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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCTACCTAGAGGCGGTCACTCAGAAGAGGATTCGCTTCTTCGAGGAGATCCAGGCAAGGCAAGCCGTCGAGCGGCTGAATATCGGCGGCGAAGTTATCAAgtgagctcttaacgatccgtttgtggtttccacacttaagtttagcttatgaaattaatatgccatcatgaaattgaaccgccgactataagtagtttttgctgtaccaactattgcttgtttgcttcataattctgattctcactcagaaccattgtttggggccatgcccttcag

Basic information

species Zea mays
transcript GRMZM2G553314_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|76021644|gb|DT948814.1|DT948814
EST:     CAGGCAAGGCAAGCCGTCGAGCGGCTGAATATCGGCGGCGAAGTTATCAA                         GGTAACTTTGCCTGATGGCGCTATCAAGGAGGGTAAGAAATGGATAACAAC
genomic: CAGGCAAGGCAAGCCGTCGAGCGGCTGAATATCGGCGGCGAAGTTATCAAgtgagctctt ... tgcccttcagGGTAACTTTGCCTGATGGCGCTATCAAGGAGGGTAAGAAATGGATAACAAC
EST: gi|149089740|gb|EE179011.2|EE179011
EST:     CAGGCAAGGCAAGCCGTCGAGCGGCTGAATATCGGCGGCGAAGTTATCAA                         GGTAACTTTGCCTGATGGCGCTATCAAGGAGGGTAAGAAATGGATAACAAC
genomic: CAGGCAAGGCAAGCCGTCGAGCGGCTGAATATCGGCGGCGAAGTTATCAAgtgagctctt ... tgcccttcagGGTAACTTTGCCTGATGGCGCTATCAAGGAGGGTAAGAAATGGATAACAAC
EST: gi|13237202|gb|BG355216.1|BG355216
EST:     CAGGCAAGGCAAGCCGTCGAGCGGCTGAATATCGGCGGCGAAGTTATCAA                         GGTAACTTTGCCTGATGGCGCTATCAAGGAGGGTAAGAAATGGATAACAAC
genomic: CAGGCAAGGCAAGCCGTCGAGCGGCTGAATATCGGCGGCGAAGTTATCAAgtgagctctt ... tgcccttcagGGTAACTTTGCCTGATGGCGCTATCAAGGAGGGTAAGAAATGGATAACAAC
EST: gi|211033167|gb|FL324568.1|FL324568
EST:     AAGCCGTCGAGCGGCTGAATATCGGCGGCGAAGTTATCAA                         GGTAACTTTGCCTGATGGCGCTATCAAGGAGGGTAAGAAATGGATAACAAC
genomic: AAGCCGTCGAGCGGCTGAATATCGGCGGCGAAGTTATCAAgtgagctctt ... tgcccttcagGGTAACTTTGCCTGATGGCGCTATCAAGGAGGGTAAGAAATGGATAACAAC
EST: gi|50334018|gb|CO529144.1|CO529144
EST:     CAGGCAAGGCAAGCCGTCGAGCGGCTGAATATCGGCGGCGAAGTTATCAA                         GGTAACTTTGCCTGATGGCGCTATCAAGGAGGGTAAGAAATGGATAACAAC
genomic: CAGGCAAGGCAAGCCGTCGAGCGGCTGAATATCGGCGGCGAAGTTATCAAgtgagctctt ... tgcccttcagGGTAACTTTGCCTGATGGCGCTATCAAGGAGGGTAAGAAATGGATAACAAC
EST: gi|211455406|gb|FL343586.1|FL343586
EST:     CAGGCAAGGCAAGCCGTCGAGCGGCTGAATATCGGCGGCGAAGTTATCAA                         GGTAACTTTGCCTGATGGCGCTATCAAGGAGGGTAAGAAATGGATAACAAC
genomic: CAGGCAAGGCAAGCCGTCGAGCGGCTGAATATCGGCGGCGAAGTTATCAAgtgagctctt ... tgcccttcagGGTAACTTTGCCTGATGGCGCTATCAAGGAGGGTAAGAAATGGATAACAAC
EST: gi|211514340|gb|FL308803.1|FL308803
EST:     CAGGCAAGGCAAGCCGTCGAGCGGCTGAATATCGGCGGCGAAGTTATCAA                         GGTAACTTTGCCTGATGGCGCTATCAAGGAGGGTAAGAAATGGATAACAAC
genomic: CAGGCAAGGCAAGCCGTCGAGCGGCTGAATATCGGCGGCGAAGTTATCAAgtgagctctt ... tgcccttcagGGTAACTTTGCCTGATGGCGCTATCAAGGAGGGTAAGAAATGGATAACAAC
EST: gi|78092217|gb|DV520591.1|DV520591
EST:     CAGGCAAGGCAAGCCGTCGAGCGGCTGAATATCGGCGGCGAAGTTATCAA                         GGTAACTTTGCCTGATGGCGCTATCAAGGAGGGTAAGAAATGGATAACAAC
genomic: CAGGCAAGGCAAGCCGTCGAGCGGCTGAATATCGGCGGCGAAGTTATCAAgtgagctctt ... tgcccttcagGGTAACTTTGCCTGATGGCGCTATCAAGGAGGGTAAGAAATGGATAACAAC

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), 48 (downstream exon)
Score: 120

CCTACCTAGAGGCGGTCACTCAGAAGAGGATTCGCTTCTTCGAGGAGATCCAGGCAAGGCAAGCCGTCGAGCGGCTGAATATCGGCGGCGAAGTTATCAAgtgagctctt ... tgcccttcagGGTAACTTTGCCTGATGGCGCTATCAAGGAGGGTAAGAAATGGATAACAACCCCAATGGATATTGCTAAGGAGATATCAAGTGGATTTGCAGCTAGTTGT


Block sizes: 44 (upstream exon), 49 (downstream exon)
Score: 77

CCTACCTAGAGGCGGTCACTCAGAAGAGGATTCGCTTCTTCGAGGAGATCCAGGCAAGGCAAGCCGTCGAGCGGCTGAATATCGGCGGCGAAGTTATCAAgtgagctctt ... tgcccttcagGGTAACTTTGCCTGATGGCGCTATCAAGGAGGGTAAGAAATGGATAACAACCCCAATGGATATTGCTAAGGAGATATCAAGTGGATTTGCAGCTAGTTGT


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

CCTACCTAGAGGCGGTCACTCAGAAGAGGATTCGCTTCTTCGAGGAGATCCAGGCAAGGCAAGCCGTCGAGCGGCTGAATATCGGCGGCGAAGTTATCAAgtgagctctt ... tgcccttcagGGTAACTTTGCCTGATGGCGCTATCAAGGAGGGTAAGAAATGGATAACAACCCCAATGGATATTGCTAAGGAGATATCAAGTGGATTTGCAGCTAGTTGT


Block sizes: 38 (upstream exon), 48 (downstream exon)
Score: 71

CCTACCTAGAGGCGGTCACTCAGAAGAGGATTCGCTTCTTCGAGGAGATCCAGGCAAGGCAAGCCGTCGAGCGGCTGAATATCGGCGGCGAAGTTATCAAgtgagctctt ... tgcccttcagGGTAACTTTGCCTGATGGCGCTATCAAGGAGGGTAAGAAATGGATAACAACCCCAATGGATATTGCTAAGGAGATATCAAGTGGATTTGCAGCTAGTTGT