTGCTTCAATGCTACTCCTAGCATTGTCCTTCACCTGGAAAGCTCTGGCA
EST: gi|60355926|gb|DN222899.1|DN222899
EST:     TGGACAAACAAGGAAGGAAAAGCCTTCTGATAACAAGCTTTTCTGGAATG                         GGTGCTTCAATGCTACTCCTAGCATTGTCCTTCACCTGGAAAGCTCTGGCA
genomic: TGGACAAACAAGGAAGGAAAAGCCTTCTGATAACAAGCTTTTCTGGAATGgtaatgccct ... tcgcttgaagGGTGCTTCAATGCTACTCCTAGCATTGTCCTTCACCTGGAAAGCTCTGGCA
EST: gi|116826239|gb|EC870015.1|EC870015
EST:     TGGACAAACAAGGAAGGAAAAGCCTTCTGATAACAAGCTTTTCTGGAATG                         GGTGCTTCAATGCTACTCCTAGCATTGTCCTTCACCTGGAAAGCTCTGGCA
genomic: TGGACAAACAAGGAAGGAAAAGCCTTCTGATAACAAGCTTTTCTGGAATGgtaatgccct ... tcgcttgaagGGTGCTTCAATGCTACTCCTAGCATTGTCCTTCACCTGGAAAGCTCTGGCA
EST: gi|67011667|gb|CO440416.1|CO440416
EST:     TGGACAAACAAGGAAGGAAAAGCCTTCTGATAACAAGCTTTTCTGGAATG                         GGTGCTTCAATGCTACTCCTAGCATTGTCCTTCACCTGGAAAGCTCTGGCA
genomic: TGGACAAACAAGGAAGGAAAAGCCTTCTGATAACAAGCTTTTCTGGAATGgtaatgccct ... tcgcttgaagGGTGCTTCAATGCTACTCCTAGCATTGTCCTTCACCTGGAAAGCTCTGGCA
EST: gi|7844519|gb|AW787741.1|AW787741
EST:     TGGACAAACAAGGAAGGAAAAGCCTTCTGATAACAAGCTTTTCTGGAATG                         GGTGCTTCAATGCTACTCCTAGCATTGTCCTTCACCTGGAAAGCTCTGGCA
genomic: TGGACAAACAAGGAAGGAAAAGCCTTCTGATAACAAGCTTTTCTGGAATGgtaatgccct ... tcgcttgaagGGTGCTTCAATGCTACTCCTAGCATTGTCCTTCACCTGGAAAGCTCTGGCA
EST: gi|211050172|gb|FL124873.1|FL124873
EST:     TGGACAAACAAGGAAGGAAAAGCCTTCTGATAACAAGCTTTTCTGGAATG                         GGTGCTTCAATGCTACTCCTAGCATTGTCCTTCACCTGGAAAGCTCTGGCA
genomic: TGGACAAACAAGGAAGGAAAAGCCTTCTGATAACAAGCTTTTCTGGAATGgtaatgccct ... tcgcttgaagGGTGCTTCAATGCTACTCCTAGCATTGTCCTTCACCTGGAAAGCTCTGGCA
EST: gi|211050170|gb|FL124871.1|FL124871
EST:     TGGACAAACAAGGAAGGAAAAGCCTTCTGATAACAAGCTTTTCTGGAATG                         GGTGCTTCAATGCTACTCCTAGCATTGTCCTTCACCTGGAAAGCTCTGGCA
genomic: TGGACAAACAAGGAAGGAAAAGCCTTCTGATAACAAGCTTTTCTGGAATGgtaatgccct ... tcgcttgaagGGTGCTTCAATGCTACTCCTAGCATTGTCCTTCACCTGGAAAGCTCTGGCA
EST: gi|60351782|gb|DN218755.1|DN218755
EST:     TGGACAAACAAGGAAGGAAAAGCCTTCTGATAACAAGCTTTTCTGGAATG                         GGTGCTTCAATGCTACTCCTAGCATTGTCCTTCACCTGGAAAGCTCTGGCA
genomic: TGGACAAACAAGGAAGGAAAAGCCTTCTGATAACAAGCTTTTCTGGAATGgtaatgccct ... tcgcttgaagGGTGCTTCAATGCTACTCCTAGCATTGTCCTTCACCTGGAAAGCTCTGGCA
EST: gi|33092425|gb|CF052419.1|CF052419
