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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttttcagtgccccttcactgagttggccacattttgtttttagttacatgattattaatatatgtatatctgataaggacatactgaacttctttgttagGAAGTGCGGATGCCGGCAGCTGGTTCCAAAGGGGCACCTAAAAACCCCAGTGAACTAAAAGATGACACAAGCTTGTCACGGGATGAAAAGCAG

Basic information

species Zea mays
transcript GRMZM2G170291_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G170291_T03 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os12g18200.1 (Oryza sativa), 3'ss of exon 1
ttttcagtgccccttcactgagttggccacattttgtttttagttacatgattattaatatatgtatatctgataaggaca-ta-ctgaacttctttgttagGAAGTGCGGATGCCGGCAGCTGGTTCCAAAGGGGCACCTAAAAACCCCAGTGAACTAAAAGATGACACAAGCTTGTCACGGGATGAAAAGCAG
 |||   |      | | |   ||  |   | ||     ||  ||  | |  ||    |  ||  || ||| |  |||| | || || |||||||||||||||||||||||||||| ||||||||||||||||||||||| ||||| ||  || |||| ||||||||||||||||  ||||| ||||||||||||
-ttttgcttttgtctgatttttttatcagtacttacaacttcattttaagtatacatgt-cataaatgtcttactaggatagtatctaaacttctttgttagGAAGTGCGGATGCCAGCAGCTGGTTCCAAAGGGGCACCAAAAAATCCTGGTCAACTGAAAGATGACACAAGCTCATCACGAGATGAAAAGCAG
















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|78105400|gb|DV523818.1|DV523818
EST:     CTTTCTCGCAGCTCGTCGCCCGCCTTGACCCCGACGTCATTTGTGTCCAG                         GAAGTGCGGATGCCGGCAGCTGGTTCCAAAGGGGCACCTAAAAACCCCAGT
genomic: CTTTCTCGCAGCTCGTCGCCCGCCTTGACCCCGACGTCATTTGTGTCCAGgtgagcgatc ... tctttgttagGAAGTGCGGATGCCGGCAGCTGGTTCCAAAGGGGCACCTAAAAACCCCAGT
EST: gi|71770443|gb|DR968380.1|DR968380
EST:     TTTCTCGCAGCTCGTCGCCCGCCTTGGACCCCGACGTCCTTTGTGTCCAG                         GAAGTGCGGATGCCGGCAGCTGGTTCCAAAGGGGCACCTAAAAACCCCAGT
genomic: TTTCTCGCAGCTCGTCGCCCGCCTTG-ACCCCGACGTCATTTGTGTCCAGgtgagcgatc ... tctttgttagGAAGTGCGGATGCCGGCAGCTGGTTCCAAAGGGGCACCTAAAAACCCCAGT
EST: gi|211194081|gb|FL030608.1|FL030608
EST:     CTTTCTCGCAGCTCGTCGCCCGCCTTGACCCCGACGTCATTTGTGTCCAG                         GAAGTGCGGATG-CGGCAGCTGGTTCCAAAGGGGCACCTAAAAACCCCAGT
genomic: CTTTCTCGCAGCTCGTCGCCCGCCTTGACCCCGACGTCATTTGTGTCCAGgtgagcgatc ... tctttgttagGAAGTGCGGATGCCGGCAGCTGGTTCCAAAGGGGCACCTAAAAACCCCAGT
EST: gi|211261839|gb|FL294946.1|FL294946
EST:     CTTTCTCGCAGCTCGTCGCCCGCCTTGACCCCGACGTCATTTGTGTCCAG                         GAAGTGCGGATGCCGGCAGCTGGTTCCAAAGGGGCACCTAAAAACCCCAGT
genomic: CTTTCTCGCAGCTCGTCGCCCGCCTTGACCCCGACGTCATTTGTGTCCAGgtgagcgatc ... tctttgttagGAAGTGCGGATGCCGGCAGCTGGTTCCAAAGGGGCACCTAAAAACCCCAGT
EST: gi|211321949|gb|FK966255.1|FK966255
EST:     CTTTCTCGCAGCTCGTCGCCCGCCTTGACCCCGACGTCATTTGTGTCCAG                         GAAGTGCGGATGCCGGCAGCTGGTTCCAAAGGGGCACCTAAAAACCCCAGT
genomic: CTTTCTCGCAGCTCGTCGCCCGCCTTGACCCCGACGTCATTTGTGTCCAGgtgagcgatc ... tctttgttagGAAGTGCGGATGCCGGCAGCTGGTTCCAAAGGGGCACCTAAAAACCCCAGT
EST: gi|94475567|gb|EB704525.1|EB704525
EST:     CTTTCTCGCAGCTCGTCGCCCGCCTTGACCCCGACGTCATTTGTGTCCAG                         GAAGTGCGGATGCCGGCAGCTGGTTCCAAAGGGGCACCTAAAAACCCCAGT
genomic: CTTTCTCGCAGCTCGTCGCCCGCCTTGACCCCGACGTCATTTGTGTCCAGgtgagcgatc ... tctttgttagGAAGTGCGGATGCCGGCAGCTGGTTCCAAAGGGGCACCTAAAAACCCCAGT
EST: gi|71431551|gb|DR812601.1|DR812601
EST:     CTTTCTCGCAGCTCGTCGCCCGCCTTGACCCCGACGTCATTTGTGTCCAG                         GAAGTGCGGATGCCGGCAGCTGGTTCCAAAGGGGCACCTAAAAACCCCAGT
genomic: CTTTCTCGCAGCTCGTCGCCCGCCTTGACCCCGACGTCATTTGTGTCCAGgtgagcgatc ... tctttgttagGAAGTGCGGATGCCGGCAGCTGGTTCCAAAGGGGCACCTAAAAACCCCAGT
EST: gi|149095617|gb|EE168978.2|EE168978
EST:     CTTTCTCGCAGCTCGTCGCCCGCCTTGACCCCGACGTCATTTGTGTCCAG                         GAAGTGCGGATGCCGGCAGCTGGTTCCAAAGGGGCACCTAAAAACCCCAGT
genomic: CTTTCTCGCAGCTCGTCGCCCGCCTTGACCCCGACGTCATTTGTGTCCAGgtgagcgatc ... tctttgttagGAAGTGCGGATGCCGGCAGCTGGTTCCAAAGGGGCACCTAAAAACCCCAGT
EST: gi|76018500|gb|DT945670.1|DT945670
EST:     CTTTCTCGCAGCTCGTCGCCCGCCTTGACCCCGACGTCATTTGTGTCCAG                         GAAGTGCGGATGCCGGCAGCTGGTTCCAAAGGGGCACCTAAAAACCCCAGT
genomic: CTTTCTCGCAGCTCGTCGCCCGCCTTGACCCCGACGTCATTTGTGTCCAGgtgagcgatc ... tctttgttagGAAGTGCGGATGCCGGCAGCTGGTTCCAAAGGGGCACCTAAAAACCCCAGT
EST: gi|40287182|gb|CK327574.1|CK327574
EST:     CTTTCTCGCAGCTCGTCGCCCGCCTTGACCCCGACGTCATTTGTGTCCAG                         GAAGTGCGGATGCCGGCAGCTGGTTCCAAAGGGGCACCTAAAAACCCCAGT
genomic: CTTTCTCGCAGCTCGTCGCCCGCCTTGACCCCGACGTCATTTGTGTCCAGgtgagcgatc ... tctttgttagGAAGTGCGGATGCCGGCAGCTGGTTCCAAAGGGGCACCTAAAAACCCCAGT
EST: gi|71771442|gb|DR969379.1|DR969379
EST:     CTTTCTCGCAGCTCGTCGCCCGCCTTGACCCCGACGTCATTTGTGTCCAG                         GAAGTGCGGATGCCGGCAGCTGGTTCCAAAGGGGCACCTAAAAACCCCAGT
genomic: CTTTCTCGCAGCTCGTCGCCCGCCTTGACCCCGACGTCATTTGTGTCCAGgtgagcgatc ... tctttgttagGAAGTGCGGATGCCGGCAGCTGGTTCCAAAGGGGCACCTAAAAACCCCAGT
EST: gi|211194080|gb|FL030607.1|FL030607
EST:     CTTTCTCGCAGCTCGTCGCCCGCCTTGACCCCGACGTCATTTGTGTCCAG                         GAAGTGCGGATGCCGGCAGCTGGTTCCAAAGGGGCACCTAAAAACCCCAGT
genomic: CTTTCTCGCAGCTCGTCGCCCGCCTTGACCCCGACGTCATTTGTGTCCAGgtgagcgatc ... tctttgttagGAAGTGCGGATGCCGGCAGCTGGTTCCAAAGGGGCACCTAAAAACCCCAGT
EST: gi|211471748|gb|FL295692.1|FL295692
EST:     CTTTCTCGCAGCTCGTCGCCCGCCTTGACCCCGACGTCATTTGTGTCCAG                         GAAGTGCGGATGCCGGCAGCTGGTTCCAAAGGGGCACCTAAAAACCCCAGT
genomic: CTTTCTCGCAGCTCGTCGCCCGCCTTGACCCCGACGTCATTTGTGTCCAGgtgagcgatc ... tctttgttagGAAGTGCGGATGCCGGCAGCTGGTTCCAAAGGGGCACCTAAAAACCCCAGT
EST: gi|91872355|gb|EB402312.1|EB402312
EST:     CTTTCTCGCAGCTCGTCGCCCGCCTTGACCCCGACGTCATTTGTGTCCAG                         GAAGTGCGGATGCCGGCAGCTGGTTCCAAAGGGGCACCTAAAAACCCCAGT
genomic: CTTTCTCGCAGCTCGTCGCCCGCCTTGACCCCGACGTCATTTGTGTCCAGgtgagcgatc ... tctttgttagGAAGTGCGGATGCCGGCAGCTGGTTCCAAAGGGGCACCTAAAAACCCCAGT
EST: gi|78074005|gb|DV502439.1|DV502439
EST:     CTTTCTCGCAGCTCGTCGCCCGCCTTGACCCCGACGTCATTTGTGTCCAG                         GAAGTGCGGATGCCGGCAGCTGGTTCCAAAGGGGCACCTAAAAACCCCAGT
genomic: CTTTCTCGCAGCTCGTCGCCCGCCTTGACCCCGACGTCATTTGTGTCCAGgtgagcgatc ... tctttgttagGAAGTGCGGATGCCGGCAGCTGGTTCCAAAGGGGCACCTAAAAACCCCAGT
EST: gi|84980468|gb|DW530817.1|DW530817
EST:     CTTTCTCGCAGCTCGTCGCCCGCCTTGACCCCGACGTCATTTGTGTCCAG                         GAAGTGCGGATGCCGGCAGCTGGTTCCAAAGGGGCACCTAAAAACCCCAGT
genomic: CTTTCTCGCAGCTCGTCGCCCGCCTTGACCCCGACGTCATTTGTGTCCAGgtgagcgatc ... tctttgttagGAAGTGCGGATGCCGGCAGCTGGTTCCAAAGGGGCACCTAAAAACCCCAGT
EST: gi|211194082|gb|FL030609.1|FL030609
EST:     CTTTCTCGCAGCTCGTCGCCCGCCTTGACCCCGACGTCATTTGTGTCCAG                         GAAGTGCGGATGCCGGCAGCTGGTTCCAAAGGGGCACCTAAAAACCCCAGT
genomic: CTTTCTCGCAGCTCGTCGCCCGCCTTGACCCCGACGTCATTTGTGTCCAGgtgagcgatc ... tctttgttagGAAGTGCGGATGCCGGCAGCTGGTTCCAAAGGGGCACCTAAAAACCCCAGT
EST: gi|76016191|gb|DT943361.1|DT943361
EST:     CTTTCTCGCAGCTCGTCGCCCGCCTTGACCCCGACGTCATTTGTGTCCAG                         GAAGTGCGGATGCCGGCAGCTGGTTCCAAAGGGGCACCTAAAAACCCCAGT
genomic: CTTTCTCGCAGCTCGTCGCCCGCCTTGACCCCGACGTCATTTGTGTCCAGgtgagcgatc ... tctttgttagGAAGTGCGGATGCCGGCAGCTGGTTCCAAAGGGGCACCTAAAAACCCCAGT
EST: gi|76021196|gb|DT948366.1|DT948366
EST:     CTTTCTCGCAGCTCGTCGCCCGCCTTGACCCCGACGTCATTTGTGTCCAG                         GAAGTGCGGATGCCGGCAGCTGGTTCCAAAGGGGCACCTAAAAACCCCAGT
genomic: CTTTCTCGCAGCTCGTCGCCCGCCTTGACCCCGACGTCATTTGTGTCCAGgtgagcgatc ... tctttgttagGAAGTGCGGATGCCGGCAGCTGGTTCCAAAGGGGCACCTAAAAACCCCAGT
EST: gi|50330655|gb|CO525781.1|CO525781
EST:     CTTTCTCGCAGCTCGTCGCCCGCCTTGACCCCGACGTCATTTGTGTCCAG                         GAAGTGCGGATGCCGGCAGCTGGTTCCAAAGGGGCACCTAAAAACCCCAGT
genomic: CTTTCTCGCAGCTCGTCGCCCGCCTTGACCCCGACGTCATTTGTGTCCAGgtgagcgatc ... tctttgttagGAAGTGCGGATGCCGGCAGCTGGTTCCAAAGGGGCACCTAAAAACCCCAGT
EST: gi|74236588|gb|DT644502.1|DT644502
EST:     CTTTCTCGCAGCTCGTCGCCCGCCTTGACCCCGACGTCATTTGTGTCCAG                         GAAGTGCGGATGCCGGCAGCTGGTTCCAAAGGGGCACCTAAAAACCCCAGT
genomic: CTTTCTCGCAGCTCGTCGCCCGCCTTGACCCCGACGTCATTTGTGTCCAGgtgagcgatc ... tctttgttagGAAGTGCGGATGCCGGCAGCTGGTTCCAAAGGGGCACCTAAAAACCCCAGT
EST: gi|50332550|gb|CO527676.1|CO527676
EST:     CTTTCTCGCAGCTCGTCGCCCGCCTTGACCCCGACGTCATTTGTGTCCAG                         GAAGTGCGGATGCCGGCAGCTGGTTCCAAAGGGGCACCTAAAAACCCCAGT
genomic: CTTTCTCGCAGCTCGTCGCCCGCCTTGACCCCGACGTCATTTGTGTCCAGgtgagcgatc ... tctttgttagGAAGTGCGGATGCCGGCAGCTGGTTCCAAAGGGGCACCTAAAAACCCCAGT
EST: gi|50325227|gb|CO520353.1|CO520353
EST:     CTTTCTCGCAGCTCGTCGCCCGCCTTGACCCCGACGTCATTTGTGTCCAG                         GAAGTGCGGATGCCGGCAGCTGGTTCCAAAGGGGCACCTAAAAACCCCAGT
genomic: CTTTCTCGCAGCTCGTCGCCCGCCTTGACCCCGACGTCATTTGTGTCCAGgtgagcgatc ... tctttgttagGAAGTGCGGATGCCGGCAGCTGGTTCCAAAGGGGCACCTAAAAACCCCAGT
EST: gi|89757612|gb|DY687140.1|DY687140
EST:     CTTTCTCGCAGCTCGTCGCCCGCCTTGACCCCGACGTCATTTGTGTCCAG                         GAAGTGCGGATGCCCGGCAGCTGGTTCCAAAGGGGCACCTAAAAACCCCAG
genomic: CTTTCTCGCAGCTCGTCGCCCGCCTTGACCCCGACGTCATTTGTGTCCAGgtgagcgatc ... tctttgttagGAAGTGCGGATGCC-GGCAGCTGGTTCCAAAGGGGCACCTAAAAACCCCAG
EST: gi|76010861|gb|DT938031.1|DT938031
EST:     CTTTCTCGCAGCTCGTCGCCCGCCTTGACCCCGACGTCATTTGTGTCCAG                         GAAGTGCGGATGCCGGCAGCTGGTTCCAAAGGGGCACCTAAAAACCCCAGT
genomic: CTTTCTCGCAGCTCGTCGCCCGCCTTGACCCCGACGTCATTTGTGTCCAGgtgagcgatc ... tctttgttagGAAGTGCGGATGCCGGCAGCTGGTTCCAAAGGGGCACCTAAAAACCCCAGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acatgattattaatatatgtatatctgataaggacatactgaacttctttgttagGAAGTGCGGATGCCGGCAGCTGGTTCCAAAGGGGCACCTAAAAACCCCAGTGAACTAAAAGATGACACAAGCTTGTCACGGGATGAAAAGCAG
                                           cttctttgtt  CT-rich tract
     attattaatatatgta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttttcagtgccccttcactgagttggccacattttgtttttagttacatgattattaatatatgtatatctgataaggacatactgaacttctttgttagGAAGTGCGGATGCCGGCAGCTGGTTCCAAAGGGGCACCTAAAAACCCCAGTGAACTAAAAGATGACACAAGCTTGTCACGGGATGAAAAGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT