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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTGTGGCACTGAGTTGGAGTACGACTCTTCAACCCGATTGATCACACTCCCAGAACCGGCTGAGGCTAAATAAGTGATGGCGTGGTTTCGgtgagtcatcatcctgctaatccatcaattaattaatgcatgatggtagaccaaagctacagtgttcttactgcatggatgttcctag

Basic information

species Zea mays
transcript GRMZM5G885392_T01
intron # 9
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|18178811|gb|BM380021.1|BM380021
EST:     ATCACACTCCCAGAACCGGCTGAGGCTAAATAAGTGATGGCGTGGTTTCG                         ATTTCGCTAGCAGGAAAGACGGCCCGGCCGGCCCGCAGATTCTTGATCGAC
genomic: ATCACACTCCCAGAACCGGCTGAGGCTAAATAAGTGATGGCGTGGTTTCGgtgagtcatc ... atgttcctagATTTCGCTAGCAGGAAAGACGGCCCGGCCGGCCCGCAGATTCTTGATCGAC
EST: gi|88748429|gb|DY532570.1|DY532570
EST:     ATCACACTCCCAGAACCGGCTGAGGCTAAATAAGTGATGGCGTGGTTTCG                         ATTTCGCTAGCAGGAAAGACGGCCCGGCCGGCCCGCAGATTCTTGATCGAC
genomic: ATCACACTCCCAGAACCGGCTGAGGCTAAATAAGTGATGGCGTGGTTTCGgtgagtcatc ... atgttcctagATTTCGCTAGCAGGAAAGACGGCCCGGCCGGCCCGCAGATTCTTGATCGAC
EST: gi|71760700|gb|DR958637.1|DR958637
EST:     ATCACACTCCCAGAACCGGCTGAGGCTAAATAAGTGATGGCGTGGTTTCG                         ATTTCGCTAGCAGGAAAGACGGCCCGGCCGGCCCGCAGATTCTTGATCGAC
genomic: ATCACACTCCCAGAACCGGCTGAGGCTAAATAAGTGATGGCGTGGTTTCGgtgagtcatc ... atgttcctagATTTCGCTAGCAGGAAAGACGGCCCGGCCGGCCCGCAGATTCTTGATCGAC
EST: gi|86468794|gb|DY235164.1|DY235164
EST:     ATCACACTCCCAGAACCGGCTGAGGCTAAATAAGTGATGGCGTGGTTTCG                         ATTTCGCTAGCAGGAAAGACGGCCCGGCCGGCCCGCAGATTCTTGATCGAC
genomic: ATCACACTCCCAGAACCGGCTGAGGCTAAATAAGTGATGGCGTGGTTTCGgtgagtcatc ... atgttcctagATTTCGCTAGCAGGAAAGACGGCCCGGCCGGCCCGCAGATTCTTGATCGAC
EST: gi|78074964|gb|DV503398.1|DV503398
EST:     ATCACACTCCCAGAACCGGCTGAGGCTAAATAAGTGATGGCGTGGTTTCG                         ATTTCGCTAGCAGGAAAGACGGCCCGGCCGGCCCGCAGATTTTTGATTGAC
genomic: ATCACACTCCCAGAACCGGCTGAGGCTAAATAAGTGATGGCGTGGTTTCGgtgagtcatc ... atgttcctagATTTCGCTAGCAGGAAAGACGGCCCGGCCGGCCCGCAGATTCTTGATCGAC
EST: gi|148942558|gb|EC887577.2|EC887577
EST:     ATCACACTCCCAGAACCGGCTGAGGCTAAATAAGTGATGGCGTGGTTTCG                         ATTTCGCTAGCAGGAAAGACGGCCCGGCCGGCCCGCAAATTTTTGATTGAC
genomic: ATCACACTCCCAGAACCGGCTGAGGCTAAATAAGTGATGGCGTGGTTTCGgtgagtcatc ... atgttcctagATTTCGCTAGCAGGAAAGACGGCCCGGCCGGCCCGCAGATTCTTGATCGAC
EST: gi|211475315|gb|FL222267.1|FL222267
EST:     ATCACACTCCCAGAACCGGCTGAGGCTAAATAAGTGATGGCGTGGTTTCG                         ATTTCGCTAGCAGGAAAGACGGCCCGGCCGGCCCGCAGATTCTTGATCGAC
genomic: ATCACACTCCCAGAACCGGCTGAGGCTAAATAAGTGATGGCGTGGTTTCGgtgagtcatc ... atgttcctagATTTCGCTAGCAGGAAAGACGGCCCGGCCGGCCCGCAGATTCTTGATCGAC
EST: gi|110538710|gb|EE042664.1|EE042664
EST:     ATCACACTCCCAGAACCGGCTGAGGCTAAATAAGTGATGGCGTGGTTTCG                         ATTTCGCTAGCAGGAAAGACGGCCCGGCCGGCCCGCAGATTTTTGATTGAC
genomic: ATCACACTCCCAGAACCGGCTGAGGCTAAATAAGTGATGGCGTGGTTTCGgtgagtcatc ... atgttcctagATTTCGCTAGCAGGAAAGACGGCCCGGCCGGCCCGCAGATTCTTGATCGAC
EST: gi|211475316|gb|FL222268.1|FL222268
EST:     ATCACACTCCCAGAACCGGCTGAGGCTAAATAAGTGATGGCGTGGTTTCG                         ATTTCGCTAGCAGGAAAGACGGCCCGGCCGGCCCGCAGATTCTTGATCGAC
genomic: ATCACACTCCCAGAACCGGCTGAGGCTAAATAAGTGATGGCGTGGTTTCGgtgagtcatc ... atgttcctagATTTCGCTAGCAGGAAAGACGGCCCGGCCGGCCCGCAGATTCTTGATCGAC

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: 46 (upstream exon), 29 (downstream exon)
Score: 11

TTGTGGCACTGAGTTGGAGTACGACTCTTCAACCCGATTGATCACACTCCCAGAACCGGCTGAGGCTAAATAAGTGATGGCGTGGTTTCGgtgagtcatc ... atgttcctagATTTCGCTAGCAGGAAAGACGGCCCGGCCGGCCCGCAGATTCTTGATCGACGACAGTACGAAGCAAGACTGTTCTTGGATCGGGTGGCAATCGTGGAGTG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 94

TTGTGGCACTGAGTTGGAGTACGACTCTTCAACCCGATTGATCACACTCCCAGAACCGGCTGAGGCTAAATAAGTGATGGCGTGGTTTCGgtgagtcatc ... atgttcctagATTTCGCTAGCAGGAAAGACGGCCCGGCCGGCCCGCAGATTCTTGATCGACGACAGTACGAAGCAAGACTGTTCTTGGATCGGGTGGCAATCGTGGAGTG


Block sizes: 25 (upstream exon), 25 (downstream exon)
Score: 1

TTGTGGCACTGAGTTGGAGTACGACTCTTCAACCCGATTGATCACACTCCCAGAACCGGCTGAGGCTAAATAAGTGATGGCGTGGTTTCGgtgagtcatc ... atgttcctagATTTCGCTAGCAGGAAAGACGGCCCGGCCGGCCCGCAGATTCTTGATCGACGACAGTACGAAGCAAGACTGTTCTTGGATCGGGTGGCAATCGTGGAGTG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 109

TTGTGGCACTGAGTTGGAGTACGACTCTTCAACCCGATTGATCACACTCCCAGAACCGGCTGAGGCTAAATAAGTGATGGCGTGGTTTCGgtgagtcatc ... atgttcctagATTTCGCTAGCAGGAAAGACGGCCCGGCCGGCCCGCAGATTCTTGATCGACGACAGTACGAAGCAAGACTGTTCTTGGATCGGGTGGCAATCGTGGAGTG