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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGTATTTGCTTTTCAGTCAACACCAGAGTTAATGTTTGGACTGTACCTTCTGTATTACTTCCGTGTGTTTGAGAGGCAGATAGGCTCTAACAAATACTCGgtaggtactttaccttttatatttctccttagtattctaatgaaatggaaaaactgtcctctccaagaacttgcaccaatattcccataaattggtgtgg...

Basic information

species Zea mays
transcript GRMZM2G157316_T03
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G157316_T03 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os01g16330.1 (Oryza sativa), 5'ss of exon 3
TGTATTTGCTTTTCAGTCAACACCAGAGTTAATGTTTGGACTGTACCTTCTGTATTACTTCCGTGTGTTTGAGAGGCAGATAGGCTCTAACAAATACTCGgtaggtactttaccttttatatttctcctt-------agtattctaatgaaatggaaaaactgtcctctccaagaacttgcaccaatattcccataaattggtgtgg
||  ||||| |||||||||||||| ||| || |||||||| | ||||| || |||||||||||||| || ||||||||||||||||||||||||||||||||| || | | |  |||| || |||||  |       | |    | || ||    |  ||  ||    |  ||  | |   | ||||  |    |            
TGGGTTTGCCTTTCAGTCAACACCGGAGCTATTGTTTGGAGTCTACCTGCTCTATTACTTCCGTGTTTTCGAGAGGCAGATAGGCTCTAACAAATACTCGgtaagtgcctcag-ttttgtacttctctctgctgtgaaatgaattgataaacaacagtaatagtatggtagaaagagtgagatcaattcttttctgggaaa------
















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|148962075|gb|EE012879.2|EE012879
EST:     TGTATTACTTCCGTGTGTTTGAGAGGCAGATAGGCTCTAACAAATACTCG                         GTTTTTTGTCTCTTCACTATCACAGCATCATCGCTCCTCGAGATCCTGTCA
genomic: TGTATTACTTCCGTGTGTTTGAGAGGCAGATAGGCTCTAACAAATACTCGgtaggtactt ... gactgtgcagGTTTTTTGTCTCTTCACTATCACAGCATCATCGCTCCTCGAGATCCTGTCA
EST: gi|76281436|gb|DV021004.1|DV021004
EST:     TGTATTACTTCCGTGTGTTTGAGAGGCAGATAGGCTCTAACAAATACTCG                         GTTTTTTGTCTCTTCACTATCACAGCATCATCGCTCCTCGAGATCCTGTCA
genomic: TGTATTACTTCCGTGTGTTTGAGAGGCAGATAGGCTCTAACAAATACTCGgtaggtactt ... gactgtgcagGTTTTTTGTCTCTTCACTATCACAGCATCATCGCTCCTCGAGATCCTGTCA
EST: gi|71305646|gb|DR788962.1|DR788962
EST:     TGTATTACTTCCGTGTGTTTGAGAGGCAGATAGGCTCTAACAAATACTCG                         GTTTTT-GTCTCTTCACTATCACAGCATCATCGCTCCTCGAGATCCTGTCA
genomic: TGTATTACTTCCGTGTGTTTGAGAGGCAGATAGGCTCTAACAAATACTCGgtaggtactt ... gactgtgcagGTTTTTTGTCTCTTCACTATCACAGCATCATCGCTCCTCGAGATCCTGTCA
EST: gi|71448463|gb|DR829513.1|DR829513
EST:     TGTATTACTTCCGTGTGTTTGAGAGGCAGATAGGCTCTAACAAATACTCG                         GTTTTTTGTCTCTTCACTATCACAGCATCATCGCTCCTCGAGATCCTGTCA
genomic: TGTATTACTTCCGTGTGTTTGAGAGGCAGATAGGCTCTAACAAATACTCGgtaggtactt ... gactgtgcagGTTTTTTGTCTCTTCACTATCACAGCATCATCGCTCCTCGAGATCCTGTCA
EST: gi|93014294|gb|EB639814.1|EB639814
EST:     TGTATTACTTCCGTGTGTTTGAGAGGCAGATAGGCTCTAACAAATACTCG                         GTTTTTTGTCTCTTCACTATCACAGCATCATCGCTCCTCGAGATCCTGTCA
genomic: TGTATTACTTCCGTGTGTTTGAGAGGCAGATAGGCTCTAACAAATACTCGgtaggtactt ... gactgtgcagGTTTTTTGTCTCTTCACTATCACAGCATCATCGCTCCTCGAGATCCTGTCA
EST: gi|149102614|gb|EE188245.2|EE188245
EST:     TGTATTACTTCCGTGTGTTTGAGAGGCAGATAGGCTCTAACAAATACTCG                         GTTTTTTGTCTCTTCACTATCACAGCATCATCGCTCCTCGAGATCCTGTCA
genomic: TGTATTACTTCCGTGTGTTTGAGAGGCAGATAGGCTCTAACAAATACTCGgtaggtactt ... gactgtgcagGTTTTTTGTCTCTTCACTATCACAGCATCATCGCTCCTCGAGATCCTGTCA
EST: gi|71305918|gb|DR789090.1|DR789090
EST:     TGTATTACTTCCGTGTGTTTGAGAGGCAGATAGGCTCTAACAAATACTCG                         GTTTTTTGTCTCTTCACTATCACAGCATCATCGCTCCTCGAGATCCTGTCA
genomic: TGTATTACTTCCGTGTGTTTGAGAGGCAGATAGGCTCTAACAAATACTCGgtaggtactt ... gactgtgcagGTTTTTTGTCTCTTCACTATCACAGCATCATCGCTCCTCGAGATCCTGTCA
EST: gi|93013209|gb|EB638729.1|EB638729
EST:     TGTATTACTTCCGTGTGTTTGAGAGGCAGATAGGCTCTAACAAATACTCG                         GTTTTTTGTCTCTTCACTATCACAGCATCATCGCTCCTCGAGATCCTGTCA
genomic: TGTATTACTTCCGTGTGTTTGAGAGGCAGATAGGCTCTAACAAATACTCGgtaggtactt ... gactgtgcagGTTTTTTGTCTCTTCACTATCACAGCATCATCGCTCCTCGAGATCCTGTCA
EST: gi|148999432|gb|EE036384.2|EE036384
EST:     TGTATTACTTCCGTGTGTTTGAGAGGCAGATAGGCTCTAACAAATACTCG                         GTTTTTTGTCTCTTCACTATCACAGCATCATCGCTCCTCGAGATCCTGTCA
genomic: TGTATTACTTCCGTGTGTTTGAGAGGCAGATAGGCTCTAACAAATACTCGgtaggtactt ... gactgtgcagGTTTTTTGTCTCTTCACTATCACAGCATCATCGCTCCTCGAGATCCTGTCA
EST: gi|74237515|gb|DT645429.1|DT645429
EST:     TGTATTACTTCCGTGTGTTTGAGAGGCAGATAGGCTCTAACAAATACTCG                         GTTTTTTGTCTCTTCACTATCACAGCATCATCGCTCCTCGAGATCCTGTCA
genomic: TGTATTACTTCCGTGTGTTTGAGAGGCAGATAGGCTCTAACAAATACTCGgtaggtactt ... gactgtgcagGTTTTTTGTCTCTTCACTATCACAGCATCATCGCTCCTCGAGATCCTGTCA
EST: gi|50336165|gb|CO531291.1|CO531291
EST:     TGTATTACTTCCGTGTGTTTGAGAGGCAGATAGGCTCTAACAAATACTCG                         GTTTTTTGTCTCTTCACTATCACAGCATCATCGCTCCTCGAGATCCTGTCA