EST:     TGGACAAACAAGGAAGGAAAAGCCTTCTGATAACAAGCTTTTCTGGAATG                         GGTGCTTCAATGCTACTCCTAGCATTGTCCTTCACCTGGAAAGCTCTGGCA
genomic: TGGACAAACAAGGAAGGAAAAGCCTTCTGATAACAAGCTTTTCTGGAATGgtaatgccct ... tcgcttgaagGGTGCTTCAATGCTACTCCTAGCATTGTCCTTCACCTGGAAAGCTCTGGCA
EST: gi|60401429|gb|DN234236.1|DN234236
EST:     TGGACAAACAAGGAAGGAAAAGCCTTCTGATAACAAGCTTTTCTGGAATG                         GGTGCTTCAATGCTACTCCTAGCATTGTCCTTCACCTGGAAAGCTCTGGCA
genomic: TGGACAAACAAGGAAGGAAAAGCCTTCTGATAACAAGCTTTTCTGGAATGgtaatgccct ... tcgcttgaagGGTGCTTCAATGCTACTCCTAGCATTGTCCTTCACCTGGAAAGCTCTGGCA
EST: gi|78179345|gb|DV549718.1|DV549718
EST:     TGGACAAACAAGGAAGGAAAAGCCTTCTGATAACAAGCTTTTCTGGAATG                         GGTGCTTCAATGCTACTCCTAGCATTGTCCTTCACCTGGAAAGCTCTGGCA
genomic: TGGACAAACAAGGAAGGAAAAGCCTTCTGATAACAAGCTTTTCTGGAATGgtaatgccct ... tcgcttgaagGGTGCTTCAATGCTACTCCTAGCATTGTCCTTCACCTGGAAAGCTCTGGCA
EST: gi|211106867|gb|FL216747.1|FL216747
EST:     TGGACAAACAAGGAAGGAAAAGCCTTCTGATAACAAGCTTTTCTGGAATG                         GGTGCTTCAATGCTACTCCTAGCATTGTCCTTCACCTGGAAAGCTCTGGCA
genomic: TGGACAAACAAGGAAGGAAAAGCCTTCTGATAACAAGCTTTTCTGGAATGgtaatgccct ... tcgcttgaagGGTGCTTCAATGCTACTCCTAGCATTGTCCTTCACCTGGAAAGCTCTGGCA
EST: gi|94472602|gb|EB701560.1|EB701560
EST:     TGGACAAACAAGGAAGGAAAAGCCTTCTGATAACAAGCTTTTCTGGAATG                         GGTGCTTCAATGCTACTCCTAGCATTGTCCTTCACCTGGAAAGCTCTGGCA
genomic: TGGACAAACAAGGAAGGAAAAGCCTTCTGATAACAAGCTTTTCTGGAATGgtaatgccct ... tcgcttgaagGGTGCTTCAATGCTACTCCTAGCATTGTCCTTCACCTGGAAAGCTCTGGCA
EST: gi|60353755|gb|DN220728.1|DN220728
EST:     AAACAAGGAAGGAAAAGCCTTTTGATAACAAGCTTTTCTGGAATG                         GGTGCTTCAATGCTACTCCTAGCATTGTCCTTCACCTGGAAAGCTTTGGCA
genomic: AAACAAGGAAGGAAAAGCCTTCTGATAACAAGCTTTTCTGGAATGgtaatgccct ... tcgcttgaagGGTGCTTCAATGCTACTCCTAGCATTGTCCTTCACCTGGAAAGCTCTGGCA
EST: gi|60358931|gb|DN225904.1|DN225904
EST:     TGGACAAACAAGGAAGGAAAAGCCTTCTGATAACAAGCTTTTCTGGAATG                         GGTGCTTCAATGCTACTCCTAGCATTGTCCTTCACCTGGAAAGCTCTGGCA
genomic: TGGACAAACAAGGAAGGAAAAGCCTTCTGATAACAAGCTTTTCTGGAATGgtaatgccct ... tcgcttgaagGGTGCTTCAATGCTACTCCTAGCATTGTCCTTCACCTGGAAAGCTCTGGCA
EST: gi|7844129|gb|AW787332.1|AW787332
EST:     TGGACAAACAAGGAAGGAAAAGCCTTCTGATAACAAGCTTTTCTGGAATG                         GGTGCTTCAATGCTACTCCTAGCATTGTCCTTCACCTGGAAAGC
genomic: TGGACAAACAAGGAAGGAAAAGCCTTCTGATAACAAGCTTTTCTGGAATGgtaatgccct ... tcgcttgaagGGTGCTTCAATGCTACTCCTAGCATTGTCCTTCACCTGGAAAGC
EST: gi|78075827|gb|DV504261.1|DV504261
EST:     GGAAGGAAAAGCCTTCTGATAACAAGCTTTTCTGGAATG                         GGTGCTTCAATGCTACTCCTAGCATTGTCCTTCACCTGGAAAGCTCTGGCA
genomic: GGAAGGAAAAGCCTTCTGATAACAAGCTTTTCTGGAATGgtaatgccct ... tcgcttgaagGGTGCTTCAATGCTACTCCTAGCATTGTCCTTCACCTGGAAAGCTCTGGCA
EST: gi|60355312|gb|DN222285.1|DN222285
EST:     TGGACAAACAAGGAAGGAAAAGCCTTCTGATAACAAGCTTTTCTGGAATG                         GGTGCTTCAATGCTACTCCTAGCATTGTCCTTCACCTGGAAAGCTCTGGCA
genomic: TGGACAAACAAGGAAGGAAAAGCCTTCTGATAACAAGCTTTTCTGGAATGgtaatgccct ... tcgcttgaagGGTGCTTCAATGCTACTCCTAGCATTGTCCTTCACCTGGAAAGCTCTGGCA
EST: gi|18963572|gb|BM660510.1|BM660510
EST:     TGGACAAACAAGGAAGGAAAAGCCTTCTGATAACAAGCTTTTCTGGAATG                         GGTGCTTCAATGCTACTCCTAGCATTGTCCTTCACCTGGAAAGCTCTGGCA
genomic: TGGACAAACAAGGAAGGAAAAGCCTTCTGATAACAAGCTTTTCTGGAATGgtaatgccct ... tcgcttgaagGGTGCTTCAATGCTACTCCTAGCATTGTCCTTCACCTGGAAAGCTCTGGCA
EST: gi|148996906|gb|EE035710.2|EE035710
EST:     TGGACAAACAAGGAAGGAAAAGCCTTCTGATAACAAGCTTTTCTGGAATG                         GGTGCTTCAATGCTACTCCTAGCATTGTCCTTCACCTGGAAAGCTCTGGCA
genomic: TGGACAAACAAGGAAGGAAAAGCCTTCTGATAACAAGCTTTTCTGGAATGgtaatgccct ... tcgcttgaagGGTGCTTCAATGCTACTCCTAGCATTGTCCTTCACCTGGAAAGCTCTGGCA
EST: gi|22545719|gb|BU098078.1|BU098078
EST:     TGGACAAACAAGGAAGGAAAAGCCTTCTGATAACAAGCTTTTCTGGAATG                         GGTGCTTCAATGCTACTCCTAGCATTGTCCTTCACCTGGAAAGCTCTGGCA
genomic: TGGACAAACAAGGAAGGAAAAGCCTTCTGATAACAAGCTTTTCTGGAATGgtaatgccct ... tcgcttgaagGGTGCTTCAATGCTACTCCTAGCATTGTCCTTCACCTGGAAAGCTCTGGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcaatcagcaaatgggggattcttctttacatattctcttttttctcgcttgaagGGTGCTTCAATGCTACTCCTAGCATTGTCCTTCACCTGGAAAGCTCTGGCACCTTATTCTGGTACTCTTGCTGTTGTTGGCACTGTTCT
                   ttcttctttacatatt  CT-rich tract
                              atattctctttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatgcccttgtgttcaacaaatcatgtgtttattttctctctcaatcagcaaatgggggattcttctttacatattctcttttttctcgcttgaagGGTGCTTCAATGCTACTCCTAGCATTGTCCTTCACCTGGAAAGCTCTGGCACCTTATTCTGGTACTCTTGCTGTTGTTGGCACTGTTCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT