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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGGAGAGGTGGGGAAATGGATTGCGATTATTGCTCTTATTCTGCGCCTATTTTTTCCGCGCCACTTCCCAGgtacatctccagtctattggtttcatcctatcaaatttccagatattggtttcatttacattgtattatttcacttaaaataacattttattaacattttgtggttttgcccttaaaataaaatagccacggttcatacatttggcttggtgactcattagcatcgtttcatcctgtgcaccag

Basic information

species Zea mays
transcript GRMZM2G052423_T01
intron # 3
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|6973434|gb|AW438128.1|AW438128
EST:     TGCGATTATTGCTGTTATTCTGCGCCTATTTTTTCCGCGCCACTTCCCAG                         ATTGGTTAGAGCTTCCCGGTTCCATCATCCTGCTCACAGCAGTCGCCCCCA
genomic: TGCGATTATTGCTCTTATTCTGCGCCTATTTTTTCCGCGCCACTTCCCAGgtacatctcc ... tgtgcaccagATTGGTTAGAGCTTCCCGGTTCCATCATCCTGCTCACAGCAGTCGCCCCCA
EST: gi|110945900|gb|EE166057.1|EE166057
EST:     TGCGATTATTGCTCTTATTCTGCGCCTATTTTTTCCGCGCCACTTCCCAG                         ATTGGTTAGAGCTTCCCGGTTCCATCATCCTGCTCACAGCAGTCGCCCCCA
genomic: TGCGATTATTGCTCTTATTCTGCGCCTATTTTTTCCGCGCCACTTCCCAGgtacatctcc ... tgtgcaccagATTGGTTAGAGCTTCCCGGTTCCATCATCCTGCTCACAGCAGTCGCCCCCA
EST: gi|12046518|gb|BF728657.1|BF728657
EST:     TTATTCTGCGCCTATTTTTTCCGCGCCACTTCCCAG                         ATTGGTTAGAGCTTCCCGGTTCCATCATCCTGCTCACAGCAGTCGCCCCCA
genomic: TTATTCTGCGCCTATTTTTTCCGCGCCACTTCCCAGgtacatctcc ... tgtgcaccagATTGGTTAGAGCTTCCCGGTTCCATCATCCTGCTCACAGCAGTCGCCCCCA
EST: gi|60395139|gb|DN228008.1|DN228008
EST:     TGCGATTATTGCTCTTATTCTGCGCCTATTTTTTCCGCGCCACTTCCCAG                         ATTGGTTAGAGCTTCCCGGTTCCATCATCCTGCTCACAGCAGTCGCCCCCA
genomic: TGCGATTATTGCTCTTATTCTGCGCCTATTTTTTCCGCGCCACTTCCCAGgtacatctcc ... tgtgcaccagATTGGTTAGAGCTTCCCGGTTCCATCATCCTGCTCACAGCAGTCGCCCCCA
EST: gi|60345305|gb|DN212278.1|DN212278
EST:     TGCGATTATTGCTCTTATTCTGCGCCTATTTTTTCCGCGCCACTTCCCAG                         ATTGGTTAGAGCTTCCCGGTTCCATCATCCTGCTCACAGCAGTCGCCCCCA
genomic: TGCGATTATTGCTCTTATTCTGCGCCTATTTTTTCCGCGCCACTTCCCAGgtacatctcc ... tgtgcaccagATTGGTTAGAGCTTCCCGGTTCCATCATCCTGCTCACAGCAGTCGCCCCCA
EST: gi|211003125|gb|FL168897.1|FL168897
EST:     TGCGATTATTGCTCTTATTCTGCGCCTATTTTTTCCGCGCCACTTCCCAG                         ATTGGTTAGAGCTTCCCGGTTCCATCATCCTGCTCACAGCAGTCGCCCCCA
genomic: TGCGATTATTGCTCTTATTCTGCGCCTATTTTTTCCGCGCCACTTCCCAGgtacatctcc ... tgtgcaccagATTGGTTAGAGCTTCCCGGTTCCATCATCCTGCTCACAGCAGTCGCCCCCA
EST: gi|211063518|gb|FL294403.1|FL294403
EST:     TGCGATTATTGCTGTTATTCTGCGCCTATTTTTTCCGCGCCACTTCCCAG                         ATTGGTTAGAGCTTCCCGGTTCCATCATCCTGCTCACAGCGGTCGCCCCCA
genomic: TGCGATTATTGCTCTTATTCTGCGCCTATTTTTTCCGCGCCACTTCCCAGgtacatctcc ... tgtgcaccagATTGGTTAGAGCTTCCCGGTTCCATCATCCTGCTCACAGCAGTCGCCCCCA

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: 179

AGGAGAGGTGGGGAAATGGATTGCGATTATTGCTCTTATTCTGCGCCTATTTTTTCCGCGCCACTTCCCAGgtacatctcc ... tgtgcaccagATTGGTTAGAGCTTCCCGGTTCCATCATCCTGCTCACAGCAGTCGCCCCCAGTCTGTTCGCACACACCTTCAGGGATGACCTCGTCGGTGTCTTCATATG


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 171

AGGAGAGGTGGGGAAATGGATTGCGATTATTGCTCTTATTCTGCGCCTATTTTTTCCGCGCCACTTCCCAGgtacatctcc ... tgtgcaccagATTGGTTAGAGCTTCCCGGTTCCATCATCCTGCTCACAGCAGTCGCCCCCAGTCTGTTCGCACACACCTTCAGGGATGACCTCGTCGGTGTCTTCATATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 98

AGGAGAGGTGGGGAAATGGATTGCGATTATTGCTCTTATTCTGCGCCTATTTTTTCCGCGCCACTTCCCAGgtacatctcc ... tgtgcaccagATTGGTTAGAGCTTCCCGGTTCCATCATCCTGCTCACAGCAGTCGCCCCCAGTCTGTTCGCACACACCTTCAGGGATGACCTCGTCGGTGTCTTCATATG


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 104

AGGAGAGGTGGGGAAATGGATTGCGATTATTGCTCTTATTCTGCGCCTATTTTTTCCGCGCCACTTCCCAGgtacatctcc ... tgtgcaccagATTGGTTAGAGCTTCCCGGTTCCATCATCCTGCTCACAGCAGTCGCCCCCAGTCTGTTCGCACACACCTTCAGGGATGACCTCGTCGGTGTCTTCATATG