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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGGGACAAGCTAGAGCGACGGACATGGGTCACCAGTAAGCCACGGTCAGGGGCATTTCAGTCCTACCTAGCAGTGGTGATGGCAAAAATCTAACATAATGgtaaatttgggatctttgcatatcattccttgtttcttttaaggtcttagatattagacagagtttcattgaaactaagatcagttggttaccccgccacacag

Basic information

species Zea mays
transcript GRMZM5G879737_T03
intron # 2
splice site 5'
intron type U2

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|211228160|gb|FK958933.1|FK958933
EST:     GGCATTTCAGTCCTACCTAGCAGTGGTGATGGCAAAAATCTAACATAATG                         ATTGAAGTGTTATCTGAATAGGAATGCTCTGGTGGATTTGCAGCAAGAAAA
genomic: GGCATTTCAGTCCTACCTAGCAGTGGTGATGGCAAAAATCTAACATAATGgtaaatttgg ... cgccacacagATTGAAGTGTTATCTGAATAGGAATGCTCTGGTGGATTTGCAGCAAGAAAA
EST: gi|149104626|gb|EE290075.2|EE290075
EST:     GGCATTTCAGTCCTACCTAGCAGTGGTGATGGCAAAAATCTAACATAATG                         ATTGAAGTGTTATCTGAATAGGAATGCTCTGGTGGATTTGCAGCAAGAAAA
genomic: GGCATTTCAGTCCTACCTAGCAGTGGTGATGGCAAAAATCTAACATAATGgtaaatttgg ... cgccacacagATTGAAGTGTTATCTGAATAGGAATGCTCTGGTGGATTTGCAGCAAGAAAA
EST: gi|91869578|gb|EB400446.1|EB400446
EST:     ATTTCAGTCCCTACCCTAGCAGTGGTGATGGCAAAAATCCTAACATAATG                         ATTGAAGTGTTATCTGAATAGGAATGCTCTGGTGGATTTGCAGCAAGAAAA
genomic: ATTTCAGTCC-TACC-TAGCAGTGGTGATGGCAAAAATC-TAACATAATGgtaaatttgg ... cgccacacagATTGAAGTGTTATCTGAATAGGAATGCTCTGGTGGATTTGCAGCAAGAAAA
EST: gi|50328435|gb|CO523561.1|CO523561
EST:     GGCATTTCAGTCCTACCTAGCAGTGGTGATGGCAAAAATCTAACATAATG                         ATTGAAGTGTTATCTGAATAGGAATGCTCTGGTGGATTTGCAGCAAGAAAA
genomic: GGCATTTCAGTCCTACCTAGCAGTGGTGATGGCAAAAATCTAACATAATGgtaaatttgg ... cgccacacagATTGAAGTGTTATCTGAATAGGAATGCTCTGGTGGATTTGCAGCAAGAAAA
EST: gi|211228159|gb|FK958932.1|FK958932
EST:     GGCATTTCAGTCCTACCTAGCAGTGGTGATGGCAAAAATCTAACATAATG                         ATTGAAGTGTTATCTGAATAGGAATGCTCTGGTGGATTTGCAGCAAGAAAA
genomic: GGCATTTCAGTCCTACCTAGCAGTGGTGATGGCAAAAATCTAACATAATGgtaaatttgg ... cgccacacagATTGAAGTGTTATCTGAATAGGAATGCTCTGGTGGATTTGCAGCAAGAAAA
EST: gi|71774704|gb|DR972582.1|DR972582
EST:     GGCATTTCAGTCCTACCTAGCAGTGGTGATGGCAAAAATCTAACATAATG                         ATTGAAGTGTTATCTGAATAGGAATGCTCTGGTGGATTTGCAGCAAGAAAA
genomic: GGCATTTCAGTCCTACCTAGCAGTGGTGATGGCAAAAATCTAACATAATGgtaaatttgg ... cgccacacagATTGAAGTGTTATCTGAATAGGAATGCTCTGGTGGATTTGCAGCAAGAAAA
EST: gi|148961114|gb|EE011820.2|EE011820
EST:     GGCATTTCAGTCCTACCTAGCAGTGGTGATGGCAAAAATCTAACATAATG                         ATTGAAGTGTTATCTGAATAGGAATGCTCTGGTGGATTTGCAGCAAGAAAA
genomic: GGCATTTCAGTCCTACCTAGCAGTGGTGATGGCAAAAATCTAACATAATGgtaaatttgg ... cgccacacagATTGAAGTGTTATCTGAATAGGAATGCTCTGGTGGATTTGCAGCAAGAAAA
EST: gi|78108982|gb|DV527399.1|DV527399
EST:     GGCATTTCAGTCCTACCTAGCAGTGGTGATGGCAAAAATCTAACATAATG                         ATTGAAGTGTTATCTGAATAGGAATGCTCTGGTGGATTTGCAGCAAGAAAA
genomic: GGCATTTCAGTCCTACCTAGCAGTGGTGATGGCAAAAATCTAACATAATGgtaaatttgg ... cgccacacagATTGAAGTGTTATCTGAATAGGAATGCTCTGGTGGATTTGCAGCAAGAAAA
EST: gi|148973633|gb|EE024744.2|EE024744
EST:     GGCATTTCAGTCCTACCTAGCAGTGGTGATGGCAAAAATCTAACATAATG                         ATTGAAGTGTTATCTGAATAGGAATGCTCTGGTGGATTTGCAGCAAGAAAA
genomic: GGCATTTCAGTCCTACCTAGCAGTGGTGATGGCAAAAATCTAACATAATGgtaaatttgg ... cgccacacagATTGAAGTGTTATCTGAATAGGAATGCTCTGGTGGATTTGCAGCAAGAAAA
EST: gi|50332809|gb|CO527935.1|CO527935
EST:     GGCATTTCAGTCCTACCTAGCAGTGGTGATGGCAAAAATCTAACATAATG                         ATTGAAGTGTTATCTGAATAGGAATGCTCTGGTGGATTTGCAGCAAGAAAA
genomic: GGCATTTCAGTCCTACCTAGCAGTGGTGATGGCAAAAATCTAACATAATGgtaaatttgg ... cgccacacagATTGAAGTGTTATCTGAATAGGAATGCTCTGGTGGATTTGCAGCAAGAAAA
EST: gi|28909778|gb|CB331096.1|CB331096
EST:     GGCATTTCAGTCCTACCTAGCAGTGG-GATGGCAAAAATCTAACATAATG                         ATTGAAGTGTTATCTGAATAGGAATGCTCTGGTGGATTTGCAGCAAGAAAA
genomic: GGCATTTCAGTCCTACCTAGCAGTGGTGATGGCAAAAATCTAACATAATGgtaaatttgg ... cgccacacagATTGAAGTGTTATCTGAATAGGAATGCTCTGGTGGATTTGCAGCAAGAAAA
EST: gi|148955107|gb|EC900621.2|EC900621
EST:     GGCATTTCAGTCCTACCTAGCAGTGGTGATGGCAAAAATCTAACATAATG                         ATTGAAGTGTTATCTGAATAGGAATGCTCTGGTGGATTTGCAGCAAGAAAA
genomic: GGCATTTCAGTCCTACCTAGCAGTGGTGATGGCAAAAATCTAACATAATGgtaaatttgg ... cgccacacagATTGAAGTGTTATCTGAATAGGAATGCTCTGGTGGATTTGCAGCAAGAAAA

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: 45 (upstream exon), 42 (downstream exon)
Score: 15

CGGGACAAGCTAGAGCGACGGACATGGGTCACCAGTAAGCCACGGTCAGGGGCATTTCAGTCCTACCTAGCAGTGGTGATGGCAAAAATCTAACATAATGgtaaatttgg ... cgccacacagATTGAAGTGTTATCTGAATAGGAATGCTCTGGTGGATTTGCAGCAAGAAAAACCTTGGAATGAATGTACAAGCCACTTAGGGTGCTGTATTAGAGCTGTA


Block sizes: 43 (upstream exon), 40 (downstream exon)
Score: 14

CGGGACAAGCTAGAGCGACGGACATGGGTCACCAGTAAGCCACGGTCAGGGGCATTTCAGTCCTACCTAGCAGTGGTGATGGCAAAAATCTAACATAATGgtaaatttgg ... cgccacacagATTGAAGTGTTATCTGAATAGGAATGCTCTGGTGGATTTGCAGCAAGAAAAACCTTGGAATGAATGTACAAGCCACTTAGGGTGCTGTATTAGAGCTGTA


Block sizes: 49 (upstream exon), 42 (downstream exon)
Score: 11

CGGGACAAGCTAGAGCGACGGACATGGGTCACCAGTAAGCCACGGTCAGGGGCATTTCAGTCCTACCTAGCAGTGGTGATGGCAAAAATCTAACATAATGgtaaatttgg ... cgccacacagATTGAAGTGTTATCTGAATAGGAATGCTCTGGTGGATTTGCAGCAAGAAAAACCTTGGAATGAATGTACAAGCCACTTAGGGTGCTGTATTAGAGCTGTA


Block sizes: 41 (upstream exon), 37 (downstream exon)
Score: 15

CGGGACAAGCTAGAGCGACGGACATGGGTCACCAGTAAGCCACGGTCAGGGGCATTTCAGTCCTACCTAGCAGTGGTGATGGCAAAAATCTAACATAATGgtaaatttgg ... cgccacacagATTGAAGTGTTATCTGAATAGGAATGCTCTGGTGGATTTGCAGCAAGAAAAACCTTGGAATGAATGTACAAGCCACTTAGGGTGCTGTATTAGAGCTGTA