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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_T03
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|71422924|gb|DR805897.1|DR805897
EST:     GATCATCGCCCAGCTCCTTACCTACCCGCTCCAGACC                         GTGAACGCGCGGCAACAGACGGAGCGCGACCCCTCCAAGCCGGCGTTCAAG
genomic: GATCATCGCCCAGCTCCTTACCTACCCGCTCCAGACCgtacgtggct ... 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|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

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 108

AGAGTACAAGCAGGGGAAGATGTCAGACGCGCTGATCAACGGCCTCGCCGGCGCCGGCGGCGGGATCATCGCCCAGCTCCTTACCTACCCGCTCCAGACCgtacgtggct ... ctcggtgcagGTGAACGCGCGGCAACAGACGGAGCGCGACCCCTCCAAGCCGGCGTTCAAGGACGGCGCCGCTCGCCAGTTGTATCTG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 106

AGAGTACAAGCAGGGGAAGATGTCAGACGCGCTGATCAACGGCCTCGCCGGCGCCGGCGGCGGGATCATCGCCCAGCTCCTTACCTACCCGCTCCAGACCgtacgtggct ... ctcggtgcagGTGAACGCGCGGCAACAGACGGAGCGCGACCCCTCCAAGCCGGCGTTCAAGGACGGCGCCGCTCGCCAGTTGTATCTG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 83

AGAGTACAAGCAGGGGAAGATGTCAGACGCGCTGATCAACGGCCTCGCCGGCGCCGGCGGCGGGATCATCGCCCAGCTCCTTACCTACCCGCTCCAGACCgtacgtggct ... ctcggtgcagGTGAACGCGCGGCAACAGACGGAGCGCGACCCCTCCAAGCCGGCGTTCAAGGACGGCGCCGCTCGCCAGTTGTATCTG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 119

AGAGTACAAGCAGGGGAAGATGTCAGACGCGCTGATCAACGGCCTCGCCGGCGCCGGCGGCGGGATCATCGCCCAGCTCCTTACCTACCCGCTCCAGACCgtacgtggct ... ctcggtgcagGTGAACGCGCGGCAACAGACGGAGCGCGACCCCTCCAAGCCGGCGTTCAAGGACGGCGCCGCTCGCCAGTTGTATCTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acctttagccctggatttctgggtcgctgatatttggaggtttccctcggtgcagGTGAACGCGCGGCAACAGACGGAGCGCGACCCCTCCAAGCCGGCGTTCAAGGACGGCGCCGCTCGCCAGTTGTATCTG
                        cgctgat  putative branch site (score: 119)
                                        tttccctc  putative PPT
                           tgatattt  TA-rich tract