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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTCGCCCGCTCATTCACCGGCGGCGTCGCCCAGCTCGGCCTCCCGCCGCCCACGGAGGCCAGGTCCCCGGGCCGCCCGCTCGGTCCGCCACGGAGGCAAGgtaaccggcgcctttctctcgatcgatcgatcgtttgtcccgcgccgatcggccgagcacgccattgcgtgtcggcgcggcacttttttcattcctcttt...

Basic information

species Zea mays
transcript GRMZM2G092991_T01
intron # 1
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|76284893|gb|DV024461.1|DV024461
EST:     CACGGAGGCCAGGTCCCCGGGCCGCCCGCTCGGTCCGCCACGGAGGCAAG                         GAATTGGTTCTTTTAGTACTTGACAGAAATAAATATATTCCAGGCATGGTG
genomic: CACGGAGGCCAGGTCCCCGGGCCGCCCGCTCGGTCCGCCACGGAGGCAAGgtaaccggcg ... tggattgtagGAATTGGTTCTTTTAGTACTTGACAGAAATAAATATATTCCAGGCATGGTG
EST: gi|211462037|gb|FK972950.1|FK972950
EST:     CACGGAGGCCAGGTCCCCGGGCCGCCCGCTCGGTCCGCCACGGAGGCAAG                         GAATTGGTTCTTTTAGTACTTGACAGAAATAAATATATTCCAGGCATGGTG
genomic: CACGGAGGCCAGGTCCCCGGGCCGCCCGCTCGGTCCGCCACGGAGGCAAGgtaaccggcg ... tggattgtagGAATTGGTTCTTTTAGTACTTGACAGAAATAAATATATTCCAGGCATGGTG
EST: gi|211464551|gb|FK972952.1|FK972952
EST:     CACGGAGGCCAGGTCCCCGGGCCGCCCGCTCGGTCCGCCACAGAGGCAAG                         GAATTGGTTCTTTTAGTACTTGACAGAAATAAATATATTCCAGGCATGGTG
genomic: CACGGAGGCCAGGTCCCCGGGCCGCCCGCTCGGTCCGCCACGGAGGCAAGgtaaccggcg ... tggattgtagGAATTGGTTCTTTTAGTACTTGACAGAAATAAATATATTCCAGGCATGGTG
EST: gi|211464550|gb|FK972951.1|FK972951
EST:     CACGGAGGCCAGGTCCCCGGGCCGCCCGCTCGGTCCGCCACAGAGGCAAG                         GAATTGGTTCTTTTAGTACTTGACAGAAATAAATATATTCCAGGCATGGTG
genomic: CACGGAGGCCAGGTCCCCGGGCCGCCCGCTCGGTCCGCCACGGAGGCAAGgtaaccggcg ... tggattgtagGAATTGGTTCTTTTAGTACTTGACAGAAATAAATATATTCCAGGCATGGTG
EST: gi|211462034|gb|FK972947.1|FK972947
EST:     CACGGAGGCCAGGTCCCCGGGCCGCCCGCTCGGTCCGCCACAGAGGCAAG                         GAATTGGTTCTTTTAGTACTTGACAGAAATAAATATATTCCAGGCATGGTG
genomic: CACGGAGGCCAGGTCCCCGGGCCGCCCGCTCGGTCCGCCACGGAGGCAAGgtaaccggcg ... tggattgtagGAATTGGTTCTTTTAGTACTTGACAGAAATAAATATATTCCAGGCATGGTG
EST: gi|211462036|gb|FK972949.1|FK972949
EST:     CACGGAGGCCAGGTCCCCGGGCCGCCCGCTCGGTCCGCCACAGAGGCAAG                         GAATTGGTTCTTTTAGTACTTGACAGAAATAAATATATTCCAGGCATGGTG
genomic: CACGGAGGCCAGGTCCCCGGGCCGCCCGCTCGGTCCGCCACGGAGGCAAGgtaaccggcg ... tggattgtagGAATTGGTTCTTTTAGTACTTGACAGAAATAAATATATTCCAGGCATGGTG
EST: gi|76920481|gb|DV168194.1|DV168194
EST:     CACGGAGGCCAGGTCCCCGGGCCGCCCGCTCGGTCCGCCACGGAGGCAAG                         GAATTGGTTCTTTTAGTACTTGACAGAAATAAATATATTCCAGGCATGGTG
genomic: CACGGAGGCCAGGTCCCCGGGCCGCCCGCTCGGTCCGCCACGGAGGCAAGgtaaccggcg ... tggattgtagGAATTGGTTCTTTTAGTACTTGACAGAAATAAATATATTCCAGGCATGGTG
EST: gi|211462031|gb|FK972944.1|FK972944
EST:     CACGGAGGCCAGGTCCCCGGGCCGCCCGCTCGGTCCGCCACAGAGGCAAG                         GAATTGGTTCTTTTAGTACTTGACAGAAATAAATATATTCCAGGCATGGTG
genomic: CACGGAGGCCAGGTCCCCGGGCCGCCCGCTCGGTCCGCCACGGAGGCAAGgtaaccggcg ... tggattgtagGAATTGGTTCTTTTAGTACTTGACAGAAATAAATATATTCCAGGCATGGTG
EST: gi|211462030|gb|FK972943.1|FK972943
EST:     CACGGAGGCCAGGTCCCCGGGCCGCCCGCTCGGTCCGCCACGGAGGCAAG                         GAATTGGTTCTTTTAGTACTTGACAGAAATAAATATATTCCAGGCATGGTG
genomic: CACGGAGGCCAGGTCCCCGGGCCGCCCGCTCGGTCCGCCACGGAGGCAAGgtaaccggcg ... tggattgtagGAATTGGTTCTTTTAGTACTTGACAGAAATAAATATATTCCAGGCATGGTG

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: 36 (upstream exon), 49 (downstream exon)
Score: 18

TTCGCCCGCTCATTCACCGGCGGCGTCGCCCAGCTCGGCCTCCCGCCGCCCACGGAGGCCAGGTCCCCGGGCCGCCCGCTCGGTCCGCCACGGAGGCAAGgtaaccggcg ... tggattgtagGAATTGGTTCTTTTAGTACTTGACAGAAATAAATATATTCCAGGCATGGTGGCGTCTTTAGACAATGTGAGGGGCTTGACTTTAGCCATGTCATCTAGTG


Block sizes: 43 (upstream exon), 43 (downstream exon)
Score: 7

TTCGCCCGCTCATTCACCGGCGGCGTCGCCCAGCTCGGCCTCCCGCCGCCCACGGAGGCCAGGTCCCCGGGCCGCCCGCTCGGTCCGCCACGGAGGCAAGgtaaccggcg ... tggattgtagGAATTGGTTCTTTTAGTACTTGACAGAAATAAATATATTCCAGGCATGGTGGCGTCTTTAGACAATGTGAGGGGCTTGACTTTAGCCATGTCATCTAGTG


Block sizes: 49 (upstream exon), 43 (downstream exon)
Score: 5

TTCGCCCGCTCATTCACCGGCGGCGTCGCCCAGCTCGGCCTCCCGCCGCCCACGGAGGCCAGGTCCCCGGGCCGCCCGCTCGGTCCGCCACGGAGGCAAGgtaaccggcg ... tggattgtagGAATTGGTTCTTTTAGTACTTGACAGAAATAAATATATTCCAGGCATGGTGGCGTCTTTAGACAATGTGAGGGGCTTGACTTTAGCCATGTCATCTAGTG


Block sizes: 44 (upstream exon), 43 (downstream exon)
Score: 34

TTCGCCCGCTCATTCACCGGCGGCGTCGCCCAGCTCGGCCTCCCGCCGCCCACGGAGGCCAGGTCCCCGGGCCGCCCGCTCGGTCCGCCACGGAGGCAAGgtaaccggcg ... tggattgtagGAATTGGTTCTTTTAGTACTTGACAGAAATAAATATATTCCAGGCATGGTGGCGTCTTTAGACAATGTGAGGGGCTTGACTTTAGCCATGTCATCTAGTG