genomic: TGTATTACTTCCGTGTGTTTGAGAGGCAGATAGGCTCTAACAAATACTCGgtaggtactt ... gactgtgcagGTTTTTTGTCTCTTCACTATCACAGCATCATCGCTCCTCGAGATCCTGTCA
EST: gi|93013635|gb|EB639155.1|EB639155
EST:     TGTATTACTTCCGTGTGTTTGAGAGGCAGATAGGCTCTAACAAATACTCG                         GTTTTTTGTCTCTTCACTATCACAGCATCATCGCTCCTCGAGATCCTGTCA
genomic: TGTATTACTTCCGTGTGTTTGAGAGGCAGATAGGCTCTAACAAATACTCGgtaggtactt ... gactgtgcagGTTTTTTGTCTCTTCACTATCACAGCATCATCGCTCCTCGAGATCCTGTCA
EST: gi|149080963|gb|EE170059.2|EE170059
EST:     TGTATTACTTCCGTGTGTTTGAGAGGCAGATAGGCTCTAACAAATACTCG                         GTTTTTTGTCTCTTCACTATCACAGCATCATCGCTCCTCGAGATCCTGTCA
genomic: TGTATTACTTCCGTGTGTTTGAGAGGCAGATAGGCTCTAACAAATACTCGgtaggtactt ... gactgtgcagGTTTTTTGTCTCTTCACTATCACAGCATCATCGCTCCTCGAGATCCTGTCA
EST: gi|149105307|gb|EE290799.2|EE290799
EST:     TGTATTACTTCCGTGTGTTTGAGAGGCAGATAGGCTCTAACAAATACTCG                         GTTTTTTGTCTCTTCACTATCACAGCATCATCGCTCCTCGAGATCCTGTCA
genomic: TGTATTACTTCCGTGTGTTTGAGAGGCAGATAGGCTCTAACAAATACTCGgtaggtactt ... gactgtgcagGTTTTTTGTCTCTTCACTATCACAGCATCATCGCTCCTCGAGATCCTGTCA
EST: gi|86470247|gb|DY236617.1|DY236617
EST:     TGTATTACTTCCGTGTGTTTGAGAGGCAGATAGGCTCTAACAAATACTCG                         GTTTTTTGTCTCTTCTCTATCACAGCATCATCGCTCCTCGAGATCCTGTCA
genomic: TGTATTACTTCCGTGTGTTTGAGAGGCAGATAGGCTCTAACAAATACTCGgtaggtactt ... gactgtgcagGTTTTTTGTCTCTTCACTATCACAGCATCATCGCTCCTCGAGATCCTGTCA
EST: gi|71327756|gb|DR800512.1|DR800512
EST:     TGTATTACTTCCGTGTGTTTGAGAGGCAGATAGGCTCTAACAAATACTCG                         GNNNNNNNGTCTCTTCACTATCACAGCATCATCGCTCCTCGAGATCCTGTC
genomic: TGTATTACTTCCGTGTGTTTGAGAGGCAGATAGGCTCTAACAAATACTCGgtaggtactt ... gactgtgcagGTTTTTT-GTCTCTTCACTATCACAGCATCATCGCTCCTCGAGATCCTGTC
EST: gi|89762002|gb|DY689797.1|DY689797
EST:     TGTATTACTTCCGTGTGTTTGAGAGGCAGATAGGCTCTAACAAATACTCG                         GTTTTTTGTCTCTTCCCTATCACAGCATCATCGCTCCTCGAGATCCTGTCC
genomic: TGTATTACTTCCGTGTGTTTGAGAGGCAGATAGGCTCTAACAAATACTCGgtaggtactt ... gactgtgcagGTTTTTTGTCTCTTCACTATCACAGCATCATCGCTCCTCGAGATCCTGTCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGTATTTGCTTTTCAGTCAACACCAGAGTTAATGTTTGGACTGTACCTTCTGTATTACTTCCGTGTGTTTGAGAGGCAGATAGGCTCTAACAAATACTCGgtaggtactttaccttttatatttctccttagtattctaatgaaatggaaaaactgtcctctccaagaacttgcaccaatattcccataaattggtgtgg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT