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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgtggctcgacgcctcgctgccgacctttagccctggatttctgggtcgctgatatttggaggtttccctcggtgcagGTGAACGCGCGGCAACAGACGGAGCGCGACCCCTCCAAGCCGGCGTTCAAGGACGGCGCCGCTCGCCAGTTGTATCTG

Basic information

species Zea mays
transcript GRMZM2G540403_T02
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G540403_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os03g15860.1 (Oryza sativa), 3'ss of exon 1
gtacgtggctcgacgcctcgctgcc--gacctttagccc-------tggatttctgggtcgct-gatatttggaggtttcc--ctcggtgc--agGTGAACGCGCGGCAACAGACGGAGCGCGACCCCTCCAAGCCGGCGTTCAAGGACGGCGCCGCTCGCCAGTTGTATCTG
||||| | | |  | ||||  | |   ||    |||          |  ||| || ||| | |  |||   |  |||||     | |||||  |||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||  |||||| |||  |||
gtacgcgccacctctcctccatccttggattgctagattgtttgggtcaattgcttggttgtttaataacggagggtttgggggtgggtgcgcagGTGAACGCGCGGCAGCAGACGGAGCGCGACCCCTCCAAGCCGGCGTTCAAGGACGGCGCCGTCCGCCAGATGTGCCTG
















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|37418570|gb|CF646954.1|CF646954
EST:     GCGCCGGCGGCGGGATCATCGCCCAGCTCCTTACCTACCCGCTCCAGACC                         GTGAACGCGCGGCAACAGACGGAGCGCGACCCCTCCAAGCCGGCGTTCAAG
genomic: GCGCCGGCGGCGGGATCATCGCCCAGCTCCTTACCTACCCGCTCCAGACCgtacgtggct ... ctcggtgcagGTGAACGCGCGGCAACAGACGGAGCGCGACCCCTCCAAGCCGGCGTTCAAG
EST: gi|149109204|gb|EE190074.2|EE190074
EST:     GCGCCGGCGGCGGGATCATCGCCCAGCTCCTTACCTACCCGCTCCAGACC                         GTGAACGCGCGGCAACAGACGGAGCGCGACCCCTCCAAGCCGGCGTTCAAG
genomic: GCGCCGGCGGCGGGATCATCGCCCAGCTCCTTACCTACCCGCTCCAGACCgtacgtggct ... ctcggtgcagGTGAACGCGCGGCAACAGACGGAGCGCGACCCCTCCAAGCCGGCGTTCAAG
EST: gi|78112113|gb|DV530509.1|DV530509
EST:     GCGCCGGCGGCGGGATCATCGCCCAGCTCCTTACCTACCCGCTCCAGACC                         GTGAACGCGCGGCAACAGACGGAGCGCGACCCCTCCAAGCCGGCGTTCAAG
genomic: GCGCCGGCGGCGGGATCATCGCCCAGCTCCTTACCTACCCGCTCCAGACCgtacgtggct ... ctcggtgcagGTGAACGCGCGGCAACAGACGGAGCGCGACCCCTCCAAGCCGGCGTTCAAG
EST: gi|149071944|gb|EE160331.2|EE160331
EST:     GCGCCGGCGGCGGGATCATCGCCCAGCTCCTTACCTACCCGCTCCAGACC                         GTGAACGCGCGGCAACAGACGGAGCGCGACCCCTCCAAGCCGGCGTTCAAG
genomic: GCGCCGGCGGCGGGATCATCGCCCAGCTCCTTACCTACCCGCTCCAGACCgtacgtggct ... ctcggtgcagGTGAACGCGCGGCAACAGACGGAGCGCGACCCCTCCAAGCCGGCGTTCAAG
EST: gi|78120502|gb|DV538886.1|DV538886
EST:     GCGCCGGCGGCGGGATCATCGCCCAGCTCCTTACCTACCCGCTCCAGACC                         GTGAACGCGCGGCAACAGACGGAGCGCGACCCCTCCAAGCCGGCGTTCAAG
genomic: GCGCCGGCGGCGGGATCATCGCCCAGCTCCTTACCTACCCGCTCCAGACCgtacgtggct ... ctcggtgcagGTGAACGCGCGGCAACAGACGGAGCGCGACCCCTCCAAGCCGGCGTTCAAG
EST: gi|211496381|gb|FL046952.1|FL046952
EST:     GCGCCGGCGGCGGGATCATCGCCCAGCTCCTTACCTACCCGCTCCAGACC                         GTGAACGCGCGGCAACAGACGGAGCGCGACCCCTCCAAGCCGGCGTTCAAG
genomic: GCGCCGGCGGCGGGATCATCGCCCAGCTCCTTACCTACCCGCTCCAGACCgtacgtggct ... ctcggtgcagGTGAACGCGCGGCAACAGACGGAGCGCGACCCCTCCAAGCCGGCGTTCAAG
EST: gi|211496383|gb|FL046954.1|FL046954
EST:     GCGCCGGCGGCGGGATCATCGCCCAGCTCCTTACCTACCCGCTCCAGACC                         GTGAACGCGCGGCAACA
genomic: GCGCCGGCGGCGGGATCATCGCCCAGCTCCTTACCTACCCGCTCCAGACCgtacgtggct ... ctcggtgcagGTGAACGCGCGGCAACA
EST: gi|88756340|gb|DY540481.1|DY540481
EST:     GCGCCGGCGGCGGGATCATCGCCCAGCTCCTTACCTACCCGCTCCAGACC                         GTGAACGCGCGGCAACAGACGGAGCGCGACCCCTCCAAGCCGGCGTTCAAG
genomic: GCGCCGGCGGCGGGATCATCGCCCAGCTCCTTACCTACCCGCTCCAGACCgtacgtggct ... ctcggtgcagGTGAACGCGCGGCAACAGACGGAGCGCGACCCCTCCAAGCCGGCGTTCAAG
EST: gi|148952677|gb|EC898511.2|EC898511
EST:     GCGCCGGCGGCGGGATCATCGCCCAGCTCCTTACCTACCCGCTCCAGACC                         GTGAACGCGCGGCAACAGACGGAGCGCGACCCCTCCAAGCCGGCGTTCAAG
genomic: GCGCCGGCGGCGGGATCATCGCCCAGCTCCTTACCTACCCGCTCCAGACCgtacgtggct ... ctcggtgcagGTGAACGCGCGGCAACAGACGGAGCGCGACCCCTCCAAGCCGGCGTTCAAG
EST: gi|91877627|gb|EB407584.1|EB407584
EST:     GCGCCGGCGGCGGGATCATCGCCCAGCTCCTTACCTACCCGCTCCAGACC                         GTGAACGCGCGGCAACAGACGGAGCGCGACCCCTCCAAGCCGGCGTTCAAG
genomic: GCGCCGGCGGCGGGATCATCGCCCAGCTCCTTACCTACCCGCTCCAGACCgtacgtggct ... ctcggtgcagGTGAACGCGCGGCAACAGACGGAGCGCGACCCCTCCAAGCCGGCGTTCAAG
EST: gi|211175056|gb|FL087597.1|FL087597
EST:     GCGCCGGCGGCGGGATCATCGCCCAGCTCCTTACCTACCCGCTCCAGACC                         GTGAACGCGCGGCAACAGACGGAGCGCGACCCCTCCAAGCCGGCGTTCAAG
genomic: GCGCCGGCGGCGGGATCATCGCCCAGCTCCTTACCTACCCGCTCCAGACCgtacgtggct ... ctcggtgcagGTGAACGCGCGGCAACAGACGGAGCGCGACCCCTCCAAGCCGGCGTTCAAG
EST: gi|8367157|gb|BE050102.1|BE050102
EST:     GCGCCGGCGGCGGGATCATCGCCCAGCTCCTTACCTACCCGCTCCAGACC                         GTGAACGCGCGGCAACAGACGGAGCGCGACCCCTCCAAGCCGGCGTTCAAG
genomic: GCGCCGGCGGCGGGATCATCGCCCAGCTCCTTACCTACCCGCTCCAGACCgtacgtggct ... ctcggtgcagGTGAACGCGCGGCAACAGACGGAGCGCGACCCCTCCAAGCCGGCGTTCAAG
EST: gi|211173388|gb|FL087593.1|FL087593
EST:     GCGCCGGCGGCGGGATCATCGCCCAGCTCCTTACCTACCCGCTCCAGACC                         GTGAACGCGCGGCAACAGACGGAGCGCGACCCCTCCAAGCCGGCGTTCAAG
genomic: GCGCCGGCGGCGGGATCATCGCCCAGCTCCTTACCTACCCGCTCCAGACCgtacgtggct ... ctcggtgcagGTGAACGCGCGGCAACAGACGGAGCGCGACCCCTCCAAGCCGGCGTTCAAG
EST: gi|71766550|gb|DR964487.1|DR964487
EST:     GCGCCGGCGGCGGGATCATCGCCCAGCTCCTTACCTACCCGCTCCAGACC                         GTGAACGCGCGGCAACAGACGGAGCGCGACCCCTCCAAGCCGGCGTTCAAG
genomic: GCGCCGGCGGCGGGATCATCGCCCAGCTCCTTACCTACCCGCTCCAGACCgtacgtggct ... ctcggtgcagGTGAACGCGCGGCAACAGACGGAGCGCGACCCCTCCAAGCCGGCGTTCAAG
EST: gi|148964459|gb|EC905815.2|EC905815
EST:     GCGCCGGCGGCGGGATCATCGCCCAGCTCCTTACCTACCCGCTCCAGACC                         GTGAACGCGCGGCAACAGACGGAGCGCGACCCCTCCAAGCCGGCGTTCAAG
genomic: GCGCCGGCGGCGGGATCATCGCCCAGCTCCTTACCTACCCGCTCCAGACCgtacgtggct ... ctcggtgcagGTGAACGCGCGGCAACAGACGGAGCGCGACCCCTCCAAGCCGGCGTTCAAG
EST: gi|76936044|gb|DV174582.1|DV174582
EST:     GCGCCGGCGGCGGGATCATCGCCCAGCTCCTTACCTACCCGCTCCAGACC                         GTGAACGCGCGGCAACAGACGGAGCGCGACCCCTCCAAGCCGGCGTTCAAG
genomic: GCGCCGGCGGCGGGATCATCGCCCAGCTCCTTACCTACCCGCTCCAGACCgtacgtggct ... ctcggtgcagGTGAACGCGCGGCAACAGACGGAGCGCGACCCCTCCAAGCCGGCGTTCAAG
EST: gi|148957275|gb|EC903307.2|EC903307
EST:     GCGCCGGCGGCGGGATCATCGCCCAGCTCCTTACCTACCCGCTCCAGACC                         GTGAACGCGCGGCAACAGACGGAGCGCGACCCCTCCAAGCCGGCGTTCAAG
genomic: GCGCCGGCGGCGGGATCATCGCCCAGCTCCTTACCTACCCGCTCCAGACCgtacgtggct ... ctcggtgcagGTGAACGCGCGGCAACAGACGGAGCGCGACCCCTCCAAGCCGGCGTTCAAG
EST: gi|211173387|gb|FL087592.1|FL087592
EST:     GCGCCGGCGGCGGGATCATCGCCCAGCTCCTTACCTACCCGCTCCAGACC                         GTGAACGCGCGGCAACAGACGGAGCGCGACCCCTCCAAGCCGGCGTTCAAG
genomic: GCGCCGGCGGCGGGATCATCGCCCAGCTCCTTACCTACCCGCTCCAGACCgtacgtggct ... ctcggtgcagGTGAACGCGCGGCAACAGACGGAGCGCGACCCCTCCAAGCCGGCGTTCAAG
EST: gi|149027549|gb|EE046558.2|EE046558
EST:     GCGCCGGCGGCGGGATCATCGCCCAGCTCCTTACCTACCCGCTCCAGACC                         GTGAACGCGCGGCAACAGACGGAGCGCGACCCCTCCAAGCCGGCGTTCAAG
genomic: GCGCCGGCGGCGGGATCATCGCCCAGCTCCTTACCTACCCGCTCCAGACCgtacgtggct ... ctcggtgcagGTGAACGCGCGGCAACAGACGGAGCGCGACCCCTCCAAGCCGGCGTTCAAG
EST: gi|211175053|gb|FL087594.1|FL087594
EST:     GCGCCGGCGGCGGGATCATCGCCCAGCTCCTTACCTACCCGCTCCAGACC                         GTGAACGCGCGGCAACAGACGGAGCGCGACCCCTCCAAGCCGGCGTTCAAG
genomic: GCGCCGGCGGCGGGATCATCGCCCAGCTCCTTACCTACCCGCTCCAGACCgtacgtggct ... ctcggtgcagGTGAACGCGCGGCAACAGACGGAGCGCGACCCCTCCAAGCCGGCGTTCAAG
EST: gi|211496382|gb|FL046953.1|FL046953
EST:     GCGCCGGCGGCGGGATCATCGCCCAGCTCCTTACCTACCCGCTCCAGACC                         GTGAAMGCGCGGCAACAGACGGAGCGCGACCCCTCCAAGCCGGCGTTCAA
genomic: GCGCCGGCGGCGGGATCATCGCCCAGCTCCTTACCTACCCGCTCCAGACCgtacgtggct ... ctcggtgcagGTGAACGCGCGGCAACAGACGGAGCGCGACCCCTCCAAGCCGGCGTTCAA
EST: gi|149013466|gb|EE042980.2|EE042980
EST:     GCGCCGGCGGCGGGATCATCGCCCAGCTCCTTACCTACCCGCTCCAGACC                         GTGAACGCGCGGCAACAGACGGAGCGCGACCCCTCCAAGCCGGCGTTCAAG
genomic: GCGCCGGCGGCGGGATCATCGCCCAGCTCCTTACCTACCCGCTCCAGACCgtacgtggct ... ctcggtgcagGTGAACGCGCGGCAACAGACGGAGCGCGACCCCTCCAAGCCGGCGTTCAAG
EST: gi|71422924|gb|DR805897.1|DR805897
EST:     GATCATCGCCCAGCTCCTTACCTACCCGCTCCAGACC                         GTGAACGCGCGGCAACAGACGGAGCGCGACCCCTCCAAGCCGGCGTTCAAG
genomic: GATCATCGCCCAGCTCCTTACCTACCCGCTCCAGACCgtacgtggct ... ctcggtgcagGTGAACGCGCGGCAACAGACGGAGCGCGACCCCTCCAAGCCGGCGTTCAAG
EST: gi|71448089|gb|DR829139.1|DR829139
EST:     GCGCCGGCGGCGGGATCATCGCCCAGCTCCTTACCTACCCGCTCCAGACC                         GTGAACGCGCGGCAACAGACGGAGCGCGACCCCTCCAAGCCGGCGTTCAAG
genomic: GCGCCGGCGGCGGGATCATCGCCCAGCTCCTTACCTACCCGCTCCAGACCgtacgtggct ... ctcggtgcagGTGAACGCGCGGCAACAGACGGAGCGCGACCCCTCCAAGCCGGCGTTCAAG
EST: gi|78121537|gb|DV539921.1|DV539921
EST:     GCGCCGGCGGCGGGATCATCGCCCAGCTCCTTACCTACCCGCTCCAGACC                         GTGAACGCGCGGCAACAGACGGAGCGCGACCCCTCCAAGCCGGCGTTCAAG
genomic: GCGCCGGCGGCGGGATCATCGCCCAGCTCCTTACCTACCCGCTCCAGACCgtacgtggct ... ctcggtgcagGTGAACGCGCGGCAACAGACGGAGCGCGACCCCTCCAAGCCGGCGTTCAAG
EST: gi|91051844|gb|EB162262.1|EB162262
EST:     GCGCCGGCGGCGGGATCATCGCCCAGCTCCTTACCTACCCGCTCCAGACC                         GTGAACGCGCGGCAACAGACGGAGCGCGACCCCTCCAAGCCGGCGTTCAAG
genomic: GCGCCGGCGGCGGGATCATCGCCCAGCTCCTTACCTACCCGCTCCAGACCgtacgtggct ... ctcggtgcagGTGAACGCGCGGCAACAGACGGAGCGCGACCCCTCCAAGCCGGCGTTCAAG
EST: gi|211175055|gb|FL087596.1|FL087596
EST:     GCGCCGGCGGCGGGATCATCGCCCAGCTCCTTACCTACCCGCTCCAGACC                         GTGAACGCGCGGCAACAGACGGAGCGCGACCCCTCCAAGCCGGCGTTCAAG
genomic: GCGCCGGCGGCGGGATCATCGCCCAGCTCCTTACCTACCCGCTCCAGACCgtacgtggct ... ctcggtgcagGTGAACGCGCGGCAACAGACGGAGCGCGACCCCTCCAAGCCGGCGTTCAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acctttagccctggatttctgggtcgctgatatttggaggtttccctcggtgcagGTGAACGCGCGGCAACAGACGGAGCGCGACCCCTCCAAGCCGGCGTTCAAGGACGGCGCCGCTCGCCAGTTGTATCTG
                        cgctgat  putative branch site (score: 4)
                                        tttccctc  putative PPT
                           tgatattt  TA-rich tract