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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttttcgtgctcagtggtcagtgcgaggtgtccacgagtcaattgaagttggtttcttattcgtacaaagcatgcaactcttgaacagtttaataactacatatttgtcggatgatcctttcttctctcttagCTTTGGCTTGTCTTGGGAGTCTTCCTAATGGCCACGAGCCTCAGAATGTATGCCACGTGCCAGCAGCTTGCTCATGCTGCAGCTGCCAACAGTTTTCTCG

Basic information

species Zea mays
transcript GRMZM2G337425_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G337425_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os03g16570.2 (Oryza sativa), 3'ss of exon 4
gtaagttttcgtgctcagtggtcagtgcgaggtgtccacgagtcaattgaagttggtttcttattcgtacaaagcatgcaactcttgaacagtttaataactacat-atttgtcggatgatcct--ttcttctctcttagCTTTGGCTTGTCTTGGGAGTCTTCCTAATGGCCACGAGCCTCAGAATGTATGCCACGTGCCAGCAGCTTGCTCATGCTGCAGCT-GCCAACAGTTTTCTCG
                                                | |  |  |   ||  | |||   |  ||||   | | |     |  |  || | ||| ||||||||| |    |    |  |||||  ||| ||||||| || ||||| || |||||||||||||| ||||| || ||||| ||||| |||||||||||  |    || |  ||  ||  ||  |      |
------------------------------------------------gtaagttatcaattgatggtatgtattatgcttatatagcttgatggagaaatttcatgatttgtcgggttgcgcggaattgtctcttgtagGTTTGGCTGGTTTTGGGTGTGTTCCTAATGGCCACCAGCCTAAGGATGTACGCCACATGCCAGCAGCTC-CAAGCGCAGGCGCAAGCTCACGCTGCAGCTG
















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|78109926|gb|DV528341.1|DV528341
EST:     TTGTTTTGTTCATGGTACTGAACTCGCACCAGATCTCTCCCAATCTTCTG                         CTTTGGCTTGTCTTGGGAGTCTTCCTAATGGCCACGAGCCTCAGAATGTAT
genomic: TTGTTTTGTTCATGGTACTGAACTCGCACCAGATCTCTCCCAATCTTCTGgtaagttttc ... tctctcttagCTTTGGCTTGTCTTGGGAGTCTTCCTAATGGCCACGAGCCTCAGAATGTAT
EST: gi|50332883|gb|CO528009.1|CO528009
EST:     TTGTTTTGTTCATGGTACTGAACTCGCACCAGATCTCTCCCAATCTTCTG                         CTTTGGCTTGTCTTGGGAGTCTTCCTAATGGCCACGAGCCTCAGAATGTAT
genomic: TTGTTTTGTTCATGGTACTGAACTCGCACCAGATCTCTCCCAATCTTCTGgtaagttttc ... tctctcttagCTTTGGCTTGTCTTGGGAGTCTTCCTAATGGCCACGAGCCTCAGAATGTAT
EST: gi|89755993|gb|DY686200.1|DY686200
EST:     TTGTTTTGTTCATGGTACTGAACTCGCACCAGATCTCTCCCAATCTTCTG                         CTTTGGCTTGTCTTGGGAGTCTTCCTAATGGCCACGAGCCTCAGAATGTAT
genomic: TTGTTTTGTTCATGGTACTGAACTCGCACCAGATCTCTCCCAATCTTCTGgtaagttttc ... tctctcttagCTTTGGCTTGTCTTGGGAGTCTTCCTAATGGCCACGAGCCTCAGAATGTAT
EST: gi|148931116|gb|EC873780.2|EC873780
EST:     TTGTTTTGTTCATGGTACTGAACTCGCACCAGATCTCTCCCAATCTTCTG                         CTTTGGCTTGTCTTGGGAGTCTTCCTAATGGCCACGAGCCTCAGAATGTAT
genomic: TTGTTTTGTTCATGGTACTGAACTCGCACCAGATCTCTCCCAATCTTCTGgtaagttttc ... tctctcttagCTTTGGCTTGTCTTGGGAGTCTTCCTAATGGCCACGAGCCTCAGAATGTAT
EST: gi|211089296|gb|FL241969.1|FL241969
EST:     TTGTTTTGTTCATGGTACTGAACTCGCACCAGATCTCTCCCAATCTTCTG                         CTTTGGCTTGTCTTGGGAGTCTTCCTAATGGCCACGAGCCTCAGAATGTA
genomic: TTGTTTTGTTCATGGTACTGAACTCGCACCAGATCTCTCCCAATCTTCTGgtaagttttc ... tctctcttagCTTTGGCTTGTCTTGGGAGTCTTCCTAATGGCCACGAGCCTCAGAATGTA
EST: gi|78083979|gb|DV512372.1|DV512372
EST:     TTGTTTTGTTCATGGTACTGAACTCGCACCAGATCTCTCCCAATCTTCTG                         CTTTGGCTTGTCTTGGGAGTCTTCCTAATGGCCACGAGCCTCAGAATGTAT
genomic: TTGTTTTGTTCATGGTACTGAACTCGCACCAGATCTCTCCCAATCTTCTGgtaagttttc ... tctctcttagCTTTGGCTTGTCTTGGGAGTCTTCCTAATGGCCACGAGCCTCAGAATGTAT
EST: gi|18164717|gb|BM334556.1|BM334556
EST:     ACTGAACTCGCACCAGATCTCT-CCAATCTTCTG                         CTTTGGCTTGTCTTGGGAGTCTTCCTAATGGCCACGAGCCTCAGAATGTAT
genomic: ACTGAACTCGCACCAGATCTCTCCCAATCTTCTGgtaagttttc ... tctctcttagCTTTGGCTTGTCTTGGGAGTCTTCCTAATGGCCACGAGCCTCAGAATGTAT
EST: gi|91048354|gb|EB158772.1|EB158772
EST:     TTGTTTTGTTCATGGTACTGAACTCGCACCAGATCTCTCCCAATCTTCTG                         CTTTGGCTTGTCTTGGGAGTCTTCCTAATGGCCACGAGCCTCAGAATGTAT
genomic: TTGTTTTGTTCATGGTACTGAACTCGCACCAGATCTCTCCCAATCTTCTGgtaagttttc ... tctctcttagCTTTGGCTTGTCTTGGGAGTCTTCCTAATGGCCACGAGCCTCAGAATGTAT
EST: gi|91876517|gb|EB406474.1|EB406474
EST:     TTGTTTTGTTCATGGTACTGAACTCGCACCAGATCTCTCCCAATCTTCTG                         CTTTGGCTTGTCTTGGGAGTCTTCCTAATGGCCACGAGCCTCAGAATGTAT
genomic: TTGTTTTGTTCATGGTACTGAACTCGCACCAGATCTCTCCCAATCTTCTGgtaagttttc ... tctctcttagCTTTGGCTTGTCTTGGGAGTCTTCCTAATGGCCACGAGCCTCAGAATGTAT
EST: gi|88756244|gb|DY540385.1|DY540385
EST:     TTGTTTTGTTCATGGTACTGAACTCGCACCAGATCTCTCCCAATCTTCTG                         CTTTGGCTTGTCTTGGGAGTCTTCCTAATGGCCACGAGCCTCAGAATGTAT
genomic: TTGTTTTGTTCATGGTACTGAACTCGCACCAGATCTCTCCCAATCTTCTGgtaagttttc ... tctctcttagCTTTGGCTTGTCTTGGGAGTCTTCCTAATGGCCACGAGCCTCAGAATGTAT
EST: gi|211086849|gb|FL241965.1|FL241965
EST:     TTGTTTTGTTCATGGTACTGAACTCGCACCAGATCTCTCCCAATCTTCTG                         CTTTGGCTTGTCTTGGGAGTCTTCCTAATGGCCACGAGCCTCAGAATGTAT
genomic: TTGTTTTGTTCATGGTACTGAACTCGCACCAGATCTCTCCCAATCTTCTGgtaagttttc ... tctctcttagCTTTGGCTTGTCTTGGGAGTCTTCCTAATGGCCACGAGCCTCAGAATGTAT
EST: gi|211089297|gb|FL241970.1|FL241970
EST:     TTGTTTTGTTCATGGTACTGAACTCGCACCAGATCTCTCCCAATCTTCTG                         CTTTGGCTTGTCTTGGGAGTCTTCCTAATGGCCACGAGCCTCAGAATGTAT
genomic: TTGTTTTGTTCATGGTACTGAACTCGCACCAGATCTCTCCCAATCTTCTGgtaagttttc ... tctctcttagCTTTGGCTTGTCTTGGGAGTCTTCCTAATGGCCACGAGCCTCAGAATGTAT
EST: gi|211089293|gb|FL241966.1|FL241966
EST:     TTGTTTTGTTCATGGTACTGAACTCGCACCAGATCTCTCCCAATCTTCTG                         CTTTGGCTTGTCTTGGGAGTCTTCCTAATGGCCACGAGCCTCAGAATGTAT
genomic: TTGTTTTGTTCATGGTACTGAACTCGCACCAGATCTCTCCCAATCTTCTGgtaagttttc ... tctctcttagCTTTGGCTTGTCTTGGGAGTCTTCCTAATGGCCACGAGCCTCAGAATGTAT
EST: gi|86467325|gb|DY233695.1|DY233695
EST:     TTGTTTTGTTCATGGTACTGAACTCGCACCAGATCTCTCCCAATCTTCTG                         CTTTGGCTTGTCTTGAGAGTCTTCCTAATGGCCACGAGCCTCAGAATGTAT
genomic: TTGTTTTGTTCATGGTACTGAACTCGCACCAGATCTCTCCCAATCTTCTGgtaagttttc ... tctctcttagCTTTGGCTTGTCTTGGGAGTCTTCCTAATGGCCACGAGCCTCAGAATGTAT
EST: gi|76288198|gb|DV027766.1|DV027766
EST:     TTGTTTTGTTCATGGTACTGAACTCGCACCAGATCTCTCCCAATCTTCTG                         CTTTGGCTTGTCTTGGGAGTCTTCCTAATGGCCACGAGCCTCAGAATGTAT
genomic: TTGTTTTGTTCATGGTACTGAACTCGCACCAGATCTCTCCCAATCTTCTGgtaagttttc ... tctctcttagCTTTGGCTTGTCTTGGGAGTCTTCCTAATGGCCACGAGCCTCAGAATGTAT
EST: gi|18166650|gb|BM336489.1|BM336489
EST:     ACTGAACTCGCACCAGATCTCT-CCAATCTTCTG                         CTTTGGCTTGTCTTGGGAGTCTTCCTAATGGCCACGAGCCTCAGAATGTAT
genomic: ACTGAACTCGCACCAGATCTCTCCCAATCTTCTGgtaagttttc ... tctctcttagCTTTGGCTTGTCTTGGGAGTCTTCCTAATGGCCACGAGCCTCAGAATGTAT
EST: gi|211089295|gb|FL241968.1|FL241968
EST:     TTGTTTTGTTCATGGTACTGAACTCGCACCAGATCTCTCCCAATCTTCTG                         CTTTGGCTTGTCTTGGGAGTCTTCCTAATGGCCACGAGCCTCAGAATGTAT
genomic: TTGTTTTGTTCATGGTACTGAACTCGCACCAGATCTCTCCCAATCTTCTGgtaagttttc ... tctctcttagCTTTGGCTTGTCTTGGGAGTCTTCCTAATGGCCACGAGCCTCAGAATGTAT
EST: gi|78085073|gb|DV513466.1|DV513466
EST:     TTGTTTTGTTCATGGTACTGAACTCGCACCAGATCTCTCCCAATCTTCTG                         CTTTGGCTTGTCTTGGGAGTCTTCCTAATGGCCACGAGCCTCAGAATGTAT
genomic: TTGTTTTGTTCATGGTACTGAACTCGCACCAGATCTCTCCCAATCTTCTGgtaagttttc ... tctctcttagCTTTGGCTTGTCTTGGGAGTCTTCCTAATGGCCACGAGCCTCAGAATGTAT
EST: gi|101389965|gb|EB816914.1|EB816914
EST:     TTGTTTTGTTCATGGTACTGAACTCGCACCAGATCTCTCCCAATCTTCTG                         CTTTGGCTTGTCTTGGGAGTCTTCCTAATGGCCACGAGCCTCAGAATGTAT
genomic: TTGTTTTGTTCATGGTACTGAACTCGCACCAGATCTCTCCCAATCTTCTGgtaagttttc ... tctctcttagCTTTGGCTTGTCTTGGGAGTCTTCCTAATGGCCACGAGCCTCAGAATGTAT
EST: gi|211089294|gb|FL241967.1|FL241967
EST:     TTGTTTTGTTCATGGTACTGAACTCGCACCAGATCTCTCCCAATCTTCTG                         CTTTGGCTTSTCTTGGGAGTCTTTCCTAATGGCCACGAGCCTCAGAATGTA
genomic: TTGTTTTGTTCATGGTACTGAACTCGCACCAGATCTCTCCCAATCTTCTGgtaagttttc ... tctctcttagCTTTGGCTTGTCTTGGGAGTCTT-CCTAATGGCCACGAGCCTCAGAATGTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttgaacagtttaataactacatatttgtcggatgatcctttcttctctcttagCTTTGGCTTGTCTTGGGAGTCTTCCTAATGGCCACGAGCCTCAGAATGTATGCCACGTGCCAGCAGCTTGCTCATGCTGCAGCTGCCAACAGTTTTCTCG
            taataac  putative branch site (score: 1)
                                  tgatcctttcttctct  putative PPT
          tttaataactacatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagttttcgtgctcagtggtcagtgcgaggtgtccacgagtcaattgaagttggtttcttattcgtacaaagcatgcaactcttgaacagtttaataactacatatttgtcggatgatcctttcttctctcttagCTTTGGCTTGTCTTGGGAGTCTTCCTAATGGCCACGAGCCTCAGAATGTATGCCACGTGCCAGCAGCTTGCTCATGCTGCAGCTGCCAACAGTTTTCTCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC