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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAGCGAGATTCGCAAGTCAGCGGAGGTACAGGTCTGGAACAACCGGATCTATGACCGCGACATGACGCCGGTTCCCAATGGGTTGCTCGACCCGCGAATGgtaatgccccgctcggtattgctgtttcgtcatgtgtattttcattgatgatttgaagatgggagttctaacataaacgtgcgtttgtggcatcgttcaagttgttgcaacttatttttcccgtgtcaaatttcag

Basic information

species Zea mays
transcript GRMZM2G080176_T01
intron # 2
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|91877388|gb|EB407345.1|EB407345
EST:     ATGACCGCGACATGACGCCGGTTCCCAATGGGTTGCTCGACCCGCGAATG                         GGAATCCCGACTAAGAGAGGCAAATGCAATACCTGCCATGGTGAATTTAGT
genomic: ATGACCGCGACATGACGCCGGTTCCCAATGGGTTGCTCGACCCGCGAATGgtaatgcccc ... caaatttcagGGAATCCCGACTAAGAGAGGCAAATGCAATACCTGCCATGGTGAATTTAGT
EST: gi|32805561|gb|CD957795.1|CD957795
EST:     ACGACCGCGACATGACGCCGGTTCCCAATGGGTTGCTCGACCCGCGAATG                         GGAATCCCGACTAAGAGAGGCAAATGCAATACCTGCCATGGCGAATTTAGT
genomic: ATGACCGCGACATGACGCCGGTTCCCAATGGGTTGCTCGACCCGCGAATGgtaatgcccc ... caaatttcagGGAATCCCGACTAAGAGAGGCAAATGCAATACCTGCCATGGTGAATTTAGT
EST: gi|211159635|gb|FL160662.1|FL160662
EST:     ATGACCGCGACATGACGCCGGTTCCCAATGGGTTGCTCGACCCGCGAATG                         GGAATCC-GACTAAGAGAGGCAAATGCAATACCTGCCATGGTGAATTTAGT
genomic: ATGACCGCGACATGACGCCGGTTCCCAATGGGTTGCTCGACCCGCGAATGgtaatgcccc ... caaatttcagGGAATCCCGACTAAGAGAGGCAAATGCAATACCTGCCATGGTGAATTTAGT
EST: gi|86474903|gb|DY241273.1|DY241273
EST:     ATGACCGCGACATGACGCCGGTTCCCAGTGGGTTGCTCGACCCGCGAATG                         GGAATCCCGACTAAGAGAGGCAAATGCAATACCTGCCGTGGTGAATTTAGT
genomic: ATGACCGCGACATGACGCCGGTTCCCAATGGGTTGCTCGACCCGCGAATGgtaatgcccc ... caaatttcagGGAATCCCGACTAAGAGAGGCAAATGCAATACCTGCCATGGTGAATTTAGT

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: 79

CAGCGAGATTCGCAAGTCAGCGGAGGTACAGGTCTGGAACAACCGGATCTATGACCGCGACATGACGCCGGTTCCCAATGGGTTGCTCGACCCGCGAATGgtaatgcccc ... caaatttcagGGAATCCCGACTAAGAGAGGCAAATGCAATACCTGCCATGGTGAATTTAGTGACTGTCCAGGTCATTTCGGCTACTTGAAGCTCGCGCTTCCAGTTTTTA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 46

CAGCGAGATTCGCAAGTCAGCGGAGGTACAGGTCTGGAACAACCGGATCTATGACCGCGACATGACGCCGGTTCCCAATGGGTTGCTCGACCCGCGAATGgtaatgcccc ... caaatttcagGGAATCCCGACTAAGAGAGGCAAATGCAATACCTGCCATGGTGAATTTAGTGACTGTCCAGGTCATTTCGGCTACTTGAAGCTCGCGCTTCCAGTTTTTA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 55

CAGCGAGATTCGCAAGTCAGCGGAGGTACAGGTCTGGAACAACCGGATCTATGACCGCGACATGACGCCGGTTCCCAATGGGTTGCTCGACCCGCGAATGgtaatgcccc ... caaatttcagGGAATCCCGACTAAGAGAGGCAAATGCAATACCTGCCATGGTGAATTTAGTGACTGTCCAGGTCATTTCGGCTACTTGAAGCTCGCGCTTCCAGTTTTTA


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 32

CAGCGAGATTCGCAAGTCAGCGGAGGTACAGGTCTGGAACAACCGGATCTATGACCGCGACATGACGCCGGTTCCCAATGGGTTGCTCGACCCGCGAATGgtaatgcccc ... caaatttcagGGAATCCCGACTAAGAGAGGCAAATGCAATACCTGCCATGGTGAATTTAGTGACTGTCCAGGTCATTTCGGCTACTTGAAGCTCGCGCTTCCAGTTTTTA