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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCCGAGAACAGTGTTGCTAGAAGATTCTCGACCGGGACTCTATCTACGATGAAATCTCATAGCAATGCACCTGCAAAATCAAACGGTTTATCTAGGACTGgtatgtttcttatgtgttttacttgggctggagcaagcaagatctacagggtttagtttgatcgtctatttcgtttaccaacattacag

Basic information

species Zea mays
transcript GRMZM2G178822_T01
intron # 17
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|148999325|gb|EE036260.2|EE036260
EST:     GAAATCTCATAGCAATGCACCTGCAAAATCAAACGGTTTATCTAGGACTG                         GTGTACAAAGAAAACTTCACTTGGATCGTCAGCCACCGCAGAAGAGTACAA
genomic: GAAATCTCATAGCAATGCACCTGCAAAATCAAACGGTTTATCTAGGACTGgtatgtttct ... aacattacagGTGTACAAAGAAAACTTCACTTGGATCGTCAGCCACCGCAGAAGAGTACAA
EST: gi|60356611|gb|DN223584.1|DN223584
EST:     AAAATCAAACGGTTTATCTAGGACTG                         GTGTACAAAGAAAACTTCACTTGGATCGTCAGCCACCGCAGAAGAGTACAA
genomic: AAAATCAAACGGTTTATCTAGGACTGgtatgtttct ... aacattacagGTGTACAAAGAAAACTTCACTTGGATCGTCAGCCACCGCAGAAGAGTACAA
EST: gi|67015254|gb|CO444003.1|CO444003
EST:     GAAATCTCATAGCAATGCACCTGCAAAATCAAACGGTTTATCTAGGACTG                         GTGTACAAAGAAAACTTCACTTGGATCGTCAGCCAACGCAGAAGAGTACAA
genomic: GAAATCTCATAGCAATGCACCTGCAAAATCAAACGGTTTATCTAGGACTGgtatgtttct ... aacattacagGTGTACAAAGAAAACTTCACTTGGATCGTCAGCCACCGCAGAAGAGTACAA
EST: gi|67022700|gb|CO451449.1|CO451449
EST:     GAAATCTCATAGCAATGCACCTGCAAAATCAAACGGTTTATCTAGGACTG                         GTGTACAAAGAAAACTTCACTTGGATCGTCAGCCAACGCAGAAGAGTACAA
genomic: GAAATCTCATAGCAATGCACCTGCAAAATCAAACGGTTTATCTAGGACTGgtatgtttct ... aacattacagGTGTACAAAGAAAACTTCACTTGGATCGTCAGCCACCGCAGAAGAGTACAA
EST: gi|67018282|gb|CO447031.1|CO447031
EST:     GAAATCTCATAGCAATGCACCTGCAAAATCAAACGGTTTATCTAGGACTG                         GTGTACAAAGAAAACTTCACTTGGATCGTCAGCCAACGCAGAAGAGTACAA
genomic: GAAATCTCATAGCAATGCACCTGCAAAATCAAACGGTTTATCTAGGACTGgtatgtttct ... aacattacagGTGTACAAAGAAAACTTCACTTGGATCGTCAGCCACCGCAGAAGAGTACAA
EST: gi|71311110|gb|DR791868.1|DR791868
EST:     GAAATCTCATAGCAATGCACCTGCAAAATCAAACGGTTTATCTAGGACTG                         GTGTACAAAGAAAACTTCACTTGGATCGTCAGCCACCGCAGAAGAGTACAA
genomic: GAAATCTCATAGCAATGCACCTGCAAAATCAAACGGTTTATCTAGGACTGgtatgtttct ... aacattacagGTGTACAAAGAAAACTTCACTTGGATCGTCAGCCACCGCAGAAGAGTACAA
EST: gi|28188021|gb|CB179631.1|CB179631
EST:     GAAATCTCATAGCAATGCACCTGCAAAATCAAACGGTTTATCTAGGACTG                         GTGTACAAAGAAAACTTCACTTGGATCGTCAGCCACCGCAGAAGAGTACAA
genomic: GAAATCTCATAGCAATGCACCTGCAAAATCAAACGGTTTATCTAGGACTGgtatgtttct ... aacattacagGTGTACAAAGAAAACTTCACTTGGATCGTCAGCCACCGCAGAAGAGTACAA
EST: gi|6269998|gb|AW157969.1|AW157969
EST:     GAAATCTCATAGCAATGCACCTGCAAAATCAAACGGTTTATCTAGGACTG                         GTGTACAAAGAAAACTTCACTTGGATCGTCAGCCAACGCAGAAGAGTACAA
genomic: GAAATCTCATAGCAATGCACCTGCAAAATCAAACGGTTTATCTAGGACTGgtatgtttct ... aacattacagGTGTACAAAGAAAACTTCACTTGGATCGTCAGCCACCGCAGAAGAGTACAA
EST: gi|24768245|gb|CA403374.1|CA403374
EST:     GAAATCTCATAGCAATGCACCTGCAAAATCAAACGGTTTATCTAGGACTG                         GTGTACAAAGAAAACTTCACTTGGATCGTCAGCCAACGCAGAAGAGTACAA
genomic: GAAATCTCATAGCAATGCACCTGCAAAATCAAACGGTTTATCTAGGACTGgtatgtttct ... aacattacagGTGTACAAAGAAAACTTCACTTGGATCGTCAGCCACCGCAGAAGAGTACAA

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: 203

TCCGAGAACAGTGTTGCTAGAAGATTCTCGACCGGGACTCTATCTACGATGAAATCTCATAGCAATGCACCTGCAAAATCAAACGGTTTATCTAGGACTGgtatgtttct ... aacattacagGTGTACAAAGAAAACTTCACTTGGATCGTCAGCCACCGCAGAAGAGTACAAAACCGACCGAGAACAGCAATAAGCTAGCTACAAATCGGGTCCCAGCCCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 129

TCCGAGAACAGTGTTGCTAGAAGATTCTCGACCGGGACTCTATCTACGATGAAATCTCATAGCAATGCACCTGCAAAATCAAACGGTTTATCTAGGACTGgtatgtttct ... aacattacagGTGTACAAAGAAAACTTCACTTGGATCGTCAGCCACCGCAGAAGAGTACAAAACCGACCGAGAACAGCAATAAGCTAGCTACAAATCGGGTCCCAGCCCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 93

TCCGAGAACAGTGTTGCTAGAAGATTCTCGACCGGGACTCTATCTACGATGAAATCTCATAGCAATGCACCTGCAAAATCAAACGGTTTATCTAGGACTGgtatgtttct ... aacattacagGTGTACAAAGAAAACTTCACTTGGATCGTCAGCCACCGCAGAAGAGTACAAAACCGACCGAGAACAGCAATAAGCTAGCTACAAATCGGGTCCCAGCCCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 191

TCCGAGAACAGTGTTGCTAGAAGATTCTCGACCGGGACTCTATCTACGATGAAATCTCATAGCAATGCACCTGCAAAATCAAACGGTTTATCTAGGACTGgtatgtttct ... aacattacagGTGTACAAAGAAAACTTCACTTGGATCGTCAGCCACCGCAGAAGAGTACAAAACCGACCGAGAACAGCAATAAGCTAGCTACAAATCGGGTCCCAGCCCG